in Oncology and Haematologydocuments.irevues.inist.fr/bitstream/handle/2042/38833/vol_12_1_2008.pdfNadia Gabellini NEIL1 (nei endonuclease VIII-like 1 (E. coli)) 53 ... Cynthia C Morton

The PDF version of the Atlas of Genetics and Cytogenetics in Oncology and Haematology is a reissue of the original articles published in collaboration with the Institute for Scientific and Technical Information (INstitut de l’Information Scientifique et Technique - INIST) of the French National Center for Scientific Research (CNRS) on its electronic publishing platform I-Revues. Online and PDF versions of the Atlas of Genetics and Cytogenetics in Oncology and Haematology are hosted by INIST-CNRS.

Atlas of Genetics and Cytogenetics in Oncology and Haematology

OPEN ACCESS JOURNAL AT INIST-CNRS

Scope The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal in open access, devoted to genes, cytogenetics, clinical entities in cancer, and cancer-prone diseases. It presents structured review articles ("cards") on genes, leukaemias, solid tumours, cancer-prone diseases, more traditional review articles on these and also on surrounding topics ("deep insights"), case reports in hematology, and educational items in the various related topics for students in Medicine and in Sciences.

Editorial correspondance Jean-Loup Huret Genetics, Department of Medical Information, University Hospital F-86021 Poitiers, France tel +33 5 49 44 45 46 or +33 5 49 45 47 67 [email protected] or [email protected]

Staff Mohammad Ahmad, Mélanie Arsaban, Mikael Cordon, Isabelle Dabin, Marie-Christine Jacquemot-Perbal, Maureen Labarussias, Anne Malo, Catherine Morel-Pair, Laurent Rassinoux, Sylvie Yau Chun Wan - Senon, Alain Zasadzinski. Database Director: Philippe Dessen, and the Chairman of the on-line version: Alain Bernheim (Gustave Roussy Institute, Villejuif, France).

The Atlas of Genetics and Cytogenetics in Oncology and Haematology (ISSN 1768-3262) is published 6 times a year by ARMGHM, a non profit organisation, and by the INstitute for Scientific and Technical Information of the French National Center for Scientific Research (INIST-CNRS) since 2008. The Atlas is hosted by INIST-CNRS (http://www.inist.fr)

http://AtlasGeneticsOncology.org

© ATLAS - ISSN 1768-3262



Editor-in-Chief

Jean-Loup Huret (Poitiers, France)

Editorial Board Sreeparna Banerjee (Ankara, Turkey) Solid Tumours Section Alessandro Beghini (Milan, Italy) Genes Section Anne von Bergh (Rotterdam, The Netherlands) Genes / Leukaemia Sections Judith Bovée (Leiden, The Netherlands) Solid Tumours Section Vasantha Brito-Babapulle (London, UK) Leukaemia Section Charles Buys (Groningen, The Netherlands) Deep Insights Section Anne Marie Capodano (Marseille, France) Solid Tumours Section Fei Chen (Morgantown, West Virginia) Genes / Deep Insights Sections Antonio Cuneo (Ferrara, Italy) Leukaemia Section Paola Dal Cin (Boston, Massachussetts) Genes / Solid Tumours Section Louis Dallaire (Montreal, Canada) Education Section Brigitte Debuire (Villejuif, France) Deep Insights Section François Desangles (Paris, France) Leukaemia / Solid Tumours Sections Enric Domingo-Villanueva (London, UK) Solid Tumours Section Ayse Erson (Ankara, Turkey) Solid Tumours Section Richard Gatti (Los Angeles, California) Cancer-Prone Diseases / Deep Insights Sections Ad Geurts van Kessel (Nijmegen, The Netherlands) Cancer-Prone Diseases Section Oskar Haas (Vienna, Austria) Genes / Leukaemia Sections Anne Hagemeijer (Leuven, Belgium) Deep Insights Section Nyla Heerema (Colombus, Ohio) Leukaemia Section Jim Heighway (Liverpool, UK) Genes / Deep Insights Sections Sakari Knuutila (Helsinki, Finland) Deep Insights Section Lidia Larizza (Milano, Italy) Solid Tumours Section Lisa Lee-Jones (Newcastle, UK) Solid Tumours Section Edmond Ma (Hong Kong, China) Leukaemia Section Roderick McLeod (Braunschweig, Germany) Deep Insights / Education Sections Cristina Mecucci (Perugia, Italy) Genes / Leukaemia Sections Yasmin Mehraein (Homburg, Germany) Cancer-Prone Diseases Section Fredrik Mertens (Lund, Sweden) Solid Tumours Section Konstantin Miller (Hannover, Germany) Education Section Felix Mitelman (Lund, Sweden) Deep Insights Section Hossain Mossafa (Cergy Pontoise, France) Leukaemia Section Stefan Nagel (Braunschweig, Germany) Deep Insights / Education Sections Florence Pedeutour (Nice, France) Genes / Solid Tumours Sections Elizabeth Petty (Ann Harbor, Michigan) Deep Insights Section Susana Raimondi (Memphis, Tennesse) Genes / Leukaemia Section Mariano Rocchi (Bari, Italy) Genes Section Alain Sarasin (Villejuif, France) Cancer-Prone Diseases Section Albert Schinzel (Schwerzenbach, Switzerland) Education Section Clelia Storlazzi (Bari, Italy) Genes Section Sabine Strehl (Vienna, Austria) Genes / Leukaemia Sections Nancy Uhrhammer (Clermont Ferrand, France) Genes / Cancer-Prone Diseases Sections Dan Van Dyke (Rochester, Minnesota) Education Section Roberta Vanni (Montserrato, Italy) Solid Tumours Section Franck Viguié (Paris, France) Leukaemia Section José Luis Vizmanos (Pamplona, Spain) Leukaemia Section Thomas Wan (Hong Kong, China) Genes / Leukaemia Sections

Atlas Genet Cytogenet Oncol Haematol. 2008;12(1)



Volume 12, Number 1, January-February 2008

Table of contents

Gene Section ACVR2 (activin receptor type 2) 1 Sarah Boles, Eddy Chau, Barbara Jung

EP400 (E1A binding protein p400) 3 Sandrine Tyteca

ENC1 (ectodermal-neural cortex (with BTB-like domain)) 5 Shalom Avraham, Seyha Seng, Shuxian Jiang, Hava Karsenty Avraham

RHOC (ras homolog gene family, member C) 8 Ahmad Faried, Leri S Faried

SAV1 (Salvador homolog 1 (Drosophila)) 10 Bernard A Callus

SNCG (synuclein, gamma (breast cancer-specific protein 1)) 12 Artur Czekierdowski, Sylwia Czekierdowska

ADAM23 (ADAM metallopeptidase domain 23) 17 Marilia de Freitas Calmon, Paula Rahal

AKT2 (v-akt murine thymoma viral oncogene homolog 2) 20 Deborah A Altomare, Joseph R Testa

AKT3 (v-akt murine thymoma viral oncogene homolog 3, Protein Kinase B gamma) 24 Mitchell Cheung, Joseph R Testa

ASCL1 (achaete-scute homolog 1 or achaete-scute complex homolog 1) 27 Jayashree S Ladha, MRS Rao

ATF2 (activating transcription factor 2) 33 Pedro A Lazo, Ana Sevilla

CTGF (connective tissue growth factor) 35 Satoshi Kubota, Masaharu Takigawa

FNIP1 (folliculin interacting protein 1) 39 Laura S Schmidt

GLMN (glomulin) 41 Virginie Aerts, Pascal Brouillard, Laurence M Boon, Miikka Vikkula

JAK3 (janus kinase 3 or just another kinase 3) 44 Ping Shi, Hesham M Amin

KLRK1 (killer cell lectin-like receptor subfamily K, member 1) 47 Lewis L Lanier

LGI1 (leucine-rich, glioma inactivated protein 1 precursor) 50 Nadia Gabellini

NEIL1 (nei endonuclease VIII-like 1 (E. coli)) 53 Masaya Suzuki, Kazuya Shinmura, Haruhiko Sugimura

Atlas Genet Cytogenet Oncol Haematol. 2008;12(1)



NLRC4 (NLR Family, CARD domain containing 4) 56 Yatender Kumar, Vegesna Radha, Ghanshyam Swarup

Leukaemia Section t(3;6)(q25;q26) 59 Jean-Loup Huret

t(3;11)(q26;p15) 60 Jean-Loup Huret

t(3;12)(q26;q21) 61 Jean-Loup Huret

Solid Tumour Section Colon: Colorectal adenocarcinoma 62 Nilufer Sayar, Sreeparna Banerjee

Uterus: Leiomyoma 68 Allison M Lynch, Cynthia C Morton

Skin Melanoma 74 Marco Castori, Paola Grammatico

Cancer Prone Disease Section Frasier syndrome (FS) 81 Mariana M Cajaiba, Miguel Reyes-Múgica

Case Report Section Translocation t(11;20)(p15;q11) detected in AML M0: A case report 85 Bani B Ganguly, Yogesh Loher, MB Agarwal

Gene Section Mini Review

Atlas Genet Cytogenet Oncol Haematol. 2008;12(1) 1



ACVR2 (activin receptor type 2) Sarah Boles, Eddy Chau, Barbara Jung

Division of Gastroenterology, University of California, San Diego 9500 Gilman Drive 0063 La Jolla, CA, 92093-0063, USA

Published in Atlas Database: June 2007

Online updated version: http://AtlasGeneticsOncology.org/Genes/ACVR2ID567ch2q22.html DOI: 10.4267/2042/38460

This work is licensed under a Creative Commons Attribution-Non-commercial-No Derivative Works 2.0 France Licence. © 2008 Atlas of Genetics and Cytogenetics in Oncology and Haematology

Identity Hugo: ACVR2A Other names: ACVRII; ACVR2A; Activin Receptor, type 2A; Activin Receptor A type 2; T ACTRII; ActR-II Location: 2q22.3 Local order: Genes flanking ACVR2A, in centromere to telomere direction on 2q22, are: PAPBPCP2 2q22.3 - polyadenylate binding protein, cytoplasmic, pseudogene 2. ACVR2 2q22.3 - activin receptor type IIA. ORC4L 2q23.1 - origin recognition complex, subunit 4.

DNA/RNA Description ACVR2 gene spans a region of 85,796 bp and has 11 exons. Exon lengths are 180, 208, 110, 155, 144, 144, 146, 115, 139, 131 and 3745 base pairs. Exon 10 contains a polyadenine tract that may be mutated in microsatellite unstable cells.

Transcription The transcript is 5217 base pairs.

Protein Description ACVR2 is a member of the transforming growth factor beta (TGF-b) receptor family. It is a 70-75kDA protein consisting of 513 amino acids. It is a transmembrane receptor for activin, with a cysteine-rich extracellular ligand-binding domain, a single pass transmembrane domain, and an intracellular domain with constitutive serine/threonine kinase activity. Upon binding activin, ACVR2 associates with and phosphorylates ACVR1.

ACVR1, in turn, phosphorylates Smad2 and/or Smad3. Phosphorylated Smad2 and Smad3 associate with Smad4, translocate to the nucleus, and regulate gene expression. There may be other non-Smad pathways in activin signal transduction. These include the RhoA-ROCK-MEKK1-JNK and MEKK1-p38 pathways. In addition to activin, other ligands such as myostatin, nodal, and bone morphogenetic protein 7 (BMP-7) may also bind to ACVR2 and affect signal transduction.

Expression Abundant expression in multiple tissues, including skeletal muscle, stomach, heart, endometrium, testes, prostate, ovary, and neural tissues. The cell surface level of ACVR2 and ACVR2B is regulated by proteins called ARIPs (activin receptor-interacting proteins).

Localisation Cell surface, spanning cytoplasmic membrane.

Function Activin signaling via its receptors has roles in cell proliferation, differentiation, apoptosis, metabolism, immune response, wound repair, and endocrine function.

Mutations Somatic Exon 10 polyadenine tract (A8-A7).

Implicated in Colon cancer Note: Colon cancer with A8-A7 deletion in exon10.

Disease Microsatellite unstable colon cancer.

ACVR2 (activin receptor type 2) Boles S et al.


Prognosis Increased tumor size.

Abnormal Protein No fusion protein; truncated non-functional protein.

Oncogenesis Occurs late in adenoma to carcinoma transition.

References Mathews LS, Vale WW. Characterization of Type II Activin Receptors. J Biol Chem 1993;268:19013-19018. Hildén K, Tuuri R, Erämaa M, Ritvos O. Expression of type II activin receptor genes during differentiation of human K562 cells and cDNA cloning of the human type IIB activin receptor. Blood 1994;83:2163-2170. Attisano L, Wrana JL, Montalvo E, Massagué J. Activation of signalling by the activin receptor complex. Mol Cell Biol 1996;16:1066-1073. Jung B, Doctolero R, Tajima A, Nguyen AK, Keku T, Sandler RS, Carethers JM. Loss of activin receptor type 2 protein expression in microsatellite unstable colorectal cancers. Gastroenterology 2004;126:654-659.

Chen YG, Wang Q, Lin SL, Chang CD, Chuang J, Ying SY. Activin signaling and its role in regulation of cell proliferation, apoptosis, and carcinogenesis. Exp Biol Med 2006;231:534-544. Jung B, Smith EJ, Doctolero RT, Gervaz P, Cerotttini JP, Bouzourene H, Goel A, Arnold CN, Boland CR, Alonso JC, Greenson JK, Carethers JM. Influence of target gene mutations on survival, stage and histology in sporadic microsatellite unstable colon cancers. Int J Cancer 2006;118:2509-2513. Liu ZH, Tsuchida K, Matsuzaki T, Bao YL, Kurisaki A, Sugino H. Characterization of isoforms of activin receptor-interacting protein 2 that augment activin signaling. J Endocrinol 2006;189:409-421. Jung B, Beck SE, Fiorino A, Doctolero RT, Smith EJ, Bocanegra M, Cabrera BL, Carethers JM. Activin type 2 receptor restoration in MSI-H colon cancer suppresses growth and enhances migration with activin. Gastroenterology 2007;132:633-644.

This article should be referenced as such:

Boles S, Chau E, Jung B. ACVR2 (activin receptor type 2). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):1-2.





EP400 (E1A binding protein p400) Sandrine Tyteca

Chromatin and Cell Proliferation group, LBCMCP-UMR 5088 CNRS, Universite Paul Sabatier, Bat 4R3B1, 118 route de Narbonne, 31062 Toulouse Cedex 9, France


Online updated version: http://AtlasGeneticsOncology.org/Genes/EP400ID40457ch12q24.html DOI: 10.4267/2042/38461


Identity Hugo: EP400 Other names: CAGH32; E1A binding protein p400; hDomino; p400; TNRC12 Location: 12q24.33

DNA/RNA Description The EP400 gene consists of 52 exons and spans 130.5 kb of genomic sequence on chromosome 12.

Transcription The predominant mRNA transcribed from this gene is 12,265 nt long. This is actually the isoform 2 of EP400. Three other isoforms generated by alternative splicing have been described:

Isoform 1 retains an alternatively spliced sequence inside intron 2. Isoform 3 lacks exon 4. Isoform 4 lacks exon 23.

Pseudogene There is an EP400 pseudogene termed 'EP400 N-terminal like' (EP400-NL) in the same locus.

Protein Description The EP400 protein (isoform 2) is 3124 amino acids long and its molecular weight is about 400 kDa. It was cloned and characterized in 2001 thanks to its interation with the E1A oncoprotein. Isoform 1 produces a 3160 aa long protein. Isoform 3 produces a 3087 aa long protein. Isoform 4 produces a 3043 aa long protein.

EP400 (E1A binding protein p400) Tyteca S


There has been no experimental confirmation for isoforms 3 and 4. The only described post-translational modification is a phosphorylation on Ser736.

Expression No data.

Localisation EP400 belongs to chromatin remodelling complexes which are located in the nucleus, so it is probably nuclear. However, its cellular localization has not been formally monitored to date.

Function EP400 belongs to the SWI2/SNF2 family of ATPases and is found in two highly related chromatin remodelling complexes: the Tip60 and p400 complexes. In these complexes, EP400 is associated with other enzymes such as the Tip60 histone acetyltransferase and/or the RuvBL1 and RuvBL2 helicases. (Note: putative specific functions of each splicing variant have not been investigated to date) Functions at the cellular level: EP400 has been implicated in cell cycle control, apoptosis and development. First, the depletion of EP400 in untransformed human fibroblasts leads to senescence through induction of the p53 - p21 pathway. Likewise, the EP400 knock-down induces a p21-dependent cell cycle arrest in human cell lines. According to these results, EP400 seems to favour cell proliferation. On the other hand, EP400 is required for E1A-mediated apoptosis. Similarly, EP400 is required for apoptosis upon DNA damage in human cell lines. Thus, EP400 also favours apoptosis, possibly through preventing cell cycle arrest. Finally, the murine homolog of EP400 appears to be involved in embryonic hematopoiesis. Functions at the molecular level: EP400 has ATP-dependent chromatin remodelling activity. Accordingly, EP400 was shown to be recruited along with the Tip60 complex on promoters by the c-myc and E2F transcription factors. Moreover, the EP400 homolog in drosophila is able to exchange specific histone variants at double-strand breaks.

Homology EP400 contains the SNF2 N-terminal domain shared by all ATPases of the SWI2/SNF2 family (SNF2, STH1, RAD16, RAD54, ISWI...). It also bears helicase-specific domains (see diagram): an helicase C-terminal domain; an HSA domain; a DEXH box which contains the ATP-binding region. Putative homologs in other species (non exhaustive):

M. musculus: Ep400 R. norvegicus: Ep400 G. gallus: EP400 D. melanogaster: DOM or domino

Implicated in Cancers Oncogenesis It was shown that EP400 is a target for the E1A viral oncoprotein transforming activity. Indeed, studies showed that the overexpression of specific EP400 fragments corresponding to the E1A binding region (the SWI2/SNF2 domain) enhance the ability of E1A to transform rat embryo fibroblasts in the presence of ras. Moreover, the same fragments are able to partially restore the transforming activity of a tranformation-defective E1A mutant.

References Fuchs M, Gerber J, Drapkin R, Sif S, Ikura T, Ogryzko V, Lane WS, Nakatani Y, Livingston DM. The p400 complex is an essential E1A transformation target. Cell 2001;106(3):297-307. Frank SR, Parisi T, Taubert S, Fernandez P, Fuchs M, Chan HM, Livingston DM, Amati B. MYC recruits the TIP60 histone acetyltransferase complex to chromatin. EMBO Rep 2003;4(6):575-580. Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci USA 2004;101(33):12130-12135. Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates JR 3rd, Abmayr SM, Washburn MP, Workman JL. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 2004;306(5704):2084-2087. Chan HM, Narita M, Lowe SW, Livingston DM. The p400 E1A-associated protein is a novel component of the p53 ---> p21 senescence pathway. Genes Dev 2005;19(2):196-201. Samuelson AV, Narita M, Chan HM, Jin J, de Stanchina E, McCurrach ME, Narita M, Fuchs M, Livingston DM, Lowe SW. p400 is required for E1A to promote apoptosis. J Biol Chem 2005;280(23):21915-21923. Tyteca S, Vandromme M, Legube G, Chevillard-Briet M, Trouche D. Tip60 and p400 are both required for UV-induced apoptosis but play antagonistic roles in cell cycle progression. EMBO J 2006;25(8):1680-1689. Flinterman MB, Mymryk JS, Klanrit P, Yousef AF, Lowe SW, Caldas C, Gaken J, Farzaneh F, Tavassoli M. p400 function is required for the adenovirus E1A-mediated suppression of EGFR and tumour cell killing. Oncogene 2007;[Epub ahead of print]. Ueda T, Watanabe-Fukunaga R, Ogawa H, Fukuyama H, Higashi Y, Nagata S, Fukunaga R. Critical role of the p400/mDomino chromatin-remodeling ATPase in embryonic hematopoiesis. Genes Cells 2007;12(5):581-592.


Tyteca S. EP400 (E1A binding protein p400). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):3-4.





ENC1 (ectodermal-neural cortex (with BTB-like domain)) Shalom Avraham, Seyha Seng, Shuxian Jiang, Hava Karsenty Avraham

Beth Israel Deaconess Medical Center, Harvard Institutes of Medicine, 4 Blackfan Circle, Boston, MA 02115, USA


Online updated version: http://AtlasGeneticsOncology.org/Genes/NRPBID40451ch5q12.html DOI: 10.4267/2042/38462


Identity Hugo: ENC1 Other names: CCL28; ENC-1; NRPB; NRP/B (Nuclear Matrix Restricted Protein/Brain); PIG10; TP53I10 Location: 5q12-13

Mapping of human NRP/B/ENC1 to 5q12-13: Chromosome 5 content of each hybrid is shown as a solid bar. Deleted segments of Chromosome 5 are indicated to the right.

DNA/RNA Description The NRP/B/ENC1 open reading frame is 1770 bp. The murine NRP/B/ENC1 gene consists of four exons interrupted by three introns that span 7.6 kb of DNA. The complete open reading frame is located in exon 3. Transcription is 5.5 kb of RNA.

Protein Description 589AA and 66130 Da. NRP/B/ENC1 is a member of a growing family of proteins that contains two major structural elements: A BTB/POZ domain in the N-terminus and kelch motif in the C-terminus [See above]. The BTB/POZ domain, consisting of approximately 115 amino acids is found in several members of the kelch family. It is involved in protein-protein interactions and mediates both dimer and heterodimer formation. The kelch domain includes six repeats (each containing about 50 amino acids), which are implicated in actin binding, protein folding and/or protein-protein interactions. NRP/B/ENC1 encodes an unusually evolutionarily conserved protein between mouse and human.

Expression NRP/B/ENC1 is expressed in the nervous system. NRP/B/ENC1 is expressed mostly in primary neurons, but not in primary astrocytes. NRP/B/ENC1 mRNA and protein expression were detected abundantly and observed in human primary brain tumors, including glioblastoma multiformae and astrocytoma, and in human neuroblastoma cell lines (IMR32, SK-N-MC, SK-N-SH), in glioblastoma cell lines (A172, T98G, U87-MG, U118-MG, U138-MG and U373-MG), and in neuroglioma (H4) and astrocytoma cell lines (CCF-STTG1 and SW1088).

Localisation Nuclear (Glioblastoma, U87-MG) and Cytosolic (Glioblastoma, GBM).

ENC1 (ectodermal-neural cortex (with BTB-like domain)) Avraham S et al


Nuclear and cytoplasmic expression of NRP/B/ENC1 were demonstrated by immunostaining with specific anti-NRP/B/ENC1 antibody. Nuclear NRP/B/ENC1: (A) Human normal adult brain (frontal cortex), (B) U87-MG human glioblastoma cells. (C) Cytoplasmic NRP/B/ENC1: primary GBM cells.

Function Evidence suggests that NRP/B/ENC1 is involved in multiple cell processes, including nervous system development, neuronal and adipocyte differentiation and brain tumorigenesis. NRP/B/ENC1 functions as an actin-binding protein that may be important in the organization of the actin cytoskeleton during neural fate specification and nervous system development, and plays a crucial role in the regulation of neuronal

process formation via association with the hypophosphorylated form of retinoblastoma protein (p110RB).

Homology NRP/B/ENC1 shares significant homology with the 'kelch' repeats found in several kelch-related genes, including the Drosophila gene which is essential for oogenesis.

Mutations

ENC1 (ectodermal-neural cortex (with BTB-like domain)) Avraham S et al


Note: p53-induced protein 10 (PIG10) was identified in DLD1 colon cancer cells. PIG10 contains multiple mutations and deletions, and is a variant form of NRP/B/ENC1. It has also been observed that there are a number of mutations and deletions occurred on the BTB, IVS and Kelch domains of NRP/B/ENC1 in human brain tumor cell lines and human brain tumors (GBM) (see tables below). The mutations on the Kelch domain are involved in brain tumor development

Implicated in Brain tumor Note: Little is known.

Disease Mutations of NRP/B/ENC1 were reported to be related to brain tumor development. NRP/B/ENC1 has been implicated in nervous system and neuronal differentiation, and these mutations of NRP/B/ENC1 may lead to neuropathology.

Oncogenesis The role of NRP/B/ENC1 in oncogenesis has been established. Evidence suggests that both amplification and alteration of NRP/B/ENC1 may lead to brain tumor development.

References Xue F, Cooley L. Kelch encodes a component of intercellular bridges in Drosophila egg chambers. Cell 1993;72:681-693. Bardwell VJ, Treisman R. The POZ domain: a conserved protein-protein interaction motif. Genes Dev 1994;8:1664-1677. Albagli O, Dhordain P, Deweindt C, Lecocq G, Leprince D. The BTB/POZ domain: a new protein-protein interaction motif common to DNA- and actin-binding proteins. Cell Growth Differ 1995;6:1193-1198.

von Bülow M, Heid H, Hess H, Franke WW. Molecular nature of calicin, a major basic protein of the mammalian sperm head cytoskeleton. Exp. Cell Res 1995;219:407-413. Hernandez MC, Andres-Barquin PJ, Martinez S, Bulfone A, Rubenstein JL, Israel MA. ENC-1: a novel mammalian kelch-related gene specifically expressed in the nervous system encodes an actin-binding protein. J. Neurosci 1997;17:3038-3051. Polyak K, Xia Y, Zweier JL, Kinzler KW, Vogelstein B. A model for p53-induced apoptosis. Nature 1997;389:300-305. Hernandez MC, Andres-Barquin PJ, Holt I, Israel MA. Cloning of human ENC-1 and evaluation of its expression and regulation in nervous system tumors. Exp. Cell Res 1998;242:470-477. Kim TA, Lim J, Ota S, Raja S, Rogers R, Rivnay B, Avraham H, Avraham S. NRP/B, a novel nuclear matrix protein, associates with p110(RB) and is involved in neuronal differentiation. J. Cell. Biol 1998;14:553-566. Hernandez MC, Andres-Barquin PJ, Kuo WL, Israel MA. Assignment of the ectodermal-neural cortex 1 gene (ENC1) to human chromosome band 5q13 by in situ hybridization. Cytogenet Cell Genet 1999;87:89-90. Hernandez M, Andres-Barquin PJ, Israel MA. Assignment of the ectodermal-neural cortex 1 gene (Enc1) to mouse chromosome band 13D1 by fluorescence in situ hybridization. Cytogenet Cell Genet 2000;89:158-159. Kim TA, Ota S, Jiang S, Pasztor LM, White RA, Avraham S. Genomic organization, chromosomal localization and regulation of expression of the neuronal nuclear matrix protein NRP/B in human brain tumors. Gene 2000;255:105-116. Haigo SL, Harland RM, Wallingford JB. A family of Xenopus BTB-Kelch repeat proteins related to ENC-1: new markers for early events in floorplate and placode development. Gene Expr. Patterns 2003;3(5):669-674. Liang XQ, Avraham HK, Jiang S, Avraham S. Genetic alterations of the NRP/B gene are associated with human brain tumors. Oncogene 2004;23:5890-5900. Kim TA, Jiang S, Seng S, Cha K, Avraham HK, Avraham S. The BTB domain of the nuclear matrix protein NRP/B is required for neurite outgrowth. J. Cell Sci 2005;118:5537-5548.


Avraham S, Seng S, Jiang S, Avraham HK. ENC1 (ectodermal-neural cortex (with BTB-like domain)). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):5-7.





RHOC (ras homolog gene family, member C) Ahmad Faried, Leri S Faried

Department of General Surgical Science (Surgery I), Graduate School of Medicine, Gunma University, Maebashi, Japan


Online updated version: http://AtlasGeneticsOncology.org/Genes/RHOCID42110ch1p13.html DOI: 10.4267/2042/38463


Identity Hugo: RHOC Other names: ARH9; ARHC; H9; MGC1448; MGC61427; RhoH9 Location: 1p13.1

DNA/RNA Description The RhoC gene contains 6 exons and 5 introns. It was predicted to span over approximately 6.3 kb of the genomic DNA with mRNA size approximately 1116 bp. This gene is related to a gene originally identified in the marine snail, Aplysia. After the original cloning of Rho gene in Aplysia californica, then several genes in mammal been identified and divided into several subfamily, among them is ( RhoA, RhoB and RhoC isoforms). In 1993, human ARH9 (RhoC), was reexamined and showed that it was present in choromosome 1. Human cDNA of RhoC proteins were isolated from the complete H9Rho (clone 9) coding sequence. Other group isolated RhoC from adult retina library.

Transcription Three alternative transcripts encoding the same protein have been identified for RhoC gene.

Protein Description The primary protein sequences of Rho-subfamily (RhoA, B and C) are about 85% identical, with most divergence close to the C-terminus. The sequence divergence among RhoA, B and C is found in the insert loop, a helix between amino acids 123 and 137. The RhoC consists of 193 amino acids corresponding to a molecular weight of 22 kDa. RhoC protein consists of

GTPase binding domain in the N-terminal. In C-terminal consists of geranylgeranyl group and carboxyl methylation extension. RhoC contains the sequence motif of GTP-binding proteins, bind to GDP and GTP with high affinity and are involved in cycle between in-active, GDP-bound and active, GTP-bound states. RhoC displays about 30% amino acids identity with Ras proteins which mainly clustered in four highly homologues internal region corresponding to the GTP binding site.

Expression The RhoC proteins are over-expressed in bladder carcinoma, breast carcinoma, and in the squamous cell carcinoma of the head and neck. At mRNA level, RhoC are over-expressed in adenocarcinoma of the ovary, pancreatic cancer and hepatocellular carcinoma.

Localisation Mainly in the cytoplasm, there is a small fraction localized in the plasma membrane of the Rat-2 fibroblast cells and associated with undefined perinuclear structures.

Function The Rho proteins are involved in multiple processes, such as organization of the cytoskeletal components, cell division or intracellular trafficking. Role of RhoC also been observed in limb development. The RhoC protein has been connected to cancer development. It is up-regulated in malignant pancreatic ductal carcinoma, inflammatory breast cancer tumors and highly metastatic melanoma. Ectopic over-expression of this gene increases the tumorigenic and metastasis properties of tumor progenitor cell. RhoC also induces the expression of angiogenic factors in human mammary epithelial cells, by facilitating the vascularization of tumors in which it is expressed.

RHOC (ras homolog gene family, member C) Faried A, Faried LS


Homology At least there are five homologues of RhoC sequences with pair-wise similarity from 80-100% at the amino acids level. Among them in dog (Canis lupus familiaris), rat (Rattus norvergicus), mouse (Mus musculus), zebrafish (Danio rerio), and chicken (Gallus gallus).

Mutations Germinal Not found in Homo sapiens.

Somatic Not found in Homo sapiens.

Implicated in Morphogenesis Note: The RhoC exhibits specific expression domain in regions undergoing major cell rearrangement process in the developing limb autopod, including the prechondrogeneic aggregates, the developing interphalangeal joints and tendons. Functional experiments indicate that RhoC is a regulator of mesenchymal cell shape and adhesiveness, acting as a modulator of digit morphogenesis and joint formation.

Malignancy Disease The RhoC reported to be over-expressed in many human cancers (see above).

Prognosis The RhoC over-expression is a predictor of poor prognosis in malignancy.

Oncogenesis The RhoC and RhoA are 94% identical, only 11 amino acids are different. RhoC plays a major role in cell locomotion compare with RhoA. Over-expression of RhoC is closely related with tumor cell invasion and metastasis.

References Madaule P, Axel R. A novel ras-related gene family. Cell 1985;41:31-40. Chardin P, Madaule P, Tavitian A. Coding sequence of human rho cDNAs clone 6 and clone 9. Nucl. Acids Res 1988;16:2717. Adamson P, Paterson HF, Hall A. Intracellular localization of the P21rho proteins. J. Cell Biol 1992;119:617-627. Morris SW, Valentine MB, Kirstein MN, Huebner K. Reassignment of the human ARH9 RAS-related gene to chromosome 1p13-p21. Genomics 1993;15:677-679. Fagan KP, Oliveira L, Pittler SJ. Sequence of rho small GTP-binding protein cDNAs from human retina and identification of novel 5' end cloning artifacts. Exp. Eye Res 1994;59:235-237. Ihara K, Muraguchi S, Kato M, Shimizu T, Shirakawa M, Kuroda S, Kaibuchi K, Hakoshima T. Crystal structure of human RhoA in a dominantly active form complexed with a GTP analogue. J. Biol. Chem 1998;273:9656-9666.

Suwa H, Ohshio G, Imamura T, Watanabe G, Arii S, Imamura M, Narumiya S, Hiai H, Fukumoto M. Overexpression of the rhoC gene correlates with progression of ductal adenocarcinoma of the pancreas. Br. J. Cancer 1998;77:147-152. Clark EA, Golub TR, Lander ES, Hynes RO. Genomic analysis of metastasis reveals an essential role for RhoC. Nature 2000;406:532-535. van Golen KL, Wu ZF, Qiao XT, Bao LW, Merajver SD. RhoC GTPase, a novel transforming oncogene for human mammary epithelial cells that partially recapitulates the inflammatory breast cancer phenotype. Cancer Res 2000;60:5832-5838. van Golen KL, Wu ZF, Qiao XT, Bao L, Merajver SD. RhoC GTPase overexpression modulates induction of angiogenic factors in breast cells. Neoplasia 2000;2:418-425. Michaelson D, Silletti J, Murphy G, D'Eustachio P, Rush M, Philips MR. Differential localization of Rho GTPases in live cells: regulation by hypervariable regions and RhoGDI binding. J. Cell Biol 2001;152:111-126. Kleer CG, van Golen KL, Zhang Y, Wu ZF, Rubin MA, Merajver SD. Characterization of RhoC expression in benign and malignant breast disease: a potential new marker for small breast carcinomas with metastatic ability. Am. J. Pathol 2002;160:579-584. Horiuchi A, Imai T, Wang C, Ohira S, Feng Y, Nikaido T, Konishi I. Up-regulation of small GTPases, RhoA and RhoC, is associated with tumor progression in ovarian carcinoma. Lab. Invest 2003;83:861-870. Kamai T, Tsujii T, Arai K, Takagi K, Asami H, Ito Y, Oshima H. Significant association of Rho/ROCK pathway with invasion and metastasis of bladder cancer. Clin. Cancer Res 2003;9:2632-2641. Wang L, Yang L, Luo Y, Zheng Y. A novel strategy for specifically down-regulating individual Rho GTPase activity in tumor cells. J. Biol. Chem 2003;278:44617-44625. Etienne-Manneville S. Actin and microtubules in cell motility: which one is in control?. Traffic 2004;5:470-477. Ikoma T, Takahashi T, Nagano S, Li YM, Ohno Y, Ando K, Fujiwara T, Fujiwara H, Kosai K. A definitive role of RhoC in metastasis of orthotopic lung cancer in mice. Clin. Cancer Res 2004;10:1192-1200. Wang W, Yang LY, Huang GW, Lu WQ, Yang ZL, Yang JQ, Liu HL. Genomic analysis reveals RhoC as a potential marker in hepatocellular carcinoma with poor prognosis. Br. J. Cancer 2004;90:2349-2355. Wheeler AP, Ridley AJ. Why three Rho proteins? RhoA, RhoB, RhoC, and cell motility. Exp. Cell Res 2004;301:43-49. Jaffe AB, Hall A. Rho GTPases: biochemistry and biology. Annu. Rev. Cell Dev. Biol 2005;21:247-269. Faried A, Faried LS, Kimura H, Nakajima M, Sohda M, Miyazaki T, Kato H, Usman N, Kuwano H. RhoA and RhoC proteins promote both cell proliferation and cell invasion of human oesophageal squamous cell carcinoma cell lines in vitro and in vivo. Eur. J. Cancer 2006;42:1455-1465. Kleer CG, Teknos TN, Islam M, Marcus B, Lee JS, Pan Q, Merajver SD. RhoC GTPase expression as a potential marker of lymph node metastasis in squamous cell carcinomas of the head and neck. Clin. Cancer Res 2006;12:4485-4490. Montero JA, Zuzarte-Luis V, Garcia-Martinez V, Hurle JM. Role of RhoC in digit morphogenesis during limb development. Dev. Biol 2007;303:325-335.


Faried A, Faried LS. RHOC (ras homolog gene family, member C). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):8-9.





SAV1 (Salvador homolog 1 (Drosophila)) Bernard A Callus

Biochemistry Department, La Trobe University, Bundoora VIC 3086, Australia


Online updated version: http://AtlasGeneticsOncology.org/Genes/SAV1ID42206ch14q13.html DOI: 10.4267/2042/38464


Identity Hugo: SAV1 Other names: Salvador; WW45; WWP4 Location: 14q13-q23 Local order: telomeric to SPG3A and centromeric to ZF405P.

DNA/RNA Description The Sav1 gene spans 34.7 kb.

Transcription The longest SAV1 mRNA transcript of 3.0 kb encodes an open reading frame (ORF) of 1152 bases and untranslated regions of 338 and 1541 bases at the 5’ and 3’ ends, respectively. No splice variants have been reported for SAV1. Smaller transcripts of 1.8 kb and 2.1 kb, encoding the identical ORF, have been isolated which may be the result of alternative sites of poly-adenylation.

