The Complex Molecular Landscape of Squamous Cell Carcinoma Martin Sos, M.D. Department of Translational Genomics Center of Integrated Oncology Köln – Bonn University of Köln martin.sos@uni-koeln.de

Disclosures Consultant of Blackfield AG, provider of cancer genomics services and genomics-based drug discovery/development Patent applications: genotype-specific drug discovery/ assays and biomarkers (including FGFR)

The efficacy of chemotherapy in stage-IV lung cancer 1.0 0.8 0.6 0.4 0.2 Cisplatin/Paclitaxel Cisplatin/Gemcitabin Cisplatin/Docetaxel Carboplatin/Paclitaxel Probability (%) 0 5 10 15 20 25 30 time (month) Therapeutisches Plateau: Gesamtüberleben < 12 Monate Schiller, et al. NEJM 2002

Mechanisms of genome alterations in cancer Meyerson et al., Nat Rev Genet 2010

EGFR-mutant lung tumors respond to EGFR inhibitors such as erlotinib and gefitinib Pre-therapy 6 weeks of erloti Paez et al., Science 2004; Lynch et al., NEJM 2004; Pao et al., PNAS 2004)

Time from randomisation (months) + 2009 EGFR mutations predict progression-free survival (IPASS trial, Tony Mok, NEJM 2009) Gefitinib EGFR M+ (n=132) Gefitinib EGFR M- (n=91) Carboplatin / paclitaxel EGFR M+ (n=129) Carboplatin / paclitaxel EGFR M- (n=85) Probability of PFS 1.0 Gefitinib, HR=0.19, 95% CI 0.13, 0.26, p<0.0001 No. events M+ = 97 (73.5%) No. events M- = 88 (96.7%) Carboplatin / paclitaxel, HR=0.78, 95% CI 0.57, 1.06, p=0.1103 No. events M+ = 111 (86.0%) No. events M- = 70 (82.4%) 0.8 0.6 0.4 0.2 0.0 4 8 12 16 20 24 Time from randomisation (months) Hazard ratio <1 implies a lower risk of progression in the M+ group than in the M- group M+, mutation positive; M-, mutation negative Slide courtesy of Tony Mok, Hongkong

Relevance of mutant kinase genes in lung cancer: the case of EML4-ALK fusions Phase I/II trial of EML4-ALK positive lung cancer patients with the c-met/ ALK inhibitor PF-02341066: 12 / 18 pts with confirmed response Kwak et al, # 83509, ASCO 2009 Detection of EML4-ALK fusion in NSCLC Rikova, Cell 2007 Soda, Nature 2007

...and more and more to come ROS fusions in lung adenos (app.1%) associated with response to crizotinib (Rikova et al., Cell 2007; Bergethon et al., J Clin Oncol 2011; Shaw et al. ASCO 2012) RET fusions in lung adenos (app.1%) associated with sensitivity to RET kinase inhibition (Ju et al., Genome Res 2012; Takeuchi et al., Nat Med 2012; Kohno et al., Nat Med 2012; Lipson et al., Nat Med 2012)

The genomic evolution of lung adenocarcinoma Pao et al., Lancet Oncol 2011

Peifer et al., Nat Genet, 2012 Hammerman et al., Nature, 2012 Imielinski et al., Cell, 2012

Genomic features of 1,000 lung tumors Chromosomes 1-22 AD CA LC SC SQ CLCGP and NGM, Sci Transl Med 2013

Automated genomics-based lung cancer diagnosis CLCGP and NGM, Sci Transl Med 2013

Genomic Targets: Adenocarcinoma versus Squamous Gene Lung Adenocarcinoma Lung Squamous Cell EGFR 14%, most at known sites, novel C-terminal deletions Amplification (7%), rare non-canonical mutation (L861Q) KRAS 31% mutation 1%, HRAS more common BRAF 10%, 2% V600/601 4%, no V600/601 PIK3CA 7% mutation 16% mutation ERBB2 5% mutation 3% non-canonical, rare amplification (<5%) FGFRs 2% mutation 10% amplification, 12% mutation DDRs 3% mutation 4% mutation Lung adenocarcinoma: ALK, RET, ROS translocations Squamous: Tumor suppressor translocations A case for comprehensive genotyping Slide courtesy of Peter Hammerman

Genomics targets in squamous cell lung cancer: DDR2 mutation S768R (25% 454 reads) Hammerman P*, Sos ML* et al., Cancer Discovery 2011 Pitini et al., Lung Cancer 2013

FGFR1 amplifications in sqamous cell cancer (SCC) of the lung: from discovery to clinical evaluation Weiss J*, Sos ML* et al. Sci Transl Med 2010 Weiss et al., Sci Transl Med 2010 Heukamp et al, Mod Pathol, 2012 Genomic discovery Preclinical validation FISH-diagnostics Chromosome 8p geography Clinical evaluation Malchers et al. Cancer Discovery 2013 FIM trial BGJ398 in FGFR1-ampl. SQLC Understanding response on the molecular level ASCO 2014, PI J. Wolf (Confidential)

RR FGFR1 amplified lung: 16% (RR FGFR-altered bladder: 40%) Lecia Sequist, AACR 2014

Massive heterogeneity of the FGFR1 amplicon Chromosome 8p geography Samples Malchers et al. Cancer Discovery 2013

MYC expression and FGFR1 dependency

MYC sensitizes FGFR1 expressing cells in vivo vehicle BGJ398 (FGFR inhibitor) vehicle BGJ398 (FGFR inhibitor) Malchers et al. Cancer Discovery 2013

MYC expression in an FGFR inhibitor responder (BGJ398 phase I trial) FGFR1 FISH 100mg BGJ398day 56 baseline Malchers and Dietlein et al., Cancer Discovery 2013

FGFR3 fusions in squamous cell lung cancer FGFR3-TACC3 fusions in squamous cell lung cancer App 2-3% of the cases Preclinical sensitivity to FGFR inhibition FGFR1 amplifications, FGFR2 mutations Kim et al., JCO 2013 Wu et al., Cancer Discovery 2013

Targeting RAS in lung cancer Picomolar affinity for GTP  >1000-fold difference to ATP-competitive TK-inhibitors “Only” Glycine-12 Cysteine mutants are being hit Allows irreversible binding with covalent inhibitors Can be used for binding affinity screens Glycine-12 Ostrem J., Peters U., Sos ML, et al., Nature 2013

Irreversible RAS-Inhibitors K-RasG12C with Ras-055 Glu-62 Gly-10 KRAS-G12C Abhängige Zellen Raf interaction Ostrem J., Peters U., Sos ML, et al., Nature 2013

Summary Genomics can guide therapeutically relevant diagnoses in lung cancer The amplicon structure of FGFR1 in squamous cell lung cancer is complex Novel drugs might enhance the window of opportunity for precision medicine in SQLC patients

POSITIONS ARE AVAILABLE!!! Shokat lab John Gordan Rebecca Levin Jonathan Ostrem Ulf Peters Arvin Dar Chloe Atreya ... Frank McCormick lab Megan Salt Al Burlingame lab Juan Oses Thanks! CIO/ University of Köln Thomas Zander Jürgen Wolf Sascha Ansén Matthias Scheffler Thomas lab Mirjam Koker Martin Peifer Felix Dietlein Florian Malchers Jonathan Weiss Stefanie Heynck Lynnette Fernandez-Cuesta CGC/ MPI Dortmund Daniel Rauh Haridas Rode Matthäus Getlik Andre Richter Sos Lab Dennis Plenker Tuya Batbayar Mex Riedel Annika Marx POSITIONS ARE AVAILABLE!!! martin.sos@uni-koeln.de