Comprehensive molecular characterization of gastric adenocarcinoma

Abstract

Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein-Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also known as PD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies.

Figure 1. Molecular subtypes of gastric cancer.

a, Gastric cancer cases are divided into subtypes: Epstein–Barr virus (EBV)-positive (red), microsatellite instability (MSI, blue), genomically stable (GS, green) and chromosomal instability (CIN, light purple) and ordered by mutation rate. Clinical (top) and molecular data (top and bottom) from 227 tumours profiled with all six platforms are depicted. b, A flowchart outlines how tumours were classified into molecular subtypes. c, Differences in clinical and histological characteristics among subtypes with subtypes coloured as in a, b. The plot of patient age at initial diagnosis shows the median, 25th and 75th percentile values (horizontal bar, bottom and top bounds of the box), and the highest and lowest values within 1.5 times the interquartile range (top and bottom whiskers, respectively). GE, gastroesophageal. PowerPoint slide

Figure 2. Molecular characteristics of EBV-positive gastric cancers.

a, The heatmap represents unsupervised clustering of DNA methylation at CpG sites for 295 tumours into four clusters: EBV-CIMP (n = 28), Gastric-CIMP (n = 77), cluster 3 (n = 73) and cluster 4 (n = 117). Profiles for non-malignant gastric mucosa are to the left of the tumours. b, The proportion of tumours harbouring PIK3CA mutation in the molecular subtypes with mutations at sites noted recurrently in this data set or in the COSMIC database marked separately (top). Locations of PIK3CA mutations with the subtype of the sample with each mutation colour-coded (bottom). PowerPoint slide

Figure 3. Significantly mutated genes in non-hypermutated gastric cancer.

a, Bars represent somatic mutation rate for the 215 samples with synonymous and non-synonymous mutation rates distinguished by colour. b, Significantly mutated genes, identified by MutSigCV, are ranked by the q value (right) with samples grouped by subtype. Mutation colour indicates the class of mutation. PowerPoint slide

Figure 4. RHOA and ARHGAP6/26 somatic genomic alterations are recurrent in genomically stable gastric cancer.

a, Missense mutations in the GTPase RHOA, including residues Y42 and D59, linked via hydrogen bond (red arc). b, Mutated regions (coloured as in panel a) mapped on the structures of RHOA and ROCK1. c, A schematic of CLDN18–ARHGAP26 translocation is shown for the fusion transcript and predicted fusion protein. SH3 denotes SRC homology 3 domain. d, The frequency of RHOA and CDH1 mutations, CLDN18–ARHGAP6 or ARHGAP26 fusions are shown across gastric cancer subtypes. e, RHOA mutations and CLDN18–ARHGAP6 or ARHGAP26 fusions are mutually exclusive in genomically stable tumours. PowerPoint slide

Figure 5. Integrated molecular description of gastric cancer.

a, Mutations, copy-number changes and translocations for select genes are shown across samples organized by molecular subtypes. Mutations that are recurrent in this data set or in the COSMIC repository are distinguished by colour. Alteration frequencies are expressed as a percentage of all cases. b, Alterations in RTK/RAS and RTK/PI(3)K signalling pathways across molecular subtypes. Red denotes predicted activation; blue denotes predicted inactivation. c, The heatmap shows NCI-PID pathways that are significantly elevated (red) or decreased (blue) in each of the four subtypes as compared with non-malignant gastric mucosa. PowerPoint slide

Figure 6. Key features of gastric cancer subtypes.

This schematic lists some of the salient features associated with each of the four molecular subtypes of gastric cancer. Distribution of molecular subtypes in tumours obtained from distinct regions of the stomach is represented by inset charts. PowerPoint slide