Protein Description Sav1 is 383 amino acids in length with an expected weight of 44,606 Da. WW1: residues 199-232; WW2: 234-267; SARAH domain: residues 321-368. The SARAH domain partially overlaps with a predicted coiled-coil domain: 344-373.

Expression SAV1 mRNA is ubiquitously expressed in adult tissues with highest expression in the placenta, pancreas, heart, kidney, lung and aorta and lowest expression in skeletal muscle. Expression was higher in fetal heart compared with adult heart.

Localisation SAV1 is localized to the centrosome during interphase and metaphase and localizes with the contractile ring during cytokinesis. SAV1 co-localizes with MST2, RASSF1A and LATS1 during anaphase, interphase, metaphase and cytokinesis.

SAV1 is encoded by five exons represented by the boxes. The blue shaded region indicates the Sav1 coding region while the untranslated regions (UTR) are shown in white.

SAV1 contains two central proline-binding WW domains (red) and a C-terminal SARAH (for Salvador/Rassf/Hippo) domain (green).

SAV1 (Salvador homolog 1 (Drosophila)) Callus BA


Function Sav1 is a scaffold protein and able to homodimerize independently of its SARAH domain. Sav1 binds to MST1 /2 kinases and RASSF1A in an interaction that requires their homologous SARAH domains. The binding of MST stabilizes SAV1 abundance and enhances the association of SAV1 with RASSF1A. SAV1 is phosphorylated by MST1/2 but the consequence of this is not known. The MST2/SAV1/RASSF1A complex can recruit LATS1 kinase resulting in the activation of LATS1 by MST2. The MST2/SAV1/RASSF1A/LATS1 complex may function in regulating cell-cycle exit. In Drosophila, dSav mutant tissue is more resistant to apoptosis and grows more quickly compared with wild type tissue suggesting dSav is a dual regulator of cell proliferation and apoptosis.

Homology mSav1 is 94% identical to hSav1. hSav1 is 31% identical and 44% similar to dSav from Drosophila melanogaster, however, the similarity increases to 59% if only the sequences comprising the WW and SARAH domains are compared. There is no recognizable orthologue of hSav1 in S.cerevisiae.

Mutations Note: The cDNA sequence for SAV1 is conflicted at codons 5 (K/Q), 18 (Q/R), 292 (L/F) and 373 (Q/stop).

Germinal No germline mutations for SAV1 have been reported.

Somatic In one study of 52 cancer cell lines, SAV1 was deleted in two renal cancer cell lines (ACHN and 786-O) and a C to A mutation at nucleotide 554 (Ala185Asp) was detected in a colon cancer cell line (HCT15). A second study from the Korean population failed to detect the C554A polymorphism or any additional mutations of SAV1 in 324 cancer cell lines. A third study failed to detect hypermethylation the SAV1 promoter in 44 soft tissue sarcomas and 6 sarcoma cell lines. These results suggest that (1) the C554A mutation found in the colon cancer cell line might be a true mutation and (2) that SAV1 is not frequently mutated in human cancers.

Implicated in To date SAV1 is not implicated in any diseases.

References Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S. Construction and characterization of a full length-enriched and a 5’-end-enriched cDNA library. Gene 1997;200:149-156. Valverde P. Cloning, Expression and Mapping of hWW45, a Novel Human WW Domain-Containing Gene. Biochem Biophyhs Res Comm 2000;276:990-998. Strausberg RL, Feingold EA, Grouse LH, et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci USA 2002;99:16899-16903. Tapon N, Harvey KF, Bell DW, Wahrer DCR, Schiripo TA, Haber DA, Hariharan IK. Salvador promotes both cell cycle exit and apoptosis in Drosophila and is mutated in human cancer cell lines. Cell 2002;110:467-478. Ebert L, Schick M, Neubert P, Schatten R, Henze S, Korn B. Cloning of human full open reading frames in Gateway (TM) system entry vector (pDONR201). Direct submission GenBank database June 2004. Yoo NJ, Soung YH, Lee JW, Park WS, Kim SY, Nam SW, Han JH, Kim SH, Lee JY, Lee SH. Mutational analysis of salvador gene in human carcinomas. APMIS 2003;111:595-598. Ota T, Suzuki Y, Nishikawa T, et al. Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet 2004;36:40-45. Chan EH, Nousiainen M, Chalamalasetty RB, Schafer A, Nigg EA, Sillje HH. The Ste20-like kinase Mst2 activates the human large tumor suppressor kinase Lats1. Oncogene 2005;24:2076-2086. Callus BA, Verhagen AH, Vaux DL. Association of mammalian sterile twenty kinases, Mst1 and Mst2, with hSalvador via C-terminal coiled-coil domains, leads to its stabilization and phosphorylation. FEBS J 2006;273:4264-4276. Guo C, Tommasi S, Liu L, Yee JK, Dammann R, Pfeifer GP. RASSF1A is part of a complex similar to the Drosophila Hippo/Salvador/Lats tumor-suppressor network. Curr Biol 2007;17:700-705. Seidel C, Schagdarsurengin U, Blümke K, Würl P, Pfeifer GP, Hauptmann S, Taubert H, Dammann R. Frequent hypermethylation of MST1 and MST2 in soft tissue sarcoma. Mol Carcinog 2007 May 30 (Epub ahead of print).


Callus BA. SAV1 (Salvador homolog 1 (Drosophila)). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):10-11.

Gene Section Review




SNCG (synuclein, gamma (breast cancer-specific protein 1)) Artur Czekierdowski, Sylwia Czekierdowska

Ist Departmentof Gynecologic Oncology and Gynecology, Medical University in Lublin, Poland (AC); Department of Clinical Immunology, Medical University in Lublin, Poland (SC)


Online updated version: http://AtlasGeneticsO.ncology.org/Genes/SNCGID42343ch10q23.html DOI: 10.4267/2042/38465


Identity Hugo: SNCG Other names: BCSG1 (Breast Cancer-Specific Gene-1 Protein); Gamma-synuclein; Persyn; PERSYN; PRSN; SR; Synoretin Location: 10q23.2 Note: Synuclein-gamma is a member of the synuclein family of proteins which are believed to be involved in the pathogenesis of neurodegenerative diseases. High levels of SNCG have been identified in advanced breast carcinomas suggesting a correlation between overexpression of SNCG and breast tumor development.

DNA/RNA Description Human SNCG gene consists of five exons that span about 5 kbp. The intron 1 contains two closely located AP1 recognition sequences. Deletion of these motifs greatly diminished the SNCG promoter activity, suggesting that AP1 is an important transactivator for SNCG transcription SNCG transcription is primarily controlled by regulatory sequences located in intron 1 and exon 1 but not in the 5' flanking region. Synuclein expression is regulated predominantly at the level of SNCG gene transcription and/or SNCG mRNA stability.

Protein Description Encoded by human SNCG Gene (Synuclein Family), the highly conserved 127-amino acid 13 kD cytoplasmic gamma-Synuclein is similar to the amyloid protein nonamyloid beta fragment and to alpha-

synuclein and beta-synuclein. The gamma-synuclein protein is the least conserved of the synuclein proteins. The human gamma-synuclein is 87.7% and 83.8% identical to the mouse and rat proteins, respectively, which are 4-amino acids shorter. As for the alpha- and beta-synuclein proteins, the region of highest homology is the amino-terminal region. The synuclein proteins contain several repeated domains that display variations of a KTKEGV consensus sequence. This motif, repeated six to seven times in the amino-terminal portion of the protein, is reminiscent of the alpha-helical domains of the apolipoproteins and suggests lipid binding properties. The very high conservation between species for a specific repeated domain of a particular protein suggests that the repeated domains have arisen from the duplication of a single domain within an ancestral synuclein gene. Later, this ancestral gene may have undergone successive duplications to give rise to the three synuclein genes in which the repeated domains may still be able to diverge. The third domain, however, remained absolutely identical, KTKEGV, in all genes throughout all species. The same type of domain is present in proteins of the rho family. However, as of today, the role of these domains remains unknown.

Expression Mammalian gamma-synuclein was first identified as the so-called Breast Cancer-Specific Gene 1 (BCSG1) in a high-throughput direct differential-cDNA-sequencing screen for markers of breast cancer. Northern blot analysis showed that the gene is principally expressed in the brain, particularly in the substantia nigra. The protein is expressed in the peripheral nervous system, mainly in primary sensory neurons, sympathetic neurons, and motor neurons. Synuclein gamma was also detected in ovarian tumors,

SNCG (synuclein, gamma (breast cancer-specific protein 1)) Czekierdowski A, Czekierdowska S


and in the olfactory epithelium. A sequence dubbed synoretin was independently isolated from ocular tissues in a screen for novel proteins regulating phototransduction and is now thought to represent the bovine ortholog of gamma-synuclein. SNCG is expressed in brain, heart, skeletal muscle, ovary, testis, colon, spleen, pancreas, kidney and lung.

Localisation The three human synuclein genes are expressed in the thalamus, the substantia nigra, the caudate nucleus, and the amygdala. Only gamma-synuclein appears strongly expressed in the subthalamic nucleus. Although gamma-synuclein is not present in senile plaques, Lewy bodies or neurofibrillary tangles, a high level of gamma-synuclein immunoreactivity is detectable in dot-like structures which are characteristic axonal lesions in the brains of patients with neurodegenerative diseases. SNCG mRNA and gamma-synuclein protein were also detected in unstimulated and phytohaemagglutinin (PHA)-stimulated cultured lymphocytes from peripheral blood of normal donors. It has been shown previously by in situ hybridization that SNCG/BCSG1 mRNA is not expressed in normal adult breast tissue, but high levels of this mRNA are present in advanced infiltrating breast tumours. In paraformaldehyde fixed cells, SNCG displayed punctuate cytoplasmic staining, a pattern that is usually associated with markers of the endoplasmic reticulum or vesicular structures. It was also found that gamma-synuclein was not co-localized with cytokeratin, actin or tubulin arrays in these cells.

Function The normal cellular function of gamma-synuclein is as yet unknown, but interestingly exogenous expression of the protein increases the invasive and metastatic potential of breast tumors. The highly conserved N-terminal region is known to be important for the lipid interactions of the synucleins and the highly acidic C-terminal region has been suggested to possess chaperone-like activity, to regulate the aggregation of synucleins and to mediate protein-protein interactions. It seems that gamma-synuclein plays a role in neurofilament network integrity and may modulate axonal architecture, also, it may increase the susceptibility of neurofilament-H to calcium-dependent proteases and may also modulate the keratin network in skin. Phosphorylation by GRK5 appears to occur on residues distinct from other kinase target residues. Synuclein gamma is likely involved in the pathogenesis of neurodegenerative diseases and SNCG is expressed at very high level in advanced infiltrating breast cancer. Sequence analysis suggests that the protein from tumour cells (BCSG1) is different from the protein expressed in the nervous system (cDNA clones 1 and 4C) and that coded by the genomic clone W6H. Substitution of two lysines by glutamates in BCSG1

changes the overall charge of the persyn molecule and disturbs EKTKEGV repeats that are highly conserved in the synuclein family. Such changes should have serious consequences for protein structure and function. The dual role of SNCG in neurodegeneration and malignancy could involve common mechanisms. Changes in organization of the cell cytoskeleton are among the most prominent characteristics of both processes. The involvement of gamma-synuclein in regulating neurofilament network integrity raises the possibility that it may also affect the intermediate filament network in malignant breast epithelial cells.

Homology There are currently almost 200 DNA and protein sequences in the sequence databases with high homology to the synuclein gene or protein. All synuclein sequences available to date from Homo sapiens, Mus musculus, and Rattus norvegicus can be assigned to three distinct protein groups: alpha beta and gamma-synuclein. Synuclein proteins have also been identified in other organisms: synelfin is the alpha-synuclein ortholog in Serinus, phosphoneuroprotein 14 (PNP14) is the beta-synuclein ortholog in Bos taurus, and the first synuclein protein described in Torpedo californica corresponds to the human gamma-synuclein. Interestingly, no homologous proteins have yet been identified in Escherichia coli, Saccharomyces cerevisiae,Caenorhabditis elegans, or Drosophila melanogaster. Each of the three family members is composed of an N-terminal lipid-binding domain, containing a series of 11-residue imperfect repeats, and an acidic C-terminal domain. Among the human family members, gamma-synuclein 50% identical and 74% homologous to alpha- synuclein and 47% identical and 66% homologous beta-synuclein The highly conserved N-terminal region is known to be important for the lipid interactions of the synucleins and the highly acidic C-terminal region has been suggested to possess chaperone-like activity, to regulate the aggregation of synuclein and to mediate protein-protein interactions. The very high degree of conservation in the lipid-binding N-terminal domains of all three synucleins strongly suggests that both beta and gamma-synuclein like alpha-synuclein bind to lipid membranes and adopt a highly helical structure. Nevertheless, differences in the sequences of the three proteins in both their N-terminal and C-terminal domains must be responsible for those differences that do exist in their individual functions, as well as for their different roles in disease.

Mutations Note: No tumor-specific mutations of the SNCG gene were found in breast tumors and tumor cell lines, but two linked polymorphisms in the coding region were detected, both in mRNA and in exons III and IV of the gene from G243C and T377A. These results reflect the



absence of two G--A (and consequently Glu--Lys) in tumor cell lines, tumors and control tissues. The above mentioned two linked polymorphic sites discriminate two alleles of the human persyn gene. The frequencies of the two alleles were the same in genomes of breast cancer and normal cells (20% G243/T377 and 80% C243/A377). Both alleles are transcriptionally active and are expressed with similar efficiency in heterozygotes.

Epigenetics Sequence analysis identified a CpG island in exon 1 of SNCG that contains 15 CpG sites, covering the region -169 to +81, relative to the translation start codon. CpG sites within the CpG island and its vicinity were partially and heterogeneously methylated in SNCG-negative breast cancer cell lines but unmethylated in SNCG-positive cells. SNCG expression correlates with complete demethylation of the exon 1 region. Specific methylation at the CpG sites 2, 5, 7, and 10-15, was sufficient to block the expression of SNCG gene in breast cell culture. Genomic sequencing and methylation-specific PCR assays have shown that SNCG CpG island is fully methylated in normal tissues of liver, esophagus, prostate, cervix, stomach, colon, and lung, but only partially methylated in breast tissue. Tumors from these tissues contain completely demethylated SNCG. Universal loss of the epigenetic control of SNCG gene expression in tumors and further demonstrating that the demethylation of SNCG CpG island is primarily responsible for the aberrant expression of SNCG protein in cancerous tissues have suggested an important role of gamma-synuclein-related epigenectic events in various malignancies. Reactivation of SNCG gene expression by DNA demethylation is a common critical contributing factor to malignant progression of many solid tumors and its expression in primary carcinomas is an effective molecular indicator of distant metastasis.

Implicated in Note: The possible involvement of gamma-synuclein in tumorigenesis first came to light when a gene named BCSG1 (Breast Cancer-Specific Gene 1) was shown to be overexpressed in advanced infiltrating carcinoma of the breast. In fact, BCSG1 and gamma-synuclein appear to be the same protein. SNCG protein is highly expressed in diversified cancer types, including the female hormone-sensitive cervical and breast cancers, male hormone-sensitive prostate cancer, four cancer types of the digestive system, and lung cancer. These cancers are currently the leading cause of mortality in both men and women. How SNCG induces disease progression in different cancer types remains elusive. Oncogenic activation of gamma-synuclein contributes to the development of breast and ovarian cancer by promoting tumor cell survival under adverse conditions

and by providing resistance to certain chemotherapeutic drugs. Overexpression of gamma-synuclein leads to constitutive activation of extracellular signal-regulated protein kinases ( ERK1 / ERK2 ) and down-regulation of c-Jun N-terminal kinase 1 (JNK1) in response to environmental stress signals. Cells expressing gamma-synuclein are significantly more resistant to the chemotherapeutic drugs paclitaxel and vinblastine as compared with the parental cells. Activation of JNK1 and its downstream caspase-3 by paclitaxel or vinblastine is significantly down-regulated in gamma-synuclein-expressing cells, indicating that the apoptosis pathway activated by vinblastine or paclitaxel is blocked by gamma-synuclein. In breast cancer cells, SNCG has been shown to act as a chaperon for estrogen receptor and stimulate estrogen receptor-a signaling pathway that leads to cell proliferation. On the other hand, the inhibitory effects of SNCG on mitotic checkpoint function are mediated through the mitotic checkpoint kinase BubR1 and are independent of the expression status of estrogen receptor-alpha. The inhibitory effects of SNCG on mitotic checkpoint can be overthrown by enforced overexpression of BubR1 in SNCG-expressing cells. SNCG intracellularly associates with BubR1 together.This observation suggests that SNCG expression compromises the mitotic checkpoint control by inhibition of the normal function of BubR1, thereby promoting genetic instability, a recognized and important contributing factor in tumorigenesis. Because all synucleins have chaperone-like activities, they may interact with different proteins in different cellular background. Identifications of specific cellular targets of SNCG in different tumor types will provide insight to delineate its oncogenic functions in human malignancies.

Breast cancer Note: Patients whose tumors expressed SNCG had a significantly shorter disease-free survival and overall survival. They also had a high probability of death when compared with those whose tumors did not express SNCG. Multivariate analysis demonstrated that SNCG is an independent predictive marker for recurrence and metastasis in breast cancer progression. SNCG is expected to be a useful marker for breast cancer progression and a potential target for breast cancer treatment. In one study it has been show that responses of 12 breast cancer cell lines to paclitaxel-induced mitotic arrest and cytotoxicity highly correlated with SNCG expression status. SNCG-positive cells exhibited a significantly higher resistance to paclitaxel-induced mitotic arrest than SNCG-negative cells. Down-regulation of SNCG expression directly increased the effectiveness of anti-microtubule drug-induced cytotoxicity in breast cancer cells without altering cell responses to doxorubicin. These new findings suggest that SNCG expression in breast



carcinomas is probably a causal factor contributing to the poor patient response to paclitaxel treatment.

Ovarian cancer Note: Several studies indicated that SNCG expression was not detectable in normal ovarian epithelium but was highly expressed in the vast majority of advanced staged ovarian carcinomas. Eighty-seven percent of ovarian carcinomas were found to express at least 1 type of synuclein, and 42% expressed all 3 synucleins (alpha, beta, and gamma) simultaneously. Highly punctate gamma synuclein expression was also observed in 20% of preneoplastic lesions of the ovary, including epithelial inclusion cysts, hyperplastic epithelium, and papillary structures, suggesting that synuclein gamma up-regulation may occur early in the development of some ovarian tumors. Demethylation is an important event in abnormal synuclein-gamma expression. The methylation pattern in ovarian cancer cells is different from that in breast cancer cells. In one of the studies that examined SNCG-nonexpressing ovarian cancer cells, all of the CpG sites were completely methylated instead of selective methylation at certain sites shown in breast cancer cells, thereby suggesting a tissue-specific methylation pattern. Recent studies indicated that the detection of SNCG mRNA in tumor-positive tumors was strongly associated with demethylation or hypometylation of SNCG gene. Methylation status was not correlated with FIGO stage or histological type of tumor. Tumor grading was strongly associated with methylation status but due to relatively small group of studied samples (43 cases) this observation requires further confirmation. Another interesting observation was that in 21% of samples both products of amplification were present and all these cases were SNCG mRNA-positive. This observation could suggested that partial methylation of SNCG probably does not influence on synuclein expression in ovarian cancer tissue. Comparison of the methylation status of SNCG and the expression of synuclein-gamma in breast and ovarian cancer cells lines in another study indicated a strong correlation between hypomethylation of the CpG island and SNCG expression in cancer cell lines. The methylation pattern in ovarian cancer cells was different from that in breast cancer cells. The analyzed CpG sites in ovarian cancer cells were all methylated in contrary to a selective methylation at certain sites shown in breast cancer cells, thereby suggesting a tissue-specific methylation pattern. Moreover, when exon 1 was partially and heterogeneously methylated, then SNCG expression in breast cancer cells was not detected.

Lung cancer Note: SNCG is not expressed in normal lung tissues, but it is highly expressed in lung tumors. It has been demonstrated that cigarette smoke extract (CSE) has strong inducing effects on SNCG gene expression in

lung cancer cells through demethylation of SNCG CpG island. CSE treatment also augments the invasive capacity of cells in an SNCG-dependent manner. These new findings demonstrate that tobacco exposure induces the abnormal expression of SNCG in lung cancer cells through downregulation of expression levels of DNA methyltransferases.

Gastric cancer Note: For the gastric cancer cell lines, SNCG mRNA expression strongly correlated with demethylation of SNCG exon 1 CpG islands. Whereas SNCG was not expressed in non-neoplastic gastric mucosal tissues obtained at autopsy, partial demethylation was present in these tissues. Demethylation occurs before malignant transformation and that only partial demethylation does not result in up-regulated SNCG mRNA expression. Thus, it appears that partial SNCG demethylation can occur in normal gastric mucosa, which then extends in some cases to become to fully demethylated, resulting in up-regulated SNCG mRNA expression.

References Ji H, Liu YE, Jia T, Wang M, Liu J, Xiao G, Joseph BK, Rosen C, Shi YE. Identification of a breast cancer-specific gene, BCSG1, by direct differential cDNA sequencing. Cancer Res 1997;57:759-764. Lavedan C, Buchholtz S, Auburger G, Albin RL, Athanassiadou A, Blancato J, Burguera JA, Ferrell RE, Kostic V, Leroy E, Leube B, Mota-Vieira L, Papapetropoulos T, Pericak-Vance MA, Pinkus J, Scott WK, Ulm G, Vasconcelos J, Vilchez JJ, Nussbaum RL, Polymeropoulos MH. Absence of mutation in the beta- and gamma-synuclein genes in familial autosomal dominant Parkinson's disease. DNA Research 1998;5:401-402. Lavedan C, Leroy E, Dehejia A, Buchholtz S, Dutra A, Nussbaum RL, Polymeropoulos MH. Identification, localization and characterization of the human gamma-synuclein gene. Hum. Genet 1998;103:106-112. Ninkina NN, Alimova-Kost MV, Paterson JW, Delaney L, Cohen BB, Imreh S, Gnuchev NV, Davies AM, Buchman VL. Organization, expression and polymorphism of the human persyn gene. Hum. Molec. Genet 1998;7:1417-1424. Bruening W, Giasson BI, Klein-Szanto AJ, Lee VM, Trojanowski JQ, Godwin AK. Synucleins are expressed in the majority of breast and ovarian carcinomas and in preneoplastic lesions of the ovary. Cancer 2000;88:2154-2163. Lu A, Zhang F, Gupta A, Liu J. Blockade of AP1 transactivation abrogates the abnormal expression of breast cancer-specific gene 1 in breast cancer cells. J Biol Chem 2002;277:31364-31372. Pan ZZ, Bruening W, Giasson BI, Lee VM, Godwin AKJ. Gamma-synuclein promotes cancer cell survival and inhibits stress- and chemotherapy drug-induced apoptosis by modulating MAPK pathways. Biol Chem 2002;277:35050-35060. Gupta A, Godwin AK, Vanderveer L, Lu A, Liu J. Hypomethylation of the synuclein gamma gene CpG island promotes its aberrant expression in breast carcinoma and ovarian carcinoma. Cancer Res 2003;63:664-673. Gupta A, Inaba S, Wong OK, Fang G, Liu J. Breast cancer-specific gene 1 interacts with the mitotic checkpoint kinase BubR1. Oncogene 2003;22:7593-7599.



Wu K, Weng Z, Tao Q, Lin G, Wu X, Qian H, Zhang Y, Ding X, Jiang Y, Shi YE. Stage-specific expression of breast cancer-specific gene gamma-synuclein. Cancer Epidemiol Biomarkers Prev 2003;12:920-925. Jiang Y, Liu YE, Goldberg ID, Shi YE. Gamma synuclein, a novel heat-shock protein-associated chaperone, stimulates ligand-dependent estrogen receptor alpha signaling and mammary tumorigenesis. Cancer Res 2004;64:4539-4546. Yanagawa N, Tamura G, Honda T, Endoh M, Nishizuka S, Motoyama T. Demethylation of the synuclein gamma gene CpG island in primary gastric cancers and gastric cancer cell lines. Clin Cancer Res 2004;10:2447-2451. Inaba S, Li C, Shi YE, Song DQ, Jiang JD, Liu J. Synuclein gamma inhibits the mitotic checkpoint function and promotes chromosomal instability of breast cancer cells. Breast Cancer Res Treat 2005;94:25-35. Liu H, Liu W, Wu Y, Zhou Y, Xue R, Luo C, Wang L, Zhao W, Jiang JD, Liu J. Loss of epigenetic control of synuclein-gamma gene as a molecular indicator of metastasis in a wide range of human cancers. Cancer Res 2005;65:7635-7643. Czekierdowski A, Czekierdowska S, Wielgos M, Smolen A, Kaminski P, Kotarski J. The role of CpG islands hypomethylation and abnormal expression of neuronal protein synuclein-gamma (SNCG) in ovarian cancer. Neuro Endocrinol Lett 2006;27:381-386.

Sung YH, Eliezer D. Secondary structure and dynamics of micelle bound beta- and gamma-synuclein. Protein Sci 2006;15:1162-1174. Zhao W, Liu H, Liu W, Wu Y, Chen W, Jiang B, Zhou Y, Xue R, Luo C, Wang L, Jiang JD, Liu J. Abnormal activation of the synuclein-gamma gene in hepatocellular carcinomas by epigenetic alteration. Int J Oncol 2006;28:1081-1088. Guo J, Shou C, Meng L, Jiang B, Dong B, Yao L, Xie Y, Zhang J, Chen Y, Budman DR, Shi YE. Neuronal protein synuclein gamma predicts poor clinical outcome in breast cancer. Int J Cancer 2007;(Epub ahead of print). Liu H, Zhou Y, Boggs SE, Belinsky SA, Liu J. Cigarette smoke induces demethylation of prometastatic oncogene synuclein-gamma in lung cancer cells by downregulation of DNMT3B. Oncogene 2007 Mar 19;(Epub ahead of print). Wu K, Quan Z, Weng Z, Li F, Zhang Y, Yao X, Chen Y, Budman D, Goldberg ID, Shi YE. Expression of neuronal protein synuclein gamma gene as a novel marker for breast cancer prognosis. Breast Cancer Res Treat 2007;101:259-67.


Czekierdowski A, Czekierdowska S. SNCG (synuclein, gamma (breast cancer-specific protein 1)). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):12-16.





ADAM23 (ADAM metallopeptidase domain 23) Marilia de Freitas Calmon, Paula Rahal

Laboratory of Genomics studies, São Paulo State University, Department of Biology, São José do Rio Preto - SP, Brasil

Published in Atlas Database: July 2007

Online updated version: http://AtlasGeneticsOncology.org/Genes/ADAM23ID44041ch2q33.html DOI: 10.4267/2042/38466


Identity Hugo: ADAM23 Other names: MDC3 Location: 2q33

DNA/RNA Description DNA contains 174312 bp composed of 26 coding exons.

Transcription 3059 bp mRNA transcribed in centromeric to telomeric

orientation; 2499 bp open reading frame. There are two isoforms of human ADAM23 (ADAM23alpha), i.e. ADAM23beta and ADAM23gamma. ADAM23beta is consistent with ADAM23alpha in domain structure except for a different transmembrane domain. ADAM23gamma, without transmembrane domain, is predicted to be a secreted form of ADAM23. ADAM23gamma is formed by skipping both exons enconding transmembrane domain in RNA splicing. Pseudogene No pseudogenes reported.

DNA of ADAM23 gene composed of 26 coding exons.

Protein

Domain structure of ADAM23. Its deduced amino acid sequence lacks essential residues conserved in metalloproteinases (Cal S. et al., 2000).

ADAM23 (ADAM metallopeptidase domain 23) Calmon MF, Rahal P


Description 832amino acid protein including a hydrophobic transmembrane domain and eight potential N-linked glycosylation sites. This protein has multiple domain structures including a pro-, a metalloproteinase-like, a desintegrin-like, a cysteine-rich, an epidermal growth factor-like, a transmembrane and a cytoplasmatic domain. Within the metalloproteinase-like domain, ADAM23 lacks HEXXHXXGXXH active-site amino acids for zinc-binding, which is critical for the proteinase activity. So, the metalloproteinase domain is inactive, suggesting that it is exclusively involved in cell adhesion processes rather than in protease-mediated events.

Expression Highly expressed in the brain and weakly expressed in the heart. In the brain, expressed prominently in the amygdala, caudate nucleus, hypothalamus, thalamus, cerebral cortex and occipital pole.

Localisation Cell membrane; single-pass type I membrane protein (Potential). Isoform Gamma: Secreted protein.

Function May play a role in cell-cell and cell-matrix interactions. This is a non-catalytic metalloprotease-like protein.

Homology H. sapiens: ADAM23; P.troglodytes: ADAM23; C.lupus: LOC607871; M.musculus: ADAM23; R.novergicus: ADAM23; G.gallus: LOC424099.

Mutations Note: There are one SNP on exon 1 in the amino acid position 1 with function start codon and two SNPs on exon 23 in the amino acid position 695 with functions synonymous and contig reference.

Implicated in Gastric tumors Note: Hypermethylation of the promoter region of ADAM 23 gene, along with decreased expression, occurs in primary gastric tumors compared with noncancerous gastric tissue.

Prognosis Not determined.

Cytogenetics Not determined.

Hybrid/Mutated Gene Not determined.

Oncogenesis Loss of ADAM23, which is likely to play an important role regard to cell-cell and cell- extracellular matrix interactions in gastric tissue as well, might be essential for the progression of gastric cancer.

Breast tumors Note: Hypermethylation of the promoter region of ADAM23 gene, along with decreased expression, occurs in primary breast tumors and primary breast tumors with a more advanced grade have higher degree of methylation.



Oncogenesis Primary breast tumors with a more advanced grade have a higher degree of methylation, suggesting that the adhesion molecule ADAM23 may be downregulated during the progression of breast cancer.

Head and neck cancer Note: Hypermethylation of the promoter region of ADAM23 gene, along with decreased expression, occurs in Head and neck cancer and the frequency of hypermethylation of ADAM23 gene is higher in primary head and neck tumors with a more advanced grade.



Oncogenesis Hypermethylation of the ADAM23 gene could lead to tumor progression, because the neoplastic cells would lose the contact inhibition. As a consequence, these cells would proliferate in an uncontrolled manner; once the proliferation of most cancer cells is no longer sensitive to density-dependent inhibition, a permissive environment for cell proliferation is created.

References Sagane K, Ohya Y, Hasegawa Y, Tanaka I. Metalloproteinase-like, disintegrin-like, cysteine-rich proteins MDC2 and MDC3: novel human cellular disintegrins highly expressed in the brain. Biochem J 1998;334:993-998. Poindexter K, Nelson N, DuBose RF, Black RA, Cerretti DP. The identification of seven metalloproteinase-disintegrin (ADAM) genes from genomic libraries. Gene 1999;237:61-70. Cal S, Freije JM López JM, Takada Y, López-Otín C. ADAM 23/MDC3, a human disintegrin that promotes cell adhesion via interaction with the alphavbeta3 integrin through an RGD-independent mechanism. Mol Biol Cell 2000;11:1457-1469. Costa FF, Verbisck NV, Salim AC, Ierardi DF, Pires LC, Sasahara RM, Sogayar MC, Zanata SM, Mackay A, O'Hare M,

ADAM23 (ADAM metallopeptidase domain 23) Calmon MF, Rahal P


Soares F, Simpson AJG, Camargo AA. Epigenetic silencing of the adhesion molecule ADAM23 is highly frequent in breast tumors. Oncogene 2004;23:1481-1488. Sun YP, Deng KJ, Wang F, Zhang J, Huang X, Qiao S, Zhao S. Two novel isoforms of Adam23 expressed in the developmental process of mouse and human brains. Gene 2004;325:171-178. Takada H, Imoto I, Tsuda H, Nakanishi Y, Ichikura T, Mochizuki H, Mitsufuji S, Hosoda F, Hirohashi S, Ohki M, Inazawa J. ADAM23, a possible tumor suppressor gene, is frequently silenced in gastric cancers by homozygous deletion or aberrant promoter hypermethylation. Oncogene 2005;24:8051-8060.

Calmon MF, Colombo J, Carvalho F, Souza FP, Filho JF, Fukuyama EE, Camargo AA, Caballero OL, Tajara EH, Cordeiro JA, Rahal P. Methylation profile of genes CDKN2A (p14 and p16), DAPK1, CDH1, and ADAM23 in head and neck cancer. Cancer Genet Cytogenet 2007;173:31-37.


Calmon MF, Rahal P. ADAM23 (ADAM metallopeptidase domain 23). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):17-19.

Gene Section Review




AKT2 (v-akt murine thymoma viral oncogene homolog 2) Deborah A Altomare, Joseph R Testa

Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA


Online updated version: http://AtlasGeneticsOncology.org/Genes/AKT2ID517ch19q13.html DOI: 10.4267/2042/38467


Identity Hugo: AKT2 Other names: PKBBETA (PKB beta); PKBB (protein kinase B, beta); RAC-PK-Beta (rac protein kinase beta) Location: 19q13.2 Note: Details concerning the local order of the human

AKT2 locus can be found at ensembl.org. Human AKT2 is found in chromosome 19, position 45,428,706-45,483,107. < or > symbols indicate the orientation of the genes. M3K10 is Mitogen-activated protein kinase kinase kinase 10 gene. CNTD2 is a gene encoding Cyclin N-terminal domain-containing protein. Location in the mouse: chromosome 7 in band B1.

DNA/RNA

Genomic organization of human AKT2. Open boxes indicate untranslated regions and shaded boxes indicate coding regions of the gene. The ATG transcription start site is located in exon 2 and the TGA termination codon is located in exon 14.

AKT2 (v-akt murine thymoma viral oncogene homolog 2) Altomare DA, Testa JR


AKT proteins contain an amino terminal pleckstrin homology (PH) domain, followed by a short helical region and kinase domain that terminates in a regulatory hydrophobic motif. Activation of AKT kinases is a multi-step process that involves both membrane translocation and phosphorylation. AKT activation occurs by means of stimulation of the growth factor receptor-associated phosphatidylinositol 3-kinase (PI3K). PI3K generates 3'-phosphorylated phosphoinositides, i.e., phosphatidylinositol-3,4,5-trisphosphate (PIP3) and phosphatidylinositol-3,4-bisphosphate (PIP2) at the plasma membrane. Both phospholipids bind with high affinity to the PH domain, mediating membrane translocation of AKT. At the membrane, AKT2 is phosphorylated at two sites, threonine 309 (T309) and serine 474 (S474).

Description The entire gene is about 54.4 Kb and contains 14 exons. The open reading frame of the coding region is 1,445 bp.

Transcription Transcript length: 4,623 bp.

Pseudogene No human pseudogene known. A mouse Akt2 pseudogene was cloned and mapped to proximal mouse chromosome 11 by fluorescence in situ hybridization.

Protein Description AKT2 protein consists of 481 amino acids, with a molecular weight of 55,769 Da.

Expression Found in all human cell types so far analyzed; insulin responsive tissues such as normal brown fat, skeletal muscle and liver exhibit the highest expression levels of AKT2/Akt2.

Localisation Predominantly cytoplasmic; also found at the plasma membrane and in the nucleus following its activation.

Function AKT proteins mediate a variety of cellular functions, ranging from control of cell proliferation and survival to modulation of intermediary metabolism and angiogenesis. Such pleiotropic effects are the consequence of phosphorylation of numerous substrates, some of which are listed below. Most substrates share the consensus sequence for AKT phosphorylation, RXRXXS/T. For example, activated AKT exerts anti-apoptotic activity in part by preventing the release of cytochrome c from mitochondria, and phosphorylating and inactivating the pro-apoptotic factors BAD and pro-caspase-9. AKT also activates IkappaB kinase (IKK), a positive regulator of NF-kappaB, which results in the transcription of anti-apoptotic genes. AKT phosphorylates and inactivates FOXO transcription factors, which mediate the

expression of genes critical for apoptosis, such as the Fas ligand gene. AKT activation mediates cell cycle progression by phosphorylation and inhibition of glycogen synthase kinase 3 beta to inhibit cyclin D1 degradation. AKT phosphorylates the cell cycle inhibitors p21WAF1 and p27Kip1 near the nuclear localization signal to induce cytoplasmic retention of these cell cycle inhibitors. Moreover, phosphorylation of AKT kinases also results in increased translation of cyclin D1, D3 and E transcripts. AKT activates the downstream mTOR kinase by inhibiting a complex formed by the tumor suppressor proteins TSC1 and TSC2, also known as hamartin and tuberin, respectively. mTOR broadly mediates cell growth and proliferation by regulating ribosomal biogenesis and protein translation and can regulate response to nutrients by restricting cell cycle progression in the presence of suboptimal growth conditions. AKT signaling also contributes to other cellular processes considered to be cancer hallmarks. AKT promotes the phosphorylation and translocation of Mdm2 into the nucleus, where it downregulates p53 and thereby antagonizes p53-mediated cell cycle checkpoints. AKT signaling is linked to tumor cell migration, and it contributes to tumor invasion and metastasis by promoting the secretion of matrix metalloproteinases. Moreover, vascular endothelial growth factor (VEGF) effects on cell survival have been shown to be mediated by the Flk1/VEGFR2 -PI3K-AKT pathway. In other cellular processes, AKT has been shown to phosphorylate human telomerase reverse transcriptase (hTERT), thereby stimulating telomerase activity and replication. Collectively, these findings implicate up-regulation of the AKT pathway in many aspects of tumorigenesis.

