ERCC2 mutations as predictors of response to cisplatin in bladder cancer
Eliezer (Eli) Van Allen, MD Instructor, Harvard Medical School Dana-Farber Cancer Institute Broad Institute of MIT and Harvard
August 8, 2015 vanallenlab.dana-farber.org @VanAllenLab Disclosures
• Advisory/Consultant role: – Syapse – Roche Ventana – Third Rock Ventures Outline
• Background • Experimental design • Genomic results • Experimental validation • Next steps Outline
• Background • Experimental design • Genomic results • Experimental validation • Next steps Clinical Computational Oncology
Prospective clinical Clinical resistance to Responders and interpretation emerging therapies non-responders Platinum chemotherapy as “Imprecision Cancer Medicine” Worldwide, estimated 750,000 patients receive a platinum- based chemotherapy each year
Wang & Lippard. Nat Rev Drug Discov. 2005. 4: 307 Intrastrand Crosslink Interstrand Crosslink MIBC and neoadjuvant platinum-based chemotherapy
Systemic treatment Diagnosis with cisplatin-based Cystectomy • Standard of care regimen for ~ 20 years • Cisplatin common to all regimens • Some patients achieve pathologic complete response at cystectomy • Improved OS
Grossman et al NEJM 2003 Low clinical uptake
• Regimen toxic • Urologic management in community
Genomic correlates of chemotherapy response lacking
Hypothesis: Somatic alterations in DNA repair genes drive selective response to platinum-based chemotherapy
David et al J Urol 2007 Outline
• Background • Experimental design • Genomic results • Experimental validation • Next steps Study design
Jonathan Rosenberg Van Allen, Mouw et al Cancer Discovery 2014 dbGaP; phs000771.v1.p1 Outline
• Background • Experimental design • Genomic results • Experimental validation • Next steps MutSig approach Case/controls studies with exome- scale data
All mutations + Alteration subset short indels
Low Low “damaging” Responders Non-responders Coverage/AF score* (n = 25) (n = 25) (e.g. PPH2 < 0.5)
Fishers exact test
BH on genes with enough events for theoretical p < 0.01
*Hodis et al, Cell 2012 Responder enrichment Responder enrichment ERCC2 and the nucleotide excision repair pathway
Compe and Egly, Nature Reviews 2012 Helicase mutation selectivity
Missense (Responders) Missense (Guo et al) Missense (TCGA)
D609G Y24C D609E N238S V242F P463L E606G G665A
1 760
Y72C S209C R286W P463S G607A H659Y G675S Q758E
M42V E86Q S246Y S44L Y14C N238S T484A/M Helicase mutation selectivity
Conserved Missense (Responders) helicase motif Missense (Guo et al) Missense (TCGA)
D609G Y24C D609E N238S V242F P463L E606G G665A
1 I IA II III IV V V 760 35-51 69-88 225-239 455-468 533-554 587-613 654-671
Y72C S209C R286W P463S G607A H659Y G675S Q758E
M42V E86Q S246Y S44L Y14C N238S T484A/M Unique mutational signature
Mutation Signatures in TCGA cohort C>A C>G C>T T>A T>C T>G 4000 3000 AP O
2000 BEC1 1000 0
1500 AP
1000 O BEC2 500 0
300 C>TCpG 200 100 Mutation Count 0
300 Unknown 200 100 0 A−A A−C A−G A−T C−A C−C C−G C−T G−A G−C G−G G−T T−A T−C T−G T−T A−A A−C A−G A−T C−A C−C C−G C−T G−A G−C G−G G−T T−A T−C T−G T−T A−A A−C A−G A−T C−A C−C C−G C−T G−A G−C G−G G−T T−A T−C T−G T−T A−A A−C A−G A−T C−A C−C C−G C−T G−A G−C G−G G−T T−A T−C T−G T−T A−A A−C A−G A−T C−A C−C C−G C−T G−A G−C G−G G−T T−A T−C T−G T−T A−A A−C A−G A−T C−A C−C C−G C−T G−A G−C G−G G−T T−A T−C T−G T−T Tri−nucleotide Sequence Motifs
Jaegil Kim, Paz Polak, Kent Mouw, Gad Getz Unique mutational signature
