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Clonal evolution of chemotherapy-resistant urothelial carcinoma

Abstract

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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Figure 1: Clinical characteristics of the study cohort.
Figure 2: Clonal mutational heterogeneity in chemotherapy-treated urothelial carcinoma.
Figure 3: Early branching evolution in urothelial carcinoma.
Figure 4: Reconstructing the spatiotemporal evolution of urothelial carcinoma over time and through different treatments.
Figure 5: Hierarchical clustering of 44 urothelial carcinoma tumor samples by copy number alterations.
Figure 6: Clonal enrichment of mutations in chemotherapy-treated urothelial carcinoma.
Figure 7: Mutagenesis in advanced urothelial carcinoma is shaped by chemotherapy and APOBECs.

References

  1. Howlader, N. et al. SEER Cancer Statistics Review, 1975–2010 (National Cancer Institute, Bethesda, Maryland, USA, 2013).

  2. von der Maase, H. et al. Long-term survival results of a randomized trial comparing gemcitabine plus cisplatin, with methotrexate, vinblastine, doxorubicin, plus cisplatin in patients with bladder cancer. J. Clin. Oncol. 23, 4602–4608 (2005).

    Article  CAS  PubMed  Google Scholar 

  3. Clark, P.E. et al. Bladder cancer. J. Natl. Compr. Canc. Netw. 11, 446–475 (2013).

    Article  CAS  PubMed  Google Scholar 

  4. Sternberg, C.N. et al. Randomized phase III trial of high-dose-intensity methotrexate, vinblastine, doxorubicin, and cisplatin (MVAC) chemotherapy and recombinant human granulocyte colony-stimulating factor versus classic MVAC in advanced urothelial tract tumors: European Organization for Research and Treatment of Cancer Protocol no. 30924. J. Clin. Oncol. 19, 2638–2646 (2001).

    Article  CAS  PubMed  Google Scholar 

  5. Sternberg, C.N. et al. Seven year update of an EORTC phase III trial of high-dose intensity M-VAC chemotherapy and G-CSF versus classic M-VAC in advanced urothelial tract tumours. Eur. J. Cancer 42, 50–54 (2006).

    Article  CAS  PubMed  Google Scholar 

  6. Bellmunt, J. et al. Phase III trial of vinflunine plus best supportive care compared with best supportive care alone after a platinum-containing regimen in patients with advanced transitional cell carcinoma of the urothelial tract. J. Clin. Oncol. 27, 4454–4461 (2009).

    Article  CAS  PubMed  Google Scholar 

  7. Bellmunt, J. & Petrylak, D.P. New therapeutic challenges in advanced bladder cancer. Semin. Oncol. 39, 598–607 (2012).

    Article  CAS  PubMed  Google Scholar 

  8. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507, 315–322 (2014).

  9. Prandi, D. et al. Unraveling the clonal hierarchy of somatic genomic aberrations. Genome Biol. 15, 439 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  10. Nixon, K.C. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15, 407–414 (1999).

    Article  PubMed  Google Scholar 

  11. Zheng, Y. et al. Identification of Pold2 as a novel interaction partner of protein inhibitor of activated STAT2. Int. J. Mol. Med. 30, 884–888 (2012).

    Article  CAS  PubMed  Google Scholar 

  12. Lee, Y.S., Gregory, M.T. & Yang, W. Human Pol ζ purified with accessory subunits is active in translesion DNA synthesis and complements Pol η in cisplatin bypass. Proc. Natl. Acad. Sci. USA 111, 2954–2959 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. van Boxtel, R. et al. FOXP1 acts through a negative feedback loop to suppress FOXO-induced apoptosis. Cell Death Differ. 20, 1219–1229 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Choi, E.J. et al. FOXP1 functions as an oncogene in promoting cancer stem cell-like characteristics in ovarian cancer cells. Oncotarget 7, 3506–3519 (2016).

    PubMed  Google Scholar 

  15. Greco, C. et al. E-cadherin/p120-catenin and tetraspanin Co-029 cooperate for cell motility control in human colon carcinoma. Cancer Res. 70, 7674–7683 (2010).