Homology All three AKT kinases belong to the more general class of AGC kinases (related to AMP/GMP kinase and protein kinase C). The kinase domain of AKT shares high similarity with other members of the AGC family of kinases such as PKA, PKC, p70 S6K, and p90 RSK. The sequence identities among the three AKTs in the



kinase domain exceed 87%. The three AKT kinases are identical in the ATP binding region, except for one residue: Ala 230 of AKT1 is conserved in AKT2 (Ala 232), but switches to Val 228 in AKT3. In addition, each of the three AKT kinases has a carboxy terminal extension of about 40 amino acids. Human AKT2 is 98.1% similar to M. musculus Akt2; 97.7% similar to the R. norvegicus homolog; 61.3% similar to D. melanogaster protein kinase RAC; 52.4% similar to C. elegans Akt/PKB serine/threonine kinase; 47.7% similar to S. cerevisiae protein kinase (see UniGene Hs.631535).

Mutations Germinal Insulin resistance and a diabetes mellitus-like syndrome have been described in knockout mice lacking Akt2.

Somatic Individuals carrying a G-to-A transition in the AKT2 gene resulting in an Arg-to-His substitution at codon 274 (R274H) were found to be markedly hyperinsulinemic. However, a large case-control study showed that variation in and around the AKT2 locus is unlikely to contribute significantly to increased risk of type 2 diabetes. Mutations in AKT2 are uncommon in human tumors. For example, AKT2 mutations have been reported in 1 of 51 gastric carcinomas and 2 of 79 lung carcinomas. The mutations consisted of one missense mutation and 2 splice site mutations in an intron.

Implicated in Various cancers Prognosis Frequent activation of AKT has been reported in a broad range of human cancers including various carcinomas, glioblastoma multiforme, and hematological malignancies. In some of these tumor types, AKT activation has been shown to correlate with advanced disease and/or poor prognosis. AKT is a major mediator of survival signals that protect cells from undergoing apoptosis and, thus, is a potentially important therapeutic target. Ovarian cancer cell lines with either constitutive AKT1 activity or AKT2 gene amplification have been shown to be highly resistant to paclitaxel compared to cells with low AKT levels.

Oncogenesis In 1992, amplification and overexpression of AKT2 was reported in a subset of ovarian carcinomas. AKT2 was shown to be amplified and overexpressed in 2 of 8 ovarian carcinoma cell lines and 2 of 15 primary ovarian tumors. Recently, amplification of AKT2 was found in 18.2% of high-grade ovarian carcinomas.

Amplification and/or overexpression of AKT2 was reported in 10-20% of primary pancreatic carcinomas and pancreatic cancer cell lines. PANC1 and ASPC1 cell lines exhibited 30-fold and 50-fold amplification of AKT2, respectively, and highly elevated levels of AKT2 RNA and protein. As an early indication of the potential importance of molecularly targeting the AKT pathway, AKT2 expression and tumorigenicity of PANC1 cells in nude mice was markedly inhibited by transfection with an antisense AKT2 construct but not with a control AKT2 construct in the sense orientation. Through the use of in vitro kinase assays, activation of the AKT2 kinase has been observed in about 40% of ovarian and pancreatic cancers.

Hyperactivation of AKT kinases have been reported in a wide assortment of human solid tumors and hematological malignancies. Activation of growth factor receptors either by ligand stimulation or receptor overexpression/mutation is one of the mechanisms leading to the upregulation of AKT signaling. Other mechanisms include activation of oncoproteins and inactivation of tumor suppressors intersecting the AKT signal transduction pathway. AKT is now known to be a central player in a signaling pathway consisting of many components that have been implicated in tumorigenesis, including upstream phosphatidylinositol 3-kinase (PI3K) and PTEN (Phosphatase and Tensin homologue deleted on chromosome Ten). Several proteins, such as AKT, eIF4E, and the subunits of PI3K, can act as oncoproteins when activated or overexpressed. Germline mutations in PTEN, LKB1, TSC2/TSC1, and VHL are linked with different dominantly-inherited cancer syndromes. Each of these tumor suppressors is a negative regulator of the AKT pathway which, when deregulated, results in altered translation of cancer-related mRNAs that regulate cellular processes such as cell cycle progression, growth, cell survival, invasion, and communication with the extracellular environment.



References Cheng JQ, Godwin AK, Bellacosa A, Taguchi T, Franke TF, Hamilton TC, Tsichlis PN, Testa JR. AKT2, a putative oncogene encoding a member of a subfamily of protein-serine/threonine kinases, is amplified in human ovarian carcinomas. Proc Natl Acad Sci USA 1992;89:9267-9271. Altomare DA, Kozak CA, Sonoda G, Testa JR. Chromosome mapping of the mouse Akt2 gene and Akt2 pseudogene. Cytogenet Cell Genet 1996;74:248-251. Cheng JQ, Ruggeri B, Klein WM, Sonoda G, Altomare DA, Watson DK, Testa JR. Amplification of AKT2 in human pancreatic cells and inhibition of AKT2 expression and tumorigenicity by antisense RNA. Proc Natl Acad Sci USA 1996;93:3636-3641. Miwa W, Yasuda J, Murakami Y, Yashima K, Sugano K, Sekine T, Kono A, Egawa S, Yamaguchi K, Hayashizaki Y, Sekiya T. Isolation of DNA sequences amplified at chromosome 19q13.1-q13.2 including the AKT2 locus in human pancreatic cancer. Biochem Biophys Res Commun 1996;225:968-974. Altomare DA, Lyons GE, Mitsuuchi Y, Cheng JQ, Testa JR. Akt2 mRNA is highly expressed in embryonic brown fat and the AKT2 kinase is activated by insulin. Oncogene 1998;16:2407-2411. Muise-Helmericks RC, Grimes HL, Bellacosa A, Malstrom SE, Tsichlis PN, Rosen N. Cyclin D expression is controlled post-transcriptionally via a phosphatidylinositol 3-kinase/Akt-dependent pathway. J Biol Chem 1998;273:29864-29872. Ruggeri BA, Huang L, Wood M, Cheng JQ, Testa JR. Amplification and overexpression of the AKT2 oncogene in a subset of human pancreatic ductal adenocarcinomas. Mol Carcinog 1998;21:81-86. Liu JP. Studies of the molecular mechanisms in the regulation of telomerase activity. FASEB J 1999;13:2091-2104. (Review). Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000;100:57-70. (Review). Page C, Lin HJ, Jin Y, Castle VP, Nunez G, Huang M, Lin J. Overexpression of Akt/AKT can modulate chemotherapy-induced apoptosis. Anticancer Res 2000;20:407-416. Thant AA, Nawa A, Kikkawa F, Ichigotani Y, Zhang Y, Sein TT, Amin AR, Hamaguchi M. Fibronectin activates matrix metalloproteinase-9 secretion via the MEK1-MAPK and the PI3K-Akt pathways in ovarian cancer cells. Clin Exp Metastasis 2000;18:423-428. Yuan ZQ, Sun M, Feldman RI, Wang G, Ma X, Jiang C, Coppola D, Nicosia SV, Cheng JQ. Frequent activation of AKT2 and induction of apoptosis by inhibition of phosphoinositide-3-OH kinase/Akt pathway in human ovarian cancer. Oncogene 2000;19:2324-2330. Cho H, Mu J, Kim JK, Thorvaldsen JL, Chu Q, Crenshaw EB 3rd, Kaestner KH, Bartolomei MS, Shulman GI, Birnbaum MJ. Insulin resistance and a diabetes mellitus-like syndrome in mice lacking the protein kinase Akt2 (PKB beta). Science 2001;292:1728-1731. Kumar CC, Diao R, Yin Z, Liu Y, Samatar AA, Madison V, Xiao L. Expression, purification, characterization and homology modeling of active Akt/PKB, a key enzyme involved in cell survival signaling. Biochim Biophys Acta 2001;1526:257-268. Testa JR, Bellacosa A. AKT plays a central role in tumorigenesis. Proc Natl Acad Sci USA 2001;98:10983-10985. (Review). Shiojima I, Walsh K. Role of Akt signaling in vascular homeostasis and angiogenesis. Circ Res 2002;90:1243-1250. (Review).

Mayo LD, Donner DB. The PTEN, Mdm2, p53 tumor suppressor-oncoprotein network. Trends Biochem Sci 2002;27:462-467. (Review). Altomare DA, Tanno S, De Rienzo A, Klein-Szanto AJ, Tanno S, Skele KL, Hoffman JP, Testa JR. Frequent activation of AKT2 kinase in human pancreatic carcinomas. J Cell Biochem 2003;88:470-476. Liang J, Slingerland JM. Multiple roles of the PI3K/PKB (Akt) pathway in cell cycle progression. Cell Cycle 2003;2:339-345. (Review). Downward J. PI 3-kinase, Akt and cell survival. Semin Cell Dev Biol 2004;15:177-182. (Review). George S, Rochford JJ, Wolfrum C, Gray SL, Schinner S, Wilson JC, Soos MA, Murgatroyd PR, Williams RM, Acerini CL, Dunger DB, Barford D, Umpleby AM, Wareham NJ, Davies HA, Schafer AJ, Stoffel M, O'Rahilly S, Barroso I. A family with severe insulin resistance and diabetes due to a mutation in AKT2. Science 2004;304:1325-1328. Pommier Y, Sordet O, Antony S, Hayward RL, Kohn KW. Apoptosis defects and chemotherapy resistance: molecular interaction maps and networks. Oncogene 2004;23:2934-2949. (Review). Whang YE, Yuan XJ, Liu Y, Majumder S, Lewis TD. Regulation of sensitivity to TRAIL by the PTEN tumor suppressor. Vitam Horm 2004;67:409-426. (Review). Altomare DA, Testa JR. Perturbations of the AKT signaling pathway in human cancer. Oncogene 2005;24:7455-7464. (Review). Astrinidis A, Henske EP. Tuberous sclerosis complex: linking growth and energy signaling pathways with human disease. Oncogene 2005;24:7475-7481. (Review). Bellacosa A, Kumar CC, Di Cristofano A, Testa JR. Activation of AKT kinases in cancer: implications for therapeutic targeting. Adv Cancer Res 2005;94:29-86. (Review). Lefranc F, Brotchi J, Kiss R. Possible future issues in the treatment of glioblastomas: special emphasis on cell migration and the resistance of migrating glioblastoma cells to apoptosis. J Clin Oncol 2005;23:2411-2422. (Review). Plas DR, Thompson CB. Akt-dependent transformation: there is more to growth than just surviving. Oncogene 2005;24:7435-7442. (Review). Ruggero D, Sonenberg N. The Akt of translational control. Oncogene 2005;24:7426-7434. (Review). Nakayama K, Nakayama N, Kurman RJ, Cope L, Pohl G, Samuels Y, Velculescu VE, Wang TL, Shih IeM. Sequence mutations and amplification of PIK3CA and AKT2 genes in purified ovarian serous neoplasms. Cancer Biol Ther 2006;5:779-785. Soung YH, Lee JW, Nam SW, Lee JY, Yoo NJ, Lee SH. Mutational Analysis of AKT1, AKT2 and AKT3 genes in common human carcinomas. Oncology 2006;70:285-289. Tan K, Kimber WA, Luan J, Soos MA, Semple RK, Wareham NJ, O'Rahilly S, Barroso I. Analysis of genetic variation in Akt2/PKB-beta in severe insulin resistance, lipodystrophy, type 2 diabetes, and related metabolic phenotypes. Diabetes 2007;56:714-719.


Altomare DA, Testa JR. AKT2 (v-akt murine thymoma viral oncogene homolog 2). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):20-23.





AKT3 (v-akt murine thymoma viral oncogene homolog 3, Protein Kinase B gamma) Mitchell Cheung, Joseph R Testa

Human Genetics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA 19111, USA


Online updated version: http://AtlasGeneticsOncology.org/Genes/AKT3ID615ch1q44.html DOI: 10.4267/2042/38468


Identity Hugo: AKT3 Other names: DKFZP434N0250; PKBG; PRKBG; RAC-PK-gamma Location: 1q44 Note: Location in the mouse: chromosome 1 in band H4-H6.

DNA/RNA Description The AKT3 gene is composed of 14 exons spanning a genomic region of 354,937 bp.

Transcription AKT3 coding sequence consists of 1,440 bp from the start codon to the stop codon.

Protein Description The AKT3 serine/threonine kinase consists of 479 amino acids with a calculated molecular weight of 55.8 kDa (approximate molecular weight of 59-60 kDa seen on a Western blot). The protein contains three important regions: the PH domain at the N terminus (residues 1-107), a kinase domain (residues 148-405), and a C-terminal regulatory domain (residues 406-479). A 465-amino acid splice variant lacking the serine 472 residue has been identified, which results from alternative splicing of an exon at the C terminus.

Expression Northern blot analysis of AKT3 indicated that it is expressed in virtually all tissues, predominantly in the brain and fetal heart and at lower levels in liver and skeletal muscle. RT-PCR analysis also indicated

expression of AKT3 in a wide variety of tissues.

Localisation Predominantly cytoplasmic; also found at the plasma membrane and in the nucleus following its activation.

Function AKT family members are serine/threonine kinases activated following stimulation by growth factors, hormones and the extracellular matrix. AKT kinases play a key role in proliferation, cell survival, and tumorigenesis. Binding of ligands (e.g., EGF) to tyrosine kinase receptors or G-protein coupled receptors leads to the recruitment and activation of the Class 1A and Class 1B PI3K (Phosphatidylinositol 3-Kinase), respectively. The pleckstrin homology domain of AKT kinases has affinity for the 3'-phosphorylated phosphoinositides 3,4,5-trisphosphate (PI-3,4,5-P3) and PI-3,4-P2 produced by PI3K, and they are activated specifically by the latter lipid. Phospholipid binding triggers the translocation of AKT kinases to the plasma membrane. There, AKT is activated through phosphorylation of a threonine (T308 in AKT1, T309 in AKT2 and T305 in AKT3) by PDK1 and on a serine (S473 on AKT1, S474 on AKT2, and S472 on AKT3) by PDK2. Activated AKT then phosphorylates a number of different substrates involved in survival, cell cycle progression, and other pathways implicated in tumorigenesis.

Homology AKT3 is a serine/threonine kinase and is a member of the AKT family that also includes AKT1 and AKT2. At the protein level, AKT3 shows overall 83.6% identity with AKT1 and 78% identity with AKT2. The three AKT kinases are identical in the ATP binding region, except for one residue: Ala 230 of AKT1 is conserved in AKT2 (Ala 232), but switches to Val 228 in AKT3.

AKT3 (v-akt murine thymoma viral oncogene homolog 3, Protein Kinase B gamma) Cheung M, Testa JR


Diagram of the AKT3 protein in scale. The numbers represent specific residues. The domains are PH (Pleckstrin Homology), a short helical region, Kinase (Catalytic Kinase), and Regulatory (Regulatory Region). Indicated are the two phosphorylation sites shown to be essential for activation of AKT3: Threonine 305 and serine 472. C: Carboxyl-terminal; N: Amino-terminal.

Mutations Note: No germline or somatic mutations were discovered through sequencing.

Implicated in Breast cancer Oncogenesis AKT3 was found to be expressed at a higher level in estrogen receptor-negative breast cancer compared to estrogen receptor-positive cancers, thus possibly contributing to the more aggressive phenotype of the former. AKT3 activity was also 30-to 60-fold higher in two estrogen receptor-negative cell lines as compared to two estrogen receptor-positive cell lines.

Hepatocellular carcinoma (Hepatitis C virus related) Oncogenesis Using array-CGH analysis, gene copy number increases of AKT3 were found in 6 out of 19 (32%) tumors, including small, well-differentiated carcinomas. Thus, increased copies of the gene may play a potentially important role in the onset of Hepatitis C-related hepatocellular carcinoma.

Melanoma Oncogenesis AKT3 was demonstrated to be the predominant AKT isoform involved in melanoma tumorigenesis. Knockdown of AKT3 with siRNA was shown to decrease total phospho-AKT levels in four melanoma cell lines and in normal melanocytes. In contrast, targeting the other two AKT proteins had no effect. AKT3 protein was overexpressed in 60% of primary melanoma tumors compared to normal melanocytes. Immunoprecipitation of AKT3 followed by immunoblotting with a phospho-specific AKT antibody indicated that 43% of primary melanomas have increased AKT3 activity compared to normal controls. Moreover, siRNA-mediated knockdown of AKT3 in a melanoma cell line led to a dramatic decrease in xenograft tumor size as a result of increased apoptosis.

Ovarian cancer Oncogenesis AKT3 was discovered to be highly expressed in 19 out of 92 (20%) primary ovarian tumors and also expressed in a number of ovarian tumor cell lines, including two cell lines having duplications of the AKT3 gene. The high expression of AKT3 in cell lines appeared to correlate with high total phospho-AKT levels, increased proliferation, and the ability to grow in serum starved conditions. SiRNA-mediated silencing of AKT3 expression in the OVCA429 and DOV13 cell lines resulted in reduced proliferation due to inhibition of the cell cycle.

Prostate cancer Oncogenesis AKT3 was found to be expressed at a higher level and with a 20- to 40-fold higher activity in androgen-insensitive prostate cancer compared to androgen-sensitive prostate cancer. The loss of PTEN expression appeared to contribute to increased AKT3 activity in one of the cell lines examined. Thus, AKT3 may play a role in the more aggressive phenotype of androgen-insensitive prostate cancers.

References Masure S, Haefner B, Wesselink JJ, Hoefnagel E, Mortier E, Verhasselt P, Tuytelaars A, Gordon R Richardson A. Molecular cloning, expression and characterization of the human serine/threonine kinase Akt-3. Eur J Biochem 1999;265(1):353-360. Nakatani K, Thompson DA, Barthel A, Sakaue H, Liu W, Weigel RJ, Roth RA. Up-regulation of Akt3 in estrogen receptor-deficient breast cancers and androgen-independent prostate cancer lines. J Biol Chem 1999;274(31):21528-21532. Murthy SS, Tosolini A, Taguchi T, Testa JR. Mapping of AKT3, encoding a member of the Akt/protein kinase B family, to human and rodent chromosomes by fluorescence in situ hybridization. Cytogenet Cell Genet 2000;88(1-2):38-40. Brodbeck D, Hill MM, Hemmings BA. Two splice variants of protein kinase B gamma have different regulatory capacity depending on the presence or absence of the regulatory phosphorylation site serine 472 in the carboxyl-terminal hydrophobic domain. J Biol Chem 2001;276(31):29550-29558. Zinda MJ, Johnson MA, Paul JD, Horn C, Konicek BW, Lu ZH, Sandusky G, Thomas JE, Neubauer BL, Lai MT, Graff JR. AKT-1, -2, and -3 are expressed in both normal and tumor tissues of the lung, breast, prostate, and colon. Clin Cancer Res 2001;7(8):2475-2479.

AKT3 (v-akt murine thymoma viral oncogene homolog 3, Protein Kinase B gamma) Cheung M, Testa JR


Bellacosa A, Testa JR, Moore R, Larue L. A portrait of AKT kinases: human cancer and animal models depict a family with strong individualities. Cancer Biol Ther 2004;3(3):268-275. (Review). Hashimoto K, Mori N, Tamesa T, Okada T, Kawauchi S, Oga A, Furuya T, Tangoku A, Oka M Sasaki K. Analysis of DNA copy number aberrations in hepatitis C virus-associated hepatocellular carcinomas by conventional CGH and array CGH. Mod Pathol 2004;17(6):617-622. Stahl JM, Sharma A, Cheung M, Zimmerman M, Cheng JQ, Bosenberg MW, Kester M, Sandirasegarane L Robertson GP. Deregulated Akt3 activity promotes development of malignant melanoma. Cancer Res 2004;64(19):7002-7010.

Altomare DA Testa JR. Perturbations of the AKT signaling pathway in human cancer. Oncogene 2005;24(50):7455-7464. (Review). Cristiano BE, Chan JC, Hannan KM, Lundie NA, Marmy-Conus NJ, Campbell IG, Phillips WA, Robbie M, Hannan RD Pearson RB. A specific role for AKT3 in the genesis of ovarian cancer through modulation of G(2)-M phase transition. Cancer Res 2006;66(24):11718-11725.


Cheung M, Testa JR. AKT3 (v-akt murine thymoma viral oncogene homolog 3, Protein Kinase B gamma). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):24-26.

Gene Section Review




ASCL1 (achaete-scute homolog 1 or achaete-scute complex homolog 1) Jayashree S Ladha, MRS Rao

Jawaharlal Nehru Centre for Advanced Scientific Research -A Deemed University- Jakkur P.O., Bangalore-560064, India


Online updated version: http://AtlasGeneticsOncology.org/Genes/ASCL1ID713ch12q23.html DOI: 10.4267/2042/38469


Identity Hugo: ASCL1 Other names: ASH1; HASH1; MASH1 Location: 12q23.2 Note: Renault B et al performed fluorescent in situ hybridisation using YAC 896h that contains ASCL1 and other chromosome 12 specific markers such as IGF1, PAH and TRA1 to localise ASCL1. They established using genetic markers that ASCL1 localises distal to Phenylalanine hydroxylase (PAH) and proximal to tumor rejection antigen (TRA1) on chromosome 12q22-q23 cytogenic interval. (Beatrice Renault et al. Genomics 30, 81-83 (1995)). LINEAGE: Eukaryota, Metazoa, Chordata, Craniata, Vertebrata, Euteleostomi, Mammalia, Eutheria, Euarchontoglires, Primates, Haplorrhini, Catarrhini, Hominidae, Homo. NCBI GI#: g119618109; g22658430; g20455478; g13111927; g12803079; g55743094; g306460; g13325212.

DNA/RNA Description 2 exons spanning 2824bp although only exon1 codes for the protein. Orientation '+' strand. Exon 1 101875594-101876910 (1317 bp), Exon 2 101877270-101878417 (1148 bp), Intron 1-2 101876911-101877269 (359 bp). Gene id= 429 (KEGG). Refseq: NM_004316.2. HASH1/ASCL1 promoter has two independent transcription start sites of which proximal INR element (YYANYY consensus binding site) plays a predominant role. The general enhancer has several Sp1 binding sites. Tissue restricted expression control comes from the repressor regions present in the distal

(over 13.5kb upstream) and proximal 5' flanking region. The proximal repressor is shown to have a class C element site to which HES1 can bind and regulate HASH1/ASCL1 expression. Variant: 158--158 Glu to Gly (E to G) Var_013179 in P50553.

Transcription 2.46 Kb mRNA, coding sequence 711 bp.

Protein Note: This gene encodes a member of the basic helix-loop-helix (bHLH) family of transcription factors. The protein activates transcription by binding to the E box (5'-CANNTG-3'). Dimerization with other bHLH proteins is required for efficient DNA binding. This protein plays a role in the neuronal commitment and differentiation and in the generation of olfactory and autonomic neurons. It is highly expressed in medullary thyroid cancer (MTC) and small cell lung cancer (SCLC) and may be a useful marker for these cancers. The proximal coding region of the cDNA contains a striking 14-copy repeat of the triplet CAG that exhibits polymorphism in human genomic DNA The presence of a CAG repeat in the gene suggests that it could play a role in tumor formation. Protein size: 237 aa, 25.45kDa. Refseq: NP_004307.2.

Description The amino terminal of the protein contains poly alanine and poly glutamine repeat rich region. The polyglutamine length polymorphism in ASCL1 has been postulated that it could influence predispositions to Parkinson's disease. The carboxy terminus of the protein contains the basic helix loop helix domain, which is important for interaction with other transcription factors.

ASCL1 (achaete-scute homolog 1 or achaete-scute complex homolog 1) Ladha JS, Rao MRS


A: Schematic representation of the ASCL1 genomic DNA depicting exons, introns, transcript and mRNA with untranslated and coding region. B: Schematic diagram showing HASH1/ASCL1 promoter with proximal and distal repressors, HASH1/ASCL1 class C site, enhancer Sp1 binding sites and transcription initiation sites (TATA box and INR (initiator) element).

Expression The gene product is expressed basically nuclear and is expressed in tissues like brain, lung and nervous system.

Function ASCL1 functions as a bHLH transcription factor that binds to E-box whose canonical sequence is 5'CANNTG 3'. It also acts as protein binding, transcription factor, and in cell differentiation. MASH1/ASCL1 is expressed during development of rat retina and interacts specifically with an E-box identified in the promoter for the opsin gene during rod photoreceptor differentiation. NOTCH1 and its downstream signal transducer HES1 regulates the transcription of HASH1/ASCL1 and is very instrumental in neuronal developmental pathways particularly dictating neuroendocrine differentiation in various organs. Interacting partners: E1A binding protein p300, Ubiquilin 1, Bone morphogenetic protein 2 (BMP2), Trancription factor 3 (TF3), Transcription factor 4 (TF4), Myocyte specific Enhancer factor 2A (MSEF2A), Neurogenin.

Homology Mus musculus Ascl1 achaete-scute complex homolog-like 1 (Drosophila) NM_008553.2; Rattus norvegicus Ascl1 achaete-scute complex homolog-like 1 (Drosophila) NM_022384.1; Canis familiaris similar to achaete-scute homolog 1 LOC482628; Danio Rerio achaete scute homolog A asha NM_131219.1.

Mutations Note: Congenital central hypoventilation syndrome is a rare disorder of the chemical control of breathing. The ASCL1--PHOX2A--PHOX2B developmental cascade was proposed as a candidate pathway for this disorder, as well as for Haddad syndrome, because the cascade controls the development of neurons with a definitive or transient noradrenergic phenotype. De Pontual et al. identified heterozygosity for mutations in the ASCL1 gene in 2 patients with CCHS and 1 patient with Haddad syndrome. The authors also developed an in vitro model of noradrenergic differentiation in neuronal progenitors derived from the mouse vagal neural crest. All Ascl1 mutant alleles result in impaired noradrenergic neuronal development when over expressed from adenoviral constructs.

Schematic representation of ASCL1 protein depicting various motifs such as poly alanine and poly glutamine repeats, a basic motif and a bHLH DNA binding motif.



ALLELIC VARIANTS

1. ASCL1 C52A, PRO18THR In a patient with CCHS, de Pontual et al identified heterozygosity for a 52C-A transversion in the ASCL1 gene, translating in a pro18-to-thr substitution. The patient was also heterozygous for a polyalanine expansion mutation in PHOX2B, which is known to induce CCHS. 2. ASCL1, 15-BP DEL, NT111 Heterozygosity for a 15-bp deletin (111-115 Del 15nt) in the ASCL1 gene was reported in a patient with CCHS by de Pontual et al. The mutation was predicted to result in loss of 5 of 13 alanine residues (ala37-ala41) in a polyalanine tract. 3. ASCL1, 24-BP DEL, NT108 Another heterozygosity for of 24-bp deletion (108-131del24nt) in the ASCL1 gene was identified in a patient with Haddad syndrome (209880), de Pontual et al The mutation was predicted to result in loss of 8 of 13 alanine residues (ala36-ala43) in a polyalanine tract. Genetic association with Parkinson's disease has been shown by Ide M et al (PMID=16021468) and that with sudden infant death syndrome or (SIDS) has been shown by Weese-Mayer DE et al (PMID= 15240857).

Implicated in Note: Upon characterization of expression of ASCL1 in several human cancer cell lines and tumors it is found that ASCL1 is highly expressed in and has been implicated to impart neuroendocrine behaviour to various NE- tumors e.g gastrointestinal NE carcinoma (NEC), Pheochromocytomas, olfactory neuroblastomas or esthesioneuroblastoma, pulmonary and thyroid carcinoids, Medullary thyroid cancer (MTC), small cell lung cell cancer (SCLC) and recently in prostate small cell carcinoma. Apart from this, ASCL1 protein is also shown to be highly upregulated in progressive secondary glioblastoma (GBM). Notch signalling down regulates ASCL1 levels but its expression is shown to be very minimal or non-existent in neuroendocrine tumors and hence inhibition of ASCL1 expression that has been implicated to impart neuroendocrine behaviour could be a therapeutic target to suppress tumor growth.

Neuroendocrine tumors Note: Neuroendocrine tumors originate from cells that are capable of amine precursor (such as dopa and 5-hydroxytryptophan) uptake and decarboxylation (APUD cells). As a result, these tumors have high intracellular levels of carboxyl groups and nonspecific esterase, which are used as a neuroendocrine marker. These tumors have NE- phenotype characterized by expression of ACTH, vasopressin, calcitonin gene related peptide (CALCA/CGRP), Gastrin releasing peptide and secretory proteins like synaptophysin and chromogranins, serotonin. HASH1/ASCL1 appears to

be cardinal/ hallmark feature of each of these tumor types. Clinically Chromogranin A is most commonly used as a marker to identify NE- tumors.

Olfactory neuroblastomas or Esthesioneuroblastoma (ENB) Note: paranasal sinus nasal cavity esthesioneuroblastoma or esthesioneurocytoma, esthesioneuroma, and esthesioneuroepithelioma.

Disease Esthesioneuroblastoma (ENB) is a rare tumor arising out of the nasal vault from cells of the developing sympathetic nervous system. When neuroblastoma cells are induced to differentiate, as indicated by neuronal morphology and upregulation of neuronal marker genes, the HASH-1/ASCL1 expression is rapidly downregulated with a concomitant, transient upregulation of HES-1. ENB is generally a slow-growing tumor with a high 5-year survival (81%). Recurrences usually occur within the first 2 years. However, late recurrences are common, and hence follow-up must be done for a prolonged time.

Prognosis HASH1/ASCL1 is expressed in immature olfactory neurons and is critical for their development. Mhawech et al found distinct expression of HASH1/ASCL1 in all estersioneuroblastoma samples as compared to the poorly differentiated tumors that were negative. They also report inverse correlation between grades of esthesioneuroblastoma and HASH1/ASCL1 mRNA levels and propose that HASH1/ASCL1 could be used as useful tool to distinguish estersioneuroblastoma from poorly differentiated tumors of sinonasal region.

Pulmonary and thyroid carcinoids Note: Carcinoid tumors or carcinoids.

Disease These tumors originate in hormone-producing cells of the gastrointestinal (GI) tract (i.e., esophagus, stomach, small intestine, colon), the respiratory tract (i.e., lungs, trachea, bronchi), the hepatobiliary system (i.e., pancreas, gallbladder, liver), and the reproductive glands (i.e., testes, ovaries). Carcinoids are classified as slow growing neuroendocrine tumors. They develop in peptide- and amine-producing cells, which release hormones like serotonin in response to signals from the nervous system. Excessive amounts of these hormones cause a condition called carcinoid syndrome in approximately 10% of patients with carcinoid tumors.

Prognosis Multiple endocrine neoplasia type 1 (MEN1) is a genetic disorder that increases the risk for neuroendocrine tumors, including carcinoids. Gastrointestinal conditions (e.g., peptic ulcer disease, pernicious anemia, atrophic gastritis, Zollinger-Ellison syndrome) increase the risk for carcinoid tumors of the



GI tract. Carcinoid patients also have an increased risk for Cushing's syndrome. Atypical Carcinoids (fast growing and potentially metastatic) express high levels of HASH1/ASCL1 (although lower than NECs) and is associated with poor prognosis for survival. RAF-1 activation is detrimental to tumorigenesis in carcinoid cells. Raf1 activation in an estrogen inducible system in pancreatic carcinoid cell line (BON) and in pulmonary cell lines leads to marked reduction in NE-markers such as 5-HT, chromogranin A, and synaptophysin and HASH1/ASCL1 has been observed.

Medullary thyroid cancer (MTC) Disease Medullary thyroid cancer is a neuroendocrine tumor derived from the parafollicular calcitonin producing C cells of thyroid and accounts for about 3% of thyroid cancers. Inheritance: About 20% of have an inherited form of the disease and familial MTC are transmitted in an autosomal dominant fashion involving mutations in the RET proto-oncogene. So far surgery remains only curative treatment modality.

Prognosis The classical tumor marker and the secreted hormone is calcitonin which is tightly regulated by Notch signalling and HASH1/ASCL1 levels. It has also been shown that by activating RAF-1 signalling mediated by MEK induction leads to complete suppression of ASCL1 and mRNA protein which is frequently upregulated in MTC. HASH1/ASCL1 over expression is linked to poor prognostic value.

Small cell lung cancer (SCLC) Note: Oat cell carcinoma.

Disease SCLC cells are small and round to fusiform with scant cytoplasm.SCLC tumors are poorly differentiated neuroendocrine tumors as compared to bronchoid carcinoid tumors and is an aggressive and highly metastatic tumor, accounting to about 20% death from lung cancer. Owing to its NE-phenotype, these tumors secrete chromogranin A, GRP and calcitonin in addition to over expressed HASH1/ASCL1. Genetically c-myc has shown to be over expressed by gene amplification and retinoblastoma (Rb) is frequently mutated in SCLC. P53 and PTEN also show aberrant expression. Loss of chromosome 3 sequences appears to occur frequently at the very earliest stages of neoplastic transformation. Losses at the short arms of chromosome 3 and 17 and the long arm of 5 are seen consistently in almost all SCLC patients. Although to date, there are no known examples of amplification or rearrangement of the HASH1/ASCL1 gene.

Prognosis HASH1/ASCL1 is associated with significantly reduced survival in small cell lung carcinoma patients and has adverse prognostic association.

Pheochromocytomas Note: Chromaffin tumors.

Disease Because pheochromocytomas arise from chromaffin cells, they are occasionally called chromaffin tumors. Pheochromocytomas are found in the adrenal medulla. The adrenal medulla normally secretes two hormones, called norepinephrine and epinephrine(also known as adrenaline). Pheochromocytomas cause the adrenal medulla to secrete too much adrenaline and often causes the adrenal glands to make excess of hormones called catechol-amines which in turn causes high blood pressure and other symptoms. Atleast in rat pheochromocytoma cell line PC12, MASH1/ASCL1 is readily detected which can be further induced by NGF treatment. Whether HASH1/ASCL1 also is over expressed in human cancers needs careful examination and distinction between tumor types. Inheritance: About 10-25% of this cancer can be familial and mutations in genes e.g. VHL, RET, NF1, SDHB and SDHD are implicated.

Prognosis Pheochromocytoma can be potentially fatal, but it is relatively uncommon (2-8 cases per million people annually). As with other neuroendocrine tumors, high levels of HASH1/ASCL1 expression seen in pheochromocytomas correlate with poor prognosis. Activation of MEK1 / MEK2 - ERK1 / ERK2 is necessary for differentiation of pheochromocytoma (PC12) cells and leads to decreased cell proliferation.

Cytogenetics Allelic losses at Chromosome 1p, 3p, 17p and 22q have been reported in sporadic and familial forms of pheochromocytomas.

Gastrointestinal neuroendocrine carcinoma (NEC) Disease Gastrointestinal NECs are defined as small cell carcinoma, morphologically similar to the small cell carcinoma of the lung. Gastrointestinal NE carcinoma (NEC) are extremely aggressive, but its pathophysiologic features remain poorly understood. Shida et al assessed HASH1/ASCL1 expression in human NECs by quantitative RT-PCR and in situ hybridisation and showed marked upregulation of HASH1/ASCL1 mRNA in NECs which was weak in



carcinoid tumors and scarcely expressed in adenocarcinomas and normal mucosa.

Prognosis Levels of HASH1/ASCL1 can be used as a more sensitive and specific marker than conventional pan-endocrine markers for clinical diagnosis of gastrointestinal tumors to differentiate among gastrointestinal tumors particularly between carcinoids, adenocarcinomas and neuroendocrine gastrointestinal tumors in addition to other NE markers.

Astrocytoma (secondary glioblastoma (GBM)) Note: Glioblastoma.

Disease Astrocytoma is the most common type of brain cancer arising from the astrocytes affecting cerebral hemispheres in adults and the brain stem in children accounting to almost 60% of brain tumors. According to the world health organization, astrocytomas are classified in to four grades: 1. Grade I or pilocytic astrocytoma (PA); 2. Grade II diffused astrocytoma (DA); 3. Grade III Anaplastic astrocyoma (AA); 4. Grade IV Glioblastoma multiforme (GBM). GBM can further be classified as being primary or secondary based on the genetic mutations, age at occurrence, tendency of progression and clinical course. Familial clustering of gliomas is frequently observed associated with defined inherited tumor syndrome incuding the Li-Fraumeni syndrome, Turcot syndrome, and the NF1 syndrome. Several genes have been associated in distinguishing one or the other form of GBM notably among which are P53, MDM2, EGFR, CDK4. LOH on chromosome 9,10, 13, 17,19, 22 frequently occur in GBMs.

