European Course in Neuroradiology - 16th Cycle Module 2

4/29/2021

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Genetics of Brain Tumors

(in children)

Zoltán Patay MD, PhD

Endowed ChairChief of Neuroimaging

Department of Diagnostic Imaging

St. Jude Children’sResearch HospitalMemphis, TN, USA

European Course in Neuroradiology - 16th Cycle Module 2 - “Tumors”

Live Online Meeting, 2-6 May 2021The speaker has no conflicts of interest to disclose with regard to

the subject matter of this presentation

St. Jude Children’s Research HospitalMemphis, TN, USA

• Outline – educational objectives– Basic concepts of the genetic underpinnings of CNS tumors

– Mechanisms of tumorigenesis (in hereditary cancer predisposition syndromes)

– Role of progenitor cells, timing and “triggering” signaling pathways in tumorigenesis (“3T concept”)

– Genetic and epigenetic mechanisms driving and modulating tumorigenesis and tumor biology

Genetics of Brain Tumors in Children

• “Buzz words” in medical imaging– Radiomics

– Radiogenomics

– Radioepigenomics

– Radiotranscriptomics

– Radioproteomics


• “Buzz words” in medical imaging– Radiomics

– Radiogenomics (aka “Imaging genomics”)• Imaging (anatomical or physiological) used as a phenotypic assay

– Assess genotype (genetic variation and differences)

– Evaluate its influence on development, physiology and pathology

– Radioepigenomics

– Radiotranscriptomics

– Radioproteomics


Genes

+

factors modifying gene expressions (spatially and temporally), function of gene products (proteins),

resultant (signaling) pathway alterations,affected cell populations,

altered metabolic processes….


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Towards pediatric neuroimaging v2

The quest for a “more perfect”capturingdescribing

characterizingand

understandingof the imaging phenotype of diseases


• Genetics in (inherited and sporadic) tumors– Germline vs somatic mutations

– Typically, not monogenic (vs metabolic diseases)• Multiple mutations on multiple genes

– Drivers

*Wu G et al. The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. Nature Genetics 46, 444–450 (2014) doi:10.1038/ng.2938




– Drivers

– Modulators





– Drivers

– Modulators

– Bystanders




– Typically, not monogenic (vs metabolic diseases)

– Clonal evolution• Evolving mutation landscape and burden over time

Korshunov A et al. LIN28A immunoreactivity is a potent diagnostic marker of embryonal tumor with multilayered rosettes (ETMR). Acta Neuropathol. 2012 Dec;124(6):875-81.

LIN28A expression patterns and outcomes (in ETMR)

in primary

ETMR

in recurrent

ETMR



– Typically, not monogenic (vs metabolic diseases)

– Clonal evolution

– Epigenetics• Functional changes to the genome that do not modify the DNA sequence

• Affect gene activity and expression, therefore influence the physiological phenotype– Methylation

– Histone modification

– Repressor proteins (binding to “silencer” regions of the DNA)

• May be induced by environmental factors

• May be temporary or last for the duration of the cell’s life or for multiple cell generations (“heritable”)


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• Knudson’ s 2-hit hypothesis: Retinoblastoma (RB)– RB gene product: retinoblastoma protein (tumor suppressor)

– Biallelic (“germline” or “somatic”) mutations (RB-/RB-) “cause” retinoblastoma

– Diagnosed before the age of 4 years (median age:18 months)• Unilateral tumors (~sporadic): median age = 2-year

• Bilateral tumors (~hereditary): median age = 8 months


• Knudson’ s 2-hit hypothesis: Retinoblastoma (RB)– RB gene product: retinoblastoma protein (tumor suppressor)

– Biallelic (“germline” or “somatic”) mutations (RB-/RB-) “cause” retinoblastoma

– Diagnosed before the age of 4 years (median age:18 months)

Knudson A, PNAS 1971


• Hereditary Cancer Predisposition Syndromes (CPS)– Susceptibility to (specific) cancers due to inherited mutations (~10%)

• Germline mutations

• Autosomal dominant or recessive inheritance

• Variable, usually incomplete penetrance (~lifetime cancer risk)

* Gabner JE, Offit K. Hereditary cancer predisposition syndromes. Journal of Clinical Oncology, 23(2):276-292, 2005


• Major CPS groups (with implicated genes and syndromes)– Genodermatoses (PTCH1, CDKN2, NF1, NF2, TSC1, TSC2)

• Gorlin syndrome (nevoid basal cell carcinoma syndrome, medulloblastoma)

• NF1, NF2, tuberous sclerosis complex (glioma, neurofibroma, meningioma, SEGA)

– Hereditary gastrointestinal malignancies (APC, MLH1, HNPCC, CDH-1)• Turcot syndrome (colon, basal cell cc, ependymoma, medulloblastoma, GBM)

