Hamidi H, Senbabaoglu Y, Beig N, Roels J, Manuel C, Guan X, Koeppen H, Assaf ZJ, Nabet BY, Waddell A, Yuen K, Maund S, Sokol E, Giltnane JM, Schedlbauer A, Fuentes E, Cowan JD, Kadel EE 3rd, Degaonkar V, Andreev-Drakhlin A, Williams P, Carter C, Gupta S, Steinberg E, Loriot Y, Bellmunt J, Grivas P, Rosenberg J, van der Heijden MS, Galsky MD, Powles T, Mariathasan S, and Banchereau R
Checkpoint inhibitors targeting programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1) have revolutionized cancer therapy across many indications including urothelial carcinoma (UC). Because many patients do not benefit, a better understanding of the molecular mechanisms underlying response and resistance is needed to improve outcomes. We profiled tumors from 2,803 UC patients from four late-stage randomized clinical trials evaluating the PD-L1 inhibitor atezolizumab by RNA sequencing (RNA-seq), a targeted DNA panel, immunohistochemistry, and digital pathology. Machine learning identifies four transcriptional subtypes, representing luminal desert, stromal, immune, and basal tumors. Overall survival benefit from atezolizumab over standard-of-care is observed in immune and basal tumors, through different response mechanisms. A self-supervised digital pathology approach can classify molecular subtypes from H&E slides with high accuracy, which could accelerate tumor molecular profiling. This study represents a large integration of UC molecular and clinical data in randomized trials, paving the way for clinical studies tailoring treatment to specific molecular subtypes in UC and other indications., Competing Interests: Declaration of interests All Genentech-affiliated authors are shareholders in Roche. H.H., S. Mariathasan., and R.B. are listed on a pending patent related to this work. P.G. is consulting for 4D Pharma, Aadi Bioscience, Asieris Pharmaceuticals, Astellas, AstraZeneca, BostonGene, Bristol Myers Squibb, CG Oncology, Dyania Health, Exelixis, Fresenius Kabi, G1 Therapeutics, Genentech, Gilead Sciences, Guardant Health, ImmunityBio, Infinity Pharmaceuticals, Janssen, Lucence, Merck KGaA, Mirati Therapeutics, MSD, Pfizer, PureTech, QED Therapeutics, Regeneron, Roche, Seattle Genetics, Silverback Therapeutics, Strata Oncology, UroGen Pharma, and receives institutional research funding from ALX Oncology, Acrivon Therapeutics, Bavarian Nordic, Bristol Myers Squibb, Clovis Oncology, Debiopharm Group, G1 Therapeutics, Gilead Sciences, GSK, Merck KGaA, Mirati Therapeutics, MSD, Pfizer, QED Therapeutics. E. Sokol. is an employee at Foundation Medicine and a shareholder in Roche. M.D.G. receives research funding from Bristol Myers Squibb, Novartis, Dendreon, Astra Zeneca, Merck, Genentech, and acts as Advisory Board/Consultant for Bristol Myers Squibb, Merck, Genentech, AstraZeneca, Pfizer, EMD Serono, SeaGen, Janssen, Numab, Dragonfly, GlaxoSmithKline, Basilea, UroGen, Rappta Therapeutics, Alligator, Silverback, Fujifilm, Curis, Gilead, Bicycle, Asieris, Abbvie, Analog Devices, Veracyte. T.P. receives honararia and research funding from Roche, Astellas, Seagen, MSD, Merck-Serono, BMS, Pfizer, Ipsen, AZ, Johnson and johnson, Mashup-Media, Exelixis, Eisai, Natera, FMI, Novartis, Bayer. J. Rosenberg is a Consultant for Aadi Bioscience; Alligator Bioscience; Astellas; AstraZeneca Pharmaceuticals LP; Boehringer Ingelheim Pharmaceuticals Inc; Bristol-Myers Squibb Company; Century Therapeutics Inc; EMD Serono Inc; Emergence Therapeutics; Genentech, a member of the Roche Group; Gilead Sciences Inc; Imvax Inc; Jiangsu Hengrui Medicine Co Ltd; Eli Lilly; Merck; Mirati Therapeutics Inc; Pfizer Inc; Seagen Inc; Tyra Biosciences, has Grant/Research support from Seagen Inc, Genentech/Roche, Astellas, Acrivon and receives honoraria from Pfizer Inc, EMD-Serono Inc, MJH Life Sciences, Research to Practice, Clinical Care Options. M.S.v.d.H. receives research funding from Bristol Myers Squibb, AstraZeneca, 4SC and Roche, and consultancy fees from Bristol Myers Squibb, Roche, Merck Sharp & Dohme, Merck, AstraZeneca, Pfizer, Janssen and Seattle Genetics, which were all paid to the Netherlands Cancer Institute., (Copyright © 2024 Elsevier Inc. All rights reserved.)