Prognosis The median survival time for a GBM individual is about 12 months and age at the time of occurrence plays a significant prognostic factor. Recently reported methylation at the O6- methyl guanine DNA methyl-transferase (MGMT) promoter has been shown to confer favourable prognostic value in terms of response to chemotherapy and longer survival. ASCL1 is highly upregulated in secondary GBMs as compared to the primary GBMs and can be thus ascribed as a distinguishing marker between the two. Concomitantly, there is repression of NOTCH1 signalling and HES1 expression in the secondary GBM. It is observed that primary GBM patients show rapid tumor progression and poor prognosis.

References Renault B, Lieman J, Ward D, Krauter K and Kucherlapati R. Localisation of human Achaete-sute Homolog gene (ASCL1) distal to Phenylalanine hydroxylase (PAH) and proximal to

tumor rejection antigen (TRA1) on chromosome 12q22-q23. Genomics 1995;30:81-83. Borges M, Linnoila RI, van de Velde HJ, Chen H, Nelkin BD, Mabry M, Baylin SB, Ball DW. An achaete-scute homologue essential for neuroendocrine differentiation in the lung. Nature 1997;386:852-855. Chen H, Biel MA, Borges MW, Thiagalingam A, Nelkin BD, Baylin SB, Ball DW. Tissue-specific expression of human achaete-scute homologue-1 in neuroendocrine tumors: transcriptional regulation by dual inhibitory regions. Cell Growth Differ 1997;8:677-686.

Linnoila RI, Zhao B, DeMayo JL, Nelkin BD, Baylin SB, DeMayo FJ, Ball DW. Constitutive achaete-scute homologue-1 promotes airway dysplasia and lung neuroendocrine tumors in transgenic mice. Cancer Res 2000;60:4005-4009. Mallolas J, Vilaseca MA, Pavia C, Lambruschini N, Cambra FJ, Campistol J, Gómez D, Carrió A, Estivill X, Milà M. Large de novo deletion in chromosome 12 affecting the PAH, IGF1, ASCL1, and TRA1 genes. J Mol Med 2001;78:721-724. Sriuranpong V, Borges MW, Strock CL, Nakakura EK, Watkins DN, Blaumueller CM, Nelkin BD, Ball DW. Notch signaling induces rapid degradation of achaete-scute homolog 1. Mol Cell Biol 2002;22:3129-3139. Westerman BA, Neijenhuis S, Poutsma A, Steenbergen RD, Breuer RH, Egging M, van Wijk IJ, Oudejans CB. Quantitative reverse transcription-polymerase chain reaction measurement of HASH1 (ASCL1), a marker for small cell lung carcinomas with neuroendocrine features. Clin Cancer Res 2002;8:1082-1086. Murray RC, Navi D, Fesenko J, Lander AD, Calof AL. Widespread defects in the primary olfactory pathway caused by loss of Mash1 function. J Neurosci 2003;23:1769-1780. Sippel RS, Carpenter JE, Kunnimalaiyaan M, Chen H. The role of human achaete-scute homolog-1 in medullary thyroid cancer cells. Surgery 2003;134:866-871; discussion 871-873. Axelson H. The Notch signaling cascade in neuroblastoma: role of the basic helix-loop-helix proteins HASH-1 and HES-1. Cancer Lett 2004;204:171-178 (Review). Ball DW. Achaete-scute homolog-1 and Notch in lung neuroendocrine development and cancer. Cancer Lett 2004;204:159-169 (Review). Hu Y, Wang T, Stormo GD, Gordon JI. RNA interference of achaete-scute homolog 1 in mouse prostate neuroendocrine cells reveals its gene targets and DNA binding sites. Proc Natl Acad Sci USA 2004;101:5559-5564. Jiang SX, Kameya T, Asamura H, Umezawa A, Sato Y, Shinada J, Kawakubo Y, Igarashi T, Nagai K, Okayasu I. hASH1 expression is closely correlated with endocrine phenotype and differentiation extent in pulmonary neuroendocrine tumors. Mod Pathol 2004;17:222-229. Mhawech P, Berczy M, Assaly M, Herrmann F, Bouzourene H, Allal AS, Dulguerov P, Schwaller J. Human achaete-scute homologue (hASH1) mRNA level as a diagnostic marker to distinguish esthesioneuroblastoma from poorly differentiated tumors arising in the sinonasal tract. Am J Clin Pathol 2004;122:100-105. Pattyn A, Simplicio N, van Doorninck JH, Goridis C, Guillemot F, Brunet JF. Ascl1/Mash1 is required for the development of central serotonergic neurons. Nat Neurosci 2004;7:589-595. Persson P, Stockhausen MT, Pahlman S, Axelson H. Ubiquilin-1 is a novel HASH-1-complexing protein that regulates levels of neuronal bHLH transcription factors in human neuroblastoma cells. Int J Oncol 2004;25:1213-1221. Chen H, Kunnimalaiyaan M, Van Gompel JJ. Medullary thyroid cancer: the functions of raf-1 and human achaete-scute homologue-1. Thyroid 2005;15:511-521. (Review). Ide M, Yamada K, Toyota T, Iwayama Y, Ishitsuka Y, Minabe Y, Nakamura K, Hattori N, Asada T, Mizuno Y, Mori N,



Yoshikawa T. Genetic association analyses of PHOX2B and ASCL1 in neuropsychiatric disorders: evidence for association of ASCL1 with Parkinson's disease. Hum Genet 2005;117:520-527. Osada H, Tatematsu Y, Yatabe Y, Horio Y, Takahashi T. ASH1 gene is a specific therapeutic target for lung cancers with neuroendocrine features. Cancer Res 2005;65:10680-10685. Shida T, Furuya M, Nikaido T, Kishimoto T, Koda K, Oda K, Nakatani Y, Miyazaki M, Ishikura H. Aberrant expression of human achaete-scute homologue gene 1 in the gastrointestinal neuroendocrine carcinomas. Clin Cancer Res 2005;11:450-458. Somasundaram K, Reddy SP, Vinnakota K, Britto R, Subbarayan M, Nambiar S, Hebbar A, Samuel C, Shetty M, Sreepathi HK, Santosh V, Hegde AS, Hegde S, Kondaiah P, Rao MR. Upregulation of ASCL1 and inhibition of Notch signaling pathway characterize progressive astrocytoma. Oncogene 2005;24:7073-7083. Kunnimalaiyaan M, Vaccaro AM, Ndiaye MA, Chen H. Overexpression of the NOTCH1 intracellular domain inhibits cell proliferation and alters the neuroendocrine phenotype of medullary thyroid cancer cells. J Biol Chem 2006;281:39819-39830.

McNay DE, Pelling M, Claxton S, Guillemot F, Ang SL. Mash1 is required for generic and subtype differentiation of hypothalamic neuroendocrine cells. Mol Endocrinol 2006;20:1623-1632. Rousseau A, Nutt CL, Betensky RA, Iafrate AJ, Han M, Ligon KL, Rowitch DH, Louis DN. Expression of oligodendroglial and astrocytic lineage markers in diffuse gliomas: use of YKL-40, ApoE, ASCL1, and NKX2-2. J Neuropathol Exp Neurol 2006;65:1149-1156. Taniwaki M, Daigo Y, Ishikawa N, Takano A, Tsunoda T, Yasui W, Inai K, Kohno N, Nakamura Y. Gene expression profiles of small-cell lung cancers: molecular signatures of lung cancer. Int J Oncol 2006;29:567-575. Watt F, Watanabe R, Yang W, Agren N, Arvidsson Y, Funa K. A novel MASH1 enhancer with N-myc and CREB-binding sites is active in neuroblastoma. Cancer Gene Ther 2007;14:287-296.


Ladha JS, Rao MRS. ASCL1 (achaete-scute homolog 1 or achaete-scute complex homolog 1). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):27-32.





ATF2 (activating transcription factor 2) Pedro A Lazo, Ana Sevilla

Instituto de Biologia Molecular y Celular del Cancer, CSIC-Universidad de Salamanca, campus Miguel de Unamuno, E-37007 Salamanca, Spain


Online updated version: http://AtlasGeneticsOncology.org/Genes/ATF2ID718ch2q31.html DOI: 10.4267/2042/38470


Identity Hugo: ATF2 Other names: CREB1; CRE-BP1; CREB2; CREBP1; HB16; MGC111558; TREB7; Cyclic AMP-dependent transcription factor ATF-2; cAMP response element-binding protein CRE- BP1 Location: 2q31.1

DNA/RNA Description Gene size: 115.93Kb.

ATF2 gene structure based on data available in the Ensembl release 44. Upstream non-coding exons (green). Coding exons (pink), 3' untranslated sequence (red). The size of the exons in nucleotides is indicated below each exon. Exon number is indicated within the exon.

Transcription Initiation codon located in exon 4. Normal message is 2109 nucleotides. Some alternatively spliced RNA messages have been detected; but they are likely to represent splicing intermediates since no protein has been detected/expressed from these alternative messages in humans.

Protein Note: Protein of 505 aminoacids and a size of 52.27 kDa. Functions as a dimer, either homodimer or heterodimer with proteins of the jun family (e.g.: c-Jun, c-Fos).

Localisation Nuclear protein.

Function Transcription factor which binds to the cAMP-responsive element (CRE) (consensus: 5'-GTGACGT[AC][AG]-3'). ATF2 binds DNA as a dimer. The specificity of the DNA target sequence that is recognized by dimers containing ATF2 is different depending on whether it is a homodimer or it forms a heterodimer with another JUN protein.

Mutations Note: Lung cancer.

Somatic G to A transition in exon 10. Val258Ile Substitution.

Implicated in Clear cell sarcoma Cytogenetics t(2;12)(q31.1;q13)

ATF2 (activating transcription factor 2) Lazo PA, Sevilla A


The arrow indicates the location of the breakpoint in chromosome 2. The ATF2 gene breaks within intron 6. In the translocation partner EWS the breakpoint occurs in intron 7. The transcript resulting from the hybrid gene fuses exon7 of EWS to exon 7 of ATF2.

Hybrid/Mutated Gene EWS -ATF2 fusion transcript.

Abnormal Protein The EWS-ATF2 fusion protein retains the ATF2 C-terminal region that contains the bZIP dimerization domain. But the fusion protein has lost the N-terminal domain of ATF2 that is kinase inducible. The N-terminal region of EWS is retained in the fusion protein but has lost both its RNA binding domain and its Zinc-finger Ran binding domain.

Structure of the EWS-ATF2 fusion protein.

Oncogenesis EWS-ATF2 may define a novel subset of clear cell sarcoma that occurs preferentially in the gastrointestinal tract and presents little or no melanocytic differentiation.

References Livingstone C, Patel G, Jones N. ATF-2 contains a phosphorylation-dependent transcriptional activation domain. Embo J 1995;14:1785-1797. Fuchs SY, Tappin I, Ronai Z. Stability of the ATF2 transcription factor is regulated by phosphorylation and dephosphorylation. J Biol Chem 2000;275:12560-12564.

Bhoumik A, Ivanov V, Ronai Z. Activating transcription factor 2-derived peptides alter resistance of human tumor cell lines to ultraviolet irradiation and chemical treatment. Clin Cancer Res 2001;7:331-342. Mayr BM, Canettieri G, Montminy MR. Distinct effects of cAMP and mitogenic signals on CREB-binding protein recruitment impart specificity to target gene activation via CREB. Proc Natl Acad Sci USA 2001;98:10936-10941. van Dam H, Castellazzi M. Distinct roles of Jun: Fos and Jun: ATF dimers in oncogenesis. Oncogene 2001;20:2453-2464. Woo IS, Kohno T, Inoue K, Ishii S, Yokota J. Infrequent mutations of the activating transcription factor-2 gene in human lung cancer, neuroblastoma and breast cancer. Int J Oncol 2002;20:527-531. Przybylski GK, Dik WA, Wanzeck J, Grabarczyk P, Majunke S, Martin-Subero JI, Siebert R, Dölken G, Ludwig WD, Verhaaf B, van Dongen JJ, Schmidt CA, Langerak AW. Disruption of the BCL11B gene through inv(14)(q11.2q32.31) results in the expression of BCL11B-TRDC fusion transcripts and is associated with the absence of wild-type BCL11B transcripts in T-ALL. Leukemia 2005;19:201-208. Antonescu CR, Nafa K, Segal NH, Dal Cin P, Ladanyi M. EWS-CREB1: a recurrent variant fusion in clear cell sarcoma--association with gastrointestinal location and absence of melanocytic differentiation. Clin Cancer Res 2006;12:5356-5362. Liu H, Deng X, Shyu YJ, Li JJ, Taparowsky EJ, Hu CD. Mutual regulation of c-Jun and ATF2 by transcriptional activation and subcellular localization. Embo J 2006;25:1058-1069. Ryan CM, Harries JC, Kindle KB, Collins HM, Heery DM. Functional interaction of CREB binding protein (CBP) with nuclear transport proteins and modulation by HDAC inhibitors. Cell Cycle 2006;5:2146-2152.


Lazo PA, Sevilla A. ATF2 (activating transcription factor 2). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):33-34.

Gene Section Review




CTGF (connective tissue growth factor) Satoshi Kubota, Masaharu Takigawa

Department of Biochemistry and Molecular Dentistry Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences Dean, Okayama University Dental School 2-5-1, Shikata-cho, Okayama, 700-8525, Japan


Online updated version: http://AtlasGeneticsOncology.org/Genes/CTGFID40192ch6q23.html DOI: 10.4267/2042/38471


Identity Hugo: CTGF Other names: CCN2; Fisp12; betaIG-M2; Hcs24; HBGF-0.8; ecogenin; IGFBP8; IGFBP-rP3 Location: 6q23.1 Note: CCN family protein 2/connective tissue growth factor (CCN2/CTGF) was initially identified in the culture supernatant of vascular endothelial cells. Subsequently, the CCN2/CTGF gene has been classified as a representative member of the CCN gene family that is an acronym of the original names of the 3 early members, Cyr61, CTGF and NOV. The mammalian genome contains 6 functional CCN family members, which were renamed based on the proposal of a unified nomenclature. CCN2/CTGF displays multiple functions via interaction with a variety of other molecules. It is important to note that CCN2/CTGF induces the development and regeneration of mesenchymal tissues including bone, cartilage and blood vessels.

DNA/RNA Description

Unlike the other CCN family members, the CCN2/CTGF gene is conserved among all of the vertebrates and several invertebrates. In Drosophila melanogaster, only one gene is designated as ccn, which is thought to have evolved from a prototypic CCN2/CTGF gene. Therefore, CCN2/CTGF may be regarded evolutionarily as an oldest gene in the CCN family. Consistent with such findings, human CCN2/CTGF gene is also quite compact. The total transcribed sequence is as short as 3.2 kb, and contains 4 intronic sequences of less than 400 bp. Transcription The mature mRNA, 2.3 kb in length, is formed by connecting 5 exons encoding a signal peptide, an IGFBP module, a VWC module, a TSP1 module and CT module in the order. The last exon yields a long 3'-untranslated region of more than1.0 kb on the mRNA, which contains the critical elements for post-transcriptional regulation. The proximal promoter area upstream of the transcription initiation site is known to contain several enhancer elements that are critical for transcriptional regulation.

Structure of human CCN2/CTGF and its mRNA. Abbreviations S, I, V, T, and C denote the coding regions for the signal peptide, IGFBP module, VWC module, TSP1 module and CT module, respectively.

CTGF (connective tissue growth factor) Kubota S, Takigawa M


Protein Description The CCN2/CTGF is composed of 4 distinct modules: the N-terminal signal peptide for secretion; insulin-like growth factor binding protein-like (IGFBP) module, von Willebrand factor type-C repeat (VWC) module, thrombospondin type 1 repeat (TSP1) module and the C-terminal cystine knot (CT) module. This is consistent with other CCN family proteins. Because of this unique structure, the 6 CCN2/CTGF-related proteins are thought to form a distinct protein class which is distinct from the IGFBP family, despite the involvement of IGFBP module. The involvement of cysteine residues that are also conserved among the CCN family members is a prominent structural characteristic. All of the 4 modules are highly interactive with other biomolecules including growth factors, cell-surface receptor molecules and extracellular matrix components. In addition, the tetramodular construction of these modules provides the structural basis for the multiple functionality of CCN2/CTGF, which is described in another section.

Interaction of each module in CCN2/CTGF with other growth factors.

Expression CCN2/CTGF is differentially expressed in certain tissues and organs, particularly in the cardiovascular, gonadal, renal and skeletal systems, during development of vertebrates. The cell population that expresses the CCN2/CTGF gene is highly restricted in each tissue; for example, this factor is produced in cartilage primarily by pre-hypertrophic and hypertrophic chondrocytes, in fact, it was previously referred to as hypertrophic chondrocyte-specific protein 24 (Hcs24).

Localisation In addition to the tissues containing the cells which express this protein described above, CCN2/CTGF is abundantly present in platelets, although its origin is still unknown.

Function Under the multiple interactions with specific molecular counterparts, CCN2/CTGF conducts the local information network of extracellular signaling molecules and exerts multiple functions, depending upon the microenvironmental conditions. Indeed, CCN2/CTGF promotes both proliferation and differentiation of mesenchymal stem cells, chondrocytes, osteoblasts, periodontal ligament cells, fibroblasts and vascular endothelial cells in vitro. As a result of these effects, this factor enhances wound healing and tissue regeneration of cartilage and bone.

Homology CCN2/CTGF is structurally homologous to the other 5 CCN family members. The cysteine residues are highly conserved among the members.

Mutations Germinal Until today, no association between mutations in the CCN2/CTGF gene and specific genetic diseases has been described. In mouse models, deletion of both CCN2/CTGF alleles results in severe skeletal malformation, leading to respiratory failure upon delivery. Histological and cell biological analysis revealed that the endochondral ossification process was specifically affected by the CCN2/CTGF deletion, particularly at the final stage that is supported by blood vessel invasion. However, no apparent phenotypic complication has been observed in CCN2/CTGF (-/+) heterozygous mice.

Somatic At present, nearly 30 SNPs have been described in the NCBI database. Among the SNPs, 35.7% and 39.3% of the total cases have been reported to exist outside of the transcribed area and in the areas of untranslated regions (UTRs) and introns, respectively. Mutation/variation in the open reading frame (ORF) was found in 25% of the total. Missense mutation occurred at a frequency of 42.7 %, whereas the other cases were silent. Excluding the UTRs, the IGFBP-encoding 2nd exon has been a hot spot of mutation and variation (57.1% of the one within ORF). In a single case, an African population was analyzed to compute the actual frequency. This demonstrated that the frequency of a mutation in the 3rd exon, which caused a missense change of amino acid 118 from asparagine to serine by an A to G transition, was 1.3%. Including these cases, no association of a SNP in the CCN2/CTGF gene with any particular human disorder has been described until now.



Implicated in Cancers Oncogenesis Although the CCN2/CTGF expression is observed in a number of different types of malignant neoplasm, the role of CCN2/CTGF in oncogenesis and its association with malignant phenotypes are quite controversial. According to a previous study, a positive correlation was observed between the level of CCN2/CTGF expression and the degree of malignancy in breast cancer and colorectal cancer cases. These findings are consistent with other recent reports describing the contribution of CCN/CTGF in developing bone metastasis of breast cancers. The ability to promote metastasis can be partially ascribed to the angiogenic activity of CCN2/CTGF. However, over expression of CCN2/CTGF in cells of the same origin is reported to induce apoptosis. Furthermore, in chondrosarcoma cases, patients with higher CCN2/CTGF expression in tumors survived longer than those with lower CCN2/CTGF expression. These findings are consistent with the observation that overexpression of CCN2/CTGF results in benign conversion of the phenotype in oral squamous carcinoma cells and induces cell cycle arrest in fibroblasts. The observations above suggest that CCN2/CTGF produced by tumor cells may exert paracrine angiogenic and autocrine/intracrine anti-proliferative effects in solid tumors.

Fibrotic disorders Disease Since its initial discovery, CCN2/CTGF has been widely known as a profibrotic factor that is involved in a variety of fibrotic disorders. CCN2/CTGF is associated with systemic sclerosis, keloids, pulmonary fibrosis, diabetic renal fibrosis, liver cirrhosis, pancreatic fibrosis, atherosclerosis, myocardial fibrosis, biliary atresia and cataracts. Since CCN2/CTGF has a positive role in wound healing and mesenchymal tissue regeneration, the fibrotic changes observed in those diseases may be regarded as a result of dysregulated regeneration of corresponding tissues.

Prognosis Fibrotic changes are usually irreversible; however, antibody-mediated molecular therapeutics against CCN2/CTGF is currently being developed to prevent the development of fibrotic lesions.

References Bradham DM, Igarashi A, Potter RL, Grotendorst GR. Connective tissue growth factor: a cysteine-rich mitogen secreted by human vascular endothelial cells is related to the SRC-induced immediate early gene product CEF-10. J Cell Biol 1991;114:1285-1294.

Grotendorst GR, Okochi H, Hayashi N. A novel transforming growth factor beta response element controls the expression of the connective tissue growth factor gene. Cell Growth Differ 1996;7:469-480. Igarashi A, Nashiro K, Kikuchi K, Sato S, Ihn H, Fujimoto M, Grotendorst GR, Takehara K. Connective tissue growth factor gene expression in tissue sections from localized scleroderma, keloid, and other fibrotic skin disorders. J Invest Dermatol 1996;106:729-733. Nakanishi T, Kimura Y, Tamura T, Ichikawa H, Yamaai Y, Sugimoto T, Takigawa M. Cloning of a mRNA preferentially expressed in chondrocytes by differential display-PCR from a human chondrocytic cell line that is identical with connective tissue growth factor (CTGF) mRNA. Biochem Biophys Res Commun 1997;234:206-210. Ito Y, Aten J, Bende RJ, Oemar BS, Rabelink TJ, Weening JJ, Goldschmeding R. Expression of connective tissue growth factor in human renal fibrosis. Kidney Int 1998;53:853-861. Tamatani T, Kobayashi H, Tezuka K, Sakamoto S, Suzuki K, Nakanishi T, Takigawa M, Miyano T. Establishment of the enzyme-linked immunosorbent assay for connective tissue growth factor (CTGF) and its detection in the sera of biliary atresia. Biochem Biophys Res Commun 1998;251:748-752. Babic AM, Chen CC, Lau LF. Fisp12/mouse connective tissue growth factor mediates endothelial cell adhesion and migration through integrin alphavbeta3, promotes endothelial cell survival, and induces angiogenesis in vivo. Mol Cell Biol 1999;19:2958-2966. di Mola FF, Friess H, Martignoni ME, Di Sebastiano P, Zimmermann A, Innocenti P, Graber H, Gold LI, Korc M, Büchler MW. Connective tissue growth factor is a regulator for fibrosis in human chronic pancreatitis. Ann Surg 1999;230:63-71. Hishikawa K, Oemar BS, Tanner FC, Nakaki T, Lüscher TF, Fujii T. Connective tissue growth factor induces apoptosis in human breast cancer cell line MCF-7. J Biol Chem 1999;274:37461-37466. Shimo T, Nakanishi T, Nishida T, Asano M, Kanyama M, Kuboki T, Tamatani T, Tezuka K, Takemura M, Matsumura T, Takigawa M. Connective tissue growth factor induces the proliferation, migration, and tube formation of vascular endothelial cells in vitro, and angiogenesis in vivo. J Biochem (Tokyo) 1999;126:137-145. Kubota S, Hattori T, Shimo T, Nakanishi T, Takigawa M. Novel intracellular effects of human connective tissue growth factor expressed in Cos-7 cells. FEBS Lett 2000;474:58-62. Kubota S, Kondo S, Eguchi T, Hattori T, Nakanishi T, Pomerantz RJ, Takigawa M. Identification of an RNA element that confers post-transcriptional repression of connective tissue growth factor/hypertrophic chondrocyte specific 24 (ctgf/hcs24) gene: similarities to retroviral RNA-protein interactions. Oncogene 2000;19:4773-4786. Nakanishi T, Nishida T, Shimo T, Kobayashi K, Kubo T, Tamatani T, Tezuka K, Takigawa M. Effects of CTGF/Hcs24, a product of a hypertrophic chondrocyte-specific gene, on the proliferation and differentiation of chondrocytes in culture. Endocrinology 2000;141:264-273. Shakunaga T, Ozaki T, Ohara N, Asaumi K, Doi T, Nishida K, Kawai A, Nakanishi T, Takigawa M, Inoue H. Expression of connective tissue growth factor in cartilaginous tumors. Cancer 2000;89:1466-1473. Xie D, Nakachi K, Wang H, Elashoff R, Koeffler HP. Elevated levels of connective tissue growth factor, WISP-1, and CYR61 in primary breast cancers associated with more advanced features. Cancer Res 2001;61:8917-8923. Abreu JG, Ketpura NI, Reversade B, De Robertis EM. Connective-tissue growth factor (CTGF) modulates cell signalling by BMP and TGF-beta. Nat Cell Biol 2002;4:599-604.



Eguchi T, Kubota S, Kondo S, Kuboki T, Yatani H, Takigawa M. A novel cis-element that enhances connective tissue growth factor gene expression in chondrocytic cells. Biochem Biophys Res Commun 2002;295:445-451. Hayashi N, Kakimuma T, Soma Y, Grotendorst GR, Tamaki K, Harada M, Igarashi A. Connective tissue growth factor is directly related to liver fibrosis. Hepatogastroenterology 2002;49:133-135. Inoki I, Shiomi T, Hashimoto G, Enomoto H, Nakamura H, Makino K, Ikeda E, Takata S, Kobayashi K, Okada Y. Connective tissue growth factor binds vascular endothelial growth factor (VEGF) and inhibits VEGF-induced angiogenesis. FASEB J 2002;16:219-221. Nishida T, Kubota S, Nakanishi T, Kuboki T, Yosimichi G, Kondo S, Takigawa M. CTGF/Hcs24, a hypertrophic chondrocyte-specific gene product, stimulates proliferation and differentiation, but not hypertrophy of cultured articular chondrocytes. J Cell Physiol 2002;192:55-63. Ivkovic S, Yoon BS, Popoff SN, Safadi FF, Libuda DE, Stephenson RC, Daluiski A, Lyons KM. Connective tissue growth factor coordinates chondrogenesis and angiogenesis during skeletal development. Development 2003;130:2779-2791. Leask A, Holmes A, Black CM, Abraham DJ. Connective tissue growth factor gene regulation. Requirements for its induction by transforming growth factor-beta 2 in fibroblasts. J Biol Chem 2003;278:13008-13015. Moritani NH, Kubota S, Nishida T, Kawaki H, Kondo S, Sugahara T, Takigawa M. Suppressive effect of overexpressed connective tissue growth factor on tumor cell growth in a human oral squamous cell carcinoma-derived cell line. Cancer Lett 2003;192:205-214. Takigawa M. CTGF/Hcs24 as a multifunctional growth factor for fibroblasts, chondrocytes and vascular endothelial cells. Drug News Perspect 2003;16:11-21. (Review). Takigawa M, Nakanishi T, Kubota S, Nishida T. Role of CTGF/HCS24/ecogenin in skeletal growth control. J Cell Physiol 2003;194:256-266. (Review).

Cicha I, Garlichs CD, Daniel WG, Goppelt-Struebe M. Activated human platelets release connective tissue growth factor. Thromb Haemost 2004;91:755-760. Gao R, Brigstock DR. Connective tissue growth factor (CCN2) induces adhesion of rat activated hepatic stellate cells by binding of its C-terminal domain to integrin alpha(v)beta(3) and heparan sulfate proteoglycan. J Biol Chem 2004;279:8848-8855. Kubota S, Kawata K, Yanagita T, Doi H, Kitoh T, Takigawa M. Abundant retention and release of connective tissue growth factor. (CTGF/CCN2) by platelets. J Biochem (Tokyo) 2004;136:279-282. Perbal B. CCN proteins: multifunctional signalling regulators. Lancet 2004;363(9402):62-64. (Review). Asano M, Kubota S, Nakanishi T, Nishida T, Yamaai T, Yosimichi G, Ohyama K, Sugimoto T, Murayama Y, Takigawa M. Effect of connective tissue growth factor (CCN2/CTGF) on proliferation and differentiation of mouse periodontal ligament-derived cells. Cell Commun Signal 2005;3:11. Wahab NA, Weston BS, Mason RM. Connective tissue growth factor CCN2 interacts with and activates the tyrosine kinase receptor TrkA. J Am Soc Nephrol 2005;16:340-351. Hoshijima M, Hattori T, Inoue M, Araki D, Hanagata H, Miyauchi A, Takigawa M. CT domain of CCN2/CTGF directly interacts with fibronectin and enhances cell adhesion of chondrocytes through integrin alpha5beta1. FEBS Lett 2006;580:1376-1382. Shimo T, Kubota S, Yoshioka N, Ibaragi S, Isowa S, Eguchi T, Sasaki A, Takigawa M. Pathogenic role of connective tissue growth factor (CTGF/CCN2) in osteolytic metastasis of breast cancer. J Bone Miner Res 2006;21:1045-1059. Kubota S, Takigawa M. Role of CCN2/CTGF/Hcs24 in bone growth. Int Rev Cytol 2007;257:1-41. (Review).


Kubota S, Takigawa M. CTGF (connective tissue growth factor). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):35-38.





FNIP1 (folliculin interacting protein 1) Laura S Schmidt

Laboratory of Immunobiology, National Cancer Institute Frederick, Bldg 560, Rm 12-69, Frederick, MD 21702, USA


Online updated version: http://AtlasGeneticsOncology.org/Genes/FNIP1ID44003ch5q23.html DOI: 10.4267/2042/38472


Identity Hugo: FNIP1 Other names: KIAA1961; MGC 667 Location: 5q23.3

DNA/RNA Description The FNIP1 gene consists of a 6655 nt mRNA (using NM 133372 derived from AC005593.1, DQ145719.1, AC008695.9 and AL832008.1, the coding sequence extends from nt143 to nt3643) and contains 18 coding exons. The initiation codon is located within exon 1.

Transcription Northern blot analysis revealed an about 7 kb FNIP1 mRNA transcript that was expressed in most major adult tissues, with strongest expression in heart, liver and placenta, and expression in kidney and lung, tissues involved in the Birt-Hogg-Dube' syndrome phenotype (see below). Several alternate transcripts lacking one or more exons have been reported. Transcript 1 is the full-length isoform. Transcript 2 lacks exon 7 (NM 001008738).

Protein Description The FNIP1 protein contains 1166 amino acids and has an estimated molecular weight of 130 kDa.

Localisation Epitope-tagged FNIP1 expressed in HeLa cells localized exclusively in the cytoplasm.

Function Coimmunoprecipitation studies to elucidate the function of folliculin (FLCN) (encoded by the tumor suppressor gene, BHD/FLCN, which is mutated in the Birt-Hogg-Dube' syndrome) identified a novel folliculin-interacting protein, FNIP1, which interacts through the C-terminus of FLCN. FNIP1 overexpression enhanced phosphorylation of FLCN and phospho-FLCN preferentially bound to FNIP1. FNIP1 is a novel protein with no domains to suggest function. By coimmunoprecipitation studies FNIP1 was also found to interact with the heterotrimer, 5'AMP-activated protein kinase (AMPK), a key molecule for energy sensing and a negative regulator of mTOR (mammalian target of rapamycin). AMPK, which

FNIP1 (folliculin interacting protein 1) Schmidt LS


bound to FNIP1, was preferentially in its phosphorylated (active) form and FNIP1 could act as a substrate for AMPK phosphorylation both in vitro and in vivo. Inhibition of AMPK kinase activity resulted in reduced FNIP1 protein expression in HEK293 cells suggesting that phosphorylation of FNIP1 by AMPK may enhance protein stability. These data suggest that FNIP1 and its interacting partner, FLCN, may be involved in energy and nutrient-sensing through the AMPK and mTOR signaling pathways. FNIP1 was also shown to interact with HSP90 by coimmunoprecipitation in HEK293 cells.

Homology A comparison of FNIP1 proteins across species identified 5 blocks of conserved sequence with at least 35% similarity. FNIP1 homologs have been identified in Mus musculus, Gallus gallus, Xenopus tropicalis, Danio rerio, Drosophila melanogaster and Caenorhabditis elegans.

Implicated in Birt-Hogg-Dube'(BHD) syndrome Note: FNIP1 interacts with FLCN, encoded by a novel tumor suppressor gene, BHD/FLCN, which is mutated in the germline of patients with BHD syndrome.

Disease Genodermatosis characterized by the triad of benign tumors of the hair follicle, spontaneous pneumothorax and kidney tumors.

References Nagase T, Kikuno R, Ohara O. Prediction of the coding sequences of unidentified human genes. XXII. The complete sequences of 50 new cDNA clones which code for large proteins. DNA Res 2001;8:319-327. Baba M, Hong SB, Sharma N, Warren MB, Nickerson ML, Iwamatsu A, Esposito D, Gillette WK, Hopkins RF, Hartley JL, Furihata M, Oishi S, Zhen W, Burke TR, Linehan WM, Schmidt LS, Zbar B. Folliculin encoded by the BHD gene interacts with a binding protein, FNIP1, and AMPK, and is involved in AMPK and mTOR signaling. Proc Natl Acad Sci USA 2006;103:15552-15557.


Schmidt LS. FNIP1 (folliculin interacting protein 1). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):39-40.





GLMN (glomulin) Virginie Aerts, Pascal Brouillard, Laurence M Boon, Miikka Vikkula

Human Molecular Genetics (GEHU) de Duve Institute, Universite catholique de Louvain, Avenue Hippocrate 74(+5), bp. 75.39, B-1200 Brussels, Belgium


Online updated version: http://AtlasGeneticsOncology.org/Genes/GLMNID43022ch1p22.html DOI: 10.4267/2042/38473


Identity Other names: GLMN; FAP68; FAP48 Location: 1p22.1 Note: The gene was identified by linkage mapping and positional cloning. There is no evidence for locus heterogeneity. Haplotype sharing has been reported for an important number of families.

DNA/RNA Description The genomic DNA of the glomulin gene spans about 55 kbp and contains 19 exons coding for 1785 bp. The first exon is non coding, the start codon is located on the second exon and the stop codon in the last exon.

Transcription In all human and murine tissues tested, a about 2 kb transcript was observed by Northern blot hybridization, suggesting that glomulin expression is ubiquitous. This could be due to the presence of glomulin-expressing blood vessels in the various tissues analysed. By in situ hybridisation on murine embryos, glomulin expression was evident at embryonic E10.5 days post-coitum (dpc) and localized to the cardiac outflow tract. Between E11.5 to 14.5 dpc, glomulin mRNA is most abundant in the walls of large vessels (e.g. dorsal aorta). At E14.5 dpc, E16.5 dpc, and in adult tissues, expression of glomulin is clearly restricted to vascular smooth muscle cells. The high level of glomulin expression in the murine vasculature indicates that glomulin may have an important role in blood vessel development and/or maintenance. A truncated form of glomulin, called FAP48, with an altered carboxy-terminal end, was isolated from a Jurkat-cell library. However FAP48, which presents

70% homology with glomulin, was not detected in other tissues and cells tested. Thus, it might be an aberrant transcript in this library.

Pseudogene In man, no paralogue exists. Yet, a pseudogene is located on chromosome 21. It contains only a few exons (exons 6 to 10), without intervening introns and with several nucleotide differences. Thus, glomulin seems to be unique in the human genome.

Protein Note: Glomulin was identified by reverse genetics, and its function is currently unknown.

Description Glomulin gene encodes a protein of 594 amino acids (68 kDa). In silico analysis reveals no known functional or structural domains, but a few potential phosphorylation and glycosylation sites.

Expression (see above, para Transcription).

Localisation By in silico analysis, no signal sequence or clear transmembrane domain in glomulin has been identified. Glomulin (FAP68) is likely an intracellular protein.

Function The exact function of glomulin is unknown. Glomulin (under the name of FAP48) has been described to interact with FKBP12, an immunophilin that binds the immunosuppressive drugs FK506 and rapamycin. FKBP12 interacts with the TGFbeta type I receptor, and prevents its phosphorylation by the type II receptor in the absence of TGFbeta. Thus, FKBP12 safeguards against the ligand-independent activation of

GLMN (glomulin) Aerts V et al


this pathway. Glomulin, through its interaction with FKBP12, could act as a repressor of this inhibition. Glomulin has also been described to interact with the last 30 amino acids of the C-terminal part of the HGF receptor, c-MET. This receptor is a transmembrane tyrosine kinase, which becomes tyrosine-phosphorylated upon activation by HGF. Glomulin interacts with the inactive, non phosphorylated form of c-MET. When c-MET is activated by HGF, glomulin is released in a phosphorylated form. This leads to p70 S6 protein kinase (p70S6K) phosphorylation. This activation occurs synergistically with the activation by the c-MET-activated PI3 kinase. It is not known whether glomulin activates p70S6K directly or indirectly. The p70S6K is a key regulator of protein synthesis. Glomulin could thereby control cellular events such as migration and cell division. The third reported glomulin partner is Cul7, a Cul1 homologue. This places glomulin in an SCF-like complex, which is implicated in protein ubiquitination and degradation.

