MINING COMPLEX SARCOMA GENOMES: LESSONS FROM OSTEOSARCOMA
Jan 01, 2016
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