– Genitourinary syndromes (HPC1, HPCX, VHL, WT1, MET)• Von Hippel-Lindau syndrome (hemangioblastoma)

– Hereditary breast cancer syndromes (BRCA1, BRCA2, TP53, PTEN)• Li-Fraumeni syndrome (sarcomas, breast, adrenal cortical, GI cancers, brain tumors)

• Cowden syndrome (multiple hamartomas, breast, thyroid, endometrial cancer, Lhermitte-Duclos)

– CNS-vascular cancer predisposition syndromes (RB1, SDHD, SDHC, INI1)• Retinoblastoma

• Rhabdoid predisposition syndrome (ATRT, “PNET”, medulloblastoma, CPC)

• Hereditary paraganglioma

– Endocrine tumor systems (MEN1, RET)• Hereditary pheochromocytoma and paraganglioma


• Tumorigenesis (in the CNS or elsewhere)• Genetic factors in brain tumors• Oncogenes• Tumor suppressors • Defective DNA replication• Altered (~ uncontrolled) DNA expression• “De novo” endogenous oncometabolites*

• Epigenetic factors

*Ming Y et al. Oncometabolites: linking altered metabolism with cancer. J Clin Invest. 2013;123(9):3652-3658.


• Tumorigenesis (in the CNS or elsewhere)• Genetic factors in brain tumors• Oncogenes - activation• Upregulated proto-oncogenes (RAS, WNT, MYC etc.)


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• WNT genes (in medulloblastoma)– “WNT”: Drosophila segment polarity gene Wg (“wingless”) and its vertebrate ortholog

Int1 (a mouse proto-oncogene)

– Encode protein growth factors (19 WNT proteins in humans)• β-catenin (one of the WNT proteins)

– Protein product of the CTNNB1 WNT gene

– Subunit of the cadherin protein complex

– Acts as an intracellular signal transducer

– “WNT signaling” (dual function)» Coordination of cell–cell adhesion

» Gene transcription (cell proliferation, death)

– Robust degradation mechanism through

phosphorylation


• WNT genes (in medulloblastoma)– “WNT”: Drosophila segment polarity gene Wg (“wingless”) and its vertebrate ortholog

Int1 (a mouse proto-oncogene)

– Encode protein growth factors (19 WNT proteins in humans)• β-catenin (one of the WNT proteins)

– Somatic CTNNB1 gene mutation (germline APC mutation in Turcot A syndrome)

» “Stable” -catenin (prevents degradation)

» Accumulation of intracellular β-catenin

» Upregulation of WNT signaling

» Uncontrolled cell proliferation

-catenin

de Bont JM et al. Biological background of pediatric medulloblastoma and ependymoma: A review from a translational research perspective. Neuro-Oncology 10, 1040–1060, 2008


• Tumorigenesis (in the CNS or elsewhere)• Role of genetic factors in brain tumors• Oncogenes - activation• Tumor suppressors - inactivation• TP53: inhibition of the cell cycle, promotion of apoptosis (Li-Fraumeni)• PTEN: cell cycle arrest or apoptosis (Cowden)• RB: inhibition of excessive cell growth until cell is ready to divide


• Li-Fraumeni syndrome• Autosomal dominant disorder

• Sarcoma, breast, leukemia and adrenal gland (SBLA) syndrome

• Germline mutations of the TP53 tumor suppressor gene• TP53 gene products: “Guardians of the genome”

• 15+ protein “isoforms” that bind to DNA, regulate gene expression and prevent mutations of the genome

• Most frequent mutated gene in human cancers (>50%)


Choroid plexus carcinoma (CPC)

Li-Fraumeni – pt. 1


Pleiomorphic xanthoastrocytoma (PXA)



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Medulloblastoma (SHH-activated MB + p53 mutation)



• Tumorigenesis (in the CNS or elsewhere)• Role of genetic factors in brain tumors• Oncogenes - activation• Tumor suppressors - inactivation• Defective DNA replication• CMMRD: DNA repair deficiency


• Constitutional mismatch repair deficiency (CMMRD)– Distinct childhood cancer predisposition syndrome

– “Generic” DNA replication error • Dysfunction of mechanisms that normally prevent error during DNA replication

– “Proofreading”» Germline mutations in the DNA polymerase epsilon and delta

– “Mismatch repair”

» Biallelic (homozygous) germline mutations in the CMMR genes


“Proofreading”:Exonuclease domains in the DNA polymerase (POLE, POLD1)

Mismatch repair system:PMS2 (58%), MLH1, MSH2, MSH6,

Tabori U et al. Clinical Management and Tumor Surveillance Recommendations of Inherited Mismatch Repair Deficiency in Childhood. Clin Cancer Res; 23(11) June 1, 2017



• “Endless” number of unrepaired mutations– High mutational burden in tumors

» Mutation rates of 100/Mb (“hypermutated” neoplasms)