Homology Glomulin seems to be an unique protein. No paralogue has been found and its lack in GVM is not compensated by another protein. Orthologues of glomulin have been identified in other species (cat, chimpanzee, cow, dog, mouse, rat, rhesus macaque, xenopus, zebrafish) and thus it is present in all vertebrates but not in insects or bacteries.

Mutations Note: There is no phenotype-genotype correlation in GVM.

Germinal To date, 29 different inherited mutations (deletions, insertions and nonsense substitutions) have been identified. The most 5' mutation are located in the first coding exon. The majority of them cause premature truncation of the protein and likely result in loss-of-function. One mutation deletes 3 nucleotides resulting in the deletion of an asparagine at position 394 of the protein. More than 70% of GVMs are caused by eight different mutations in glomulin: 157delAAGAA (40,7%), 108C>A (9,3%), 1179delCAA (8,1%), 421insT and 738insT (4,65% each), 554delA+556delCCT (3,5%), 107insG and IVS5-1(G>A) (2,3% each).

Somatic The phenotypic variability observed in GVM could be explained by the need of a somatic second-hit mutation. Such a mechanism was discovered in one GVM (somatic mutation 980delCAGAA), suggesting that the lesion is due to a complete localized loss-of-function of glomulin. This concept can explain why some patients have bigger lesions than others, why new lesions appear, and why they are multifocal. This could also explain, why some mutation carriers are unaffected.

Schematic representation of glomulin: The two stars (*) indicate the start and the stop codons, in exon 2 and 19 respectively. All known mutations are shown. Somatic second hit is in blue.

GLMN (glomulin) Aerts V et al


Implicated in Glomuvenous malformation (GVM) Note: GVM is often, if not always, hereditary, and transmitted as an autosomal dominant disorder.

Disease GVM is a localized bluish-purple cutaneous vascular lesion, histologically consisting of distended venous channels with flattened endothelium surrounded by variable number of maldifferentiated smooth muscle-like 'glomus cells' in the wall. GVM account for 5% of venous anomalies referred to centers for vascular anomalies. Seven features characterize GVM lesions: (1) Colour: GVMs can be pink in infants, the most are bluish-purple; (2) Affected tissues: the lesions are localized to the skin and subcutis; (3) Localization: lesions are more often located on the extremities; (4) Appearance: lesions are usually nodular and multifocal. They are often hyperkeratotic; (5) The lesions are not compressible; (6) The lesions are painful on palpation; (7) New lesions can appear with time, likely after trauma. GVM has no neoplastic histological characteristics and never becomes malignant.

References Goodman TF, Abele DC. Multiple glomus tumors. A clinical and electron microscopic study. Arch Dermatol 1971;103(1):11-23. Chambraud B, Radanyi C, Camonis JH, Shazand K, Rajkowski K, Baulieu EE. FAP48, a new protein that forms specific complexes with both immunophilins FKBP59 and FKBP12. Prevention by the immunosuppressant drugs FK506 and rapamycin. J biol Chem 1996;271(51):32923-32929. Chen YG, Liu F, Massague J. TGFbeta receptor inhibition by FKBP12. EMBO J 1997;16(13):3866-3876. Boon LM, Brouillard P, Irrthum A, Karttunen L, Warman ML, Rudolph R, Mulliken JB, Olsen BR, Vikkula M. A gene for inherited cutaneous venous anomalies ('glomangiomas') localizes to chromosome 1p21-22. Am J Hum Genet 1999;65(1):125-133. Brouillard P, Olsen BR, Vikkula M. High-resolution physical and transcript map of the locus for venous malformations with

glomus cells (VMGLOM) on chromosome 1p21-p22. Genomics 2000;67(1):96-101. Grisendi S, Chambraud B, Gout I, Comoglio PM, Crepaldi T. Ligand-regulated binding of FAP68 to the hepatocyte growth factor receptor. J Biol Chem 2001;276(49):46632-46638. Irrthum A, Brouillard P, Enjolras O, Gibbs NF, Eichenfield LF, Olsen BR, Mulliken JB, Boon LM, Vikkula M. Linkage disequilibrium narrows locus for venous malformation with glomus cells (VMGLOM) to a single 1.48 Mbp YAC. Eur J Hum Genet 2001;9(1):34-38. Brouillard P, Boon LM, Mulliken JB, Enjolras O, Ghassibé M, Matthew L, Warman O, Tan T, Olsen BR, Vikkula M. Mutations in a novel factor, Glomulin, are responsible for glomuvenous malformations ('Glomangiomas'). Am J Hum Genet 2002;70:866-874. Arai T, Kasper JS, Skaar JR, Ali SH, Takahashi C, DeCaprio JA. Targeted disruption of P185/Cul7 gene results in abnormal vascular morphogenesis. Proc Natl Acad Sci USA 2003;100(17):9855-9860. Boon LM, Mulliken JB, Enjolras O, Vikkula M. Glomuvenous malformations (glomangioma) and Venous malformations, Distinct clinicopathologic and genetic entities. Arch Dermatol 2004;140:971-976. McIntyre BA, Brouillard P, Aerts V, Gutierrez-Roelens I, Vikkula M. Glomulin is predominantly expressed in vascular smooth muscle cells in the embryonic and adult mouse. Gene Expr Patterns 2004;4(3):351-358. Brouillard P, Ghassibé M, Penington A, Boon LM, Dompmartin a, Temple IK, Cordisco M, Adams D, Piette F, Harper JI, Syed S, Boralevi F, Taïeb A, Danda S, Baselga E, Enjolras O, Mulliken JB, Vikkula M. Four common glomulin mutation cause two thirds of glomuvenous malformations ('familial glomangiomas'): evidence for a founder effect. J Med Genet 2005;42(2):e13. Boon LM, Vanwijck R. Medical and surgical treatment of venous malformations. Ann Chir Plast Esthet 2006;51(4-5):403-411. Mallory SB, Enjolras O, Boon LM, Rogers E, Berk DR, Blei F, Baselga E, Ros AM, Vikkula M. Congenital plaque-type glomuvenous malformations presenting in childhood. Arch Dermatol 2006;142(7):892-896. Brouillard P, Enjolras O, Boon LM, Vikkula M. GLMN and Glomuvenous Malformation. Inborn Errors of Development 2e, edited by Charles Epstein, Robert Erickson and Anthony Wynshaw-Boris, Oxford University Press, Inc.


Aerts V, Brouillard P, Boon LM, Vikkula M. GLMN (glomulin). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):41-43.





JAK3 (janus kinase 3 or just another kinase 3) Ping Shi, Hesham M Amin

Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA


Online updated version: http://AtlasGeneticsOncology.org/Genes/JAK3ID41032ch19p13.html DOI: 10.4267/2042/38474


Identity Hugo: JAK3 Other names: JAK-3; JAK_HUMAN; L-JAK; LJAK; EC 2.7.10.2 Location: 19p13.1 Local order: chr19: 17788,324-17819800.

DNA/RNA Description JAK3 is a functioning gene that comprises 23 exons spanning roughly 21 kb of genomic DNA with an open reading frame of 3372 bp.

Transcription 4025 bp mRNA. 7 transcript variants encoding 7 distinct proteins.

Protein Note: 3 isoforms produced by alternative splicing: JAK3S, JAK3B, JAK3M.

Description 1124 amino acids, 125099 Da. JAK3 is comprised of 7 JAK homology (JH) domains. JH1 contains the C terminus kinase domain and an SH2 or SH3 binding motif; JH2 contains a pseudokinase domain tandemly linked to the N site of the JH1 domain; 5 more JH domains. The N terminus region (JH6 and JH7) is critical for receptor binding and signal transduction.

Expression JAK3 is expressed in 12 normal human tissues (bone marrow, spleen, thymus, brain, spinal cord, heart, skeletal muscle, liver, pancreas, prostate, kidney, and lung). JAK3S is more commonly seen in hematopoietic cells, whereas JAK3B and JAK3M are detected in cells of hematopoietic or epithelial origin.

Localisation Intracellular, membrane-associated through association with interleukin (IL) receptor common gamma chain (gamma-c).

Function Tyrosine kinase of the non-receptor type. Involved in the signaling of ILs that contain the gamma-c chain in their respective receptors, including IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21. Induces tyrosine phosphorylation of a number of proteins, of which most widely studied are signal transducers and activators of transcriptions (STAT). JAK3 has also been shown to phosphorylate insulin receptor substrate-1 (IRS-1), IRS-2, and PI3K/Akt.

Homology JAK3 is the most recently identified member of the mammalian Janus kinase subfamily (TYK2, JAK1, JAK2, and JAK3); JAK3 paralogs to JAK1 and JAK2; human JAK3 orthologs to murine Jak3.

Mutations Note: Mostly point mutations were identified affecting all 7 structural JH domains of JAK3.

Somatic Mutations of JAK3 were generally associated with the same cellular phenotype of the more frequently encountered X-linked SCID due to gamma-c deficiency. It was confirmed with the identification of 34 mutations in JAK3-SCID patients from Europe and the US. JAK3-SCID is inherited as autosomal recessive disease. It is estimated to account for approximately 7-14% of heritable SCID. JAK3 mutations are seemingly sporadic, and neither preferential gene locations (i.e. gene 'hot-spots') nor founder effects have yet been documented.

JAK3 (janus kinase 3 or just another kinase 3) Shi P, Amin HM


Different mutations identified in all of the 7 domains of JAK3. The mutations in 'black color' are the mutations reported in JAK3-SCID; 'red color and italic' identifies mutations reported in acute megakaryoblastic leukemia; and 'orange color and underline' highlights one mutation that has been reported in both JAK3-SCID and acute megakaryoblastic leukemia.

The majority of JAK3-SCID patients are compound heterozygotes, having inherited a distinct mutation from each parent, although some individuals are homozygous for their mutations as a result of parental consanguinity. Most mutations have dramatic effects on protein expression of JAK3, but some missense mutations or small in-frame deletions allow for some protein expression. These mutations affect kinase activity, receptor binding, and intracellular trafficking. In addition, 7 mutations of JAK3 have been recently described in 5 patients with acute megakaryoblastic leukemia with or without Down syndrome. These mutations are in general activation mutations. The Down syndrome patients presented initially with transient myeloproliferative disease.

Implicated in Severe combined immunodeficiency (SCID) Note: 34 unique mutations of JAK3 have been identified in cases of JAK3-SCID, occurring in all of its 7 structural JH domains. No hotspots have been reported and multiple types of mutations have been identified: 21 missense/nonsense mutations, 7 splice site mutations, 3 small deletions, 2 gross deletions and 1 insertion.

Disease Defects in JAK3 are associated with the autosomal recessive T-cell negative/B-cell positive type of severe combined immunodeficiency (SCID); a condition characterized by the absence of circulating mature T-

lymphocytes and NK cells, normal to elevated numbers of nonfunctional B-lymphocytes, and marked hypoplasia of lymphoid tissues.

Prognosis SCID due to JAK3 deficiency is generally a lethal disorder. The advent of hematopoietic stem cell transplant revolutionized the outcome of JAK3-SCID, and at present it is still the treatment of choice. Acute megakaryoblastic leukemia Note: 7 unique mutations of JAK3 have also been identified in patients with acute megakaryoblastic leukemia. These mutations occur in the JH2, JH6, and JH7 domains.

Disease Also, defects in JAK3 have been recently described in some cases of acute megakaryoblastic leukemia with or without Down syndrome. Acute megakaryoblastic leukemia is a type of acute leukemia where more than 50% of the blasts are of megakaryocytic lineage. The exact role of JAK3 in this disease is not completely known.

Prognosis Acute megakaryoblastic leukemia demonstrates a bad clinical outcome.

References Johnston JA, Kawamura M, Kirken RA, Chen YQ, Blake TB, Shibuya K, Ortaldo JR, McVicar DW, O'Shea JJ. Phosphorylation and activation of the Jak-3 Janus kinase in response to interleukin-2. Nature 1994;370:151-152.

JAK3 (janus kinase 3 or just another kinase 3) Shi P, Amin HM


Kawamura M, McVicar DW, Johnston JA, Blake TB, Chen YQ, Lal BK, Lloyd AR, Kelvin DJ, Staples JE, Ortaldo JR, O'Shea JJ. Molecular cloning of L-JAK, a Janus family protein-tyrosine kinase expressed in natural killer cells and activated leukocytes. Proc Natl Acad Sci USA 1994;91:6374-6378. Rane SG, Reddy EP. JAK3: a novel JAK kinase associated with terminal differentiation of hematopoietic cells. Oncogene 1994;9:2415-2423. Johnston JA, Wang LM, Hanson EP, Sun XJ, White MF, Oakes SA, Pierce JH, O'Shea JJ. Interleukins 2, 4, 7, and 15 stimulate tyrosine phosphorylation of insulin receptor substrates 1 and 2 in T cells. Potential role of JAK kinases. J Biol Chem 1995;270:28527-28530. Macchi P, Villa A, Giliani S, Sacco MG, Frattini A, Porta F, Ugazio AG, Johnston JA, Candotti F, O'Shea JJ, Vezzoni P, Notarangelo LD. Mutations of Jak-3 gene in patients with autosomal severe combined immune deficiency. Nature 1995;377:65-68. Russell SM, Tayebi N, Nakajima H, Riedy MC, Roberts JL, Aman MJ, Migone TS, Noguchi M, Markert ML, Buckley RH, O'Shea JJ, Leonard WJ. Mutation of Jak3 in a patient with SCID:essential role of Jak3 in lymphoid development. Science 1995;270:797-799. Riedy MC, Dutra AS, Blake TB, Modi W, Lal BK, Davis J, Bosse A, O'Shea JJ, Johnston JA. Genomic sequence, organization, and chromosomal localization of human JAK3. Genomics 1996;37:57-61. Candotti F, Oakes SA, Johnston JA, Giliani S, Schumacher RF, Mella P, Fiorini M, Ugazio AG, Badolato R, Notarangelo LD, Bozzi F, Macchi P, Strina D, Vezzoni P, Blaese RM, O'Shea, JJ, Villa A. Structural and functional basis for JAK3-deficient severe combined immunodeficiency. Blood 1997;90:3996-4003. Bozzi F, Lefranc G, Villa A, Badolato R, Schumacher RF, Khalil G, Loiselet J, Bresciani S, O'Shea JJ, Vezzoni P, Notarangelo LD, Candotti F. Molecular and biochemical characterization of JAK3 deficiency in a patient with severe combined immunodeficiency over 20 years after bone marrow transplantation: implications for treatment. Br J Haematol 1998;102:1363-1366. Brooimans RA, van der Slot AJ, van den Berg AJAM, Zegers BJM. Revised exon-intron structure of human JAK3 locus. Europ J Hum Genet 1999;7:837-840. Buckley RH, Schiff SE, Schiff RI, Markert L, Williams LW, Roberts JL, Myers L A, Ward FE. Hematopoietic stem-cell transplantation for the treatment of severe combined immunodeficiency. N Eng J Med 1999;340:508-516. Schumacher RF, Mella P, Badolato R, Fiorini M, Savoldi G, Giliani S, Villa A, Candotti F, Tampalini A, O'Shea JJ, Notarangelo LD. Complete genomic organization of the human JAK3 gene and mutation analysis in severe combined immunodeficiency by single-strand conformation polymorphism. Hum Genet 2000;106:73-79. Vihinen M, Villa A, Mella P, Schumacher RF, Savoldi G, O'Shea JJ, Candotti F, Notarangelo LD. Molecular modeling of the Jak3 kinase domains and structural basis for severe combined immunodeficiency. Clin Immunol 2000;96:108-118. Fehniger TA, Caligiuri MA. Interleukin 15: biology and relevance to human disease. Blood 2001;97:14-32. Gennery AR, Cant AJ. Diagnosis of severe combined immunodeficiency. J Clin Pathol 2001;54:191-195. Notarangelo LD, Mella P, Jones A, de Saint Basile G, Savoldi G, Cranstonb T, Vihinen M, Schumacher RF. Mutations in severe combined immune deficiency (SCID) due to JAK3 deficiency. Hum Mutat 2001;18:255-263. Grimwood J, Gordon LA, Olsen AS, Terry A, Schmutz J, Lamerdin JE, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, Aerts A, Altherr M, Ashworth L, Bajorek E, Black S,

Branscomb E, Caenepeel S, Carrano AV, Caoile C, Lucas SM. The DNA sequence and biology of human chromosome 19. Nature 2004;428:529-535. O'Shea JJ, Husa M, Li D, Hofmann SR, Watford W, Roberts JL, Buckley RH, Changelian P, Candotti F. Jak3 and the pathogenesis of severe combined immunodeficiency. Mol Immunol 2004;41:727-737. Roberts JL, Lengi A, Brown SM, Chen M, Zhou YJ, O'Shea JJ, Buckley RH. Janus kinase 3 (JAK3) deficiency: clinical, immunologic, and molecular analyses of 10 patients and outcomes of stem cell transplantation. Blood 2004;103:2009-2018. Yamaoka K, Saharinen P, Pesu M, Holt VE, Silvennoinen O, O'Shea JJ. The Janus kinases (Jaks). Genome Biol 2004;5:253. Mangan JK, Reddy EP. Activation of the Jak3 pathway and myeloid differentiation. Leuk Lymphoma 2005;46:21-27. Mori D, Nakafusa Y, Miyazaki K, Tokunaga O. Differential expression of Janus kinase 3 (JAK3), matrix metalloproteinase 13 (MMP13), heat shock protein 60 (HSP60), and mouse double minute 2 (MDM2) in human colorectal cancer progression using human cancer cDNA microarrays. Pathol Res Pract 2005;201:777-789. Notarangelo LD. JAK3 deficiency, (SCID T-B+). Orphanet encyclopedia, 2005;pp1-6. Pesu M, Candotti F, Husa M, Hofmann SR, Notarangelo LD, O'Shea JJ. Jak3, severe combined immunodeficiency, and a new class of immunosuppressive drugs. Immunol Rev 2005;203:127-142. Han Y, Amin HM, Franko B, Frantz C, Shi X, Lai R. Loss of SHP1 enhances JAK3/STAT3 signaling and decreases proteosome degradation of JAK3 and NPM-ALK in ALK+ anaplastic large-cell lymphoma. Blood 2006;108:2796-2803. Krejsgaard T, Vetter-Kauczok CS, Woetmann A, Lovato P, Labuda T, Eriksen KW, Zhang Q, Becker JC, Ødum N. Jak3- and JNK-dependent vascular endothelial growth factor expression in cutaneous T-cell lymphoma. Leukemia 2006;20:1759-1766. Qiu L, Lai R, Lin Q, Lau E, Thomazy DM, Calame D, Ford RJ, Kwak LW, Kirken RA, Amin HM. Autocrine release of interleukin-9 promotes Jak3-dependent survival of ALK+ anaplastic large-cell lymphoma cells. Blood 2006;108:2407-2415. Walters DK, Mercher T, Gu TL, O'Hare T, Tyner JW, Loriaux M, Goss VL, Lee KA, Eide CA, Wong MJ, Stoffregen EP, McGreevey L, Nardone J, Moore SA, Crispino J, Boggon TJ, Heinrich MC, Deininger MW, Polakiewicz RD, Gilliland DG, Druker BJ. Activating alleles of JAK3 in acute megakaryoblastic leukemia. Cancer Cell 2006;10:65-75. Choi YL, Kaneda R, Wada T, Fujiwara S, Soda M, Watanabe H, Kurashina K, Hatanaka H, Enomoto M, Takada S, Yamashita Y, Mano H. Identification of a constitutively active mutant of JAK3 by retroviral expression screening. Leuk Res 2007;31:203-209. Kiyoi H, Yamaji S, Kojima S, Naoe T. JAK3 mutations occur in acute megakaryoblastic leukemia both in Down syndrome children and non-Down syndrome adults. Leukemia 2007;21:574-576. Mjaanes CM, Hendershot RW, Quinones RR, Gelfand EW. A novel mutation of intron 22 in Janus kinase 3-deficient severe combined immunodeficiency. J Allergy Clin Immunol 2007;119:1542-1545.


Shi P, Amin HM. JAK3 (janus kinase 3 or just another kinase 3). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):44-46.





KLRK1 (killer cell lectin-like receptor subfamily K, member 1) Lewis L Lanier

UCSF, Department of Microbiology and Immunology, San Francisco, CA 94143-0414, USA


Online updated version: http://AtlasGeneticsOncology.org/Genes/KLRK1ID41094ch12p13.html DOI: 10.4267/2042/38475


Identity Hugo: KLRK1 Other names: CD314; D12S2489E; NKG2D; NKG2-D. Location: 12p13.2 Local order: KLRK1 is flanked by KLRD1 (CD94) on the centromeric and KLRC4 (NKG2F) on the telomeric side. The 3' end of the KLRC4 transcript includes the first non-coding exon found at the 5' end of the adjacent KLRK1 gene transcript. Note: KLRK1 is on chromosome 12p13.2-p12.3 at 10,416,857-10,454,012. KLRK1 is a member of the C-type lectin-like family of type II cell surface glycoproteins. It is expressed by NK cells, CD8+ T cells, gamma/delta-TcR+ T cells, and a minor subset of CD4+ T cells. KLRK1 associates with the DAP10 transmembrane adapter protein and transmits activating signalings into these lymphocytes.

DNA/RNA Note: KLRK1 is present on chromosome 12 within a cluster of genes referred to as the 'NK complex' (NKC) because several genes that are preferentially expressed by NK cells are located in this region, including on the centromeric side KLRD1 (CD94) and on the telomeric side KLRC4 (NKG2F), KLRC3 (NKG2E), KLRC2 (NKG2C), and KLRC1 (NKG2A).

Description The KLRK1 gene is 37,793 bases located on the negative strand of chromosome 12 spanning 10,416,219 to 10,454,012 bp. ENTREZ database predicts 12 exons. Three alleles of KLRK1 differing by substitutions at only two nucleotide positions, of which one is nonsynonymous and the other synonymous, have been reported.

Transcription There is evidence for alternative splicing of KLRK1, but only one isoform encoding a functional protein has been described in humans. In one of the KLRK1 splice variants the fourth exon of KLRC4 is spliced to the 5-prime end of KLRK1. KLRK1 is transcribed by NK cells, gamma/delta-TcR+ T cells, CD8+ T cells and some CD4+ T cells. Transcription of KLRK1 is enhanced by stimulation of NK cells with IL-2 or IL-15 and decreased by culture with TGF-beta.

Protein Note: KLRK1 is a type II membrane glycoprotein expressed as a disulfide-bonded homodimer on the cell surface. Expression of KLRK1 on the cell surface requires its association with DAP10, which is a type I adapter protein expressed as a disulfide-bonded homodimer. On the cell surface, the receptor complex is a hexamer; two disulfide-bonded KLRK1/NKG2D homodimers each paired with two DAP10 disulfide-bonded homodimers. A charged amino acid residue (aspartic acid) centrally located within the transmembrane region of DAP10 forms a salt bridge with a charged amino acid residue (arginine) in the transmembrane region of KLRK1/NKG2D to stabilize the receptor complex.

Description KLRK1 is a type II membrane protein comprising 216 amino acids with a predicted molecular weight of 25143 kD. The protein has an N-terminal intracellular region, a transmembrane domain, and a C-terminal extracellular region with a single C-type lectin-like domain. KLRK1 is expressed on the cell surface as a disulfide-bonded homodimer with a molecular weight of

KLRK1 (killer cell lectin-like receptor subfamily K, member 1) Lanier LL


approximately 42 kd when analyzed under reducing conditions and approximately 80 kd under non-reducing conditions. A cysteine residue just outside the transmembrane region forms the disulfide bond joining the two subunits of the homodimer. There are three potential sites for N-linked glycosylation in the extracellular region of KLRK1. Treatment of the KLRK1 glycoprotein with N-glycanase reduces the molecular weight to approximately the size of the core polypeptide. The protein has an N-terminal intracellular region, a transmembrane domain, a membrane-proximal stalk region, and an extracellular region with a single C-type lectin-like domain.

Expression KLRK1 is transcribed by NK cells, gamma/delta-TcR+ T cells, CD8+ T cells and some CD4+ T cells.

Localisation KLRK1 is expressed as a type II glycoprotein on the cell surface of NK cells, gamma/delta-TcR+ T cells, CD8+ T cells and some CD4+ T cells.

Function KLRK1 binds to at least seven distinct ligands: MICA, MICB, ULBP-1, ULBP-2, ULBP-3, ULBP-4, and RAET1G. These ligands are type I glycoproteins with homology to MHC class I. The KLRK1 ligand are frequently over-expressed on tumor cells, virus-infected cells, and 'stressed' cells. The crystal structure of KLRK1 bound to MICA has been reported. After binding to its ligand, KLRK1 transmits an activating signal via the DAP10 adapter subunit. DAP10 has a YxxM motif in its cytoplasmic domain, which upon tyrosine phosphorylation binds to Vav and the p85 subunit of PI3-kinase, causing a downstream cascade of signaling in T cells and NK cells.

Homology NKG2-D type II integral membrane protein [Pan troglodytes] NP_001009059; NKG2D protein [Macaca mulatta] NP_001028061; NKG2D receptor [Macaca fascicularis] CAD19993; NKG2D [Callithrix jacchus] ABN45890; NKG2D [Papio anubis] ABO09749; NKG2-D type II integral membrane protein [Pongo pygmaeus] Q8MJH1; putative immunoreceptor NKG2D [Bos taurus] CAJ27114; NKG2-D type II integral membrane protein [Sus scrofa] Q9GLF5; NKG2-D isoform a [Mus musculus] NP_149069; NKG2-D isoform b [Mus musculus] NP_001076791; killer cell lectin-like receptor subfamily K, member 1 [Rattus norvegicus] NP_598196.

Mutations Note: None identified.

Implicated in Cancer Note: Many types of cancer (carcinomas, sarcomas, lymphomas, leukemias) over-express the ligands for KLRK1. In some cases, this renders the tumor cells susceptible to killing by activated KLRK1-bearing NK cells. Some tumors shed or secrete soluble ligands that bind to KLRK1 and down-regulate expression of the KLRK1 receptor on NK cells and T cells, potentially to evade attack by these immune effector cells.

Viral infection Note: Viral infection of cells can induce transcription and cell surface expression of ligands for KLRK1, rendering these infected cells susceptible to attack by NK cells and T cells. Some viruses, for example cytomegalovirus, encodes proteins that intercept the ligand proteins intracellularly and prevent their expression on the surface of virus-infected cells.

Rheumatoid arthritis Note: An expansion of CD4+, CD28- T cells expressing KLRK1 was observed in the joints of patients with rheumatoid arthritis and KLRK1 ligands were detected on synovial cells in the inflamed tissue.

Type I diabetes Note: Peripheral blood NK cells and T cells in patients with type I diabetes demonstrate a slightly decreased amount of expression of KLRK1 on the cell surface, independent disease duration, similar to prior observations in the NOD mouse.

References Houchins JP, Yabe T, McSherry C, Bach FH. DNA sequence analysis of NKG2, a family of related cDNA clones encoding type II integral membrane proteins on human natural killer cells. J Exp Med 1991;173(4):1017-1020. Glienke J, Sobanov Y, Brostjan C, Steffens C, Nguyen C, Lehrach H, Hofer E, Francis F. The genomic organization of NKG2C, E, F, and D receptor genes in the human natural killer gene complex. Immunogenetics 1998;48(3):163-173. Bauer S, Groh V, Wu J, Steinle A, Phillips JH, Lanier LL, Spies T. Activation of NK cells and T cells by NKG2D, a receptor for stress-inducible MICA. Science 1999;285(5428):727-729. Wu J, Song Y, Bakker AB, Bauer S, Spies T, Lanier LL, Phillips JH. An activating immunoreceptor complex formed by NKG2D and DAP10. Science 1999;285(5428):645-647. Cosman D, Müllberg J, Sutherland CL, Chin W, Armitage R, Fanslow W, Kubin M, Chalupny NJ. ULBPs, novel MHC class I-related molecules, bind to CMV glycoprotein UL16 and stimulate NK cytotoxicity through the NKG2D receptor. Immunity 2001;14(2):123-133. Li P, Morris DL, Willcox BE, Steinle A, Spies T, Strong RK. Complex structure of the activating immunoreceptor NKG2D

KLRK1 (killer cell lectin-like receptor subfamily K, member 1) Lanier LL


and its MHC class I-like ligand MICA. Nat Immunol 2001;2(5):443-451. Groh V, Wu J, Yee C, Spies T. Tumour-derived soluble MIC ligands impair expression of NKG2D and T-cell activation. Nature 2002;419(6908):734-738. Groh V, Bruhl A, El-Gabalawy H, Nelson JL, Spies T. Stimulation of T cell autoreactivity by anomalous expression of NKG2D and its MIC ligands in rheumatoid arthritis. Proc Natl Acad Sci USA 2003;100(16):9452-9457. Garrity D, Call ME, Feng J, Wucherpfennig KW. The activating NKG2D receptor assembles in the membrane with two

signaling dimers into a hexameric structure. Proc Natl Acad Sci USA 2005;102(21):7641-7646. Rodacki M, Svoren B, Butty V, Besse W, Laffel L, Benoist C, Mathis D. Altered natural killer cells in type 1 diabetic patients. Diabetes 2007;56(1):177-185.


Lanier LL. KLRK1 (killer cell lectin-like receptor subfamily K, member 1). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):47-49.

Gene Section Review




LGI1 (leucine-rich, glioma inactivated protein 1 precursor) Nadia Gabellini

University of Padua, Department of Biological Chemistry, Viale G. Colombo, 3, 35121, Padua, Italy


Online updated version: http://AtlasGeneticsOncology.org/Genes/LGI1ID311ch10q23.html DOI: 10.4267/2042/38476


Identity Hugo: LGI1 Other names: ADPEAF; EPT; Epitempin-1; ETL1; IB1099; uc001kjc.1 Location: 10q23.33 Local order: Plus strand orientation, between C10orf4 (protein isoform FRA10AC1-2) and TMEM20 (Transmembrane protein 20).

DNA/RNA Note: LGI1 gene spans a 40,274 bp region of chromosome 10 (95,507,632 - 95,547,906). NCBI assembly annotation: NC_000010.9; NT_030059.12. Alternate Celera assembly: AC_000053.1; NW_924884.1. LGI1 is considered a metastasis suppressor gene; it is also implicated in Autosomal Dominant Lateral Temporal Lobe Epilepsy (ADLTE).

Description The LGI1 gene was isolated by positional cloning from a glioblastoma cell line (T98G) bearing a balanced translocation t(10;19)(q24;q13). LGI1 gene comprises 8 exons. Exon 1 contains the 5’UTR (224 bp) and encodes the start methione. The size of exon 8 and the position of the stop codon are

different in isoform 1 and 2. The 3’UTR consists of 356 bp in isoform 1 and of 386 bp in isoform 2. A minimal promoter region is located immediately upstream of the TSS. Two Poly (A) sites are predicted by SVM from UCSC Genome Browser at the following positions: chr10:95547796-95547828 and chr10:95547881-95547919. STS markers: IB1099; EST307318; RH51322; SHGC-155057.

Transcription Isoform 1 mRNA is composed of 2290 bases. Alternative splicing produces isoform 2 consisting of 1456 bases with a shorter exon 8 (425 bases).

Pseudogene None.

Protein Note: The unprocessed precursor of LGI1 comprises 557 Amino Acids with a Molecular weight of 63818 Da (isoform 1, UniProtKB/Swiss-Prot). Three potential N-linked glycosilation sites have been identified at AA positions: 192, 277 and 422. Isoform 2 includes a sequence variation (AA: 280-291) and lacks the C-terminal AA stretch (292-557) yielding a protein length of 291 AA (Isoform ID: O95970-2). Isoform 1 is potentially secreted.

Organization of LGI1 gene, depicting isoform 1 exons (1-8); exon size: (bp); red: translated region; blue: 5'UTR and 3'UTR.

LGI1 (leucine-rich, glioma inactivated protein 1 precursor) Gabellini N


Predicted domains of LGI1 protein (isoform 1): signal peptide (SP, AA: 1-34); N-terminal LRRNT (AA: 41-71); LRRs domains 1-3 (AA: 90-113, 114-137 and 138-161); C-terminal LRRCT (AA: 173-222). The C-terminal half includes the EAR/EPTP repeats 1-7 (AA: 224-267, 270-313, 316-364, 365-415, 418-462, 463-506, and 509-552).

Description The N-terminal sequence of LGI1 precursor consists of a cleavable N-terminal signal peptide and of three leucine-rich repeats (LRRs) flanked by N-terminal and C-terminal cysteine-rich domains (LRRNT and LRRCT). The LRR domains are structurally similar to arcs and are generally involved in protein-protein interaction. The C-terminal portion of LGI1 contains 7 repeats, termed Epilepsy Associated Repeats (EAR) or Epitempin (EPTP). The repeats potentially fold as beta-sheet and form a seven-bladed beta-propeller structure. Similar domains, identified in a number of proteins, probably represent protein interfaces. Isoform 2 lacks the six C-terminal EAR/EPTP domains.

Expression LGI1 is highly expressed in neural tissue, particularly in specific brain regions comprising both neurons and glial cells; strong expression is also reported in some areas of the prostate, kidney, sebaceous glands, islets of Langerhans, endometrium, ovary and testis. Expression is low or absent in the majority of glioma, glioblastoma, neuroblastoma, melanoma and breast cancer cell lines. The decrease of LGI1 expression correlates with the increasing grade of malignancy in astrocytic gliomas. DNA microarray data substantiate high expression in brain, spinal cord, DRG, and in pituitary gland. The expression profiles by SAGE and EST number support high expression in cerebellum and cerebrum, peripheral nerve, and also in B-lymphocytes, eye, lung, muscle, testis, and thymus; low or absent expression in neoplasia and tumors.

Localisation Isoform 1 can be secreted, whereas a shorter isoform (which might correspond to isoform 2) is retained within the cell. Some mutants of LGI1 (isoform 1) linked to ADLTE, fail to be secreted and remain in the endoplasmic reticulum and Golgi.

Function LGI1 is involved in the control of cell proliferation, cell migration and neurogenesis. Like other neuronal LRR proteins LGI1 may modulate synaptic function.

Re-expression in LGI1-null glioblastoma cells decreases cell proliferation through the inhibition of the ERK1/2 pathway and consequent down-regulation of matrix metalloproteinases. Increased expression in neuroblastoma cells reduces proliferation and triggers intrinsic apoptosis by inhibiting the PI3K/AKT pathway. LGI1 forms membrane complexes with Kv1.1 potassium channels within the cell antagonizing the N-type inactivation by the Kvbeta1 subunit. It has been recognized as a ligand of the trans-membrane protein receptor ADAM22, which also causes seizure when mutated.

Homology It belongs to a family comprising four highly homologous members denoted LGI1, LGI2, LGI3, and LGI4. LRR repeats flanked by cysteine rich regions, are also part of adhesive proteins and receptors of the LRR superfamily. With respect to this domain LGI1 is particularly related to the Drosophila protein slit, involved in growth-cone guidance and neuronal migration; and to the portion of the mammalian Trk receptors involved in neurotrophin binding. These proteins are crucial for the development of the nervous system. A comparable role for LGI1 is consistent with its involvement in epilepsy and tumors. The C-terminal seven-fold repeat shows the largest identity with the other members of the LGI protein family, and with a segment of the G protein coupled receptor MASS1/VLGR1, which carries mutations in a mouse model of audiogenic epilepsy.

Mutations Note: The human LGI1 gene disclosed about 200 Single Nucleotide Polimorphism (SNP), NCBI Assembly Reference Cluster Report: rs1111820 - rs3083468. Heterozygous point mutations are associated with ADLTE. Large-scale homozygous mutations are linked to the development of brain malignancy. Apparently the incidence of brain tumors is not increased in ADLTE.

LGI1 (leucine-rich, glioma inactivated protein 1 precursor) Gabellini N


Germinal Several loss of function mutations (missense/nonsense, splicing, small deletions and insertions) have been reported in ADLTE patients. Somatic Complete loss of LGI1 expression is associated with malignant brain tumors. Rearrangement or deletion of the region 10q23-q26, following the complete loss of one copy of chromosome 10, frequently occurs in high-grade gliomas. Genetic abnormalities in this region, comprising tumor suppressor genes such as PTEN and DMBT next to the metastasis suppressor LGI1 gene, enhance the malignant progression. Even if rearrangements or mutations of LGI1 locus are absent in low-grade tumors LGI1 expression is often reduced, possibly due to epigenetic silencing.

Implicated in Malignant brain tumors Epilepsy with auditory features (ADLTE)

To be noted Note: Consultation of “The Cancer Genome Anatomy Project” (CGAP) for breakpoints of region 10q24 associated with cancer yielded several balanced and unbalanced abnormalities, raising the possibility that interruption of LGI1 gene may be implicated in additional cancer pathologies.