    CAS  PubMed  Google Scholar 

  16. Wei, L., Li, Y. & Suo, Z. TSPAN8 promotes gastric cancer growth and metastasis via ERK MAPK pathway. Int. J. Clin. Exp. Med. 8, 8599–8607 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Zöller, M. Tetraspanins: push and pull in suppressing and promoting metastasis. Nat. Rev. Cancer 9, 40–55 (2009).

    Article  PubMed  CAS  Google Scholar 

  18. Kinsella, R.J. et al. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford) 2011, bar030 (2011).

    Article  CAS  Google Scholar 

  19. Plimack, E.R. et al. Defects in DNA repair genes predict response to neoadjuvant cisplatin-based chemotherapy in muscle-invasive bladder cancer. Eur. Urol. 68, 959–967 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Eke, I. & Cordes, N. Focal adhesion signaling and therapy resistance in cancer. Semin. Cancer Biol. 31, 65–75 (2015).

    Article  CAS  PubMed  Google Scholar 

  21. Maiuthed, A. & Chanvorachote, P. Cisplatin at sub-toxic levels mediates integrin switch in lung cancer cells. Anticancer Res. 34, 7111–7117 (2014).

    CAS  PubMed  Google Scholar 

  22. Seguin, L., Desgrosellier, J.S., Weis, S.M. & Cheresh, D.A. Integrins and cancer: regulators of cancer stemness, metastasis, and drug resistance. Trends Cell Biol. 25, 234–240 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Tsutsumi, S. et al. L1 cell adhesion molecule (L1CAM) expression at the cancer invasive front is a novel prognostic marker of pancreatic ductal adenocarcinoma. J. Surg. Oncol. 103, 669–673 (2011).

    Article  CAS  PubMed  Google Scholar 

  24. Weidle, U.H., Eggle, D. & Klostermann, S. L1-CAM as a target for treatment of cancer with monoclonal antibodies. Anticancer Res. 29, 4919–4931 (2009).

    CAS  PubMed  Google Scholar 

  25. Meier, B. et al. C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency. Genome Res. 24, 1624–1636 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Szikriszt, B. et al. A comprehensive survey of the mutagenic impact of common cancer cytotoxics. Genome Biol. 17, 99 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  27. Alexandrov, L.B. et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979–993 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Kim, J. et al. Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors. Nat. Genet. 48, 600–606 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Roberts, S.A. et al. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat. Genet. 45, 970–976 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Liu, D. et al. Clinical validation of chemotherapy response biomarker ERCC2 in muscle-invasive urothelial bladder carcinoma. JAMA Oncol. 2, 1094–1096 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  32. Van Allen, E.M. et al. Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma. Cancer Discov. 4, 1140–1153 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Hoopes, J.I. et al. APOBEC3A and APOBEC3B preferentially deaminate the lagging strand template during DNA replication. Cell Rep. 14, 1273–1282 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Lackey, L. et al. APOBEC3B and AID have similar nuclear import mechanisms. J. Mol. Biol. 419, 301–314 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Chelico, L., Pham, P. & Goodman, M.F. Stochastic properties of processive cytidine DNA deaminases AID and APOBEC3G. Phil. Trans. R. Soc. Lond. B 364, 583–593 (2009).

    Article  CAS  Google Scholar 

  36. Harris, R.S. & Liddament, M.T. Retroviral restriction by APOBEC proteins. Nat. Rev. Immunol. 4, 868–877 (2004).

    Article  CAS  PubMed  Google Scholar 

  37. Faltas, B.M., Karir, B.S., Tagawa, S.T. & Rosenberg, J.E. Novel molecular targets for urothelial carcinoma. Expert Opin. Ther. Targets 19, 515–525 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Knowles, M.A. & Hurst, C.D. Molecular biology of bladder cancer: new insights into pathogenesis and clinical diversity. Nat. Rev. Cancer 15, 25–41 (2015).

