Genomic DNA Variation

Computer-Aided Discovery Methods

Baylor College of Medicine course 311-405Term 3, 2010/2011

Lecture on Wednesday, February 2nd, 2011

Aleksandar Milosavljevic, PhDAleksandar Milosavljevic, PhDhttp://www.brl.bcm.tmc.eduhttp://www.brl.bcm.tmc.edu

Cancer Genome Variation: Methods

Cancer Genome Variation:Sequencing Provides Comprehensive

Tumor Characterization

Chromosome Aberrations: References 1 of 2

Background reviews

[Balmain 2001] Balmain, A., Cancer genetics: from Boveri and Mendel to microarrays. Nat Rev Cancer, 2001. 1(1): p. 77-82.

[Albertson et al. 2003] Albertson, D.G., et al., Chromosome aberrations in solid tumors. Nat Genet, 2003. 34(4): p. 369-76.

[Rabbitts et al. 2003] Rabbitts, T.H. and M.R. Stocks, Chromosomal translocation products engender new intracellular therapeutic technologies. Nat Med, 2003. 9(4): p. 383-6.

[Kumar-Sinha et al. 2008] Kumar-Sinha, C., S. A. Tomlins, et al. (2008). "Recurrent gene fusions in prostate cancer." Nat Rev Cancer 8(7): 497-511.

•

Chromosome Aberrations References 2 of 2

Research articles

[Chin et al. 2006] Chin K. et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies, Cancer Cell 10:529-541 2006

[Tomlins et al. 2005] Tomlins SA et al., Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science, 2005. 310(5748): p. 644-8.

[TCGA 2008] The Cancer Genome Atlas Network "Comprehensive genomic characterization defines human glioblastoma genes and core pathways." Nature 455(7216): 1061-1068.

[Miller et al.] Miller C.A. et al. Discovering functional modules by identifyingrecurrent and mutually exclusive mutational patterns in tumors [in review].

Cancer Genome Variationobject of discovery

single gene

pathway / module /gene set

background knowledge employed in discovery

none expression and other attributes of individual genes

networks /modules /gene sets

[Miller et al.]

[Chin et al. 2006]

[Tomlins et al. 2005][Kumar-Sinha et al.

2008]

[TCGA 2008]

Boveri, one century ago …

Multiple cell poles cause unequalsegregation of chromosomes.

a | Fertilization of sea-urchin eggs bytwo sperm results in multiple cell poles.

b | Chromosomes are aberrantly segregated

[Balmain 2001]

Chromosomal aberrations

[Albertson et al.]

Chromosomal aberrations

[Albertson et al.]

Cancer Genome Variation: Methods

(Array) Comparative Genome Hybridization (array CGH)

Cancer Genome Variationobject of discovery

single gene

pathway / module /gene set

background knowledge employed in discovery

none expression and other attributes of individual genes

networks /modules /gene sets

[Miller et al.]

[Chin et al. 2006]

[Tomlins et al. 2005][Kumar-Sinha et al.

2008]

[TCGA 2008]

Genomic and transcriptional aberrations linked to breast cancer pathophysiologies [Chin et al. 2006]

• 100+ aggressively treated early stage breast tumors

1989-1997, before ERBB2 antagonist Trastuzumab (Herceptin) was approved for treating ERBB2+ breast cancer

ERBB2 heuristic (“paradigm”) formulated in last sentence of Chin K. et al.

“Taking ERBB2 as the paradigm (recurrently amplified, overexpressed, associated with outcome and with demonstrated functional importance in cancer) suggests FGFR1, TACC1, ADAM9, IKBKB, PNMT, and GRB7 as high-priority therapeutic targets in these regions of amplification.”

“Taking ERBB2 as the paradigm (recurrently amplified, overexpressed…

Array CGH (~3K BAC array)

Gene expression (Affymetrix U133A array)

“Taking ERBB2 as the paradigm (recurrently amplified…

“Taking ERBB2 as the paradigm (… associated with outcome…)

“Taking ERBB2 as the paradigm (… associated with outcome…)

Deletions, amplifications induce aberrant fusions

…but…

Some aberrant fusion-producing rearrangements ( reciprocal translocations, inversions ) may not affect copy number

Going beyond copy-number changes

Cancer Genome Variationobject of discovery

single gene

pathway / module /gene set

background knowledge employed in discovery

none expression and other attributes of individual genes

networks /modules /gene sets

[Miller et al.]