References Kobe B, Deisenhofer J. The leucine-rich repeat: a versatile binding motif. Trends Biochem Sci 1994;19:415-421. (Review). Chernova OB, Somerville RP, Cowell JK. A novel gene, LGI1, from 10q24 is rearranged and downregulated in malignant brain tumors. Oncogene 1998;17:2873-2881. Somerville RP, Chernova O, Liu S, Shoshan Y, Cowell JK. Identification of the promoter, genomic structure, and mouse ortholog of LGI1. Mamm Genome 2000;11:622-627. Battye R, Stevens A, Perry RL, Jacobs JR. Repellent signaling by Slit requires the leucine-rich repeats. J Neurosci 2001;21:4290-4298. Gu W, Wevers A, Schröder H, Grzeschik KH, Derst C, Brodtkorb E, de Vos R, Steinlein OK. The LGI1 gene involved in lateral temporal lobe epilepsy belongs to a new subfamily of leucine-rich repeat proteins. FEBS Lett 2002;519:71-76. Kalachikov S, Evgrafov O, Ross B, Winawer M, Barker-Cummings C, Martinelli Boneschi F, Choi C, Morozov P, Das K, Teplitskaya E, Yu A, Cayanis E, Penchaszadeh G, Kottmann AH, Pedley TA, Hauser WA, Ottman R, Gilliam TC. Mutations in LGI1 cause autosomal-dominant partial epilepsy with auditory features. Nat Genet 2002;30:335-341. Krex D, Hauses M, Appelt H, Mohr B, Ehninger G, Schackert HK, Schackert G. Physical and functional characterization of the human LGI1 gene and its possible role in glioma development. Acta Neuropathol (Berl) 2002;103:255-266. McMillan DR, Kayes-Wandover KM, Richardson JA, White PC. Very large G protein-coupled receptor-1, the largest known cell surface protein, is highly expressed in the developing central nervous system. J Biol Chem 2002;277:785-792.

Morante-Redolat JM, Gorostidi-Pagola A, Piquer-Sirerol S, Sáenz A, Poza JJ, Galán J, Gesk S, Sarafidou T, Mautner VF, Binelli S, Staub E, Hinzmann B, French L, Prud'homme JF, Passarelli D, Scannapieco P, Tassinari CA, Avanzini G, Martí-Massó JF, Kluwe L, Deloukas P, Moschonas NK, Michelucci R, Siebert R, Nobile C, Pérez-Tur J, López de Munain A. Mutations in the LGI1/Epitempin gene on 10q24 cause autosomal dominant lateral temporal epilepsy. Hum Mol Genet 2002;11:1119-1128. Scheel H, Tomiuk S, Hofmann K. A common protein interaction domain links two recently identified epilepsy genes. Hum Mol Genet 2002;11:1757-1762. Staub E, Pérez-Tur J, Siebert R, Nobile C, Moschonas NK, Deloukas P, Hinzmann B. The novel EPTP repeat defines a superfamily of proteins implicated in epileptic disorders. Trends Biochem Sci 2002;27:441-444. (Review). Besleaga R, Montesinos-Rongen M, Perez-Tur J, Siebert R, Deckert M. Expression of the LGI1 gene product in astrocytic gliomas: downregulation with malignant progression. Virchows Arch 2003;443:561-564. Brodtkorb E, Nakken KO, Steinlein OK. No evidence for a seriously increased malignancy risk in LGI1-caused epilepsy. Epilepsy Res 2003;56:205-208. Kunapuli P, Chitta KS, Cowell JK. Suppression of the cell proliferation and invasion phenotypes in glioma cells by the LGI1 gene. Oncogene 2003;22:3985-3991. Kunapuli P, Kasyapa CS, Hawthorn L, Cowell JK. LGI1, a putative tumor metastasis suppressor gene, controls in vitro invasiveness and expression of matrix metalloproteinases in glioma cells through the ERK1/2 pathway. J Biol Chem 2004;279:23151-23157. Erratum in J Biol Chem 2007;282:2752. Rossi MR, Huntoon K, Cowell JK. Differential expression of the LGI and SLIT families of genes in human cancer cells. Gene 2005;356:85-90. Senechal KR, Thaller C, Noebels JL. ADPEAF mutations reduce levels of secreted LGI1, a putative tumor suppressor protein linked to epilepsy. Hum Mol Genet 2005;14:1613-1620. Fukata Y, Adesnik H, Iwanaga T, Bredt DS, Nicoll RA, Fukata M. Epilepsy-related ligand/receptor complex LGI1 and ADAM22 regulate synaptic transmission. Science 2006;313:1792-1795. Gabellini N, Masola V, Quartesan S, Oselladore B, Nobile C, Michelucci R, Curtarello M, Parolin C, Palu G. Increased expression of LGI1 gene triggers growth inhibition and apoptosis of neuroblastoma cells. J Cell Physiol 2006;207:711-721. Schulte U, Thumfart JO, Klöcker N, Sailer CA, Bildl W, Biniossek M, Dehn D, Deller T, Eble S, Abbass K, Wangler T, Knaus HG, Fakler B. The epilepsy-linked Lgi1 protein assembles into presynaptic Kv1 channels and inhibits inactivation by Kvbeta1. Neuron 2006;49:697-706. Sirerol-Piquer MS, Ayerdi-Izquierdo A, Morante-Redolat JM, Herranz-Pérez V, Favell K, Barker PA, Pérez-Tur J. The epilepsy gene LGI1 encodes a secreted glycoprotein that binds to the cell surface. Hum Mol Genet 2006;15:3436-3445. Head K, Gong S, Joseph S, Wang C, Burkhardt T, Rossi MR, Laduca J, Matsui SI, Vaughan M, Hicks DG, Heintz N, Cowell JK. Defining the expression pattern of the LGI1 gene in BAC transgenic mice. Mamm Genome. 2007;18 (5):328-337. Ko J, Kim E. Leucine-rich repeat proteins of synapses. J Neurosci Res. 2007 Oct;85(13):2824-32.


Gabellini N. LGI1 (leucine-rich, glioma inactivated protein 1 precursor). Atlas Genet Cytogenet Oncol Haematol.2008; 12(1):50-52.





NEIL1 (nei endonuclease VIII-like 1 (E. coli)) Masaya Suzuki, Kazuya Shinmura, Haruhiko Sugimura

Department of Pathology, Hamamatsu University School of Medicine, 1-20-1, Handayama, Hamamatsu, Shizuoka 431-3192, Japan


Online updated version: http://AtlasGeneticsOncology.org/Genes/NEIL1ID41519ch15q24.html DOI: 10.4267/2042/38477


Identity Hugo: NEIL1 Other names: FLJ22402; FPG1; hFPG1; NEH1; NEI1 Location: 15q24.2

DNA/RNA Description The NEIL1 gene maps on chromosome 15q24.2 spanning 8,179bp. It contains 11 exons, and the orientation is plus strand.

Transcription The transcript of 1,828bp, expressed in Brain, Liver, Lung, Kidney, Colon, and Stomach. The NEIL1 gene is up-regulated during S-phase.

Protein Description NEIL1 encodes 390 amino acids, theoretical molecular weight is 43684 Da, Formamidopyrimidine-DNA glycosylase N-terminal domain and Formamidopyrimidine-DNA glycosylase H2TH domain.

Localisation Nucleus, centrosome, and mitotic condensed chromosomes.

Function (1) Bifunctional DNA glycosylase and apurinic/apyrimidinic (AP) lyase that catalyzes beta- and delta-elimination reactions at the site of damaged base. (2) Reported substrates: thymine glycol (Tg), 5-hydroxycytosine, 5-hydroxyuracil, 5,6-dihydrouracil, 5,6-dihydrothymine, 2,6-diamino-4-hydroxy-5-

formamidopyrimidine (FapyG), 4,6-diamino-5-formamidopyrimidine (FapyA), 5-formyluracil, 5-hydroxymethyluracil, spiroiminodihydantoin (Sp), guanidinohydantoin, (Gh) and 8-hydroxyguanine. (3) Since NEIL1 catalyzes beta- and delta-elimination reactions, the protein generates DNA strand breaks with 3' phosphate termini. In mammalian cells, this 3' phosphate is removed by polynucleotide kinase, but not by APE1. NEIL1 stably interacts with other BER proteins, DNA polymerase beta and DNA ligase III alpha. (4) In mammalian BER, DNA glycosylases generate abasic (AP) sites, which are then converted to deoxyribo-5'-phosphate (dRP) and excised by a dRP lyase (dRPase) activity of DNA polymerase beta. Since NEIL1 also has dRPase activity, NEIL1 has a role as a backup dRPase in mammalian cells. (5) NEIL1 has a repair activity for oxidized bases in single-strand DNA and bubble DNA, suggesting a possibility that NEIL1 is preferentially involved in repair of lesions in DNA bubbles generated during transcription and/or replication. (6) Proteins that associate and stimulate the repair activity of NEIL1: a) The Werner syndrome protein (WRN), a member of RecQ family of DNA helicases, b) Rad9, Rad1, and Hus1 as individual proteins and as the 9-1-1 complex. (7) The major DNA glycosylase for the excision of 8-hydroxyguanine is OGG1. In the repair of 8-ydroxyguanine by OGG1, after excising the base lesion, OGG1 remains bound to the resulting AP site and does not turn over efficiently. The APE1, which cleaves the phosphodiester bond 5' to the AP site, displaces the bound OGG1 and thus increases its turnover. NEIL1 stimulates turnover of OGG1 in a fashion similar to that of APE1, and carries out beta/delta- elimination at the AP site.

NEIL1 (nei endonuclease VIII-like 1 (E. coli)) Suzuki M et al


(8) Although OGG1 has limited activity on 8-hydroxyguanine lesion located in the vicinity of the 3' end of a DNA single-strand break, NEIL1 effectively excises the 3' end proximal 8-hydroxyguanine lesion. NEIL1 also effectively excises 5-hydroxyuracil lesions located in the proximity of the 3'-end of a DNA single-strand break. (9) The NEIL1 gene is induced by reactive oxygen species.

Homology Homo sapiens: NEIL2 (NP_659480, 20.1%), NEIL3 (NP_060718, 15.0%) using the CLUSTALW software.

Implicated in Gastric cancer Note: The following is the abstract of the paper by Shinmura K. et al. (Carcinogenesis, 2004). Oxidized DNA base lesions, such as thymine glycol (Tg) and 8-hydroxyguanine, are often toxic and mutagenic and have been implicated in carcinogenesis. To clarify whether NEIL1 protein, which exhibits excision repair activity towards such base lesions, is involved in gastric carcinogenesis, we examined 71 primary gastric cancers from Japanese patients and four gastric cancer cell lines for mutations and genetic polymorphisms of the NEIL1 gene. We also examined 20 blood samples from Chinese patients for NEIL1 genetic polymorphisms. Three mutations (c.82_84delGAG:p.Glu28del, c.936G > A and c.1000A > G:p.Arg334Gly) and two genetic polymorphisms were identified. When the excision repair activity towards double-stranded oligonucleotide containing a Tg:A base pair was compared among six types of recombinant NEIL1 proteins, p.Glu28del-type NEIL1, found in a primary case, was found to exhibit an extremely low activity level. Moreover, c.936G > A, located in the last nucleotide of exon 10 and detected in the KATO-III cell line, was shown to be associated with a splicing abnormality using an in vivo splicing assay. An immunofluorescence analysis showed that the wild-type NEIL1 protein, but not the truncated protein encoded by the abnormal transcript arising from the c.936G > A mutation, was localized in the nucleus, suggesting that the truncated protein is unlikely to be capable of repairing nuclear DNA. An expression analysis revealed that NEIL1 mRNA expression was reduced in six of 13 (46%) primary gastric cancer specimens that were examined. These results suggest

that low NEIL1 activities arising from mutations and reduced expression may be involved in the pathogenesis in a subset of gastric cancers.

References Bandaru V, Sunkara S, Wallace SS, Bond JP. A novel human DNA glycosylase that removes oxidative DNA damage and is homologous to Escherichia coli endonuclease VIII. DNA Repair (Amst) 2002;1(7):517-529. Hazra TK, Izumi T, Boldogh I, Imhoff B, Kow YW, Jaruga P, Dizdaroglu M, Mitra S. Identification and characterization of a human DNA glycosylase for repair of modified bases in oxidatively damaged DNA. Proc Natl Acad Sci USA 2002;99(6):3523-3528. Hazra TK, Kow YW, Hatahet Z, Imhoff B, Boldogh I, Mokkapati SK, Mitra S, Izumi T. Identification and characterization of a novel human DNA glycosylase for repair of cytosine-derived lesions. J Biol Chem 2002;277(34):30417-30420. Morland I, Rolseth V, Luna L, Rognes T, Bjørås M, Seeberg E. Human DNA glycosylases of the bacterial Fpg/MutM superfamily: an alternative pathway for the repair of 8-oxoguanine and other oxidation products in DNA. Nucleic Acids Res 2002;30(22):4926-4936. Takao M, Kanno S, Kobayashi K, Zhang QM, Yonei S, van der Horst GT, Yasui A. A back-up glycosylase in Nth1 knock-out mice is a functional Nei (endonuclease VIII) homologue. J Biol Chem 2002;277(44):42205-42213. Dou H, Mitra S, Hazra TK. Repair of oxidized bases in DNA bubble structures by human DNA glycosylases NEIL1 and NEIL2. J Biol Chem 2003;278(50):49679-49684. Kroeger KM, Hashimoto M, Kow YW, Greenberg MM. Cross-linking of 2-deoxyribonolactone and its beta-elimination product by base excision repair enzymes. Biochemistry 2003;42(8):2449-2455. Rosenquist TA, Zaika E, Fernandes AS, Zharkov DO, Miller H, Grollman AP. The novel DNA glycosylase, NEIL1, protects mammalian cells from radiation-mediated cell death. DNA Repair (Amst) 2003;2(5):581-591. Bandaru V, Cooper W, Wallace SS, Doublié S. Overproduction, crystallization and preliminary crystallographic analysis of a novel human DNA-repair enzyme that recognizes oxidative DNA damage. Acta Crystallogr D Biol Crystallogr 2004;60(Pt 6):1142-1144. Doublié S, Bandaru V, Bond JP, Wallace SS. The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity. Proc Natl Acad Sci USA 2004;101(28):10284-10289. Inoue M, Shen GP, Chaudhry MA, Galick H, Blaisdell JO, Wallace SS. Expression of the oxidative base excision repair enzymes is not induced in TK6 human lymphoblastoid cells after low doses of ionizing radiation. Radiat Res 2004;161(4):409-417. Jaruga P, Birincioglu M, Rosenquist TA, Dizdaroglu M. Mouse NEIL1 protein is specific for excision of 2,6-diamino-4-hydroxy-5-formamidopyrimidine and 4,6-diamino-5-formamidopyrimidine from oxidatively damaged DNA. Biochemistry 2004;43(50):15909-15914.

NEIL1 (nei endonuclease VIII-like 1 (E. coli)) Suzuki M et al


Katafuchi A, Nakano T, Masaoka A, Terato H, Iwai S, Hanaoka F, Ide H. Differential specificity of human and Escherichia coli endonuclease III and VIII homologues for oxidative base lesions. J Biol Chem 2004;(14):14464-14471. Miller H, Fernandes AS, Zaika E, McTigue MM, Torres MC, Wente M, Iden CR, Grollman AP. Stereoselective excision of thymine glycol from oxidatively damaged DNA. Nucleic Acids Res 2004;32(1):338-345. Mokkapati SK, Wiederhold L, Hazra TK, Mitra S. Stimulation of DNA glycosylase activity of OGG1 by NEIL1: functional collaboration between two human DNA glycosylases. Biochemistry 2004;43(36):11596-11604. Shinmura K, Tao H, Goto M, Igarashi H, Taniguchi T, Maekawa M, Takezaki T, Sugimura H. Inactivating mutations of the human base excision repair gene NEIL1 in gastric cancer. Carcinogenesis 2004;25(12):2311-2317. Wiederhold L, Leppard JB, Kedar P, Karimi-Busheri F, Rasouli-Nia A, Weinfeld M, Tomkinson AE, Izumi T, Prasad R, Wilson SH, Mitra S, Hazra TK. AP endonuclease-independent DNA base excision repair in human cells. Mol Cell 2004;15(2):209-220. Ali MM, Hazra TK, Hong D, Kow YW. Action of human endonucleases III and VIII upon DNA-containing tandem dihydrouracil. DNA Repair (Amst) 2005;4(6):679-686. Das A, Hazra TK, Boldogh I, Mitra S, Bhakat KK. Induction of the human oxidized base-specific DNA glycosylase NEIL1 by reactive oxygen species. J Biol Chem 2005;280(42):35272-35280. Hailer MK, Slade PG, Martin BD, Rosenquist TA, Sugden KD. Recognition of the oxidized lesions spiroiminodihydantoin and guanidinohydantoin in DNA by the mammalian base excision repair glycosylases NEIL1 and NEIL2. DNA Repair (Amst) 2005;4(1):41-50. Hu J, de Souza-Pinto NC, Haraguchi K, Hogue BA, Jaruga P, Greenberg MM, Dizdaroglu M, Bohr VA. Repair of formamidopyrimidines in DNA involves different glycosylases: role of the OGG1, NTH1, and NEIL1 enzymes. J Biol Chem 2005;280(49):40544-40551. Parsons JL, Zharkov DO, Dianov GL. NEIL1 excises 3' end proximal oxidative DNA lesions resistant to cleavage by NTH1 and OGG1. Nucleic Acids Res 2005;33(15):4849-4856. Zhang QM, Yonekura S, Takao M, Yasui A, Sugiyama H, Yonei S. DNA glycosylase activities for thymine residues oxidized in the methyl group are functions of the hNEIL1 and hNTH1 enzymes in human cells. DNA Repair (Amst) 2005;4(1):71-79. Broderick P, Bagratuni T, Vijayakrishnan J, Lubbe S, Chandler I, Houlston RS. Evaluation of NTHL1, NEIL1, NEIL2, MPG, TDG, UNG and SMUG1 genes in familial colorectal cancer predisposition. BMC Cancer 2006;6:243. Grin IR, Khodyreva SN, Nevinsky GA, Zharkov DO. Deoxyribophosphate lyase activity of mammalian endonuclease VIII-like proteins. FEBS Lett 2006;580(20):4916-4922.

Hazra TK, Mitra S. Purification and characterization of NEIL1 and NEIL2, members of a distinct family of mammalian DNA glycosylases for repair of oxidized bases. Methods Enzymol 2006;408:33-48. Ocampo-Hafalla MT, Altamirano A, Basu AK, Chan MK, Ocampo JE, Cummings A Jr, Boorstein RJ, Cunningham RP, Teebor GW. Repair of thymine glycol by hNth1 and hNeil1 is modulated by base pairing and cis-trans epimerization. DNA Repair (Amst) 2006;5(4):444-454. Vartanian V, Lowell B, Minko IG, Wood TG, Ceci JD, George S, Ballinger SW, Corless CL, McCullough AK, Lloyd RS. The metabolic syndrome resulting from a knockout of the NEIL1 DNA glycosylase. Proc Natl Acad Sci USA 2006;103(6):1864-1869. Akbari M, Otterlei M, Peña-Diaz J, Krokan HE. Different organization of base excision repair of uracil in DNA in nuclei and mitochondria and selective upregulation of mitochondrial uracil-DNA glycosylase after oxidative stress. Neuroscience 2007;145(4):1201-1212. Bandaru V, Zhao X, Newton MR, Burrows CJ, Wallace SS. Human endonuclease VIII-like (NEIL) proteins in the giant DNA Mimivirus. DNA Repair (Amst) 2007;[Epub ahead of print]. Daviet S, Couvé-Privat S, Gros L, Shinozuka K, Ide H, Saparbaev M, Ishchenko AA. Major oxidative products of cytosine are substrates for the nucleotide incision repair pathway. DNA Repair (Amst) 2007;6(1):8-18. Das A, Boldogh I, Lee JW, Harrigan JA, Hegde ML, Piotrowski J, de Souza-Pinto N, Ramos W, Greenberg MM, Hazra TK, Mitra S, Bohr VA. The human werner syndrome protein stimulates repair of oxidative DNA base damage by the DNA glycosylase Neil1. J Biol Chem 2007;[Epub ahead of print]. Guan X, Bai H, Shi G, Theriot CA, Hazra TK, Mitra S, Lu AL. The human checkpoint sensor Rad9-Rad1-Hus1 interacts with and stimulates NEIL1 glycosylase. Nucleic Acids Res 2007;35(8):2463-2472. Hildrestrand GA, Rolseth V, Bjørås M, Luna L. Human NEIL1 localizes with the centrosomes and condensed chromosomes during mitosis. DNA Repair (Amst) 2007;[Epub ahead of print]. Jia L, Shafirovich V, Geacintov NE, Broyde S. Lesion specificity in the base excision repair enzyme hNeil1: modeling and dynamics studies. Biochemistry 2007;46(18):5305-5314. Parsons JL, Kavli B, Slupphaug G, Dianov GL. NEIL1 is the major DNA glycosylase that processes 5-hydroxyuracil in the proximity of a DNA single-strand break. Biochemistry 2007;46(13):4158-4163. Roy LM, Jaruga P, Wood TG, McCullough AK, Dizdaroglu M, Lloyd RS. Human polymorphic variants of the NEIL1 DNA glycosylase. J Biol Chem 2007;282(21):15790-15798.


Suzuki M, Shinmura K, Sugimura H. NEIL1 (nei endonuclease VIII-like 1 (E. coli)). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):53-55.





NLRC4 (NLR Family, CARD domain containing 4) Yatender Kumar, Vegesna Radha, Ghanshyam Swarup

Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad - 500 007, India


Online updated version: http://AtlasGeneticsOncology.org/Genes/NLRC4ID43189ch2p22.html DOI: 10.4267/2042/38478


Identity Hugo: NLRC4 Other names: Ipaf; CARD12; CLAN; CLR2.1 Location: 2p22.3 Local order: Galactose enzyme activator 2p22-p11; Solute carrier family 30(Zinc transporter), member 2p22.3; RH-II GuB pseudogene 2p22-p21; NLRC4 2p22-p21; Yip domain family, member 4 2p22.3.

Human Chromosome 2 map depicting the position of NLRC4.

NLRC4 (NLR Family, CARD domain containing 4) Kumar Y et al


DNA/RNA

Schematic showing genome organization of NLRC4 gene.

Description The NLRC4 gene is comprised of 9 exons, spanning 41.3kb on chromosome 2p21-p22.

Transcription Four isoforms arising due to alternate splicing of NLRC4/CLAN cDNA have been identified in Homo sapiens. The longest transcript termed CLAN-A is 3.370kb with an ORF encoding 1024 amino acids. CLAN-B, C and D have exon 4 spliced selectively to other exons forming shorter transcripts. Tumor suppressor p53 activates transcription of full length NLRC4 mRNA by binding to a site in the minimal promoter.

Pseudogene Not Known.

Protein Description NLRC4 encodes a protein of 1024 residues with a predicted molecular mass of 112kDa. NLRC4 contains an N-terminal CARD (caspase activation and recruitment domain), a central NBD (nucleotide binding domain) and an LRR (leucine rich repeat) domain containing 13 leucine rich repeats at its carboxy terminus. The NBD is essential for activation of caspase-1. The CARD of NLRC4 is involved in interaction with itself and other CARD containing proteins and LRR domain is believed to be a regulatory domain.

Expression NLRC4 is highly expressed in the bone marrow and lung and to a lesser extent in lymph nodes, placenta, and spleen. TNF-a, Doxorubicin, UV radiation and p53

or p73 over expression induce mRNA of NLRC4 in many cell lines. NLRC4 is also induced by over expression of the tyrosine phosphatase, TC-45, which activates p53. P53 response elements have been identified upstream of the transcription start site of the NLRC4 gene.

Localisation Cytosolic.

Function NLRC4 associates with caspase-1 and several other CARD containing proteins, including ASC. The LRR domain may exert an auto inhibitory function on NLRC4 as truncation of this domain makes the protein constitutively active. NLRC4 is involved in the regulation of caspase-1, which is activated within the 'inflammasome', a complex comprising several adaptors and permitting pro-IL-1beta processing and secretion of mature IL-1beta. It is required for the activation of caspase-1 and IL-1beta secretion in response to bacterial flagellin. It is involved in restriction of Legionella replication through the regulation of phagosome maturation. NLRC4 knock out mice are resistant to Salmonella typhimurium induced endotoxic shock. NLRC4 is one of the mediators of the p53-induced apoptosis. It is also known to have caspase-1 independent functions.

Homology The CARD of NLRC4 bears significant homology to the CARDs of Caspase-1, cIAP-1 and cIAP-2, and ICEBERG. The NBD domain of NLRC4 shows high similarity to the NBD domains of NAIP, NOD1 and NOD2.

Schematic showing domain organization of NLRC4 protein.

NLRC4 (NLR Family, CARD domain containing 4) Kumar Y et al


Mutations Germinal Not known in H. sapiens.

Somatic Not known in H. sapiens.

References Damiano JS, Stehlik C, Pio F, Godzik A, Reed JC. CLAN, a novel human CED-4-like gene. Genomics 2001;75(1-3):77-83. Geddes BJ, Wang L, Huang WJ, Lavellee M, Manji GA, Brown M, Jurman M, Cao J, Morgenstern J, Merriam S, Glucksmann MA, DiStefano PS, Bertin J. Human CARD12 is a novel CED4/Apaf-1 family member that induces apoptosis. Biochem Biophys Res Commun 2001;284(1):77-82. Poyet JL, Srinivasula SM, Tnani M, Razmara M, Fernandes-Alnemri T, Alnemri ES. Identification of Ipaf, a human caspase-1-activating protein related to Apaf-1. J Biol Chem 2001;276(30):28309-28313. Masumoto J, Dowds TA, Schaner P, Chen FF, Ogura Y, Li M, Zhu L, Katsuyama T, Sagara J, Taniguchi S, Gumucio DL, Nunez G, Inohara N. ASC is an activating adaptor for NF-kappa B and caspase-8-dependent apoptosis. Biochem Biophys Res Commun 2003;303(1):69-73. Damiano JS, Newman RM, Reed JC. Multiple roles of CLAN (caspase-associated recruitment domain, leucine-rich repeat, and NAIP CIIA HET-E, and TP1-containing protein) in the mammalian innate immune response. J Immunol 2004;173(10):6338-6345. Damiano JS, Oliveira V, Welsh K, Reed JC. Heterotypic interactions among NACHT domains: implications for regulation of innate immune responses. Biochem J 2004;381(Pt 1):213-219. Gutierrez O, Pipaon C, Fernandez-Luna JL. Ipaf is upregulated by tumor necrosis factor-alpha in human leukemia cells. FEBS Lett 2004;568(1-3):79-82. Mariathasan S, Newton K, Monack DM, Vucic D, French DM, Lee WP, Roose-Girma M, Erickson S, Dixit VM. Differential activation of the inflammasome by caspase-1 adaptors ASC and Ipaf. Nature 2004;430(6996):213-218. Inohara, Chamaillard, McDonald C, Nunez G. NOD-LRR proteins: role in host-microbial interactions and inflammatory disease. Annu Rev Biochem 2005;74:355-383. (Review). Lu C, Wang A, Wang L, Dorsch M, Ocain TD, Xu Y. Nucleotide binding to CARD12 and its role in CARD12-mediated caspase-1 activation. Biochem Biophys Res Commun 2005;331(4):1114-1119. Sadasivam S, Gupta S, Radha V, Batta K, Kundu TK, Swarup G. Caspase-1 activator Ipaf is a p53-inducible gene involved in apoptosis. Oncogene 2005;24(4):627-636. Franchi L, Amer A, Body-Malapel M, Kanneganti TD, Ozoren N, Jagirdar R, Inohara N, Vandenabeele P, Bertin J, Coyle A, Grant EP, Nunez G. Cytosolic flagellin requires Ipaf for activation of caspase-1 and interleukin 1beta in salmonella-infected macrophages. Nat Immunol 2006;7(6):576-582. Fritz JH, Ferrero RL, Philpott DJ, Girardin SE. Nod-like proteins in immunity, inflammation and disease. Nat Immunol 2006;7(12):1250-1257. (Review). Miao EA, Alpuche-Aranda CM, Dors M, Clark AE, Bader MW, Miller SI, Aderem A. Cytoplasmic flagellin activates caspase-1 and secretion of interleukin 1beta via Ipaf. Nat Immunol 2006;7(6):569-575.

Ogura Y, Sutterwala FS, Flavell RA. The inflammasome: first line of the immune response to cell stress. Cell 2006;126(4):659-662. (Review). Roy CR, Zamboni DS. Cytosolic detection of flagellin: a deadly twist. Nat Immunol 2006;7(6):549-551. Thalappilly S, Sadasivam S, Radha V, Swarup G. Involvement of caspase 1 and its activator Ipaf upstream of mitochondrial events in apoptosis. FEBS J 2006;273(12):2766-2778. Werts C, Girardin SE, Philpott DJ. TIR, CARD and PYRIN: three domains for an antimicrobial triad. Cell Death Differ 2006;13(5):798-815. (Review). Amer A, Franchi L, Kanneganti TD, Body-Malapel M, Ozoren N, Brady G, Meshinchi S, Jagirdar R, Gewirtz A, Akira S, Nunez G. Regulation of Legionella phagosome maturation and infection through flagellin and host Ipaf. J Biol Chem 2006;281(46):35217-35223. Coers J, Vance RE, Fontana MF, Dietrich WF. Restriction of Legionella pneumophila growth in macrophages requires the concerted action of cytokine and Naip5/Ipaf signalling pathways. Cell Microbiol 2007 May 15;[Epub ahead of print]. Delbridge LM, O'Riordan MX. Innate recognition of intracellular bacteria. Curr Opin Immunol 2007;19(1):10-16. (Review). Kanneganti TD, Lamkanfi M, Kim YG, Chen G, Park JH, Franchi L, Vandenabeele P, Nunez G. Pannexin-1-mediated recognition of bacterial molecules activates the cryopyrin inflammasome independent of Toll-like receptor signaling. Immunity 2007;26(4):433-443. Lamkanfi M, Amer A, Kanneganti TD, Munoz-Planillo R, Chen G, Vandenabeele P, Fortier A, Gros P, Nunez G. The Nod-Like Receptor Family Member Naip5/Birc1e Restricts Legionella pneumophila Growth Independently of Caspase-1 Activation. J Immunol 2007;178(12):8022-8027. Lamkanfi M, Kanneganti TD, Franchi L, Nunez G. Caspase-1 inflammasomes in infection and inflammation. J Leukoc Biol 2007;82(2):220-225. Mariathasan S. ASC, Ipaf and Cryopyrin/Nalp3: bona fide intracellular adapters of the caspase-1 inflammasome. Microbes Infect 2007;9(5):664-671. Martinon F, Tschopp J. Inflammatory caspases and inflammasomes: master switches of inflammation. Cell Death Differ 2007;14(1):10-22. (Review). Mayor A, Martinon F, De Smedt T, Petrilli V, Tschopp J. A crucial function of SGT1 and HSP90 in inflammasome activity links mammalian and plant innate immune responses. Nat Immunol 2007;8(5):497-503. Neish AS. TLRS in the gut. II. Flagellin-induced inflammation and antiapoptosis. Am J Physiol Gastrointest Liver Physiol 2007;292(2):G462-G466. Paliwal P, Radha V, Swarup G. Regulation of p73 by Hck through kinase-dependent and independent mechanisms. BMC Mol Biol 2007;8(1):45. Petrilli V, Papin S, Dostert C, Mayor A, Martinon F, Tschopp J. Activation of the NALP3 inflammasome is triggered by low intracellular potassium concentration. Cell Death Differ 2007 Jun 29;[Epub ahead of print]. Rescigno M, Nieuwenhuis EE. The role of altered microbial signaling via mutant NODs in intestinal inflammation. Curr Opin Gastroenterol 2007;23(1):21-26. (Review).


Kumar Y, Radha V, Swarup G. NLRC4 (NLR Family, CARD domain containing 4). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):56-58.

Leukaemia Section Short Communication




t(3;6)(q25;q26) Jean-Loup Huret

Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

Published in Atlas Database: May 2007

Online updated version: http://AtlasGeneticsOncology.org/Anomalies/t0306q25q26ID1211.html DOI: 10.4267/2042/38479


Clinics and pathology Disease Acute myeloid leukaemia (AML) and treatment related acute myeloid leukaemia (t-AML).

Epidemiology Only 2 cases to date, a 41 year old female patient with M1 AML, and a 70 year old male patient with t-AML.

Prognosis No data.

Cytogenetics Cytogenetics, morphological Sole anomaly in the t-AML case, accompanied with del(7q) and a complex karyotype in the other case.

Genes involved and Proteins Note: The partner of EVI1 is yet unknown.

EVI1 Location: 3q26.2

Protein Transcrition factor; EVI1 targets include:GATA2, ZBTB16 /PLZF, ZFPM2/FOG2, JNK and the PI3K/AKT pathway. Role in cell cycle progression, likely to be cell-type dependant; antiapoptotic factor; involved in neuronal development organogenesis; role in hematopoietic differsntiation.

References Van Limbergen H, Poppe B, Michaux L, Herens C, Brown J, Noens L, Berneman Z, De Bock R, De Paepe A, Speleman F. Identification of cytogenetic subclasses and recurring chromosomal aberrations in AML and MDS with complex karyotypes using M-FISH. Genes Chromosomes Cancer 2002;33:60-72. Poppe B, Dastugue N, Vandesompele J, Cauwelier B, De Smet B, Yigit N, De Paepe A, Cervera J, Recher C, De Mas V, Hagemeijer A, Speleman F. EVI1 is consistently expressed as principal transcript in common and rare recurrent 3q26 rearrangements. Genes Chromosomes Cancer 2006;45:349-356. Wieser R. The oncogene and developmental regulator EVI1: expression, biochemical properties, and biological functions. Gene 2007;396:346-357.


Huret JL. t(3;6)(q25;q26). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):59.





t(3;11)(q26;p15) Jean-Loup Huret



Online updated version: http://AtlasGeneticsOncology.org/Anomalies/t0311q26p15ID1474.html DOI: 10.4267/2042/38480


Clinics and pathology Disease Chronic myelogenous leukaemia with t(9;22)(q34;q11).

Epidemiology Only one case to date, a 64 year old male patient.

Prognosis No data.

Cytogenetics Cytogenetics, morphological Anomaly accompanying the t(9;22)(q34;q11).




References Poppe B, Dastugue N, Vandesompele J, Cauwelier B, De Smet B, Yigit N, De Paepe A, Cervera J, Recher C, De Mas V, Hagemeijer A, Speleman F. EVI1 is consistently expressed as principal transcript in common and rare recurrent 3q26 rearrangements. Genes Chromosomes Cancer 2006;45:349-356. Wieser R. The oncogene and developmental regulator EVI1: expression, biochemical properties, and biological functions. Gene 2007;396:346-357.


Huret JL. t(3;11)(q26;p15). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):60.





t(3;12)(q26;q21) Jean-Loup Huret



Online updated version: http://AtlasGeneticsOncology.org/Anomalies/t0312q26q21ID1280.html DOI: 10.4267/2042/38481


Clinics and pathology Disease Treatment related acute myeloid leukaemia (t-AML).

Epidemiology Only one case to date, a 47 year old male patient.

Prognosis No data.

Cytogenetics Cytogenetics, morphological Sole anomaly.




References Poppe B, Dastugue N, Vandesompele J, Cauwelier B, De Smet B, Yigit N, De Paepe A, Cervera J, Recher C, De Mas V, Hagemeijer A, Speleman F. EVI1 is consistently expressed as principal transcript in common and rare recurrent 3q26 rearrangements. Genes Chromosomes Cancer 2006;45:349-356. Wieser R. The oncogene and developmental regulator EVI1: expression, biochemical properties, and biological functions. Gene 2007 Jul 15;396(2):346-57.


Huret JL. t(3;12)(q26;q21). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):61.

Solid Tumour Section Review




Colon: Colorectal adenocarcinoma Nilufer Sayar, Sreeparna Banerjee

Department of Molecular Biology and Genetics, Middle East Technical University, Ankara 06531 Turkey (NS); Department of Biological Sciences, Middle East Technical University, Ankara 06531, Turkey (SB)

Published in Atlas Database: Update -May 2007

Online updated version: http://AtlasGeneticsOncology.org/Tumors/colon5006.html DOI: 10.4267/2042/38482

This article is an update of: Hamelin R. Colon: Colorectal adenocarcinoma. Atlas Genet Cytogenet Oncol Haematol.1998;2(4):144-145. This work is licensed under a Creative Commons Attribution-Non-commercial-No Derivative Works 2.0 France Licence. © 2008 Atlas of Genetics and Cytogenetics in Oncology and Haematology

Classification Note: Hereditary colorectal cancers can be broadly classified into three types: 1- Familial adenomatous polyposis (FAP): characterized by the development of hundreds of polyps at a very early age, due to mutations in the APC gene. 2- Attenuated familial adenomatous polyposis (AFAP): Fewer polyps, and later onset of cancer than FAP. The difference is due to extreme 5' mutations in APC gene. 3- Hereditary nonpolyposis colon cancer (HNPCC) or Lynch syndrome: develops without the polyps, due to germline mutations in genes intervening in the repair of DNA mismatches occurring during replication (mostly hMSH2 and hMLH1 on 2p16 and 3p21 respectively).