TCGA DFCI/MSK BGI 5 ERCC2 ● ERCC2 ● ERCC2 ● 4 WDFY3 ● ● ● ● ● 3 ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ●● ●● ● ● ●● ● ● ●●●●●● ●●●●●● ● ●●●●●●● 2 ●● ● ●●● ● ●● ● ● ● ● ● ●● ●●● ●●●●●●●●● −Log(P) ● ● ●●●●●●●● ●● ● ● ● ● ● ●●●●●● ● ● ●●● ● ● ● ●●●●● ● ● ● ● ●● ● ●●●●● ● ● ● ● ●● ● ●●●●●●●● ● ● ● ● ● ● ● ●●●●● ●●● ●● ● ●●● ● ●● ●● ●●●●● ●●● ● ● ●●● ● ● ● ●● ●● ●● ● ●●●● ● ● ● ●● ●● ● ● ● ● ●● ●●●●●●● ● ●● ● ● ● ●●● ● ● ● ●●●●●● ●●● ●●● ●● ● ●●● ● ● ● ●●● ● ● ● ●● ●● ●● ●●●● ●●●●● ● ● ● ● ● ●●● ● ● ● ● ●●●●● ● ●● ● ● ● ● ● ● ● ● ● ●●●● ● ●● ●● ●● ●● ●● ●● ● 1 ● ●● ● ● ●● ● ● ●● ●●●●● ● ●● ●● ● ● ● ● ● ●● ●● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ●● ●●●●● ●●● ●● ● ● ●● ● ● ● ● ●●● ● ●●●●● ● ● ● ●● ●●●●● ● ●● ●● ●● ● ●● ●● ● ● ● ● ● ● ● ●● ● ● ●● ●●● ● ●●● ● ●●●●● ●●●●● ●● ●●● ● ● ● ●● ● ● ●● ● ● ●●●●●● ●●●● ●● ●●●●● ● ● ● ● ● ●● ●●● ● ● ● ●● ●●● ●● ● ●●● ●● ● ●●●● ● ● ●● ●● ● ● ● ● ● ●●● ● ● ● ●● ●●● ●●●● ● ●● ●● ● ● ● ●●● ●●● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ●●●● ● ●● ● ●● ●●● ● ● ● ● ● ● ● ● ● ●● ● ● ●●●●● ● ●●●● ● ● ● ● ●● ●● ●● ● ● ● ● ●● ●●● ●● ●●● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ●●● ●●●●● ●●● ● ●●●● ● ● ● ● ● ● ● ●● ● ● ●● ● ●●● ● ●● ● ●● ● ● ● ●● ●●●● ●● ● ● ● ● ● ● ●● ● ● ● ● ●● ●●●● ● ●● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ●● ●●● ● ● ●● ●●●●● ● ● ●● ● ●● ● ● ● ● ● ● ●● ●●● ● ●● 0 ● ● ● ● 1 10 100 1 100 1 10 Median differences in No. Unknown Signature Mutations
Jaegil Kim, Paz Polak, Kent Mouw, Gad Getz Outline
• Background • Experimental design • Genomic results • Experimental validation • Next steps Experimental work
• Use ERCC2 null cell line derived from xeroderma pigmentosum patient • Transfect with WT or mutants seen in patients • Assess change in sensitivity to perturbation in different scenarios
Kent Mouw Alan D’Andrea ERCC2 and cisplatin sensitivity
Kent Mouw Alan D’Andrea Outline
• Background • Experimental design • Genomic results • Experimental validation • Next steps External Clinical Validation? External Clinical Validation?
• Carbo < Cis clinically in bladder CA • Carbo < Cis potency + DNA target • Specifically excluded in our study • Focusing on matching cohorts -> 6/16 vs. 0/16
• Need larger sample size for wider application • Still likely doesn’t capture the full story A window into broader DNA repair defects underlying response?
Plimack et al Eur Urol 2015 Next steps
• Expanding clinical validation – Clonal v. subclonal effect? – Towards development of genomic “signature” for platinum response1 – Metastatic cohorts • Experimentally: – What is the selective advantage of mutating ERCC2 for the tumor? – Are other NER genes involved? • Therapeutic potential?
1Plimack et al Eur Urol 2015 Let’s work together! vanallenlab.dana-farber.org [email protected] @vanallenlab
Clinical computational Broad DFCI + Center for Cancer oncology team Institute Precision Medicine MSKCC
Ali Amin-Mansour Genomics Platform Levi A. Garraway Jonathan Rosenberg Andrea Garofalo Picard Team Joaquim Bellmunt Gopa Iyer Diana Miao Firehose Team Kent Mouw Hikmat Al-Ahmadie Travis Zack Gad Getz Alan D’Andrea Many others… David Liu Gregory Kryukov David Kwiatkowski Alma Imamovic Jill Mesirov Philip Kantoff Brendan Reardon Manaswi Gupta Mary-Ellen Taplin Funding Daniel Keliher Jasmine Mu GU Oncology team Kris Cibulskis Judy Garber Will Gibson Many others… Adam Keizun Scott Carter Many others…