[Chin et al. 2006]

[Tomlins et al. 2005][Kumar-Sinha et al.

2008]

[TCGA 2008]

Two significant types of aberrant fusions

[Rabbitts et al.]

aberrantlyamplified

expression

aberrantactivation

of signaling protein

BCR-ABL fusion in Chronic Myeloid Leukaemia: four decades from lesion discovery

to Imatinib ( Gleevec)

1960: Philadelphia chromosome discovered

1973: Chromosome translocation t(9;22) identified

1983: Activated oncogene ABL identified

2001: Drug inhibiting BCR-ABL fusion identified

Fourfold significance of recurrent chromosomal aberrations

Prognostic Marker

Drug target

Pointing to biological pathway

Early diagnostic marker

Case Study: Prostate Cancer [Tomlins et al. 2005]

Recurrent ( > 50% cases) chromosomal aberrations discovered in leukaemias, lymphomas, and sarcomas

Carcinomas more complex: -- more rearrangements-- submicroscopic structure

Gene overexpression recurrent chromosomal aberration present in > 50% prostate carcinomas [Tomlins et al. 2005]

Cancer Outlier Profile Analysis (COPA) using Oncomine database reveals overexpression of

ETV1 and ERG

[Tomlins et al.]

Frequent gene amplifications and losses in receptor tyrosine kinase-mediated signaling

ETV1

ERG

Recurrent TMPRSS2:ETV1 and TMPRSS2:ERG fusions

revealed by the study of rearrangements involving ETV1 and ERG

Expression of TMPRSS2 is regulated by androgen

[Tomlins et al. 2005]

Exclusivity of rearrangement:either ETV1 or ERG

[Tomlins et al. 2005]

TMPRSS2 translocation associated with:

• Aggressive disease

Cancer Res 66:8347-51, 2006

• Reduced disease free survival

Cancer Biol Ther 6, 2007

• Higher rate of prostate cancer specific death

TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort. Oncogene, 2007

Expanding gamut of fusions in prostate cancer [Kumar-Sinha et al. 2009]

Cancer Genome Variationobject of discovery

single gene

pathway / module /gene set

background knowledge employed in discovery

none expression and other attributes of individual genes

networks /modules /gene sets

[Miller et al.]

[Chin et al. 2006]

[Tomlins et al. 2005][Kumar-Sinha et al.

2008]

[TCGA 2008]

Study: aberrations in the context of interaction networks [Kumar-Sinha et al. 2008]

Cancer Genome Variationobject of discovery

single gene

pathway / module /gene set

background knowledge employed in discovery

none expression and other attributes of individual genes

networks /modules /gene sets

[Miller et al.]

[Chin et al. 2006]

[Tomlins et al. 2005][Kumar-Sinha et al.

2008]

[TCGA 2008]

Integrating basepair-level and copy number alterations in study of 206 glioblastoma tumors

[TCGA 2008]

Recurrent mutually exclusive mutational patterns identified in pathways [TCGA 2008]

Cancer Genome Variationobject of discovery

single gene

pathway / module /gene set

background knowledge employed in discovery

none expression and other attributes of individual genes

networks /modules /gene sets

[Miller et al.]

[Chin et al. 2006]

[Tomlins et al. 2005][Kumar-Sinha et al.

2008]

[TCGA 2008]

Hallmarks of cancer (“acquired capabilities”) are acquired by positive selection

Hallmarks of cancer (“acquired capabilities”) cause

recurrent mutually exclusive mutational patterns

RME (“recurrent mutually exclusive”) pattern discovery algorithm

RME algorithm

Sensitivity and Specificity of the RME algorithm

Applying RME algorithm to glioblastoma

Effect of EP300 expression on survival in glioblastoma

Laboratory exercise this week: array CGH ( Chia-Chin Wu)

Analysis of array CGH data from a set of tumor samples using Genboree

– Upload array CGH data– Perform segmentation (invoke Bioconductor tool)– Subtract polymorphisms (databases, current literature)– Identify recurrent amplifications or deletions– Study correlation with gene expression