Comprehensive Molecular Characterization Reveals Genomic and Transcriptomic Subtypes of Metastatic Urothelial Carcinoma

J. Alberto Nakauma-González, Maud Rijnders, Job van Riet, Michiel S. van der Heijden, Jens Voortman, Edwin Cuppen, Niven Mehra, Sandra van Wilpe, Sjoukje F. Oosting, L. Lucia Rijstenberg, Hans M. Westgeest, Ellen C. Zwarthoff, Ronald de Wit, Astrid A.M. van der Veldt, Harmen J.G. van de Werken*, Martijn P.J. Lolkema*, Joost L. Boormans*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

Recent molecular characterization of primary urothelial carcinoma (UC) may guide future clinical decision-making. For metastatic UC (mUC), a comprehensive molecular characterization is still lacking. We analyzed whole-genome DNA and RNA sequencing data for fresh-frozen metastatic tumor biopsies from 116 mUC patients who were scheduled for palliative systemic treatment within the context of a clinical trial (NCT01855477 and NCT02925234). Hierarchical clustering for mutational signatures revealed two major genomic subtypes: GenS1 (67%), which was APOBEC-driven; and GenS2 (24%), which had a high fraction of de novo mutational signatures related to reactive oxygen species and is putatively clock-like. Significantly mutated genes (SMGs) did not differ between the genomic subtypes. Transcriptomic analysis revealed five mUC subtypes: luminal-a and luminal-b (40%), stroma-rich (24%), basal/squamous (23%), and a nonspecified subtype (12%). These subtypes differed regarding expression of key genes, SMGs, oncogenic pathway activity, and immune cell infiltration. We integrated the genomic and transcriptomic data to propose potential therapeutic options by transcriptomic subtype and for individual patients. This in-depth analysis of a large cohort of patients with mUC may serve as a reference for subtype-oriented and patient-specific research on the etiology of mUC and for novel drug development. Patient summary: We carried out an in-depth analysis of the molecular and genetic features of metastatic cancer involving the cells that line the urinary tract. We showed that this is a heterogeneous disease with different molecular subtypes and we identified possible targets for therapy for each subtype.

Original languageEnglish
Pages (from-to)331-336
Number of pages6
JournalEuropean Urology
Volume81
Issue number4
DOIs
Publication statusE-pub ahead of print - 25 Jan 2022

Bibliographical note

Funding/Support and role of the sponsor:
This research was funded by the Barcode for Life Foundation through a grant to Martijn P.J. Lolkema. Harmen J.G. van de Werken, J. Alberto Nakauma-González, and the Erasmus MC Cancer Computational Biology Center were financed through a grant from the Daniel den Hoed Foundation and the Dutch Uro-Oncology Study group. This study was also partly financed by a grant from Merck Sharpe & Dome (Kenilworth, NJ, USA) to Martijn P.J. Lolkema. The sponsors had no influence on the design and conduct of the study; collection, management, analysis, and interpretation of the data; and preparation, review, or approval of the manuscript.

© 2022 The Authors. Published by Elsevier B.V. on behalf of European Association of Urology.

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