Division Faculty Meeting
March 29, 2011
Initial Findings in The
Cancer Genome Atlas
(TCGA)
for Colorectal Cancer
Stan Hamilton, MD
Head, Pathology and Laboratory Medicine
The University of Texas M. D. Anderson Cancer Center
1
AACR Meeting
Raju Kucherlapati
Harvard Medical School
April 5, 2011
(With additions and modifications)
2
Molecular characteristics of colorectal cancer
• Chromosomal instability type
• Microsatellite instability type
• DNA methylation type
• Heterogeneity
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4
5
TCGA for Colorectal Cancer
Tumor/Normal pairs from colonic and rectal tumors (80% from
Germany)
Low pass whole genome sequencing for copy number variation and
chromosomal aberrations (Harvard) – 90 pairs
SNP arrays for copy number variation (Dana Farber CI/Broad) – 160
pairs
Array and RNA-Seq for expression profiling (U No Carolina) -250
pairs
Infinium arrays for methylation studies (U So Cal/Johns Hopkins) –
250 pairs
Sequence based methods for miRNA (British Columbia CC) – 250
pairs
Whole exome sequencing of all samples and whole genome
sequencing on a subset (Baylor Houston and Washington U St.
Louis) – 139 pairs
Microsatellite instablity status (MD Anderson CC) – 202 pairs
6Analysis (Broad, Memorial Sloan-Kettering CC, UCSC, Institute for
Systems Biology, MD Anderson CC)
Microsatellite instability status
• Seven marker panel of four mononucs (BAT25, BAT26, BAT40,
TGFbRII) and three dinucs (D2S123, D5S346, D17S250) from NCI
Consensus Conference on MSI
• 0 markers altered = MS-Stable
• 1 to 3 altered = MSI-Low and add 6 dinucs on 18q (no changes in
classification)
• 5 to 7 altered = MSI-High
• 71.8% MSS
• 14.9% MSI-L (30% mononucs only, 50% dinucs only, 20% both)
• 13.4% MSI-H
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CNV profiles from 3-5X coverage WGS
Sequencing (3000 base fixed window)
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Copy number profiles
8q gain
13 gain
18q loss
20q gain
Colon
Rectal
No differences between colonic and rectal tumors
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Focal amplifications
IGF2/Insulin
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ASCL2
ERBB2 amplifications
ERBB2
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Chromosomal translocations
Confirmed by
RNA Seq
PRSS3-TMEM45B
t (9;11)(p11;q24.3)
PTPN14-AP3S1
t (1;5)(q32.2;q22)
TGFb-signaling
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“Low”
“High”
Expression profiles by
RNA Seq
CIN
CIMP
Inter
mediate
Loss of Chr 18, Chr 5
Loss of Chr 22, Chr 11
Gain of Chr 20 (20q)
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Mutation in miRNA maturation regulatory
genes (RNASEN, DICER Complexes)
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hgnc_symbol
Frequency
RNASEN
2
Frequency(67
NonHyperMut Samples)
NA
DGCR8
2
1
DDX17
6
3
PRKRA
1
NA
TARBP2
1
NA
TARBP1
1
1
DICER1
NA
NA
ZCCHC11
6
3
Multiple aberrations in miRNA biogenesis
 miR-17-92
 miR-1247
•Ago1/2/3/4, MOV10, TNRC6A and
TNRC6B mutation
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


•DGCR8, RNASEN and DDX17 mutation
•DICER1*, TRBP1 and TRBP2 mutation
Somatic mutation frequencies in tumors
colon
rectum
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Mutations in genes of the Wnt signaling pathway
Moon et al. Nat Rev Genet. 2004 5: 689-699.
113 patients
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Mutations in the ERBB and MAPK pathway genes
91 patients
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ErbB family of genes including amplications of ErbB2
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PI3Kinase pathway mutations including PTEN
deletions
47%
38%
2%
1%
1%
4%
6%
• PI3K and Ras mutations include all the family members
• PIK3CA only from Illumina patients (13 mut in 55 pts)
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Annu Rev Pathol. Mech. Dis. 2009. 4:127-50
TGF-B signaling pathway mutations
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Location of SMAD mutations
MH2 domain: protein interaction, homo- and heterooligomerization
MH1: DNA binding domain
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IDH mutations
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Conclusions
• TCGA is generating comprehensive genetic/genomic
data from analysis of colorectal tumor/normal pairs. The
data are deposited at DbGap and TCGA’s DCC.
http://www.ncbi.nlm.nih.gov/gap and
http://cancergenome.nih.gov/.
• CNV, expression profiling, and miRNA analysis reveal no
significant differences between colon and rectal tumors.
• 15% of the tumors have high somatic mutation rates
resulting from mutations in DNA mismatch repair genes,
most with MSI-H.
• MicroRNA biogenesis might be altered in colorectal
tumors.
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Conclusions
• Translocations involving TTC28 gene (chr 22)
• Four methylation clusters: CIMP-High, CIMP-Low, NonCIMP with two different patterns
• Mutation rate groups with >40/Mb, 10 to 40/Mb, and
<10/Mb
• >40/Mb and 10 to 40/Mb usually MSI-H and CIMP-H, but
occasional hypermutated cancers without MSI-H
• Occasional cancers with methylation of MLH1 lack MSIH and hypermutation
• MSI-H with five pathway markers: Myc/Max,
HIF1a/ARNT, FOXA1, Myb, and Delta-notch
• Beta-catenin pathway marker in MSS cancers
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Conclusions
• Key pathways that are critical for the
initiation and progression of colorectal
cancer are modified in diverse ways.
• Extensive genomic analysis of individual
tumors will help stratify patients for
targeted therapies.
• Integrative analyses are in progress.
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Acknowledgements
Broad/DFCI
ISB
MDA
MSKCC
UCSC
BCCA
Broad
Harvard
UNC
USC/JHU
BCM
Broad
Wash U
Project Team
DCC
Tissue Source sites
Disease working group
Analysis working group
IGC and NCH
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