MINING COMPLEX SARCOMA GENOMES:

LESSONS FROM OSTEOSARCOMA

LARGE MARKER CHROMOSOMES IN ADULT SARCOMA

TWO WAYS OF THINKING ABOUT SARCOMA

TEICHER 2012

DEVELOPMENTAL BIOLOGY VIEW OF SARCOMA

GENOMIC VIEW OF SARCOMA

GENOMIC VIEW OF SARCOMA

A

CLEARLY

DEFINED

ONCOGENIC

PATHWAY

GENOMIC VIEW OF SARCOMA

NO

SINGLE

CLEARLY

DEFINED

ONCOGENIC

PATHWAY

APPROACHES TO COMPLEXITY

• LARGE INTEGRATED GENOMICS STUDIES

• INTEGRATION WITH GWAS STUDIES

• COMPARATIVE ONCOLOGY

• COMMONALITIES AMONG COMPLEX SARCOMAS

• GOAL: A PATH TO CLINICAL RELEVANCE

ENDOCHONDRAL OSSIFICATION

MEMBRANOUS OSSIFICATION

NORMAL TUMOR

GLOBAL INCIDENCE

International Journal of CancerVolume 125, Issue 1, pages 229-234, 3 FEB 2009 DOI: 10.1002/ijc.24320http://onlinelibrary.wiley.com/doi/10.1002/ijc.24320/full#fig1

EPIDEMIOLOGY CONNECTS BONE GROWTH TO TUMOR RISK

Mirabello et al.Cancer Causes Control. 2011 Jun;22(6):899-908.

MINIMAL SURVIVAL IMPROVEMENT IN RECENT DECADES

Whelan Ann. Oncol 2011

OSTEOCYTE OSTEOBLAST 2PREOSTEOBLAST

MSC

OSTEOBLAST 1

CHONDROBLAST

CHONDROCYTE

BONE DIFFERENTIATION GENES

A CONCEPTUAL FRAMEWORK FOR OSTEOSARCOMA

OSTEOCYTE OSTEOBLAST 2PREOSTEOBLAST

MSC

OSTEOBLAST 1

CHONDROBLAST

CHONDROCYTE

BONE DIFFERENTIATION GENES

MORPHOGENETIC,GROWTH

ANDDIFFERENTIATION

REGULATING SIGNALS

A CONCEPTUAL FRAMEWORK FOR OSTEOSARCOMA

ENDOCRINE

AUTOCRINE

PARACRINE

OSTEOCYTE OSTEOBLAST 2PREOSTEOBLAST

MSC

OSTEOBLAST 1

CHONDROBLAST

CHONDROCYTE

BONE DIFFERENTIATION GENES

A CONCEPTUAL FRAMEWORK FOR OSTEOSARCOMA

OSTEOSARCOMA

OSTEOCYTE OSTEOBLAST 2PREOSTEOBLAST

MSC

OSTEOBLAST 1

CHONDROBLAST

CHONDROCYTE

BONE DIFFERENTIATION GENES

A CONCEPTUAL FRAMEWORK FOR OSTEOSARCOMA

OSTEOSARCOMA

• DERANGED GROWTH• INVASIVE• ABERRANT DIFFERENTIATION• MASSIVE GENOME INSTABILITY• GROSSLY PERTURBED GENE EXPRESSION

OSTEOCYTE OSTEOBLAST 2PREOSTEOBLAST

MSC

OSTEOBLAST 1

CHONDROBLAST

CHONDROCYTE

BONE DIFFERENTIATION GENES

A CONCEPTUAL FRAMEWORK FOR OSTEOSARCOMA

OSTEOSARCOMA

• MASSIVE GENOME INSTABILITY• DERANGED GROWTH• INVASIVE• ABERRANT DIFFERENTIATION

A SHATTERED GENOME

OSTEOCYTE OSTEOBLAST 2PREOSTEOBLAST

MSC

OSTEOBLAST 1

CHONDROBLAST

CHONDROCYTE

BONE DIFFERENTIATION GENES

DISTINCT COPY NUMBER PROFILES EMERGE

OSTEOSARCOMA

• MASSIVE GENOME INSTABILITY• DERANGED GROWTH• INVASIVE• ABERRANT DIFFERENTIATION

OSTEOCYTE OSTEOBLAST 2PREOSTEOBLAST

MSC

OSTEOBLAST 1

CHONDROBLAST

CHONDROCYTE

BONE DIFFERENTIATION GENES

A CONCEPTUAL FRAMEWORK FOR OSTEOSARCOMA

OSTEOSARCOMA

OSTEOCYTE OSTEOBLAST 2PREOSTEOBLAST

MSC

OSTEOBLAST 1

CHONDROBLAST

CHONDROCYTE

BONE DIFFERENTIATION GENES

A CONCEPTUAL FRAMEWORK FOR OSTEOSARCOMA

OSTEOSARCOMA

EVIDENCE BASED CATEGORIES OF GENES ALTERED IN OS OR WHICH CONFER PREDISPOSITION TO OS THAT

CAN CONTRIBUTE TO THE TUMOR PHENOTYPE:

• CELL CYCLE, DNA REPLICATION AND REPAIR

• SIGNAL TRANSDUCTION

• BONE DIFFERENTIATION

OSTEOCYTE OSTEOBLAST 2PREOSTEOBLAST

MSC

OSTEOBLAST 1

CHONDROBLAST

CHONDROCYTE

BONE DIFFERENTIATION GENES

A CONCEPTUAL FRAMEWORK FOR OSTEOSARCOMA

OSTEOSARCOMA

CELL CYCLE, DNA REPLICATION AND REPAIR

GENE EVIDENCE

TP53 GERMLINE MUTATION, TUMOR MUTATION, MOUSE MODELS

RB1 GERMLINE MUTATION, TUMOR MUTATION, MOUSE MODELS

CDKN2A DELETIONCCNE1 AMPLIFICATIONCDK4 AMPLIFICATIONMDM2 AMPLIFICATIONCDC5L AMPLIFICATIONCOPS3 AMPLIFICATIONREQL4 GERMLINE MUTATION

OSTEOCYTE OSTEOBLAST 2PREOSTEOBLAST

MSC

OSTEOBLAST 1

CHONDROBLAST

CHONDROCYTE

BONE DIFFERENTIATION GENES

A CONCEPTUAL FRAMEWORK FOR OSTEOSARCOMA

OSTEOSARCOMA

SIGNAL TRANSDUCTION

GENE EVIDENCE

PTEN DELETION

PIK3CA MUTATION

RAS MUTATION

IGF1R AMPLIFICATION

TRANSCRIPTION FACTORS IN BONE DIFFERENTIATION

PPARGCEBP’s

SOX 5,6,9

RUNX2 SP7 (OSX)

RUNX2

OSTEOCYTE OSTEOBLAST 2PREOSTEOBLAST

MSC

OSTEOBLAST 1

CHONDROBLAST

CHONDROCYTE

BONE DIFFERENTIATION GENES

OTHER TF’SSATB2TWISTDLXMSXAP1EGR2ATF4

OSTEOCYTE OSTEOBLAST 2PREOSTEOBLAST

MSC

OSTEOBLAST 1

CHONDROBLAST

CHONDROCYTE

BONE DIFFERENTIATION GENES

A CONCEPTUAL FRAMEWORK FOR OSTEOSARCOMA

OSTEOSARCOMA

BONE DIFFERENTIATION

GENE EVIDENCE

RUNX2 AMPLIFICATION

SATB2 LOSS

RB1 MODELS

TP53 MODELS

OSTEOCYTE OSTEOBLAST 2PREOSTEOBLAST

MSC

OSTEOBLAST 1

CHONDROBLAST

CHONDROCYTE

BONE DIFFERENTIATION GENES

A CONCEPTUAL FRAMEWORK FOR OSTEOSARCOMA

OSTEOSARCOMA

UNCERTAIN FUNCTION

GENE EVIDENCE

LSAMP DELETION(REGION?)