Clinics and pathology Disease Adenocarcinoma

Etiology 75% colorectal cancers occur sporadically. 25% are associated with family history. 5-6% through genetic mutations. 85% arise from chromosomal instability, 15% due to microsatellite instability. Most arise from adenomatous polyps. History with ulcerative colitis, breast, uterine and ovarian cancers. Personal or familial history of colon cancer increases the risk (23% of all colorectal cancers). High fat diet, obesity, smoking may also increase the risk.

Epidemiology Colorectal cancer is the third most frequent cancer in the world in both sexes and the third most frequent cause of cancer related deaths. Until age 50, men and women are susceptible at same levels, but after 50 years of age, men are more susceptible.

Clinics The majority of colorectal cancers arise from pre-existing adenomatous polyps.

Pathology Dukes's staging system, modified by Astler-Coller. Detection through colonoscopy, flexible sigmoidoscopy, barium enema, chest x-ray, faecal occult blood testing (FOBT).

Treatment Surgery is the most common method. - For colon cancer, the tumour together with a small portion of the surrounding tissue is removed with the adjacent lymph nodes. - For rectal cancer, rectum is totally removed and replaced with colostomies. After surgery, micrometastasis can be experienced, which requires chemotherapy to destroy the metastatic cells (adjuvant chemotherapy). 5FU is the most frequently used drug. Radiotherapy may be used for rectal cancer, but it is not useful in colon cancer.

Prognosis Survival, although improving is not much more than 50% after 5 years, depending mainly of the stage of tumour growth at the time of diagnosis. Metastasis

Colon: Colorectal adenocarcinoma Sayar N, Banerjee S


resulting from penetration of the tumor through the bowel wall of the colon is very common with lymph node involvement. Patients with early colon cancer can survive with surgery (more than 80%). For patients with metastasis, 5 year survival rate is less than 10%. Genetic alterations have been studied in relation to prognosis with contradictory results. Loss of heterozygosity (LOH) of chromosomes 18q and 17p and overexpression and mutation of the p53 gene result in poorer prognosis in primary cancer patients.

Cytogenetics Cytogenetics morphological There are two types of colorectal cancers, according to the ploidy: - Aneuploid tumours showing numerous allelic losses; - Aneuploidy, loss and rearrangements of chromosome 1p (about 70%), 5q (55%, loss of APC), 15q, 18q (65%, loss of DCC), 17p (80%, TP53), and 17q (30%); and abnormalities in 7q(25%) and 8p (55%). Reciprocal translocation t(5;10)(q22;q25), inv(5)(q22-q31.3). Diploid tumours without frequent allelic losses.

Genes involved and Proteins Note: A number of genes are known to be implicated in tumour progression in colorectal cancers. They are either oncogenes or tumour suppressor genes. A model for the genetic basis of colorectal tumourigenesis is proposed.

APC Location: 5q21-22

DNA/RNA 16 exons, 10702 bp mRNA.

Protein Tumour suppressor protein composed of 2843 amino acids; the APC interacts with the adherens junction proteins a and beta-catenin suggesting involvement in cell adhesion. APC may also inhibit the pathway regulated by the beta-catenin /Tcf complex. Other functions include anterior-posterior pattern formation, axis specification, cell cycle, cell migration, apoptosis, chromosome segregation and spindle assembly.

Germinal mutations Point mutations in APC gene results in the generation of stop codons, small deletions, LOH, 1-2 bp insertions. Most mutations result in a truncated protein, mostly in the first half. Results in FAP and AFAP.

Somatic mutations The APC gene is mutated in about 50% of sporadic colorectal tumours. Most mutations are frameshifts of nonsense mutations resulting in premature stop codons.

Some mutations on beta-catenin have been described in tumours and cell lines without mutations in the APC gene. APC loss may also be due to interstitial deletion or mitotic recombination, LOH, and nonsense mutations. Most of the somatic mutations are clustered in the exon 15 in mutation cluster region (MCR). about 20% of APC mutations are observed with mutation of TP53. Methylation of the promoter may be related.

P53 Location: 17p13

DNA/RNA 11 exons.

Protein Tumour suppressor has essential role in cell cycle regulation, in G1 DNA damage checkpoint. 5 highly-conserved regions containing a transactivation domain, a DNA-binding domain, nuclear localization signals and a tetramerization domain. P53 is thus a transcriptional regulator regulating the transcription of genes whose products inhibit cell growth and proliferation and induce apoptosis. It is also called the guardian of the genome preventing cells from dividing before DNA damage is repaired.

Somatic mutations Mutations of P53 are mostly located in exons 4 to 8 with hotspots at codons 175, 245, 248, 273 and 282. They can be either missense mutations, or non-sense, deletions, insertions and splicing mutations resulting in a truncated p53 protein. Mutant form of p53 is found to be overexpressed in primary colon cancer. p53 mutation is observed in 40-50% of colorectal carcinomas, and is associated with aggressive carcinomas. p53 mutation or LOH of chromosome 17p is observed mostly in carcinoma rather then adenoma, in both familial and non-familial patients. 80% of mutations result from deamination of methylated cytosine in CpG region of the gene (codons 175, 248 and 273).

MLH1 Location: 3p21.3


Protein Human homolog of E. coli DNA mismatch repair gene MutL. Defects observed in 30% of HNPCC.

Germinal mutations Results in HNPCC. Deletion of codons 578 to 632 (they constitute a single exon), deletion and frameshifts, nonsense mutations, insertions, truncated protein. Both of the genes should be impaired for phenotype to occur. Mutations give rise to microsatellite instability.



Somatic mutations Methylation of the promoter, mostly responsible for HNPCC.

MSH2 Location: 2p22-p21

DNA/RNA 16 exons.

Protein Human homolog of E. coli MutS protein, functional in mismatch repair, defects observed in about 60% of HNPCC.

Germinal mutations Truncated protein, nonsense mutation, results in HNPCC.

MSH6 Location: 2p16

DNA/RNA 10 exons.

Protein Functions in mismatch binding.

Germinal mutations Deletion (of CT at nucleotide 3052 in exon 4), frameshift mutations, truncated protein.

PMS2 Location: 7p22.2

DNA/RNA 15 exons.

Protein Functional in mismatch repair.

Germinal mutations In frame deletion, out of frame deletion, point mutation. The mutations give rise to microsatellite instability.

AXIN2 Location: 17q23-q24


Protein The protein has role in regulation of beta-catenin pathway.

Somatic mutations Axin2 is mutated in MMR deficient CRC cells. The mutations result in the stabilization of beta catenin and activation of the T-cell factor signaling. Also epigenetic silencing is associated with CRC.

STK11 Location: 19p13.3


Protein Tumor suppressor serine-threonine kinase, functions in cell cycle arrest. Mutations result in Peutz-Jeghers syndrome.

Germinal mutations Nonsense, missense, frameshift mutations.

Somatic mutations Mutations give rise to Peutz-Jeghers syndrome, which results in polyps in gastrointestinal tract.

PTEN Location: 10q23.3

DNA/RNA 9 exons, 3417bp mRNA.

Protein Tumor suppressor protein, which negatively regulates AKT/PKB signaling. Also known as 'mutated in multiple advanced cancers' since mutations are found in many cancers. The protein is a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase, removing phosphates from serine, tyrosine and threonine.

Germinal mutations Results in Cowden Syndrome, a cancer prone syndrome and Bannayan-Riley-Ruvalcaba Syndrome.

Somatic mutations Somatic mutations of PTEN are a result of MLH1-MSH2 deficiency in HNPCC patients. Frameshift mutations in MMR deficient cells. Nonsense, missense, and splice-site mutations.

BMPR1A Location: 10q22.3

DNA/RNA 13 exons, 3616bp mRNA.

Protein Transmembrane serine-threonine kinase, type1 receptor.

Germinal mutations Nonsense, missense, frameshift and splice-site mutations.

SMAD4 Location: 18q21.1


Protein Protein is coded from 11 exons. A tumor suppressor, functioning in TGFbeta signaling, mediating signals from cell surface to nucleus.



Germinal mutations Result in juvenile polyps.

Somatic mutations Deletion of SMAD4 results in epithelial cancers. Minimally lost region on chromosome 18q21, containing the SMAD4 gene is found in colorectal cancers. 4-basepair deletion in exon 9 of SMAD4 is found in colon cancers, resulting in a new stop codon.

MYH Location: 1p34.1


Protein DNA glycosylase. Functions in oxidative DNA damage repair (base excision repair), nicks A-G mismatches, as well as A-8oxoG and A-C mismatches.

Germinal mutations Tyr82-Cys and Gly253 -Asp transitions affect glycosylase activity, resulting in APC mutations in somatic cells. Nonsense mutations, missense and truncated protein mutations. Mutations cause 93-fold increase in colorectal cancer risk.

DCC Location: 18q21.3


Protein DCC is thought to be receptor for neptin-1 (axonal chemoattractant). In absence of ligand, it induces apoptosis but when neptin-1 is bound, it prevents apoptosis.

Germinal mutations Chromosome 18 sequences are frequently (74%) lost in colorectal carcinoma. Loss of DCC is mostly observed in metastatic cancers.

KRAS2 (or Ki-ras) Location: 12p12.1

DNA/RNA 3 exons.

Protein Ki-ras belongs to the ras gene family containing also Ha-ras and N-ras; they encode for closely related 21-kDa (189 amino acids) GTP-binding proteins with a role in growth signal transduction; oncogenes.

Somatic mutations These genes are activated by point mutations at codons 12, 13 and 61, and, in the case of colorectal cancers, Ki-ras is mutated on codons 12 or 13 in about 40% of the cases.

Homozygous deletion of 5' end, point mutation in one of the introns (for example intron 13), probably interfering with splicing, DNA insertions.

To be noted - The RER+ sporadic colon cancers are mostly diploid, without LOH, with few mutations of p53 and APC and right-sided; they contain mutations in repetitive coding sequences of a number of genes such as the TGFbeta type II receptor, the receptor of the Insulin-like growth factor and the BAX gene implicated in apoptosis. - The RER- are polyploid, with LOH (5q, 17p, 18q), mutations in p53, and more often left-sided, they have a worse prognosis.

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Sayar N, Banerjee S. Colon: Colorectal adenocarcinoma. Atlas Genet Cytogenet Oncol Haematol.2008;12(1):62-67.





Uterus: Leiomyoma Allison M Lynch, Cynthia C Morton

Brigham and Women's Hospital, Harvard New Research Building, 77 Avenue Louis Pasteur, Room 160, Boston, MA 02115, USA

Published in Atlas Database: Update -May 2007

Online updated version: http://AtlasGeneticsOncology.org/Tumors/leiomyomID5031.html DOI: 10.4267/2042/38483

This article is an update of: Vanni R. Uterus: Leiomyoma. Atlas Genet Cytogenet Oncol Haematol.2002;6(2):138-142. This work is licensed under a Creative Commons Attribution-Non-commercial-No Derivative Works 2.0 France Licence. © 2008 Atlas of Genetics and Cytogenetics in Oncology and Haematology

Identity Other names: Uterine fibroids; Uterine fibromyoma; fibroids; fibroma; fibroleiomyoma; myoma Note: Uterine Leiomyomata (UL), benign smooth muscle tumors of the uterus, are the most common pelvic tumors in women. UL are symptomatic in approximately 25% of reproductive age females and are the primary indicator for hysterectomy in the United States accounting for over 200,000 procedures annually. Careful pathologic examination of the uterus shows over 75% of reproductive age females have UL with the average affected uterus containing six to seven fibroids. UL are frequent in women older than 30 years of age, very rare in woman below the age of 18, and tend to regress after menopause. Rarely are UL estimated to become malignant leiomyosarcoma. They are steroid-hormone dependent tumors and especially sensitive to estrogen and progesterone actively impacting their overall growth and development. See WebPath leiomyoma, leiomyomata, and degeneration.

Classification Note: Classification of leiomyomas is based on location within the uterus (see figures below). Uterine Layer - Subserous: located just beneath the serosal surface. They grow out toward the peritoneal cavity, and can be sessile (broad-based) or pedunculated (attached to the surface by a narrow stalk). The pedunculated ones may attach themselves to adjacent structures like the bowel, omentum or mesentery, and develop a secondary blood supply, loosing its primary uterine blood supply (parasitic leiomyoma). Subserous leiomyomas may also

extend into the broad ligament (intraligamentary leiomyomas). - Intramural: are the most common type of UL, found primarily within the thick myometrium. - Submucous: are the most symptomatic form of UL, located beneath the endometrium (uterine mucosa). Like subserosal UL, they may be sessile or pedunculated. The pedunculated nodules may protrude through the cervical os, and may undergo torsion, infarction, and separation from the uterus. Submucous leiomyoma are often associated with an abnormality of the endometrium, resulting in a disturbed bleeding pattern.

Clinics and pathology Epidemiology Ethnic predisposition studies show leiomyomas are more frequent (from three to nine fold) in women of African origin than women of other ethnic groups. African American women are reported to have an earlier age of UL diagnosis, larger and more abundant tumors, greater symptom severity and higher rates of hysterectomy. Risk factors for UL include early age of menarche, nulliparity, oral contraceptive use and obesity.

Clinics Clinical presentation depends upon size, location and number of lesions. UL may occur singly but often are multiple, with variations in size. They may manifest with profuse menstrual bleeding, pelvic pain and pressure, and reproductive dysfunction causing significant medical and social morbidity. UL may be a cause of pregnancy complications, such as abortion, hemorragic degeneration, disseminated intravascular

Uterus: Leiomyoma Lynch AM, Morton CC


(Source of images: http://www.fibroids.net/aboutfibroids.html#basic )

coagulation, hemoperitoneum, premature rupture of membranes, dystocia, inversion of the uterus, antepartum and postpartum hemorrhage, breech presentation, placental abruption and postpartum sepsis. They are steroid-hormone dependent and have high estrogen concentrations, elevated numbers of estrogen receptors and more bound estrogen. UL increase in size when exposed to high estrogen levels, such as during the reproductive years and diminish in the presence of low estrogen levels, following menopause or during GnRH agonist therapy. Having more progesterone receptors than normal myometrium, UL also grow in the presence of high progesterone concentrations. Growth hormone (GH) and prolactin (PRL) are thought to promote UL growth, but require further investigation.

Pathology Leiomyomas are dense, well-circumscribed nodules consisting of myometrial-derived smooth muscle cells

and extracellular matrix (e.g. collagen, fibronectin, proteoglycan). The cut surfaces are white to tan in color, with a whorled trabecular pattern. The appearance is often altered by degenerative changes. Microscopically, they consist of whorled, anastomosing fascicles of uniform, spindle-shaped, smooth muscle cells. Cells have indistinct borders and abundant fibrillar, eosinophilic cytoplasm. The nuclei are elongated and have finely dispersed chromatin. They may show areas of hemorrage, as well as cystic degeneration and microcalcification in a minority of lesions. Despite the variety in the histologic subtypes of leiomyomas, all are grossly similar. In addition to histologically typical UL, several other specific subtypes are distinguished, some of which are very rare: - Cellular leiomyoma (composed of densely cellular

fascicles of smooth muscle with little intervening collagene).



- Atypical leiomyoma (containing atypical cells, clustered or distributed through the lesion).

- Epithelioid leiomyoma (composed of round or poligonal cells rather than spindle-shaped. This subtype includes leiomyoblastoma, clear cell leiomyoma, plexyform leiomyoma).

- Myxoid leiomyoma (containing abundant amorphous myxoid substance between the smooth muscle cells).

- Vascular leiomyoma (containing dense proliferations of large, caliber, thick-walled vessels).

- Lipoleiomyoma (consisting of a mixture of mature adipocytes and smooth muscle cells).

- Leiomyoma with tubules (containing tubular structures).

- Benign metastasizing leiomyoma (occurrence of multiple smooth-muscle nodules, most often located in the lung after previous hysterectomy).

Microscopic pathology: see WebPath leiomyoma

Treatment Only UL that are symptomatic, enlarge rapidly, or pose diagnostic problems, are typically removed. The traditional and most definitive treatment for UL is hysterectomy (surgical removal of the uterus). Myomectomy is another surgical option for women with fewer and smaller tumors wanting to remove UL, yet maintain fertility. Uterine Artery Embolization (UAE) is a radiological alternative especially effective at treating intramural UL that are difficult to access surgically, yet the impact on pregnancy and future fertility is unclear. Despite being expensive and having limited availability, a noninvasive thermoablative procedure known as MRI-guided focused ultrasound (MRIgFUS) has recently been shown to target specific UL effectively and decrease recovery time. Certain medications, such as gonadotropin releasing hormone agonists (GnRHa), can alleviate UL symptoms by decreasing estrogen levels to a menopausal-like state. However, current medical therapies cannot prevent recurrence.

Genetics Note: Familial aggregation and twin studies support the heritability of these tumors. First-degree relatives of women with UL are 2.5 times more likely to develop these tumors than women with unaffected relatives, suggesting a possible predisposition. Glucose-6-phosphate dehydrogenase isoenzyme and androgen receptor polymorphism studies have demonstrated that UL develop as independent clonal lesions. Accordingly, UL may be found with different chromosomal aberrations in the same uterus.

Cytogenetics Note: Approximately 40% of cytogenetically investigated cases show abnormal karyotypes, usually with single or few changes. Rarely, they may show complex karyotypes. The cytogenetic heterogeneity of UL can be attributed to various clonal chromosomal changes such as translocations, deletions and trisomies. Subgroups of common cytogenetic rearrangements include a translocation between chromosomes 12 and 14, trisomy 12, deletions of portions of the long arms of chromosomes 3 or 7 and the short arm of chromosome 1, rearrangements of the short arm of chromosome 6 and rearrangements of chromosomes 1, 3, 10, 13 and X. Although the initiating event for tumorigenesis remains unknown, the variety of cytogenetic abnormalities displayed in UL suggests multiple genetic pathways may be involved. Correlations between cytogenetics and clinical phenotype: - Myoma location/incidence of abnormal karyotype:

- intramural - 35%; - subserosal - 29%; - submucosal - 12%.

- Type of chromosome abnormality/ tumor mean size: - tumors with normal karyotype - 5.4 cm; - tumors with del(7q) - 5cm; - tumors with t(12; 14) rearrangements - 8.5 cm.

Cytogenetics morphological t(12;14)(q14-15;q22-24) subgroup. It is found in approximately 20% of the abnormal cases. The t(12;14)(q14-15;q22-24) translocation is the first chromosome alteration reported in uterine leiomyoma. It may be observed as the sole cytogenetic abnormality, or together with other clonal changes, such as del(7q). The chromosome segment 12q14-15 may be rearranged with other translocation partners (such as chromosomes X, 2, 8, 9, 10, 22) or may undergo pericentric inversion. Myoma cells with this abnormality are responsive to the immortalization by the 'early region' of the SV40 genome. t(12;14)(q14-15;q22-24) subgroup - molecular findings: In this subgroup dysregulation of the HMGA2 (formerly HMGIC) gene located at 12q15 has been observed. Chromosome 12 breakpoint is often located 10 kb up to 100 kb 5' to HMGA2, and in a majority of cases there is no fusion transcript. However, in a number of cases the gene is altered: - case with pericentric inversion: HMGA2 exon 3 is

fused to ALDH2 exon 13 (12q24.2). - case with apparently normal karyotype: HMGA2

exon 3 is fused to retrotransposon-like sequences RTVLH 3' LTRs.



- case with complex karyotype including chromosome 12 and 14 rearrangements: cumulative dosage effect of a RAD51L1/HMGA2 fusion and RAD51L1 loss.

- case without cytogenetic analysis: HMGA2 exon 3 is fused to COX6C exon 2 (8q22-23).

- cases without cytogenetic analysis: HMGA2 exon 2 or 3 is fused to RAD51L1 exon 7 (14q23.3-24).

- cases without cytogenetic analysis: HMGA2 isoforms due to aberrant alternative splicing.

- case without cytogenetic analysis: HMGA2 exon 2 is fused to the 3' portion of the HEI10 gene, located at 14q11.

del(7)(q22-32) subgroup. It is found in approximately 17% of the karyotypically abnormal cases. It may be observed as the sole cytogenetic abnormality, or together with other changes. It is often associated with t(12;14) or alterations of the chromosome segment 12q14-15. The del(7q) clone is almost invariably found together with a normal clone. A few cases with translocations involving 7q22 have been described. Myoma cells with del(7q) are not responsive to the immortalization by the 'early region' SV40 virus, unless they also contain 12q14-15 abnormalities. Myoma with del(7q) tend to be smaller than those showing 12q14-15 abnormalities. del(7)(q22-32) subgroup - molecular findings: Conflicting minimal deletion regions have been proposed by multiple loss-of-heterozygosity (LOH) analyses using polymorphic microsatellite markers. The resultant tumor suppressor candidate genes, including CUTL1, ORL5L, PAI1, PCOLCE and LHFPL3, were not consistently altered in expression. Most recently, a study using 7q tiling path CGH microarrays confined the minimal deletion region to 2.79 Mb at 7q22 and also proposed a second region of loss at 7q34. However, no pathogenic coding variation was detected in the genes encompassed by the proposed region. At the present time the tumor-suppressor gene(s) responsible for del(7q) fibroid growth has not been identified despite much effort. This raises the possibility that a mechanism other than loss of tumor-suppressor gene function could be responsible for development of del(7q) fibroid tumors. 6p21 rearrangement subgroup. Aberrations of the 6p21, including deletions, translocations, and inversions are found in less than 10% of the abnormal cases. 6p21 rearrangements may be observed as the sole cytogenetic abnormality, or together with other clonal changes. Simple and complex rearrangements of 6p21 have been observed. Complex rearrangements are sometimes definable only by FISH analysis. The most frequent translocation partners are chromosomes 1, 2, 4, 10 and 14 with rearrangements

including t(1;6)(q23;p21), t(6;14)(p21;q24), and t(6;10)(q21;q22). 6p21 rearrangement subgroup - molecular findings: HMGA1 (formerly HMGIY) (6p21.3) is the pathogenic sequence. No hybrid gene has been described yet. A genomic PAC clone containing the gene spans the 6p21.3 breakpoint. The breakpoint seems to be extragenic, located within an 80 kb region 3' of HMGA1. One case of aberrant transcript with truncation of 1295 bp from the 3' UTR has been described. del(1)(p11p36) subgroup: This subgroup is characterized by an almost complete loss of the short arm of chromosome 1. Rearrangements are often observed with additional cytogenetic abnormalities such as the loss of chromosomes 19 and/or 22. del(1p) subgroup - molecular findings: Transcriptional profiles with loss of 1p in UL resemble those of leiomyosarcoma suggesting a similar pathway for tumorigenesis. LOH analysis of polymorphic microsatellites confirmed deletion of the 1p region.

Karyotypic representation of specific chromosomal aberrations in UL. (Modified from Lobel et al., 2006).

(A): t(6;14)(p21;q24) has been observed in UL and other mesenchymal tumors, and implicates HMGA1 at band 6p21. (B): Tumors with del(7)(q22q32) abnormalities are generally smaller in size than tumors with t(12;14) translocations. (C): A minor cytogenetic subgroup of UL, t(10;17)(q22-q24;q21-q22), has been observed in a subset of tumors and involved the MORF gene at the 10q22 breakpoint.



Genes involved and Proteins Note: Elevated levels of HMGA expression have been observed in tumor cells and during embryonic tissue development suggesting that HMGA proteins influence cell growth. Dysregulation of HMGA2 (12q15) and HMGA1 (6p21.3) genes have been observed in uterine leiomyomas. Mechanisms leading to dysregulation include fusion transcript formation, HMGA2 truncation, and disruption of HMGA2 regulatory sequences. It has been suggested that the expression of HMGA1 and HMGA2 is controlled by regulatory elements within their 3'UTR: luciferase assays with HMGA1 3'UTRs of different length show an increase in luciferase activity by truncation of the 3'UTR. Of interest, HMGA1 and HMGA2 have been shown to contain multiple sites in their 3'UTRs predicted to be targets of micro RNAs, which likely play an important role in their regulation. UL are also associated with insufficiency of FH (fumarate hydratase). FH encodes fumarase, involved in the key metabolic pathway of the Krebs cycle and may play a role in tumor development as a tumor suppressor gene. Structural rearrangements of 1q42.1 leading to missense mutations and various deletions (i.e., protein-truncating, large germline and in-frame) of FH can lead to haploinsufficiency and subsequent absent expression if the other FH allele is mutated

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Brosens I, Johannisson E, Dal Cin P, Deprest J, Van den Berghe. Analysis of the karyotype and desoxyribonucleic acid content of uterine myomas in premenopausal, menopausal, and gonadotropin-releasing hormone agonist-treated females. H Fertil Steril 1996;66:376-379. Kazmierczak B, Pohnke Y, Bullerdiek J. Fusion transcripts between the HMGIC gene and RTVL-H related sequences in mesenchymal tumors without cytogenetic aberrations. Genomics 1996;38:223-226. Sourla A, Polychronakos C, Zeng WR, Nepveu A, Kukuvitis A, Naud F, Koutsilieris M. Plasminogen activator inhibitor 1 messenger RNA expression and molecular evidence for del(7)(q22) in uterine leiomyomas. Cancer Res 1996 1;56:3123-3128. Ishwad CS, Ferrell RE, Hanley K, Davare J, Meloni AM, Sandberg AA, Surti U. Two discrete regions of deletion at 7q in uterine leiomyomas. Genes Chromosomes Cancer 1997;19:156-160. Vanni R, Marras S, Schoenmakers EF, Dal Cin P, Kazmierczak B, Senger G, Bullerdiek J, Van de Ven WJ, Van den Berghe H. Molecular cytogenetic characterization of del(7q) in two uterine leiomyoma-derived cell lines. Genes Chromosomes Cancer 1997;18:155-161. Wanschura S, Dal Cin P, Kazmierczak B, Barnitzke S, Van den berghe H, Bullerdiek J. Hidden paracentric inversions of chromosome arm 12 q affecting the HMGIC gene. Genes Chromosomes Cancer 1997;18:322-323. Zeng WR, Scherer SW, Koutsilieris M, Huizenga JJ, Filteau F, Tsui LC, Nepveu A. Loss of heterozygosity and reduced expression of the CUTL1 gene in uterine leiomyomas. Oncogene 1997;14:2355-2365. Brosens I, Deprest J, Dal Cin P, Van den Berghe H. Clinical significance of cytogenetic abnormalities in uterine myomas. H. Fertil Steril 1998;69:232-235. Kazmierczak B, Dal Cin P, Wanschura S, Borrmann L, Fusco A, Van den Berghe H, Bullerdiek J. HMGIY is the target of 6p21.3 rearrangements in various benign mesenchymal tumors. Genes Chromosomes Cancer 1998;23:279-285. Quintana DG, Thome KC, Hou ZH, Ligon AH, Morton CC, Dutta A. ORC5L, a new member of the human origin recognition complex, is deleted in uterine leiomyomas and malignant myeloid diseases. J Biol Chem 1998 Oct 16;273:27137-27145. Rein MS, Powell WL, Walters FC, Weremowicz S, Cantor RM, Barbieri RL, Morton CC. Cytogenetic abnormalities in uterine myomas are associated with myoma size. Mol Hum Reprod 1998;4:83-86. Van der Heijden O, Chiu HC, Park TC, Takahashi H, LiVolsi VA, Risinger JI, Barrett JC, Berchuck A, Evans AC, Behbakht K, Menzin AW, Liu PC, Benjamin I, Morgan MA, King SA, Rubin SC, Boyd J. Allelotype analysis of uterine leiomyoma: localization of a potential tumor suppressor gene to a 4-cM region of chromosome 7q. Mol Carcinog 1998;23:243-247. Hennig Y, Deichert U, Bonk U, Thode B, Bartnitzke S, Bullerdiek J. Chromosomal translocations affecting 12q14-15 but not deletions of the long arm of chromosome 7 associated with a growth advantage of uterine smooth muscle cells. Mol Hum Reprod 1999;50:1150-1154. Ingraham SE, Lynch RA, Kathiresan S, Buckler AJ, Menon AG. hREC2, a RAD51-like gene, is disrupted by t(12;14) (q15;q24.1) in a uterine leiomyoma. Cancer Genet Cytogenet 1999;115:56-61. Klotzbücher M, Wasserfall A, Fuhrmann U. Misexpression of wild-type and truncated isoforms of the high-mobility group I proteins HMGI-C and HMGI(Y) in uterine leiomyomas. Am J Pathol 1999;155:1535-1542.



Schoenmakers EFPM, Huysmans C, Van de Ven WJM. Allelic knokout of novel splice variants of human recombination repair gene RAD51B in t(12;14) uterine leiomyomas. Cancer Res 1999;59:19-23. Sornberger KS, Weremowicz S, Williams AJ, Quade BJ, Ligon AH, Pedeutour F, Vanni R, Morton CC. Expression of HMGIY in three uterine leiomyomata with complex rearrangements of chromosome 6. Cancer Genet Cytogenet 1999;114:9-16. Vanni R, Schoenmakers EF, Andria M. Deletion 7q in uterine leiomyoma: fluorescence in situ hybridization characterization on primary cytogenetic preparations. Cancer Genet Cytogenet 1999;113:183-187. Kurose K, Mine N, Doi D, Ota Y, Yoneyama K, Konoshi H, Araki T, Emi M. Novel gene fusion of COX6C at 8q22-23 to HMGIC in a uterine leiomyoma. Genes Chromosomes Cancer 2000;27:303-307. Tietze L, Günther K, Hörbe A, Pawlik C, Klosterhalfen B, Handt S, Merkelbach-Bruse S. Benign metastasizing leiomyoma: a cytogenetically balanced but clonal disease. Hum Pathol 2000;3:126-128. Amant F, Debiec-Rychter M, Schoenmakers EF, Hagemeijer-Hausman A, Vergote I. Cumulative dosage effect of a RAD51l1/HMGA2 fusion and RAD51l1 loss in a case of pseudo-Meigs' syndrome. Genes Chromosomes Cancer 2001;32:324-329. Borrmann L, Wilkening S, Bullerdiek J. The expression of HMGA genes is regulated by their 3'UTR. Oncogene 2001;20:4537-4541. Kurose K, Mine N, Iida A, Nagai H, Harada H, Araki T, Emi M. Three aberrant splicing variants of the HMGIC gene transcribed in uterine leiomyomas. Genes Chromosomes Cancer 2001;30:212-217. Ligon AH, Morton CC. Genetics of uterine leiomyomata. Genes Chromosomes Cancer 2000;28(3):235-245. Borrmann L, Wilkening S, Bullerdiek J. The expression of HMGA genes is regulated by their 3'UTR. Oncogene 2001;20(33):4537-4541.

Mine N, Kurose K, Konishi H, Araki T, Nagai H, Emi M. Fusion of a sequence from HEI10 (14q11) to the HMGIC gene at 12q15 in a uterine leiomyoma. Jpn J Cancer Res 2001;92:135-139. Mine N, Kurose K, Nagai H, Doi D, Ota Y, Yoneyama K, Konishi H, Araki T, Emi M. Gene fusion involving HMGIC is a frequent aberration in uterine leiomyomas. J Hum Genet 2001;46:408-412. Takahashi T, Nagai N, Oda H, Ohama K, Kamada N, Miyagawa K. Evidence for RAD51L1/HMGIC fusion in the pathogenesis of uterine leiomyoma. Genes Chromosomes Cancer 2001;30:196-201. Christacos NC, Quade BJ, Dal Cin P, Morton CC. Uterine leiomyomata with deletions of Ip represent a distinct cytogenetic subgroup associated with unusual histologic features. Genes Chromosomes Cancer 2006;45(3):304-312. Lobel MK, Somasundaram P, Morton CC. The genetic heterogeneity of uterine leiomyomata. Obstet Gynecol Clin North Am 2006;33(1):13-39. (Review). Huyck KL, Morton CC. Uterine leiomyoma, cellular and genetic characteristics. In:Schwab M, editor. Encyclopedic Reference of Cancer. Berlin: Springer, 2007, in press. Vanharanta S, Wortham NC, Langford C, El-Bahrawy M, van der Spuy Z, Sjöberg J, Lehtonen R, Karhu A, Tomlinson IP, Aaltonen LA. Definition of a minimal region of deletion of chromosome 7 in uterine leiomyomas by tiling-path microarray CGH and mutation analysis of known genes in this region. Genes Chromosomes Cancer 2007;46(5):451-458. Wang T, Zhang X, Obijuru L, Laser J, Aris V, Lee P, Mittal K, Soteropoulos P, Wei JJ. A micro-RNA signature associated with race, tumor size, and target gene activity in human uterine leiomyomas. Genes Chromosomes Cancer 2007;46(4):336-347.


Lynch AM, Morton CC. Uterus: Leiomyoma. Atlas Genet Cytogenet Oncol Haematol.2008;12(1):68-73.





Skin Melanoma Marco Castori, Paola Grammatico

Laboratory of Molecular and Cell Biology, Isituto Dermopatico dell'Immacolata, IRCCS, Via dei Monti di Creta, 104, 00168 Rome, Italy (MC); Medical Genetics, Institute of Experimental Medicine, Universitá La Sapienza, San Camillo-Forlanini Hospital, Rome, Italy (PG)


Online updated version: http://AtlasGeneticsOncology.org/Tumors/SkinMelanomID5416.html DOI: 10.4267/2042/38484


Identity Other names: Cutaneous melanoma; Melanoma skin cancer

Classification Note: Skin melanoma is a relatively common human cancer with an increasing incidence trend and originates from skin melanocytes, which are neural crest derived cells. Melanoma arises in more than 95% of cases in the skin, although other sites of primary extracutaneous melanoma include uvea, oral and genital mucosae, gastrointestinal and genitourinary tracts, leptomeninges and lymph nodes.

Clinics and pathology Embryonic origin Neural crest cells (this embryonic origin is valid for all forms of melanoma, except for uveal melanoma, which derives from neuroectodermal cells.

Etiology A wide spectrum of risk factors for skin melanoma has been unravelled in the last decades. They are classically distinguished in 'host' and environmental factors. The strongest 'host' conditions are positive family history for melanoma (especially in first-degree relatives and in a number of 3 or more), multiple benign (often more than 100) or atypical nevi (the so-called 'dysplastic nevus syndrome'), and a previous melanoma. The first two risk factors may coexist in the same pedigree, thus delineating the Familial Atypical Mole - Multiple Melanoma syndrome (or FAMMM syndrome). Among these families, 30-40% of them display mutations in the CDKN2A gene, while a few kindreds are mutated in

CDK4. Other 'host' factors that may increase the risk of developing melanoma are previous non-melanoma skin cancer and immunosuppression (such as, transplant recipients or patients with AIDS). However, solar UVR exposure remains the leading cause for developing skin melanoma. In fact, skin melanoma is strikingly more common in patients with type I skin, freckling, blue eyes and red hair. This evidence demonstrates that 'host' and environmental risk factors cooperate in determining the onset and evolution of skin melanoma (this interaction has been recently demonstrated at the molecular level. In fact, ultraviolet exposure stimulates tanning in part inducing the action of the alpha-melanocyte-stimulating hormone (POMC) on the melanocortin receptor 1 - MC1R. Light-skinned and readheaded people carry specific MC1R polymorphisms that reduce its activity). Accumulated evidences support that intermittent sun exposure is a major determinant for melanoma in contrast with cumulative sun exposure, as well as a history of blistering sunburn, especially in young age (i.e. three or more episodes before 20 years). The risk related to non-solar UVR exposure is still debated.

Epidemiology Melanoma is the fifth most common cancer in men and the sixth in women (note that this ranking may slightly vary among distinct populations and different epidemiological studies). It accounts for nearly 4% of all dermatologic cancers, but represents the major cause of death for skin cancer. The overall incidence of melanoma ranges from 10 to 42 new cases for 100.000 per year. This apparent wide variability may essentially relay on the ethnic background of the population studied. The incidence of melanoma is rising by 3-8% per year in most people of European origin. Melanoma affects young and middle aged people, with a median

Skin Melanoma Castori M, Grammatico P


age at diagnosis of 57 years. The cancer incidence increase progressively after the age of 15 years until the age of 50 and then slows, especially in females, who are slightly less affected than men (males are approximately 1.5 times more likely to develop melanoma than females). Nearly half of the patients have an age comprised from 35 and 65 years at diagnosis.

Clinics Melanoma should be considered for every suspicious pigmented skin lesions. There are specific characteristics to be taken into account for identifying suspicious lesions which request further investigations. The acronym ABCDE summarizes five cardinal features, including: (i) Asymmetry; (ii) Border irregularity; (iii) Color variation; (iv) Diameter above 6 mm; and (v) Evolving, which encompasses any significant change in size, shape, surface, shades of color or symptoms (such as, itching). Clinical suspicion must be supported by assistive optical devices, such as dermatoscopes, epiluminescent microscopes and/or other portable scanning units using visible, infrared and UV sources. However, a firm diagnosis is reached only by excision and histologic examination.

