Bladder Urothelial Carcinoma — Weill Cornell (2016)

Overview

A prospective longitudinal cohort of 72 urothelial carcinoma (UC) tumors from 32 patients collected at Weill Cornell Medicine, designed to capture matched pre- and post-chemotherapy samples from advanced-stage disease. The cohort enriches for chemotherapy-treated metastatic UC; 16 patients contributed matched primary/advanced sets and 2 underwent rapid autopsy. Data were generated to interrogate how platinum-based chemotherapy reshapes UC clonal architecture. BAMs are deposited in dbGaP phs001087.v1.p1. PMID:27749842

Composition

Assays / panels (linked)

Papers using this cohort

  • PMID:27749842 — Faltas et al., Nat Genet 2016: Clonal evolution of chemotherapy-resistant urothelial carcinoma; whole-exome sequencing of 72 matched pre/post-chemotherapy tumors from 32 patients.

Notable findings derived from this cohort

  • Only ~28% of mutations shared between matched pre- and post-chemotherapy samples on average (range 0.2%–76.4%); even canonical UC drivers (PIK3CA, KMT2D, ATM, TP53) were inconsistently shared, implying that pre-treatment biopsy is insufficient to define actionable targets in chemotherapy-resistant disease. PMID:27749842
  • Early branching evolution: phylogenetic analysis placed the primary tumor as a branch (not trunk) of every patient’s tree, indicating multiple lineages diverged from an ancestral clone in parallel before diagnosis. PMID:27749842
  • Post-chemotherapy clonal enrichment: post-chemotherapy samples showed significantly increased clonal mutations (P=0.0134, Fisher’s exact); GSEA identified L1CAM signaling (OR=1.9, FDR=0.12) and integrin signaling (OR=2.8, FDR=0.02) as enriched — 83% and 90% missense, respectively, suggesting gain-of-function. PMID:27749842
  • ATM/RB/FANCC signature depleted by chemotherapy: present in 73.3% of pre-chemotherapy vs 37.9% of post-chemotherapy tumors (P=0.05), suggesting selective elimination of ATM/RB1/FANCC-altered clones. PMID:27749842
  • APOBEC3A dominates post-chemotherapy mutagenesis: significant enrichment of APOBEC3A YTCA-context mutations (P=1×10⁻⁵) and APOBEC3B RTCA-context mutations (P=0.0395) post-chemotherapy; APOBEC3G mutagenesis decreased. PMID:27749842
  • WCM117 rapid autopsy (12 samples): CDKN2A deletion progressed from sub-clonal heterozygous in the primary to clonal homozygous in distant metastases; TSPAN8 mutation acquired at the primary-to-metastasis transition node. PMID:27749842
  • Copy-number landscape more stable than SNV landscape: hierarchical CN clustering yields two stable clusters — Cluster A (9p21 CDKN2A/CDKN2B/MTAP deletions in a euploid background) and Cluster B (1q21.1 SETDB1/MLLT11 amplifications, 6p22.3 E2F3 amplifications; enriched for TP53 mutations). PMID:27749842

Sources

  • dbGaP accession: phs001087.v1.p1
  • cBioPortal study ID: blca_cornell_2016
  • Faltas et al., Nat Genet 2016 — DOI: 10.1038/ng.3682

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