APPROACHES TO COMPLEXITY

• LARGE INTEGRATED GENOMICS STUDIES

• INTEGRATION WITH GWAS STUDIES

• COMPARATIVE ONCOLOGY

• COMMONALITIES AMONG COMPLEX SARCOMAS

• GOAL: A PATH TO CLINICAL RELEVANCE

TARGET OSTEOSARCOMA PROJECT

TARGET OSTEOSARCOMA PROJECT

• COMPREHENSIVE GENOMIC ANALYSIS

• ARRAYS: mRNA,miRNA, DNA Methylation, SNPS

•SEQUENCING: EXOME, TRANSCRIPTOME,

WHOLE GENOME ON SELECT SAMPLES

OS

NBL

THE TURBULENT GENOME OF OSTEOSARCOMA

WHOLE GENOME SEQUENCING

SOMATIC STRUCTURAL VARIATIONS

WHOLE GENOME SEQUENCING

SOMATIC STRUCTURAL VARIATIONS

WHOLE GENOME SEQUENCING

STRUCTURAL VARIATIONS: COPY NUMBER LOSS

WHOLE GENOME SEQUENCINGCOPY NUMBER

| ||| || | ||||| | | | | |

APPROACHES TO COMPLEXITY

• LARGE INTEGRATED GENOMICS STUDIES

• INTEGRATION WITH GWAS STUDIES

• COMPARATIVE ONCOLOGY

• COMMONALITIES AMONG COMPLEX SARCOMAS

• GOAL: A PATH TO CLINICAL RELEVANCE

OsteosarcomaNormal Tissues

Human Dog

APPROACHES TO COMPLEXITY

• LARGE INTEGRATED GENOMICS STUDIES

• INTEGRATION WITH GWAS STUDIES

• COMPARATIVE ONCOLOGY

• COMMONALITIES AMONG COMPLEX SARCOMAS

• MAPPING A PATH TO CLINICAL RELEVANCE

PROFILING ADULT PLEOMORPHIC SARCOMAS

• HIGH DENSITY SNP ARRAYS

• TARGETED SEQUENCING OF 1300 GENES

MANY COMMONALITIES WITH OSTEOSARCOMA

•FEW TARGETABLE POINT MUTATIONS

• STRUCTURAL COMPLEXITY

• SHARED REGIONS OF CNA

• SHARED SNV’S (TP53, RB1)

• TELOMERE MAINTENANCE MECHANISMS

COMPLEX GENOME OF UPS

RB1 DELETION IN UPS

CHROMOSOME 12 AMPLIFICATION IN A LEIOMYOSARCOMA

TWO MODES OF TELOMERE MAINTENANCE

IMMORTALITY

PROGENITOR CELL

TELOMERASEACTIVATION

ALTERNATIVELENGTHENING OF TELOMERES

TWO MODES OF TELOMERE MAINTENANCE

IMMORTALITY

MESENCHYMAL STEM CELL(LOW TELOMERASE EXPRESSION)

TELOMERASEACTIVATION

ALTERNATIVELENGTHENING OF TELOMERES

TELOMERE MAINTENANCE IN SARCOMA

Heaphy et al,AJP 179:1609 (2011)

Durant, J. Cancer3:67 2012

FREQUENCY OF ALT IN SARCOMA

Heaphy et al,AJP 179:1609 (2011)

%

Embryonic Kidney w/Adenovirus

Pancreatic Cell Line

Normal DNA

Osteosarcoma

RNA SEQ REVEALS A TRUNCATED RNA SEQ TRANSCRIPT IN SAOS2

DIRECTION OF TRANSCRIPTION

ATRX INACTIVATION BY AN INTRACHROMOSOMAL REARRANGEMENTIN SAOS2

ATRX INACTIVATION BY A DELETION IN LEIOMYOSARCOMA

WORKING MODEL OF COMPLEX SARCOMA GENESIS

PROGENITOR RECOMBINATION PRONE PROGENITOR

•DEFECTIVE TELOMERE MAINTENANCE• LOW BASELINE TERT

RECOMBINATION COMPETENT PROGENITOR•DEFECTIVE TELOMERE MAINTENANCE• CELL CYCLE CHECKPOINT DEFECTS

PROLIFERATINGTUMOR CELL

• ALT ACTIVATION• MASSIVE CNA• DYSREGULATED GENE EXPRESSION• ACCUMULATION OF POINT MUTATIONS

APPROACHES TO COMPLEXITY

• LARGE INTEGRATED GENOMICS STUDIES

• INTEGRATION WITH GWAS STUDIES

• COMPARATIVE ONCOLOGY

• COMMONALITIES AMONG COMPLEX SARCOMAS

• MAPPING A PATH TO CLINICAL RELEVANCE

• HIGH COMPLEXITY = NEED FOR TUMOR SAMPLING.

• PROGNOSTIC SIGNATURES (OF ANY TYPE).

• EXPLORE SYNTHETIC LETHALITY WITH TSG DEFICIENCY.

• DOES ALT CREATE A THERAPEUTIC OPPORTUNITY?

• IDENTIFY SUBSETS WITH GAIN OF FUNCTION ALTERATIONS WHICH MAY BE TARGETED (e.g. MDM2).

• IDENTIFY VULNERABILITIES WHICH ARE RELATED TOTHE DIFFERENTIATION STATE OF A GIVEN SARCOMA.

• WEAK LINKS IN THE METASTATIC CHAIN.

COLLABORATORS

NCI Genetics Branch

Rizzoli Institute

Luca SangiorgiPiero Picci

TARGET PROJECT

Ching LauMark KrailoDon BarkauskasLisa TeotLaura MonovichJulie Gestier-FosterChand KhannaRichard GorlickTim TricheGreg ReamanNeyssa MarinaLee HelmanIrene AndrulisJay WunderJaime Guidry-AuvilDaniela GerhardMalcolm Smith

Sean DavisSven BilkeJack ZhuJosh WaterfallYevgeniy Gindin

Robert WalkerMarbin PinedaMark MackiewiczYuan JiangSo Young MoonPrincy Francis

NCI DCEG

Sharon SavageLisa Mirabello