    Article  CAS  PubMed  Google Scholar 

  39. Yoon, H. et al. L1 cell adhesion molecule and epidermal growth factor receptor activation confer cisplatin resistance in intrahepatic cholangiocarcinoma cells. Cancer Lett. 316, 70–76 (2012).

    Article  CAS  PubMed  Google Scholar 

  40. Stoeck, A. et al. L1-CAM in a membrane-bound or soluble form augments protection from apoptosis in ovarian carcinoma cells. Gynecol. Oncol. 104, 461–469 (2007).

    Article  CAS  PubMed  Google Scholar 

  41. Sebens Müerköster, S. et al. Drug-induced expression of the cellular adhesion molecule L1CAM confers anti-apoptotic protection and chemoresistance in pancreatic ductal adenocarcinoma cells. Oncogene 26, 2759–2768 (2007).

    Article  PubMed  CAS  Google Scholar 

  42. Sebens Müerköster, S. et al. alpha5-integrin is crucial for L1CAM-mediated chemoresistance in pancreatic adenocarcinoma. Int. J. Oncol. 34, 243–253 (2009).

    PubMed  Google Scholar 

  43. Kiefel, H. et al. L1CAM: a major driver for tumor cell invasion and motility. Cell Adh. Migr. 6, 374–384 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  44. Gast, D. et al. The RGD integrin binding site in human L1-CAM is important for nuclear signaling. Exp. Cell Res. 314, 2411–2418 (2008).

    Article  CAS  PubMed  Google Scholar 

  45. Voura, E.B., Ramjeesingh, R.A., Montgomery, A.M. & Siu, C.H. Involvement of integrin alpha(v)beta(3) and cell adhesion molecule L1 in transendothelial migration of melanoma cells. Mol. Biol. Cell 12, 2699–2710 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Burgett, M.E. et al. Direct contact with perivascular tumor cells enhances integrin αvβ3 signaling and migration of endothelial cells. Oncotarget http://dx.doi.org/10.18632/oncotarget.9700 (2016).

  47. Hodkinson, P.S. et al. ECM overrides DNA damage-induced cell cycle arrest and apoptosis in small-cell lung cancer cells through beta1 integrin-dependent activation of PI3-kinase. Cell Death Differ. 13, 1776–1788 (2006).

    Article  CAS  PubMed  Google Scholar 

  48. Sethi, T. et al. Extracellular matrix proteins protect small cell lung cancer cells against apoptosis: a mechanism for small cell lung cancer growth and drug resistance in vivo. Nat. Med. 5, 662–668 (1999).

    Article  CAS  PubMed  Google Scholar 

  49. Zhang, H. et al. Beta 1-integrin protects hepatoma cells from chemotherapy induced apoptosis via a mitogen-activated protein kinase dependent pathway. Cancer 95, 896–906 (2002).

    Article  CAS  PubMed  Google Scholar 

  50. Argyris, E.G. et al. The interferon-induced expression of APOBEC3G in human blood-brain barrier exerts a potent intrinsic immunity to block HIV-1 entry to central nervous system. Virology 367, 440–451 (2007).

    Article  CAS  PubMed  Google Scholar 

  51. Shain, K.H. & Dalton, W.S. Cell adhesion is a key determinant in de novo multidrug resistance (MDR): new targets for the prevention of acquired MDR. Mol. Cancer Ther. 1, 69–78 (2001).

    CAS  PubMed  Google Scholar 

  52. Damiano, J.S. Integrins as novel drug targets for overcoming innate drug resistance. Curr. Cancer Drug Targets 2, 37–43 (2002).

    Article  CAS  PubMed  Google Scholar 

  53. Hazlehurst, L.A. & Dalton, W.S. Mechanisms associated with cell adhesion mediated drug resistance (CAM-DR) in hematopoietic malignancies. Cancer Metastasis Rev. 20, 43–50 (2001).

    Article  CAS  PubMed  Google Scholar 

  54. Hehlgans, S., Haase, M. & Cordes, N. Signalling via integrins: implications for cell survival and anticancer strategies. Biochim. Biophys. Acta 1775, 163–180 (2007).

