Frequent somatic CDH1 loss-of-function mutations in plasmacytoid-variant bladder cancer

Authors

Hikmat A. Al-Ahmadie

Gopa Iyer

Byron H. Lee

Sasinya N. Scott

Rohit Mehra

Aditya Bagrodia

Emmet J. Jordan

Sizhi Paul Gao

Ricardo Ramirez

Eugene K. Cha

Neil B. Desai

Emily C. Zabor

Irina Ostrovnaya

Anuradha Gopalan

Ying-Bei Chen

Samson W. Fine

Satish K. Tickoo

Anupama Gandhi

Joseph Hreiki

Agnès Viale

Maria E. Arcila

Guido Dalbagni

Jonathan E. Rosenberg

Bernard H. Bochner

Dean F. Bajorin

Michael F. Berger

Victor E. Reuter

Barry S. Taylor

David B. Solit

Doi

10.1038/ng.3503

PMID: 26901067 · DOI: 10.1038/ng.3503 · Journal: Nature Genetics (2016)

TL;DR

Al-Ahmadie et al. characterized the mutational landscape of plasmacytoid-variant bladder cancer (SRCBC), an aggressive histologic variant excluded from TCGA. Combining whole-exome and targeted sequencing of 31 plasmacytoid tumors at MSKCC, they discovered that truncating somatic CDH1 mutations occur in 84% of plasmacytoid carcinomas — a finding completely absent from 127 conventional urothelial carcinoma, NOS tumors in the TCGA cohort. E-cadherin loss (by mutation or promoter hypermethylation) was universal across the 31 plasmacytoid tumors examined by IHC. CRISPR/Cas9 knockout of CDH1 in RT4 and MGHU4 bladder cancer cell lines enhanced cell migration, providing a mechanistic explanation for the variant’s distinctive peritoneal pattern of spread and poor prognosis.

Cohort & data

  • Discovery cohort: 6 plasmacytoid-variant bladder tumors with matched normal tissue, profiled by whole-exome sequencing (SureSelect XT Human All Exon V4, HiSeq 2500, ~63M read pairs/sample, 94.4% of targets at ≥30X) PMID:26901067.
  • Validation cohort: 19 additional plasmacytoid-variant tumors profiled by a 300-gene exon-capture panel (targeted DNA-seq), plus 6 plasmacytoid-variant tumors profiled with the CLIA-certified MSK-IMPACT 341-gene panel PMID:26901067.
  • Prospective clinical cohort: 62 patients with invasive bladder cancer prospectively sequenced at MSKCC underwent centralized histologic review; 6 had plasmacytoid-variant histology and 56 had urothelial carcinoma, NOS PMID:26901067.
  • Comparator: 121 muscle-invasive urothelial carcinoma, NOS samples from the urothelial TCGA cohort (127 tumors total) PMID:26901067.
  • Clinical outcome cohort: 53 MSKCC patients with predominantly plasmacytoid histology treated 7/1994–4/2014; 37 included in survival analyses (16 with metastases at presentation and 2 with outside follow-up excluded). Compared against 978 patients with pure urothelial carcinoma treated 5/2001–3/2010. Median follow-up among survivors: 71.8 months PMID:26901067.
  • Cancer type: Plasmacytoid/Signet Ring Cell Bladder Carcinoma (SRCBC) — a variant of bladder urothelial carcinoma.
  • Dataset: blca_plasmacytoid_mskcc_2016.

