Chemotherapy-resistant urothelial carcinoma has no uniformly curative therapy. Understanding how selective pressure from chemotherapy directs the evolution of urothelial carcinoma and shapes its clonal architecture is a central biological question with clinical implications. To address this question, we performed whole-exome sequencing and clonality analysis of 72 urothelial carcinoma samples, including 16 matched sets of primary and advanced tumors prospectively collected before and after chemotherapy. Our analysis provided several insights: (i) chemotherapy-treated urothelial carcinoma is characterized by intra-patient mutational heterogeneity, and the majority of mutations are not shared; (ii) both branching evolution and metastatic spread are very early events in the natural history of urothelial carcinoma; (iii) chemotherapy-treated urothelial carcinoma is enriched with clonal mutations involving L1 cell adhesion molecule (L1CAM) and integrin signaling pathways; and (iv) APOBEC-induced mutagenesis is clonally enriched in chemotherapy-treated urothelial carcinoma and continues to shape the evolution of urothelial carcinoma throughout its lifetime.

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We would like to thank our patients and their families for participation in this study. We would like to thank B. Sleckman for constructive review of the manuscript. We would also like to acknowledge D. Scherr and C. Barbieri for contributing samples, our research and clinical pathology fellows J. Fontugne, M. Kossai, C. Pauli, K. Hennrick and K. Park for their assistance during rapid autopsies, and S.S. Chae and D. Wilkes for technical assistance and constructive comments. We would also like to thank T.Y. MacDonald, J. Padilla and T. Fedrizzi for technical assistance. Work was partially supported by the Translational Research Program at WCMC Pathology and Laboratory Medicine. This work was supported by a Conquer Cancer Foundation and the John and Elizabeth Leonard Family Foundation Young Investigator Award (B.M.F.), NIH/NCATS KL2TR000458 (B.M.F.), Early Detection Research Network US NCI 5U01 CA111275-09 (J.M.M., M.A.R. and F.D.), Damon Runyon Cancer Research Foundation Clinical Investigator Award CI-67-13 (H.B.), and H2020 European Research Council ERC-CoG 648670 (F.D.).

Author information

Author notes

    • Bishoy M Faltas
    •  & Davide Prandi

    These authors contributed equally to this work.

    • Himisha Beltran
    • , Francesca Demichelis
    •  & Mark A Rubin

    These authors jointly directed this work.


  1. Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital–Weill Cornell Medicine, New York, New York, USA.

    • Bishoy M Faltas
    • , Scott T Tagawa
    • , Ana M Molina
    • , David M Nanus
    • , Juan Miguel Mosquera
    • , Brian Robinson
    • , Olivier Elemento
    • , Andrea Sboner
    • , Himisha Beltran
    • , Francesca Demichelis
    •  & Mark A Rubin
  2. Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York, USA.

    • Bishoy M Faltas
    • , Scott T Tagawa
    • , Ana M Molina
    • , David M Nanus
    •  & Himisha Beltran
  3. Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine, New York, New York, USA.

    • Bishoy M Faltas
    • , Scott T Tagawa
    • , David M Nanus
    • , Himisha Beltran
    •  & Mark A Rubin
  4. Centre for Integrative Biology, University of Trento, Trento, Italy.

    • Davide Prandi
    •  & Francesca Demichelis
  5. Department of Medical Oncology, San Camillo–Forlanini Hospital, Rome, Italy.

    • Cora Sternberg
  6. Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • Jonathan Rosenberg
  7. Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA.

    • Juan Miguel Mosquera
    • , Brian Robinson
    • , Andrea Sboner
    •  & Mark A Rubin
  8. Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA.

    • Olivier Elemento
  9. Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA.

    • Olivier Elemento
    • , Andrea Sboner
    •  & Francesca Demichelis


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Initiation and design of study: B.M.F., H.B., M.A.R. and F.D. Subject enrollment and sample and clinical data collection: B.M.F., H.B., D.M.N., S.T.T., A.M.M., C.S., J.M.M. and B.R. Statistical and bioinformatics analyses: D.P., O.E., A.S. and F.D. Supervision of research: B.M.F., M.A.R., J.R. and F.D. Writing of the first draft of the manuscript: B.M.F., D.P., H.B., M.A.R. and F.D. All authors contributed to the writing and editing of the revised manuscript and approved the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Francesca Demichelis or Mark A Rubin.

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