    CAS  PubMed  Google Scholar 

  55. Cho, S. et al. Generation, characterization and preclinical studies of a human anti-L1CAM monoclonal antibody that cross-reacts with rodent L1CAM. MAbs 8, 414–425 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Min, J.K. et al. L1 cell adhesion molecule is a novel therapeutic target in intrahepatic cholangiocarcinoma. Clin. Cancer Res. 16, 3571–3580 (2010).

    Article  CAS  PubMed  Google Scholar 

  57. Schäfer, H. et al. Combined treatment of L1CAM antibodies and cytostatic drugs improve the therapeutic response of pancreatic and ovarian carcinoma. Cancer Lett. 319, 66–82 (2012).

    Article  PubMed  CAS  Google Scholar 

  58. Golubovskaya, V.M. Targeting FAK in human cancer: from finding to first clinical trials. Front. Biosci. (Landmark Ed.) 19, 687–706 (2014).

    Article  CAS  Google Scholar 

  59. Schultze, A. & Fiedler, W. Therapeutic potential and limitations of new FAK inhibitors in the treatment of cancer. Expert Opin. Investig. Drugs 19, 777–788 (2010).

    Article  CAS  PubMed  Google Scholar 

  60. Rezaee, M., Sanche, L. & Hunting, D.J. Cisplatin enhances the formation of DNA single- and double-strand breaks by hydrated electrons and hydroxyl radicals. Radiat. Res. 179, 323–331 (2013).

    Article  CAS  PubMed  Google Scholar 

  61. Zellweger, R. et al. Rad51-mediated replication fork reversal is a global response to genotoxic treatments in human cells. J. Cell Biol. 208, 563–579 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Roberts, S.A. & Gordenin, D.A. Hypermutation in human cancer genomes: footprints and mechanisms. Nat. Rev. Cancer 14, 786–800 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Chan, K. et al. An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers. Nat. Genet. 47, 1067–1072 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Lipinski, K.A. et al. Cancer evolution and the limits of predictability in precision cancer medicine. Trends Cancer 2, 49–63 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  65. Beltran, H. et al. Whole-exome sequencing of metastatic cancer and iomarkers of treatment response. JAMA Oncol. 1, 466–474 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  66. Demichelis, F. et al. SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines. Nucleic Acids Res. 36, 2446–2456 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Beltran, H. et al. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat. Med. 22, 298–305 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Futreal, P.A. et al. A census of human cancer genes. Nat. Rev. Cancer 4, 177–183 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Rubio-Perez, C. et al. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities. Cancer Cell 27, 382–396 (2015).

    Article  CAS  PubMed  Google Scholar 

  70. Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31, 213–219 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Jiang, Y., Soong, T.D., Wang, L., Melnick, A.M. & Elemento, O. Genome-wide detection of genes targeted by non-Ig somatic hypermutation in lymphoma. PLoS One 7, e40332 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Romanel, A., Lago, S., Prandi, D., Sboner, A. & Demichelis, F. ASEQ: fast allele-specific studies from next-generation sequencing data. BMC Med. Genomics 8, 9 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  73. Ramos, A.H. et al. Oncotator: cancer variant annotation tool. Hum. Mutat. 36, E2423–E2429 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  74. Eilbeck, K. et al. The sequence ontology: a tool for the unification of genome annotations. Genome Biol. 6, R44 (2005).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

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Acknowledgements

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.).

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Authors and Affiliations

Authors

Contributions

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.

Corresponding authors

Correspondence to Francesca Demichelis or Mark A Rubin.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Analysis of mutated genes as reported in TCGA bladder study.

Each row represents a gene harboring frequent SNVs (middle panel) or somatic copy number (bottom panel). Annotation rows include, from top to bottom, tumor ploidy, treatment information, biopsy site, patient’s gender, matched samples. Top bars report the otal number of non-silent SNVs in each sample. Bars on the left indicate the per-sample frequency of aberration in the cohort. NA, not available.

Supplementary Figure 2 SNVs burden comparison.

