Large-scale Analysis of CDH1 mutations defines a distinctive molecular subset in gastric cancer (GC)


Jingyuan Wang, Joanne Xiu, Hiroyuki Arai, Francesca Battaglin, Kelsey Poorman, Ryuma Tokunaga, Wu Zhang, Zoran Gatalica, W. Michael Korn and Heinz-Josef Lenz


Although histological and molecular (genomic and transcriptomic) classifications have been well studied for gastric cancer (GC), targeted therapies for GC are still limited. E-cadherin (encoded by CDH1) is a member of the cadherin family of calcium dependent cell adhesion molecules and plays a major role in the process of intercellular adhesion between epithelial cells. Frequent CDH1 mutations are characteristics of genomically stable gastric tumors and are associated with poor prognosis, but lack effective therapies. Most of the earlier works on CDH1 mutation of GC had been on familial cases and focused on the germline mutation, which is a known risk factor for hereditary DGC. Lack of sufficient studies explored the molecular features of CDH1-mutated (MT) GC, and identified potential druggable targets for these cohort. Herein we aim to understand the specific mutation profile and enriched pathways in CDH1-MT GC, which could help to discover novel drug targets.


  • NGS was performed on genomic DNA isolated from FFPE tumor samples using the NextSeq (592-genes) (Illumina, Inc., San Diego, CA). All variants were detected with greater than 99% confidence based on allele frequency and amplicon coverage, with an average sequencing depth of coverage of greater than 500 and an analytic sensitivity of 5%.
  • Microsatellite instability (MSI) was calculated with a combination of MSI by NGS and Fragment analysis and IHC (MLH1, PMS2, MSH2, MSH6). – Tumor mutational burden (TMB) was estimated from 592 genes (1.4 megabases [MB] sequenced per tumor) by counting all non-synonymous missense mutations found per tumor that had not been previously described as germline alterations.
  • IHC was performed on FFPE sections of glass slides. PD- L1 testing was performed using the SP142 (Ventana, Tucson, AZ) or 22c3 (DAKO, Santa Clara, CA) anti-PD-L1 clone. HER2 testing was performed using 4B5, Ventana Medical Systems.
  • Chromogenic In Situ Hybridization (CISH) was applied for the scores of HER2/neu. -Gene fusion was evaluated using Archer or Whole Transcriptome Sequencing. – Chi-square and Wilcoxon Rank were used for comparative analyses using R version 3.5.0


This is the largest study to investigate the distinct genomic landscape between CDH1-MT and WT GC. Our data indicate GC patients with CDH1 mutation could potentially benefit from agents targeting DNA repair pathway, while immunotherapy may be of lower efficacy in this cohort based on lower CPS score. Efficiency of these therapeutic targets and enriched pathways in CDH1- Mut GC warrant further investigation.

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