» (As compared with <10/Mb in most childhood cancers)



“Proofreading”:Exonuclease domains in the DNA polymerase (POLE, POLD1)

Mismatch repair system:PMS2 (58%), MLH1, MSH2, MSH6,

• Mutation burden in pediatric cancer (MMR and POL vs WT)• “Wild type” (<10/Mb)• Proofreading• Mismatch repair• Both (>100/Mb)

Campbell BB et al. Comprehensive Analysis of Hypermutation in Human Cancer . Cell, 171(5):1042-1056, 2017




• “Endless” number of unrepaired mutations– High mutational burden in tumors

» Mutation rates of 100/MB (“hypermutated” neoplasms)

» (As compared with <10/MB in most childhood cancers)

– Some (but not all!) potentially oncogenic» Malignant and non-malignant features



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• Constitutional mismatch repair deficiency (CMMRD)– Clinical features (phenotypic spectrum)

Wimmer K et al. Diagnostic criteria for constitutional mismatch repair deficiency syndrome: suggestions of the European consortium ‘Care for CMMRD’ (C4CMMRD) J Med Genet 2014;51:355–365.








Pt. 1

Pt. 2

• Imaging phenotypic clues to suggest CMMRD– Multifocal tumors (~95%)

Kerpel A et al. Neuroimaging Findings in Children with Constitutional Mismatch Repair Deficiency Syndrome. AJNR (under review)


Pt. 1 Pt. 2


– FASIs (focal areas of signal intensity, NF1-like, ~30%)





– Non-specific subcortical T2 hyperintensities (~70%)



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– DVAs (~85%, typically multiple)

CMMRD – pt. 1



CMMRD – pt. 1





– DVAs (~85%, typically multiple)


• Tumorigenesis (in the CNS or elsewhere)• Role of genetic factors in brain tumors• Oncogenes - activation• Tumor suppressors - inactivation• Defective DNA replication• Altered (~ uncontrolled) DNA expression• DICER1: mRNA silencing deficiency (DICER1)


• DICER1 syndrome– Defective post-translational regulation of gene expression

– DICER1 gene product: DICER1 protein• Participates in the production of mature microRNAs (miRNAs)

• Mature microRNAs are part of the RNA-Induced Silencing Complex (miRISC)


• DICER1 syndrome– Defective post-translational regulation of gene expression

– DICER1 gene product: DICER1 protein• Participates in the production of mature microRNAs (miRNAs)

• Mature microRNAs are part of the RNA-Induced Silencing Complex (miRISC)• miRISCs control gene expression by attaching to (“silencing”) or breaking down specific messenger RNA (mRNA)

molecules

• miRNAs stop protein synthesis (post-transcriptionally)


• DICER1 syndrome– DICER1 mutations• DICER1 mutations lead to abnormal (short) DICER1 protein that is unable to produce mature miRNA

(and miRISC)

• Without regulation at the mRNA level, genes may be overexpressed, leading to uncontrolled cells growth, proliferation and tumor formation

Klein SD et al. Hotspot Mutations in DICER1 Causing GLOW Syndrome-Associated Macrocephaly via Modulation of Specific MicroRNA Populations Result in the Activation PI3K/ATK/mTOR Signaling. MicroRNA, 2020, 9, 70-80.


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• DICER1 syndrome– Common tumors

• Lungs (pleuropulmonary blastoma)

• Kidneys (nephroblastoma aka Wilms tumor, cystic nephroma, sarcoma)

• Ovaries (Sertoli-Leydig tumor, a rare, testosterone releasing androblastoma)

• CNS: pituitary blastoma and pineoblastoma (5%)

• Thyroid (multinodular goiter)


• Natural “cancer prevention” mechanisms– Before transcription• TP53 – preservation of “genomic integrity”

– During transcription• “Proofreading” and “mismatch repair” (POLE, PMS2)

– After transcription – during translation• “Last minute censoring” of gene expression by miRNAs (DICER1)


• Tumorigenesis (in the CNS or elsewhere)• Role of genetic factors in brain tumors• Oncogenes (activation)• Tumor suppressors (inactivated)• Defective DNA replication• Altered DNA expression• “De novo” endogenous oncometabolites*• Accumulation of metabolic intermediates which cause metabolic and non-metabolic dysregulation leading to

tumorigenesis

*Ming Y et al. Oncometabolites: linking altered metabolism with cancer. J Clin Invest. 2013;123(9):3652-3658.


• Carcinogenesis by “oncometabolites”• Most common oncometabolites• 2-hydroxyglutarate, succinate, fumarate

Pt.1 Pt.2 Pt.3


• 3T concept (P. Lasjaunias)– Target (”where”)

– Timing (”when”)

– Trigger (“how”)


• 3T concept (P. Lasjaunias)– Target (”where”) - location

• Progenitor cell population (mutation, selective vulnerability)– Protein function alteration (loss of function, gain of function etc.)