Per sample number of all SNVs (left boxplot) and only non-silent SNVs (right boxplot) in pre-chemotherapy and post-chemotherapy tumors. No statistical difference.

Supplementary Figure 3 Single nucleotide variants (SNV) validation by targeted sequencing (N250 panel).

Each dot represents a genomic position corresponding to an SNV sequenced with WES and with N250 approaches. Reported values are the ratios between the number of reads supporting the alternative base and the coverage. SNVs from the same patient are represented with the same color.

Supplementary Figure 4 Discordance in the SNVs between chemotherapy-naive and chemotherapy-treated UC tumors.

(a) Percentage of shared and unique SNVs in matched chemotherapy-naive and chemotherapy-treated UC tumors (same of Fig. 2a). (b) Detail of the specific amino acid change in matched chemotherapy-naive and chemotherapy-treated UC tumors. Each column represents a matched pair of pre- and post- chemotherapy tumors. Row reports the specific amino acid change. The figure highlights the wide divergence in the mutational landscape of pre- and post-chemotherapy samples.

Supplementary Figure 5 Phylogenetic trees of patients with two sequenced tumor samples.

Phylogenetic trees from 15 patients with two samples per patient.

Supplementary Figure 6 Hierarchical clusters of 131 UC tumor samples by copy-number alterations.

The plot extends Fig. 5a considering samples from both WCM and TCGA cohorts. Copy number gains are represented in red and copy number losses are represented in blue. Each column represents one tumor sample. Clinical annotations include treatment, biopsy site, cohort, and the presence of TP53 SNV.

Supplementary Figure 7 Hierarchical clusters of 86 UC tumor samples by copy-number alterations.

The plot shows allele specific copy number clusters as in Fig. 5a while considering samples from the TCGA cohort. Copy number gains are represented in red and copy number losses are represented in blue. Each column represents one tumor sample. Each row represents one of the 2503 genes used to compute TCGA clusters (Fig. S4.1 from Nature 507, 315–322, 2014)). Annotations include presence of TP53 SNV and TCGA clusters.

Supplementary Figure 8 Pairwise comparison of SNVs clonality.

Top right scatter plot reports the clonality of SNVs in matched pre-chemotherapy and post-chemotherapy samples. Bottom and left boxplots show clonality of SNVs that are private to pre-chemotherapy and post-chemotherapy samples, respectively.

Supplementary Figure 9 Comparison of FFPE and Fresh samples.

(left) Boxplot of the purity in FFPE and Fresh samples (p>0.05, Wilcoxon test). (right) Boxplot of the number of non-silent SNVs in FFPE and Fresh samples (p>0.05, Wilcoxon test).

Supplementary Figure 10 Landscape of somatic SNVs identified.

Landscape of somatic SNVs identified.

Supplementary Figure 11 Comparison of shared and local SNVs considering silent and non-silent SNVs.

Comparison of the percentage of shared and local SNVs in matched chemotherapy-naive and chemotherapy-treated UC tumors when considering only non-silent SNVs (top) or all SNVs (bottom).

Supplementary Figure 12 Early branching evolution in UC using silent and non-silent SNVs.

Phylogenetic trees (top), shared and private clonally-adjusted mutations (bottom) from 6 patients with three or more tumor samples per patient.

Supplementary Figure 13 Phylogenetic tree of case WCM117 using silent and non-silent SNVs.

Silent and non-silent SNVs across 12 tumor samples (top) collected at various time points and from various anatomical locations. Fractions of tumor cells harboring each mutation represented by shades of green. Reconstruction of evolutionary tree (bottom).

Supplementary Figure 14 Clonal enrichment of mutations in chemotherapy-treated UC considering silent and non-silent SNVs.

Clonal enrichment of mutations in chemotherapy-treated UC considering silent and non-silent SNVs.

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Faltas, B., Prandi, D., Tagawa, S. et al. Clonal evolution of chemotherapy-resistant urothelial carcinoma. Nat Genet 48, 1490–1499 (2016). https://doi.org/10.1038/ng.3692

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