Key findings

  • CDH1 truncating mutations are pathognomonic for plasmacytoid-variant bladder cancer. All 6 discovery-cohort tumors harbored nonsense CDH1 mutations; 14/19 (74%) of the targeted-sequencing validation cohort were CDH1-mutant. Across the prospective clinical cohort, CDH1 mutations were found in 6/6 plasmacytoid tumors and 0/56 non-plasmacytoid tumors PMID:26901067.
  • E-cadherin loss is universal in plasmacytoid tumors regardless of CDH1 mutation status. All 31 plasmacytoid tumors across the three cohorts showed loss of E-cadherin expression by IHC, including 5 CDH1 wild-type tumors PMID:26901067.
  • Promoter hypermethylation accounts for most CDH1 wild-type cases. Bisulfite sequencing of the CDH1 promoter CpG island (whole-genome-bisulfite-seq workflow, Sanger readout) detected promoter hypermethylation in 4/5 CDH1 wild-type plasmacytoid tumors and 0 CDH1-mutant or urothelial NOS tumors PMID:26901067.
  • E-cadherin loss is restricted to the invasive component. IHC staining was absent in invasive plasmacytoid regions but retained in in situ regions of the same tumors (Supplementary Figure 5) PMID:26901067.
  • Plasmacytoid co-mutation pattern resembles conventional urothelial carcinoma. Aside from CDH1, the genomic profile of plasmacytoid-variant tumors was not substantially different from 183 urothelial NOS tumors in TCGA / MSKCC cohorts, with frequent mutations in TP53, RB1, ARID1A, ERBB2, and PIK3CA PMID:26901067.
  • Lobular breast and diffuse gastric carcinomas — which also harbor frequent CDH1 mutations — show distinct co-mutation patterns from plasmacytoid bladder cancer apart from CDH1 itself (Supplementary Figure 2) PMID:26901067.
  • Plasmacytoid-variant and conventional urothelial regions of the same tumor share a common precursor. Multi-region exon capture of one mixed tumor revealed CDKN1A (A45fs) and PIK3C2G (S48R) as truncal alterations shared by both regions, while CDH1 Y68fs together with PTEN, NOTCH2, and FAT4 mutations were unique to the plasmacytoid component PMID:26901067.
  • No germline CDH1 alterations were detected, in contrast to hereditary diffuse gastric cancers where germline CDH1 mutations are causal PMID:26901067.
  • Plasmacytoid-variant patients have higher cumulative incidence of local recurrence and cancer-specific mortality than patients with pure urothelial carcinoma, NOS (Figure 2a–b) and a distinct peritoneal pattern of spread PMID:26901067.
  • CRISPR/Cas9 CDH1 knockout enhances bladder cancer cell migration. Knockout of CDH1 (LentiCRISPR v2 nickase, D10A Cas9) in MGHU4 cells increased migratory capability in a wound-healing scratch assay, and both RT4 and MGHU4 CDH1 knockouts displayed enhanced migration in a Boyden chamber assay (p < 0.05) compared with parental lines PMID:26901067.

Genes & alterations

  • CDH1 — Truncating somatic loss-of-function mutations (nonsense, frameshift) in 84% of plasmacytoid-variant bladder cancers (vs. 0% in 127 TCGA urothelial NOS tumors). Promoter hypermethylation accounts for 4/5 mutation-negative cases. The defining molecular event of the plasmacytoid variant; mutation or methylation produces E-cadherin loss that drives the variant’s enhanced migratory and invasive phenotype PMID:26901067.
  • TP53 — Frequently mutated in plasmacytoid-variant tumors at frequencies similar to urothelial carcinoma, NOS PMID:26901067.
  • RB1 — Frequently mutated in plasmacytoid-variant tumors at frequencies similar to urothelial carcinoma, NOS PMID:26901067.
  • ARID1A — Recurrent chromatin-remodeler mutations in plasmacytoid-variant tumors, comparable to urothelial NOS PMID:26901067.
  • ERBB2 — Recurrent alterations in plasmacytoid-variant tumors; flagged by the authors as a clinically actionable target supporting early use of targeted agents PMID:26901067.
  • PIK3CA — Recurrent alterations in plasmacytoid-variant tumors; flagged as clinically actionable PMID:26901067.
  • TSC1 — Listed by the authors among clinically actionable alterations recurrent in plasmacytoid-variant tumors PMID:26901067.
  • CDKN1A — A45fs mutation observed as a truncal alteration shared between plasmacytoid and adjacent urothelial NOS components in a mixed tumor PMID:26901067.
  • PIK3C2G — S48R mutation observed as a truncal alteration shared between plasmacytoid and adjacent urothelial NOS components in the same mixed tumor PMID:26901067.
  • PTEN — Mutation unique to the plasmacytoid component of a mixed tumor (alongside CDH1 Y68fs) PMID:26901067.
  • NOTCH2 — Mutation unique to the plasmacytoid component of a mixed tumor PMID:26901067.
  • FAT4 — Mutation unique to the plasmacytoid component of a mixed tumor PMID:26901067.