Pathology Pathologic staging of skin melanoma is crucial for prognosis definition and management planning. The Clark's model identifies 5 steps in the progression from benign nevus and metastatic melanoma: step 1: benign nevus; step 2: dysplastic nevus; step 3: radial-growth phase melanoma; step 4: vertical-growth phase melanoma; step 5: metastatic melanoma. This model also denotes qualitative anatomic levels of invasion: In level I melanoma, all tumor cells are above the basement membrane (malignant melanoma in situ). Level II melanoma invades into the papillary dermis. Level III melanoma fills and expands the papillary dermis. Level IV melanoma invades the reticular dermis, while level V melanoma reaches the subcutaneous adipose tissue. Actually, for the T staging of melanoma the primary determinant is the Breslow's technique, that provides a quantitative measurement of the depth of invasion by measuring the tumor thickness with an ocular micrometer (in millimeters). T1 melanomas are = 1.0 mm in thickness, T2 between 1.01 and 2.00 mm, T3 between 2.01 and 4.00 mm, and

T4 above 4.0 mm. To date, the Clark's level system is the primary prognostic method only for T1 melanomas. The melanoma clinical staging include four stages. Stage I melanomas are those with thickness that are 1 mm or less with no evidence of metastases. Stage II melanoma is diagnosed in patients with thicker cancers without evidence of metastases. Stage III melanomas are those with regional lymph nodes and/or an in-transit or satellite metastasis. Stage IV cancer is diagnosed when the melanoma spreads to distant sites. Specific determinants define the N and M axes for stage III and IV melanomas. There are unusual variants of melanoma (for which the standard prognostic factors should be taken into account), that must be differentiated form epithelial or mesenchymal neoplasms. These variants include: desmoplastic melanoma, mucosal melanoma, malignant blue nevus, nevoid melanoma, minimal deviation melanoma, small cell melanoma, spitzoid melanoma, dermal melanoma, amelanotic melanoma, myxoid melanoma, signet ring melanoma, balloon cell melanoma, rhabdoid melanoma, pigment-synthesizing animal melanoma, osteoid melanoma, chondroid and cartilagineous melanoma, and basomelanocytic tumor.

Treatment After histologic diagnosis of melanoma, the first step is the extent of excision. The radius of this excision depends on the tumor thickness (Breslow's technique). Sentinel lymph node biopsy is requested in melanomas of Stage I. In melanomas with thickness above 2 mm, elective lymph node dissection is also recommended. Surgical excision could be considered also for local recurrences, in-transit metastases, regional metastases and in patients with metastatic disease. In stage III patients, the eradication of clinical undetectable micrometastases at the time of diagnosis may be obtained using adjuvant therapy, including interferon-alpha and ganulocyte-macrophage colony-stimulating factor. In stage IV cancers the systemic therapy is based on decarbazide, interleukin-2, in isolation or in combination with other chemotherapeutic agents. Novel therapeutic regimens include cancer vaccines, angiogenesis inhibitors and novel cytotoxic agents.

Evolution Usually, skin melanomas show two distinct phases of local invasion: (i) the radial-growth phase, during which tumor cells acquire the ability to proliferate intraepidermally; (ii) the vertical-growth phase, which is characterized by tumor invasion of the dermis in form of an expansile nodule.



Local invasive melanomas may reach distant skin areas and subcutis. The invasion of lymph vessels leads to lymph node metastases. Finally, metastatic melanomas may metastasize to lungs, liver, central nervous system and other organs.

Prognosis The prognosis (i.e. % of 10-year survival rate) is directly related to the Pathologic stage. This range from 100% for melanoma in situ to less than 6% for patients with a stage IV melanoma with distant metastases.

Cytogenetics Cytogenetics morphological Numerical and structural changes visible by standard cytogenetics are common in sporadic melanoma, which is frequently aneuploid with a modal chromosomal set usually ranging from 24 to more than 100. The most common abnormality involves chromosome 1 with deletions and translocations usually including the region 1p12-22. A recurrent t(1;19) translocation has been also described in a subset of sporadic melanomas. Deletions or translocations involving the long arm of one or both chromosome 6, commonly affecting the 6q16-23 region, are observed in nearly 80% of skin melanomas. The 6 chromosome short arm is generally retained in form of an isochromosome (i6p). The gain of the short arm of chromosome 6 may have a role in cancer progression, especially for metastastic evolution (in fact, the NEDD9 gene, whose overexpression in associated to metastatic melanomas, maps in 6p25-p24). An equally common alteration is the gain of copies of chromosome 7. This finding is usually associated with late stages of skin melanoma. A second set of chromosome abnormalities includes alterations of chromosome 2, 3, 9, 10 and 11. Among them, a recurrent site of alterations (predominantly deletions) in both premalignant nevi and metastatic melanomas is the short arm of chromosome 9, particularly the region 9q21. Loss of chromosome 10, especially involving the region 10q24-26, seems to be implicated in both the early and late stages of melanocytic neoplasia. In late stage melanomas, chromosome 10 loss often accompanies chromosome 7 gain. At the standard cytogenetic level, the rate of involvement of other chromosomes (i.e. 2, 3 and 11) is less consistent.

Cytogenetics molecular A large number of studies have searched for loss of heterozygosity (LOH), homozygous deletions (HD) and amplifications in cutaneous melanomas, events that are difficult or impossible to identify at the standard cytogenetic level. Over the years, the improvement of laboratory techniques has collected a wide range of different

approaches, including fluorescent in situ hybridization, standard microsatellite analysis on specific genomic regions and conventional chromosome-based comparative genomic hybridization array. Actually, the most sensitive technique is the high-density whole-genome single nucleotide polymorphism array, which is able to detect variations in number of copies of genomic DNA within an interval of only 9 kb. Therefore, the results of this type of analysis is by far the most sensitive among all available approaches. Overall, whole chromosome arm LOH is most common on 9p, 9q, 10p and 10q, occurring in 40-50% of the cases. Considering focal (i.e. small portion of chromosome arms) LOH, these chromosome regions are involved in 49-72% of the cases. Over 40% of analyzed melanomas show LOH on 6q, 11q and 17p, while 33% on 5q. A broad spectrum of HD has been also registered and involves regions containing both well known melanoma progression associated genes (such as, CDKN2A and PTEN - for more details, see 'Genes Involved and Proteins' section), and other genes, whose role in cancer evolution awaits further elucidations. In more that one fourth (25%) of melanomas there are chromosome gains involving 7p, 20q and 22q. Amplifications of single genes may be also detected by this technique, but these data will be discussed in the next section. The 8q region, in which maps the C-MYC gene, is amplified in nearly 14% of the cases.

Genes involved and Proteins Note: Several genes have been discovered as involved in the progression of cutaneous melanoma. Two major groups of genes have been identified: tumor suppressor genes and proto-oncogenes. In order to describe melanoma progression implicated genes, the present section follows this classification. In addition to those here described, other genes, such as NF1, NF2, TTC4, NME2, CDKN1A, and RAB8A, have been sporadically studied in melanomas, but the present data are still very limited and not completely conclusive. Note: Tumor suppressor genes:

B2M Location: 15q21.1 Note: Escape by melanoma cells from T cell recognition through a complete lack of HLA class I antigen can be ascribed to beta-2-microglobulin (encoded by the B2M gene) aberrations. The combination of LOH and somatic mutation leading to a biallelic inactivation of B2M is not uncommon in melanoma cells.

CDC2L1 Location: 1p36.1 Note: This genes maps in a chromosome region (i.e. 1q36) frequently deleted in melanoma. However,



mutations in this gene are rare and the role of this gene in tumor progression is probably very limited.

CDKN2A Location: 9p21 Note: The CDKN2A locus shows LOH in nearly 50% of melanomas, while point mutations of this gene are extremely rare, probably because other mechanisms are involved in its inactivation (such as promoter methylation or homozygous deletion).

CDKN2B Location: 9q21 Note: CDKN2B maps nearly to CDKN2A and shares with this gene an high sequence homology. Although CDKN2B maps in a commonly deleted region in melanoma, the frequency of point mutations is relatively low and the actual knowledge about the role of this gene in melanoma progression is limited.

MEN1 Location: 11q13 Note: Mutations in menin, the gene responsible for the multiple endocrine neoplasia type I (MEN1), results mutated in nearly 1% of the analyzed melanomas.

PTEN Location: 10q23.31 Note: The chromosome region in which this gene maps is deleted in about 30-50% of melanomas, while somatic PTEN mutations have been identified in approximately 3% primary melanomas and 8% metastatic melanomas.

RB1 Location: 13q14.1-14.2 Note: Although the implications of CDKN2A and CDK4 (see below) is crucial in melanoma progression, the actual rate of mutations or rearrangement involving this gene, which is implicated in the same pathway, is extremely rare and confined to sporadic cases.

TFAP2A Location: 6p24 Note: Loss of AP2-alpha (the protein encoded by TFAP2A) expression is a crucial event in the melanoma development. However, the frequency of TFAP2A somatic mutations in melanomas is extremely low, thus suggesting that the AP2-alpha underexpression is very probably caused by the caspasis activity.

TP53 Location: 17p13.1 Note: TP53 mutations in melanomas are rare, occurring in 0-24% (mean 7%) of the analyzed tumors. However, UVR is very likely the cause of these mutations, as well as in other non-melanocytic skin tumors.

Wnt signalling pathway tumor suppressor genes. Location: Variable (see text). Note: The involvement of this pathway in melanoma progression is clearly demonstrated by the overexpression of beta-catenin in nearly 30% of the cases. Several genes coding for proteins implicated in the modulation of this pathway has been studied for somatic mutations in relation with melanoma. Among them, the most frequently somatically mutated gene is LKB1 (i.e. the gene responsible of Peutz-Jeghers syndrome ; location: 19p13.3) with an overall mutation frequency in melanoma of 4%. Other related genes, namely PPP2R1A (location: 19q13.4), APC (whose germline mutations are associated with the familial adenomatous polyposis; location: 5q21-q22) and ICAT (location: 1p36.22), are only rarely mutated in melanomas. Note: Proto-oncogenes

CDK4 Location: 12q14 Note: The primary role of the protein encoded by CDK4 is to inactivate pRB. Mutations that constitutively activate the kinase, in particular those involving the K22 and R24 aminoacid residues, have been identified in a variable proportion, ranging from 1/60 to 5/48, of the cases.

CTNNB1 Location: 3p22-p21.3 Note: This gene encodes for beta-catenin. As this protein is overexpressed in about one third of the cases, several studies investigated the presence of somatic mutations in this gene. The overall frequency of CTNNB1 somatic mutations in melanoma is 2-5%.

MAPK signalling pathway proto-oncogenes. Location: Variable (see text). Note: This pathway may be simplified as follows. The growth factor receptor interaction with its ligand induces the activation of RAS. Its activation stimulates phosphorylation of RAF proteins (including BRAF), that in turn activate MEK1 and MEK2. The final step of this cascade is the transcription factors activation by ERK 1 and ERK 2, which are phosphorilated by MEK proteins. BRAF (location: 7q34) mutations have been identified in more than 60% of melanomas and approximately 80% of these mutations occur at a single site, leading to the substitution of valine at position 600 with glutamic acid (V600E). This change mimics phosphorylation within the activation segment and results in constitutive activation of BRAF. The frequency of BRAF mutations in melanocytic nevi is similar to that in melanomas, suggesting that BRAF function perturbation is an early



event in melanoma development and is not sufficient to determine the neoplastic switch. The rate of BRAF mutation varies among melanoma subtypes and is highest in nodular melanoma and superficial spreading melanoma. BRAF mutations appear to be less common in sun-exposed areas. BRAF mutations are mutually exclusive to those occurring in the NRAS gene (1p13.2). The most common sites of mutation in this gene are codon 12, 13, 18 and 61. In contrast to BRAF mutations, NRAS alterations are more common in sun-exposed areas. This fact suggests that NRAS mutations may arise as a result of UVR-induced mutagenesis. HRAS (location: 11p15.5) mutations are less commonly observed and occurs in no more than 1.5-3% of melanomas. Activating changes in KRAS2 (location: 12p12.1) have been observed in rare cases and often associate with mutations in other RAS genes (i.e. NRAS and HRAS). Therefore, KRAS2 in a not powerful oncogene in melanoma progression.

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suppressor genes on chromosome 11 by use of homozygosity mapping-of-deletions analysis. Am J Hum Genet 2000;67:417-431. Jimenez P, Cantón J, Concha A, Cabrera T, Fernández M, Real LM, García A, Serrano A, Garrido F, Ruiz-Cabello F. Microsatellite instability analysis in tumors with different mechanisms for total loss of HLA expression. Cancer Immunol Immunother 2000;48:684-690. Nord B, Platz A, Smoczynski K, Kytola S, Robertson G, Calender A, Murat A, Weintraub D, Burgess J, Edwards M, Skogseid B, Owen D, Lassam N, Hogg D, Larsson C, Teh BT. Malignant melanoma in patients with multiple endocrine neoplasia type 1 and involvement of the MEN1 gene in sporadic melanoma. Int J Cancer 2000;87:463-467. Ries LA, Wingo PA, Miller DS, Howe HL, Weir HK, Rosenberg HM, Vernon SW, Cronin K, Edwards BK. The annual report to the nation on the status of cancer, 1973-1997, with a special section on colorectal cancer. Cancer 2000;88:2398-2424. Demunter A, Ahmadian MR, Libbrecht L, Stas M, Baens M, Scheffzek K, Degreef H, De Wolf-Peeters C, van Den Oord JJ. A novel N-ras mutation in malignant melanoma is associated with excellent prognosis. Cancer Res 2001;61:4916-4922. Demunter A, Stas M, Degreef H, De Wolf-Peeters C, van den Oord JJ. Analysis of N- and K-ras mutations in the distinctive tumor progression phases of melanoma. J Invest Dermatol 2001;117:1483-1489. Kennedy C, ter Huurne J, Berkhout M, Gruis N, Bastiaens M, Bergman W, Willemze R, Bavinck JN. Melanocortin 1 receptor (MC1R) gene variants are associated with an increased risk for cutaneous melanoma which is largely independent of skin type and hair color. Invest Dermatol 2001;17:294-300. Kraehn GM, Utikal J, Udart M, Greulich KM, Bezold G, Kaskel P, Leiter U, Peter RU. Extra c-myc oncogene copies in high risk cutaneous malignant melanoma and melanoma metastases. Br J Cancer 2001;84:72-79. Kumar R, Smeds J, Berggren P, Straume O, Rozell BL, Akslen LA, Hemminki K. A single nucleotide polymorphism in the 3'untranslated region of the CDKN2A gene is common in sporadic primary melanomas but mutations in the CDKN2B, CDKN2C, CDK4 and p53 genes are rare. Int J Cancer 2001;95:388-393. Omholt K, Platz A, Ringborg U, Hansson J. Cytoplasmic and nuclear accumulation of beta-catenin is rarely caused by CTNNB1 exon 3 mutations in cutaneous malignant melanoma. Int J Cancer 2001;92:839-842. Poetsch M, Dittberner T, Woenckhaus C. Does the PITSLRE gene complex contribute to the pathogenesis of malignant melanoma of the skin? A study of patient-derived tumor samples. Cancer Genet Cytogenet 2001;128:181-182. Pollock PM, Welch J, Hayward NK. Evidence for three tumor suppressor loci on chromosome 9p involved in melanoma development. Cancer Res 2001;61:1154-1161. Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, Teague J, Woffendin H, Garnett MJ, Bottomley W, Davis N, Dicks E, Ewing R, Floyd Y, Gray K, Hall S, Hawes R, Hughes J, Kosmidou V, Menzies A, Mould C, Parker A, Stevens C, Watt S, Hooper S, Wilson R, Jayatilake H, Gusterson BA, Cooper C, Shipley J, Hargrave D, Pritchard-Jones K, Maitland N, Chenevix-Trench G, Riggins GJ, Bigner DD, Palmieri G, Cossu A, Flanagan A, Nicholson A, Ho JW, Leung SY, Yuen ST, Weber BL, Seigler HF, Darrow TL, Paterson H, Marais R, Marshall CJ, Wooster R, Stratton MR, Futreal PA. Mutations of the BRAF gene in human cancer. Nature 2002;417:949-954. Maitra A, Gazdar AF, Moore TO, Moore AY. Loss of heterozygosity analysis of cutaneous melanoma and benign melanocytic nevi: laser capture microdissection demonstrates clonal genetic changes in acquired nevocellular nevi. Hum Pathol 2002;33:191-197.



Reifenberger J, Knobbe CB, Wolter M, Blaschke B, Schulte KW, Pietsch T, Ruzicka T, Reifenberger G. Molecular genetic analysis of malignant melanomas for aberrations of the WNT signaling pathway genes CTNNB1, APC, ICAT and BTRC. Int J Cancer 2002;100:549-556. Bastian BC, Olshen AB, LeBoit PE, Pinkel D. Classifying melanocytic tumors based on DNA copy number changes. Am J Pathol 2003;163:1765-1770. de Vries E, Schouten LJ, Visser O, Eggermont AM, Coebergh JW; Working Group of Regional Cancer Registries. Rising trends in the incidence of and mortality from cutaneous melanoma in the Netherlands: a Northwest to Southeast gradient?. Eur J Cancer 2003;9:1439-1446. Kefford RF, Mann GJ. Is there a role for genetic testing in patients with melanoma?. Curr Opin Oncol 2003;15:157-161. Maldonado JL, Fridlyand J, Patel H, Jain AN, Busam K, Kageshita T, Ono T, Albertson DG, Pinkel D, Bastian BC. Determinants of BRAF mutations in primary melanomas. J Natl Cancer Inst 2003;95:1878-1890. Paschen A, Mendez RM, Jimenez P, Sucker A, Ruiz-Cabello F, Song M, Garrido F, Schadendorf D. Complete loss of HLA class I antigen expression on melanoma cells: a result of successive mutational events. Int J Cancer 2003;103:759-767. van Dijk M, Sprenger S, Rombout P, Marres H, Kaanders J, Jeuken J, Ruiter D. Distinct chromosomal aberrations in sinonasal mucosal melanoma as detected by comparative genomic hybridization. Genes Chromosomes Cancer 2003;36:151-158. Woenckhaus C, Giebel J, Failing K, Fenic I, Dittberner T, Poetsch M. Expression of AP-2alpha, c-kit, and cleaved caspase-6 and -3 in naevi and malignant melanomas of the skin. A possible role for caspases in melanoma progression?. J Pathol 2003;201:278-287. Jemal A, Tiwari RC, Murray T, Ghafoor A, Samuels A, Ward E, Feuer EJ, Thun MJ; American Cancer Society. Cancer statistics, 2004. CA Cancer J Clin 2004;54:8-29. Naysmith L, Waterston K, Ha T, Flanagan N, Bisset Y, Ray A, Wakamatsu K, Ito S, Rees JL. Quantitative measures of the effect of the melanocortin 1 receptor on human pigmentary status. J Invest Dermatol 2004;122:423-428. Worm J, Christensen C, Grønbaek K, Tulchinsky E, Guldberg P. Genetic and epigenetic alterations of the APC gene in malignant melanoma. Oncogene 2004;23:5215-5226. de Snoo FA, Hayward NK. Cutaneous melanoma susceptibility and progression genes. Cancer Lett 2005;230:153-186.

Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S, Beroukhim R, Milner DA, Granter SR, Du J, Lee C, Wagner SN, Li C, Golub TR, Rimm DL, Meyerson ML, Fisher DE, Sellers WR. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 2005;436:117-122. Namiki T, Yanagawa S, Izumo T, Ishikawa M, Tachibana M, Kawakami Y, Yokozeki H, Nishioka K, Kaneko Y. Genomic alterations in primary cutaneous melanomas detected by metaphase comparative genomic hybridization with laser capture or manual microdissection: 6p gains may predict poor outcome. Cancer Genet Cytogenet 2005;157:1-11. Thompson JF, Scolyer RA, Kefford RF. Cutaneous melanoma. Lancet 2005;365:687-701. Kim M, Gans JD, Nogueira C, Wang A, Paik JH, Feng B, Brennan C, Hahn WC, Cordon-Cardo C, Wagner SN, Flotte TJ, Duncan LM, Granter SR, Chin L. Comparative oncogenomics identifies NEDD9 as a melanoma metastasis gene. Cell 2006;125:1269-1281. Miller AJ, Mihm MC Jr. Melanoma. N Engl J Med 2006;355:51-65. Markovic SN, Erickson LA, Rao RD, Weenig RH, Pockaj BA, Bardia A, Vachon CM, Schild SE, McWilliams RR, Hand JL, Laman SD, Kottschade LA, Maples WJ, Pittelkow MR, Pulido JS, Cameron JD, Creagan ET; Melanoma Study Group of the Mayo Clinic Cancer Center. Malignant melanoma in the 21st century, part 1: epidemiology, risk factors, screening, prevention, and diagnosis. Mayo Clin Proc 2007;82:364-380. Markovic SN, Erickson LA, Rao RD, Weenig RH, Pockaj BA, Bardia A, Vachon CM, Schild SE, McWilliams RR, Hand JL, Laman SD, Kottschade LA, Maples WJ, Pittelkow MR, Pulido JS, Cameron JD, Creagan ET; Melanoma Study Group of Mayo Clinic Cancer Center. Malignant melanoma in the 21st century, part 2: staging, prognosis, and treatment. Mayo Clin Proc 2007;82:490-513. Stark M, Hayward N. Genome-wide loss of heterozygosity and copy number analysis in melanoma using high-density single-nucleotide polymorphism arrays. Cancer Res 2007;67:2632-2642.


Castori M, Grammatico P. Skin Melanoma. Atlas Genet Cytogenet Oncol Haematol.2008;12(1):74-80.

Cancer Prone Disease Section Mini Review




Frasier syndrome (FS) Mariana M Cajaiba, Miguel Reyes-Múgica

Program of Pediatric and Developmental Pathology, Yale University School of Medicine, 430 Congress Avenue, New Haven, CT 06520-8023, USA


Online updated version: http://AtlasGeneticsOncology.org/Kprones/FrasierID10035.html DOI: 10.4267/2042/38485


Identity Inheritance: Sporadic occurrence, with possible cases of autosomal dominant inheritance

Clinics Phenotype and clinics Clinical presentation usually occurs between 2nd and 3rd decades; most cases at puberty. - Exceptional cases in younger children; youngest example at 6 months of age. Male pseudohermaphroditism; phenotypically female patients presenting with amenorrhea. - XY karyotype: - Streak (dysgenetic) gonads with gonadoblastoma. - Normal external female genitalia; clitoris enlargement and ambiguous genitalia may be present. - Small uterus (often with an inactive/atrophic endometrium) and fallopian tubes. Nephrotic syndrome with slowly progressing renal disease, resulting in end-stage renal failure. - Focal and segmental glomerulosclerosis; in later stages of renal disease, only chronic, nonspecific findings may be present in kidney biopsy. XX karyotype: patients with less severe phenotype, frequently not clinically identified as FS. - Normal and functioning female genitalia. - Clinically present only with renal disease.

Neoplastic risk Gonadoblastomas are present in virtually all XY patients; usually bilateral.

Germ cell tumors (dysgerminomas) may arise from gonadoblastoma within dysgenetic gonads. Wilms tumors are exceptional, and in these cases the diagnosis of FS is controversial (differential diagnosis with Denys-Drash syndrome; vide infra).

Treatment Prophylactic bilateral gonadectomy (may be laparoscopic if there is no evidence of overgrowth by a germ cell tumor); hysterectomy is not necessary. The renal disease is usually steroid-resistant, requiring dialysis and renal transplantation. Chemotherapy may be needed in cases with germ cell tumors. In XY patients, menstruation can be induced with cyclic hormone replacement therapy; there are reported cases of successful pregnancy following in vitro fertilization procedures in these patients.

Evolution The end-stage renal disease is usually the major cause of morbidity in FS patients. The focal and segmental glomerulosclerosis progresses slowly (often for more than 10 years) and leads to terminal renal failure, requiring dialysis therapy and renal transplantation which can result in complications and increased morbidity. There are limited data regarding the clinical outcome after renal transplantation in these patients. The occurrence of germ cell neoplasia in FS patients can affect their prognosis. However, there is no evidence that FS-associated germ cell tumors have a different clinical outcome in comparison with sporadic tumors.

Frasier syndrome (FS) Cajaiba MM, Reyes-Múgica M


Figure 1. Surgical appearance of the internal genitalia in a patient with Frasier syndrome. A) Small but normally shaped uterus. B) A streak gonad is seen at the tip of the surgical instrument (courtesy of Dr. Masoud Azodi, Yale University School of Medicine).

Figure 2. A-B: Kidney biopsy showing focal and segmental glomerulosclerosis (FSGS). A: Masson trichrome stain (400X). B: Semi-thin section stained with toluidine blue (400X). C-D: Gonadectomy specimens. C: Streak gonad with gonadoblastoma (H & E 40X). D: Gonadoblastoma nodule displaying Call-Exner body-like structures, surrounded by Leydig-like cells (H & E 200X). E-F: Histological aspect of dysgerminoma arising in gonadoblastoma. E: Gonadectomy specimen showing both, gonadoblastoma and dysgerminoma (H & E 100X). F: Peritoneal metastasis of dysgerminoma (H & E 200X).



Genes involved and Proteins WT1 (Wilms Tumor 1) Location: 11p13

DNA/RNA Description: 10 exons; spans approximately 50 kb. Encodes 4 zinc finger domains. Transcription: Alternative splicing in two different sites (exons 5 and 9) leads to variable insertion of exon 5 and/or insertion of 9 nucleotides in exon 9, resulting in transcription of four different isoforms.

Protein Description: Transcription factor: contains 4 zinc finger domains. Four different isoforms, ranging from 52 to 54 kDa (429-449 aminoacids). Alternative splicing in exon 9: variable insertion of aminoacids lysine (K), threonine (T) and serine (S) between 3rd and 4th zinc fingers results in either +KTS or -KTS isoforms. Expression: During embryonal life, the WT1 protein is mainly expressed in the metanephros and developing kidney, gonadal ridges, coelomic surfaces, heart, spleen, liver, thymus, uterus and muscles of the abdominal wall. An adequate ratio of +KTS/-KTS expression is essential for the wild type function of WT1. Localisation: Nuclear (transcription factor function). Function: WT1 functions mainly as a transcription factor, with many different downstream target genes; a post-transcriptional regulatory function of some target mRNAs has been also proposed. In mammalian embryos, expression of the -KTS isoform induces gonadal ridge formation through proliferation of the coelomic epithelium, resulting in the bipotential gonad. In XY individuals, expression of the +KTS isoform will activate the transcription of the SRY gene located on Y chromosome, which induces the expression of anti-mYllerian hormone by the developing Sertoli cells. Expression of the anti-mYllerian hormone in the developing testis results in formation of seminiferous cords, allowing sex-specific gonadal development, and regression of mYllerian structures (which give rise to the female genitalia). During early kidney development in mammal embryos, the -KTS isoform promotes proliferation of the primordial mesenchyme, epithelial-mesenchymal interactions and ureteric bud branching. In later phases of kidney development, expression of +KTS leads to differentiation of podocytes and glomerular capillaries.

Mutations Most of the WT1 gene mutations in FS are located in positions 2, 4, 5 or 6 of the second splice donor site in intron 9.

These mutations lead to a decrease in the +KTS isoform, affecting the zinc fingers' DNA binding affinity. A decrease in +KTS is in keeping with the phenotype observed in FS, in which there seems to be a defect in antimüllerian hormone expression resulting in abnormal genital development in XY individuals. Also, defective expression of this isoform could explain the glomerular lesion observed in FS.

To be noted The classical clinical picture of FS is that of a phenotypically female adolescent patient presenting with either amenorrhea or nephrotic syndrome, or both. However, the clinical presentation may be atypical, with cases occurring at earlier ages or in XX patients, resulting in the presence of only renal disease. These atypical cases must be differentiated from sporadic forms of nephrotic syndrome, and from other entities such as Denys-Drash syndrome (DDS), which is also related to WT1 mutations but features rapidly progressive renal disease at earlier ages. It is important to establish a differential diagnosis between FS and DDS, since they carry different tumor risks requiring specific clinical management: while in FS there is an increased risk for the development of gonadal neoplasms, in DDS there is an increased risk for the development of Wilms tumors; while FS mutations affect a splice site in intron 9, DDS results from missense mutations in exons 8 and 9 of WT1. In these atypical cases, molecular analysis may be of extreme importance to reveal the specific genetic defect in the WT1 gene, allowing an accurate diagnosis.

References Frasier SD, Bashore RA, Mosier HD. Gonadoblastoma associated with pure gonadal dysgenesis in monozygotic twins. J Pediatr 1964;64:740-745. Moorthy AV, Chesney RW, Lubinsky M. Chronic renal failure and XY gonadal dysgenesis: 'Frasier' syndrome Ñ a commentary on reported cases. Am J Med Genet 1987;3:297-302. (Review). Haber DA, Sohn RL, Buckler AJ, Pelletier J, Call KM, Housman DE. Alternative splicing and genomic structure of the Wilms' tumor gene WT1. Proc Natl Acad Sci USA 1991;88:9618-9622. Barbaux S, Niaudet P, Gubler MC, Grunfeld JP, Jaubert F, Kuttenn F, Fekete CN, Souleyreau-Therville N, Thibaud E, Fellous M, McElreavey K. Donor splice-site mutations in WT1 are responsible for Frasier syndrome. Nat Genet 1997;17:467-470. Klamt B, Koziell A, Poulat F, Wieacker P, Scambler P, Berta P, Gessler M. Frasier syndrome is caused by defective alternative splicing of WT1 leading to an altered ratio of WT1 +/-KTS splice isoforms. Hum Mol Genet 1998;7:709-714. Demmer L, Primack W, Loik V, Brown, R, Therville N, McElreavey K. Frasier syndrome: A cause of focal segmental glomerulosclerosis in a 46,XX female. J Am Soc Nephrol 1999;10:2215-2218.



Mrowka C, Schedl A. Wilms' tumor suppressor gene WT1: from structure to renal pathophysiologic features. J Am Soc Nephrol 2000;11 (Suppl 2):S106-115. (Review). Scharnhorst V, van der Eb AJ, Jochemsen AG. WT1 proteins: functions in growth and differentiation. Gene 2001;273:141-161. (Review). Auber F, Lortat-Jacob S, Sarnacki S, Jaubert F, Salomon R, Thibaud E, Jeanpierre C, Nihoul-Fékété C. Surgical management and genotype/phenotype correlations in WT1 gene-related diseases (Drash, Frasier syndromes). J Pediatr Surg 2003;38:124-129. Brennan J, Capel B. One tissue, two fates: molecular genetic events that underlie testis versus ovary development. Nature Rev Genet 2004;5:509-521. (Review). Chen MJ, Yang JH, Mao TL, Ho HN, Yang YS. Successful pregnancy in a gonadectomized woman with 46,XY gonadal dysgenesis and gonadoblastoma. Fertil Steril 2005;84:217.

Rivera MN, Haber DA. Wilms tumour: connecting tumorigenesis and organ development in the kidney. Nature Rev Cancer 2005;5:699-712. (Review). Wang NJ, Song HR, Schanen NC, Litman NL, Frasier SD. Frasier syndrome comes full circle: genetic studies performed in an original patient. J Pediatr 2005;146:843-844. Gwin K, Cajaiba MM, Caminoa-Lizarralde A, Picazo ML, Nistal M, Reyes-Múgica M. Expanding the clinical spectrum of Frasier syndrome. Pediatr Dev Pathol 2007;10:Epub ahead of print.


Cajaiba MM, Reyes-Múgica M. Frasier syndrome (FS). Atlas Genet Cytogenet Oncol Haematol.2008;12(1):81-84.

Case Report Section Paper co-edited with the European LeukemiaNet




Translocation t(11;20)(p15;q11) detected in AML M0: A case report Bani B Ganguly, Yogesh Loher, MB Agarwal

MGM Centre for Genetic Research and Diagnosis, MGM's New Bombay Hospital, Navi Mumbai, India (BBG); Hemato-oncology Department, Bombay Hospital and Research Centre, Mumbai, India (YL, MBA)

Published in Atlas Database: April 2007

Online updated version: http://AtlasGeneticsOncology.org/Reports/1120GangulyID100028.html DOI: 10.4267/2042/38486


Clinics Age and sex: 28 years old female patient. Previous History: - no preleukemia; - no previous malignant disease; - no inborn condition of note. Organomegaly: - no hepatomegaly; - no splenomegaly; - no enlarged lymph nodes; - no central nervous system involvement.

Blood Blasts: 52%

Cytopathology classification Cytology: AML Immunophenotype: Positive for CD13, CD33 and CD117 Rearranged Ig or Tcr: - Pathology: MPO and SBB negative Precise diagnosis: AML-M0 (FAB)

Survival Date of diagnosis: 03-2007. Treatment: 7+3 protocol (7 days of cytosine arabinoside continuous infusion + 3 doses of Daunorubicin), patient did not respond. Hence, she was treated with high dose of cytosine arabinoside together with etoposide; however, she didn't respond. In view of poor prognosis, she was discharged on 25/03/2007 and died on 26/03/2007.

Complete remission: none Treatment related death: - Relapse: - Status: Dead Survival: 1 month

Karyotype Sample: Bone marrow Culture time: 24/48h Banding: G-banding Results: 46,XX,t(11;20)(p15;q11) [100%, 24/24 cell]. Other molecular cytogenetic techniques: FISH with WCP probes for chromosome 11. Other molecular cytogenetics results: Three spots of 11 in interphase cells. Due to low mitotic index metaphases could not be spotted. No more material could be tested for NUP98 and TOP1 fusion.

Comments Chromosomal rearrangement between 11p15 and 20q11 has been reported in hematologic malignancies (Lam and Aplan, 2001), which results in fusion of the nucleoporin gene, NUP98 on chromosome 11p15 with topoisomerase 1, TOP1 gene located at 20q11. The NUP98 is a member of nuclear pore complex and involved in nuclear-cytosolic transport of RNA and protein complexes, and TOP1 is a protein whose c-terminus site of active tyrosine forms phosphodiester bond with 3'-strand of DNA and generates transient single strand DNA breaks (Wang 2002). In t(11;20), the rearrangement generates NUP98-TOP1 fusion protein from fusion of N-terminal portion of NUP98 (1-

Translocation t(11;20)(p15;q11) detected in AML M0: A case report Ganguly BB, et al.


G-banding shows t(11;20)(p15;q11); Interphase FISH with three signals of chromosome 11.

514) with most of TOP1 gene (170-765), including core, linker and catalytic domains (Gurevich et al. 2004). It has been suggested that the NUP98-TOP1 has leukemogenic activities independent of topoisomerase activity. The t(11;20) has also been described in patients with polycythemia vera, T-MDS and acute myeloid leukemia (Chen et al. 2003, Potenza et al. 2004, Panagopoulos et al. 2002). Our case aged 28 years with 60 kg weight has been reported with AML-M0 and probable NUP98 and TOP1 fusion. In addition, del(3p), inv(X) and der(7) was observed in one single cell. Short survival of 2.5 - 30 months was reported after diagnosis (Sekikawa and Horiguchi-yamada, 2005). Our patient got the shortest survival of 23 days after diagnosis

References Lam DH, Aplan PD. NUP98 gene fusions in hematologic malignancies. Leukemia 2001, 15:1689-1695. Panagopoulos I, Fioretos T, Isaksson M, Larsson G, Billström R, Mitelman F, Johansson B. Expression of NUP98/TOP1, but not of TOP1/NUP98, in a treatment-related myelodysplastic

syndrome with t(10;20;11)(q24;q11;p15). Genes Chromosome Cancer 2002;34(2):249-254. Wang JC. Cellular roles of DNA topoisomerases: a molecular perspective. Nat Rev Mol Cell Biol 2002;3:430-440. Chen S, Xue Y, Chen Z, Guo Y, Pan J. Generation of the NUP98-TOP1 fusion transcript by the t(11;20)(p15;q11) in a case of acute monocytic leukemia. Cancer Genet Cytogenet 2003;140(2):153-156. Gurevich RM, Aplan PD, Humphries RK. NUP98-Topoisomerase 1 acute myeloid leukemia-associated fusion gene has potent leukemogenic activities independent of an engineered catalytic site mutation. Blood 2004;104:1127-1136. Potenza L, Sinigaglia B, Luppi M, Morselli M, Saviola A, Ferrari A, Riva G, Giacobbi F, Emilia G, Temperani P, Torelli G. A t(11;20)(p15;q11) may identify a subset of nontherapy-related acute myeloid leukemia. Cancer Genet Cytogenet 2004;149(2):164-168. Sekikawa T, Horiguchi-Yamada J. t(11;20)(p15;q11). Atlas Genet Cytogenet Oncol Haematol 2005;9(2).


Ganguly BB, Loher Y, Agarwal MB. Translocation t(11;20)(p15;q11) detected in AML M0: A case report. Atlas Genet Cytogenet Oncol Haematol.2008;12(1):85-86.



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