– Pathway alteration (upregulation, downregulation, silencing etc.)


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• SHH-activated MB: Developmental neurobiology– Progenitor cells: in upper rhombic lip (rhombomere 1)

• Glutamate-ergic granule neuron progenitor cells (Glut+ GNPCs)


Hovestadt V et al. Medulloblastomics revisited: biological and clinical insights from thousands of patients. Nature Reviews Cancer 2020, https://doi.org/10.1038/s41568-019-0223-8

• The “next big thing”: Cell lineage tracking (transcriptomics)– Single cell RNA sequencing (sc-RNA seq) to identify distinctly different cell lineages and

types in the cerebellum (in mice)

– Link those to tumor subtypes (in humans) based on similarity





– Timing (”when”) - age (e.g. during early development or later)• “Permissive” genetic-molecular context (age-in vs age-out)


• Aging in?

Genomic landscape of DIPG and pediatric non-brainstem high-grade glioma*

Genetic alterations detected in 19 genes, including ACVR1 (activin A receptor type 1) and the genes most recurrently mutated in the pathways indicated on the left, are displayed.






– Timing (”when”) - age (e.g. during early development)• “Permissive” genetic-molecular context (age-in vs age-out)

– Trigger (“how”) - genetic, epigenetic (environmental factors…)


• Applied genetic-molecular profiling of embryonal CNS tumors


WHO 2016

WHO 2007

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Korshunov A et al. Embryonal tumor with abundant neuropil and true rosettes (ETANTR), ependymoblastoma, and medulloepithelioma share molecular similarity and comprise a single clinicopathological entity. Acta Neuropathol. 2014 Aug;128(2):279-89.


• Embryonal tumor with multilayered rosettes (ETMR)– Genetic “common denominator”: C19MC-alteration• Focal amplification at 19q13.42 (C19MC cluster)

Microscopyy and immunohistochemistry of ETMR.a: Paucicellular areas intermixed with undifferentiated cell components and rosettes (H-E; ×40). b: Typical multilayered rosette surrounded by neuropil with neurocytic cells and small “blue” cells (H-E; ×400).


• Additional features– TP53 mutation

Korshunov A et al. Embryonal tumor with abundant neuropil and true rosettes (ETANTR), ependymoblastoma, and medulloepithelioma share molecular similarity and comprise a single clinicopathological entity. Acta Neuropathol. 2014 Aug;128(2):279-89.

Microscopyy and immunohistochemistry of ETMR.a: Paucicellular areas intermixed with undifferentiated cell components and rosettes (H-E; ×40). b: Typical multilayered rosette surrounded by neuropil with neurocytic cells and small “blue” cells (H-E; ×400).

Microscopy and immunohistochemistry of ETMR.c: Strong heterogeneous staining with p53. Marked expression within rosettes (p53; ×200), d: In neuropil areas, background diffusely stained by synaptophysin antibody (Synaptophysin; ×100).



• Additional features– TP53 mutation

– LIN28A positivity (translational enhancer)*

in primary

ETMR

in recurrent

ETMR

Korshunov A et al. LIN28A immunoreactivity is a potent diagnostic marker of embryonal tumor with multilayered rosettes (ETMR). Acta Neuropathol. 2012 Dec;124(6):875-81.


Cancer Cell 2015 27, 613-615DOI: (10.1016/j.ccell.2015.04.015), Copyright © 2015 Elsevier Inc.


• Chromosome 1q gain: an unfavorable prognostic factor– Ependymoma-PF-A


Merchant TE et al. Conformal Radiation Therapy for Pediatric Ependymoma, Chemotherapy for Incompletely Resected Ependymoma, and Observation for Completely Resected, Supratentorial Ependymoma. J Clin Oncol 37:974-983, 2019







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Chiang J et al. Chromosome arm 1q gain is an adverse prognostic factor in localized and diffuse leptomeningeal glioneuronal tumors with BRAF gene fusion and 1p deletion. Acta Neuropathol 137, 179–181 (2019). https://doi.org/10.1007/s00401-018-1940-x

• Chromosome 1q gain: an unfavorable prognostic factor– Ependymoma PF-A

– Localized and diffuse DLGNT (with BRAF fusion and 1p deletion)


• Key points– The genetic underpinnings of CNS tumors are increasingly elucidated

– Hereditary cancer predisposition syndromes are good model conditions to understand mechanisms of tumorigenesis

– The “3T concept” works for tumorigenesis too

– Genetic (and epigenetic) mechanisms may drive or modulate tumorigenesis and tumor biology


Memphis, TN

Thank you!

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European Course in Neuroradiology - 16th Cycle Module 2