Clinical implications

  • Histology + sequencing should jointly trigger CDH1 testing. A patient with plasmacytoid-variant bladder histology has an ~84% probability of harboring a somatic CDH1 truncating mutation, and an essentially universal probability of E-cadherin loss PMID:26901067.
  • Worse prognosis warrants more aggressive multi-modality treatment. Plasmacytoid-variant patients have higher cumulative incidence of local recurrence and cancer-specific mortality than urothelial NOS patients; the authors recommend considering early use of targeted agents as part of multi-modality treatment PMID:26901067.
  • Targetable co-alterations are present. Recurrent ERBB2, PIK3CA, and TSC1 alterations in plasmacytoid tumors imply potential benefit from anti-HER2, PI3K-pathway, or mTOR-pathway agents — though the paper does not test specific agents PMID:26901067.
  • Mechanistic rationale for peritoneal spread. CRISPR knockout of CDH1 in bladder cancer lines increases migration, plausibly explaining the variant’s distinctive pattern of peritoneal dissemination and supporting CDH1 / E-cadherin loss as the molecular driver of the aggressive clinical course PMID:26901067.
  • No germline screening indication. Unlike hereditary diffuse gastric cancer, the authors found no germline CDH1 alterations, suggesting no immediate hereditary-cancer screening implication for plasmacytoid bladder probands PMID:26901067.

Limitations & open questions

  • Small absolute sample size. The molecular cohort comprises 31 plasmacytoid-variant tumors (6 WES + 19 targeted-panel + 6 IMPACT341); statistical comparisons against TCGA NOS rest on this modest n PMID:26901067.
  • Single-institution provenance. All plasmacytoid samples come from a single MSKCC pathology archive; centralized histologic review reduces diagnostic-criteria variability but the discovery may not generalize uniformly across institutions.
  • No matched-comparator targeted treatment data. The authors recommend early use of targeted agents but do not test ERBB2-, PIK3CA-, or TSC1-directed therapy in this cohort; outcomes by treatment class remain an open question.
  • Cell-line phenotype is migration only. CRISPR knockout demonstrates increased migration in two urothelial cell lines (RT4, MGHU4); it does not directly model the peritoneal-spread phenotype or test whether re-expression of CDH1 would reverse it in plasmacytoid-derived models.
  • Mechanism of E-cadherin loss in 1/5 promoter-unmethylated CDH1-WT tumor is unexplained; alternative regulatory mechanisms (e.g., post-translational, miRNA, transcriptional repressors) are not investigated PMID:26901067.
  • Cell of origin not formally established. The mixed-tumor multi-region analysis (n=1) is suggestive of a common precursor with the urothelial NOS component, but a single tumor cannot generalize.
  • Functional consequence of the co-altered NOTCH2 / FAT4 / PTEN mutations in the plasmacytoid-only component is not dissected.

Citations from this paper used in the wiki

  • “truncating somatic alterations in the CDH1 gene occur in 84% of plasmacytoid carcinomas and are specific to this histologic variant” (Abstract).
  • “Six plasmacytoid-variant bladder tumors were initially analyzed by whole exome sequencing and all 6 harbored nonsense mutations in CDH1” (p. 2).
  • “no CDH1 truncating mutations were detected within 127 bladder tumors in the TCGA cohort comprised of urothelial carcinoma, not otherwise specified (NOS)” (p. 2).
  • “we performed targeted exon capture and sequencing of 19 additional plasmacytoid-variant bladder tumors … 14 (74%) of which harbored CDH1 mutations” (p. 2).
  • “CDH1 mutations were identified in 6 patients, all of whose tumors exhibited the plasmacytoid-variant histology, whereas no CDH1 alterations were observed in the 56 non-plasmacytoid-variant samples” (p. 2).
  • “frequent mutations in the tumor suppressors TP53 and RB1, the chromatin remodeler ARID1A, and the targetable kinases ERBB2 and PIK3CA” (pp. 2–3).
  • “All 31 plasmacytoid tumors from the whole exome, validation, and prospective cohorts exhibited loss of E-cadherin expression, including 5 CDH1 wild-type tumors” (p. 3).
  • “CDH1 promoter hypermethylation was present in 4 of 5 CDH1 wild-type plasmacytoid tumors but in none of the CDH1 mutant or urothelial carcinoma, NOS specimens examined” (p. 3).
  • “Both histologic regions shared mutations in CDKN1A (A45fs) and PIK3C2G (S48R) … A CDH1 Y68fs mutation alongside PTEN, NOTCH2, FAT4, and other gene mutations were, however, unique to the plasmacytoid component” (p. 3).
  • “we identified no germline CDH1 alterations in the plasmacytoid-variant bladder cancers” (p. 3).
  • “both RT4 and MGHU4 CDH1 knockouts displayed enhanced migration across a Boyden chamber membrane (Figure 2f) as compared to the parental lines” (p. 4).
  • “The frequent presence of clinically actionable alterations in genes such as ERBB2, PIK3CA, and TSC1 and the poor prognosis of patients with this disease imply that early use of targeted agents, as part of a multi-modality treatment approach, should be considered” (p. 4).

This page was processed by crosslinker on 2026-05-14.