Programme for optimized treatment of Norwegian cancer patients Status, challenges and opportunities Ola Myklebost OUS - Norwegian Radium Hospital Cancer Crosslinks Jan 12th 2012 All cancers are different • Each cancer type is recognized as having many subtypes, with different cellular origins or reflecting different cellular phenotypes • Within these subtypes there are vast differences in mutation spectra and which cellular pathways are deranged • Even within each tumour and its metastases, there is enormous heterogeneity in geno- and phenotypes among cancer cell subpopulations These give rise to resistant tumours All patients are different • Germ-line genetic variation impinges on Cancer development or progression immune responses stroma interactions Response to therapy Adverse and late side effects • Deep sequencing reveals a large number of rare, “private” gene variants in each individual Their impact is not yet understood New targeted therapies • Mechanistic understanding means sensitive tumours can be identified and treated resistant tumours can be allocated to better treatment • Expensive treatments may become cost effective • Cancers of other types having the targeted properties may potentially have benefit New diagnostic options • Traditional pathology Testing a few markers for each cancer type Usually only certain mutations of each gene Each new assay needs effort • High-throughput methods Can scan large numbers of relevant markers Can identify mutations genome-wide Sensitivity, speed and capacity improving dramatically Prices falling rapidly Easily scalable Deep sequencing-based tumour mutation detection • Sample tumour and blood • Sequence candidate genes in both • Compare sequence and identify somatic mutations in tumours • Are “actionable” proteins mutated? • Are the mutations likely or known to make the phenotype targetable by an available drug? Norwegian initiatives toward personalized cancer care • Oslo Cancer Cluster Initiative from Pfizer to make a Norwegian “Stratified Medicine Initiative” • National Collaboration Group for Health Research National proposal to use tumour gene profiles to determine cancer treatment • Norw. Radium Hospital pilot study Establishment of technology Determine the complete sequence of all kinases and a number of cancer-related genes in 100 lung cancers Example results Lung cancer study • Project start late 2010 • 100 patients, DNA from tumour + blood Samples from Helland and Brustugun OUS • Sequenced all kinase genes + 100 “cancer genes” Meza-Zepeda et al. HSØ Core Eight first pairs processed The technology works perfectly • Bioinformatic analysis Hovig HSØ et al. Core Multiple possibly actionable mutations detected Kinases targeted in clinical trials The majority of targets for specific cancer therapy are kinases Oleg Fedorov, Susanne Müller & Stefan Knapp Genes included in “Kinome Set” PIK3 Inositol PROTEIN REGULATORY polyphospha KINASE GENES PI3K DOMAIN DIGLYCERIDE COMPONENTS te kinases PIP4/PIP5 (517) PROTEINS (12) KINASES (13) (6) (9) kinases (9) AAK1 517 12 13 9 6 ADDITIONAL MORE BREAST CANCER CANCER GENES (16) GENES (11) CANCER GENES (20) 9 16 20 10 PIK3C2A AGK PIK3R1 IP6K1 PIKFYVE CDC6 COL1A1 CCND1 ATM AATK PIK3C2B CERK PIK3R2 IP6K2 PIP4K2A CHD3 GAB1 CCND2 ABL1 AXL ABL2 CDKs PIK3C2G DGKA PIK3R3 IP6K3 PIP4K2B HRAS HAUS3 CCND3 PIK3C3 DGKB PIK3R4 IPMK PIP4K2C KRAS IRS2 ESR1 ACTR2 EGFR ACVR1 FGFRs ACVR1B FLTs ACVR1C IGF1R ACVR2A PIK3CA DGKD PIK3R5 IPPK PIP5K1A NRAS IRS4 ESR2 PIK3CB DGKE PIK3R6 ITPK1 PIP5K1B PTEN KIAA1468 FBXW7 PIK3CD DGKG ITPKA PIP5K1C CDH1 KLHL4 IDH1 PIK3CG DGKH ITPKB PIP5KL1 TP53 NFKB1 IDH2 PI4KA DGKI ITPKC PIPSL CDKN2A NFKBIA MLH1 JAK1 ACVR2B KIT ACVRL1 PI4KB DGKQ CDKN2B NFKBIE TERT PI4K2B DGKZ APC PALB2 ADCK1 MAPKs ADCK4 MET PI4K2A SPHK1 RB1 RHEB SPHK2 CTNNB1 RNF220 BRCA1 SNX4 BRCA2 SP1 NF1 USP28 ADCK5 MTOR ADRBK1 PDGFRs ADRBK2 RAF1 AKT1 TGFBRs AKT2 Total 3,2 Mbp NF2 GATA3 AKT3 MYC ALK INPP4A TOTAL GENES 612 Filtering of “private” genetic variation Patient Change from human reference sequence After exclusion of known variants* Real somatic mutations 3 6684 5706 3 17 6157 5216 67 22 6209 5219 26 27 6100 5070 50 35 6137 5171 58 39 6065 5123 30 48 6318 5373 6 90 6344 5471 65 * dbSNP (Including non-exonic flanking sequence) Example findings Tumour mutations in first 8 lung cancers: Gene PTEN ERBB4 CDKN2A DDR2 JAK2 Protein name phosphatase and tensin homolog erythroblastic leukemia viral oncogene homolog 4 cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) discoidin domain receptor tyrosine kinase 2 Janus kinase 2 epidermal growth factor EGFR receptor c-abl oncogene 1, nonABL1 receptor tyrosine kinase JAK1 Janus kinase 1 kinase insert domain KDR (VEGFR) receptor phosphoinositide-3PIK3CG kinase, gamma peptide Pati ent Mut Mut type AA AA Candidate therapy chng pos 17 stopgain GAG>TAG E>X sirolimus, imatinib, cisplatin, docetaxel, fluorouracil, leucov 256 levamisole, trastuzumab, pioglitazone, rosiglitazone 17 missense GAC>TAC D>Y 376 trastuzumab, neratinib 27 missense GAA>GCA E>A 35 stopgain GAA>TAA E>X 35 missense TTG>TTC L>F 48 missense CTG>CGG L>R Validated 858 Erlotinib, gefitinib, Pertuzumab, Cetuximab 90 missense GAG>AAG 90 missense CCG>CTG E>K P>L 704 imatinib 430 CYT387,Tofacitinib,Ruxolitinib,LY3009104 90 missense GCA>TCA A>S 90 missense GAC>GAA D>E 94 busulfan, cisplatin, gemcitabine, troglitazone 786 imatinib 1082 Lestaurtinib,CYT387,Pacritinib,LY3009104,TG101348,Ruxoli 1324 pazopanib,sorafenib,vatalanib,axitinib,sunitinib 500 exenatide Vanderbilt: MyCancerGenome.org DDR2 mutation National cooperation group for health research (NSG) • ”Cancer task force” (”Skrivegruppen”) Stein Kvaløy, OUS (Head) Roy Bremnes, UNN and UiTromsø Stein Kaasa, St Olav and NTNU Ragnhild A. Lothe, OUS and UiO Per Eystein Lønning, Haukeland and UiB • Proposed national initiative ”Development of diagnostics and personalized cancer treatment based on genetic analyses” Based on deep sequencing of tumours • Endorsed by the National cooperation group for health research • Personalized cancer therapy chosen by the National council for health priorities for grant call through the Research council Norwegian Cancer Genomics Consortium • Joint application from Oslo, Bergen and Trondheim • Key investigators Ola Myklebost, PI, OUS Ragnhild Lothe, OUS Harald Holte, OUS Translational Per Eystein Lønning, Haukeland medicine group Anders Waage, St Olavs Giske Ursin, Norw. Cancer Registry Leonardo Meza-Zepeda, OUS, Sequencing Technology Eivind Hovig, OUS, Bioinformatics Plans • Applying for a budget for 4000 tumour/blood pairs • Will design custom gene capture set Kinome + 5-600 others • Cancer types Breast cancer Lymphoma Leukemia Colorectal cancer Malignant melanoma Sarcoma Multiple myeloma Gynecological cancers Prostate cancer Main objectives I • Provide a national network for implementation of personalised cancer medicine in Norway • Provide and disseminate methodology for deep sequencing of tumour material and identification of somatic mutations • Initiate a number of research projects to determine the applicability of mutation profiles from the individual tumour for therapeutic decisions Main objectives II • Provide the bioinformatics tools necessary to make mutation spectra clinically interpretable and for national data logistics • Establish a nation-wide cancer mutation database in collaboration with the Cancer Registry • Provide a dialogue on the clinical implementation of personal mutation data • Analyse the health economic impacts of improved and standardised access to molecular targeted therapies nation-wide NCGC Web Page Project plan Phase Activity Issues 1 Retrospective studies 3000 sample pairs Technology dissemination Standardization of technologies and results Sample and data logistics Stepwise introduction of molecular pathology Communication of relevant findings to clinicians 2 Prospective studies 1000 sample pairs Application of standardized protocols Scientific hypotheses, approved treatments Close interaction with clinicians Clinical monitors Clinical trial units (OUS, Haukeland) Data transfer to Cancer registry 3 Evaluation Frequency of “actionable” mutations Potential for targeted treatment Possible impact on health economy Possible health benefits 4 Clinical implementation What is learned, and what should be implemented Transfer of technology to routine cancer pathology NCGC data logistics Myeloma Bioinformatics Sequence Lymphoma OUS Leukemia Colon Melanoma National mutation database Haukeland Prostate Breast St Olavs Cancer registry Sarcoma Clinical data Others? Accumulated national data Added values from national collaboration • • • • • Population-based data Standardized genome analysis Equal patient access nation-wide Standardized treatment choices National follow-up of multiple N=1 trials (compassionate use) • National evaluation of mutation frequencies and health-economic consequences • Over time accumulation of outcome data of personalized treatments and other therapies stratified by mutation profiles National Cancer Genomics Consortium Haukeland Hospital Pharma? St Olavs Hospital NCE Oslo Cancer Cluster Norwegian Cancer Registry