Distinct esophageal adenocarcinoma molecular subtype has subtype-specific gene expression and mutation patterns

Abstract

Background: Esophageal carcinoma (EC), consists of two histological types, esophageal squamous carcinoma (ESCC) and esophageal adenocarcinoma (EAC). EAC accounted for 10% of EC for centuries; however, the prevalence of EAC has alarmingly risen 6 times and increased to about 50% of EC in recent 30 years in the western countries, while treatment options for EAC patients are still limited. Stratification of molecular subtypes by gene expression profiling methods had offered opportunities for targeted therapies. However, the molecular subtype in EAC has not been defined. Hence, Identification of EAC molecular subtypes is needed and will provide important insights for future new therapies.

Results: We performed meta-analysis of gene expression profiling data on three independent EAC cohorts and showed that there are two common molecular subtypes in EAC. Each of the two EAC molecular subtypes has subtype specific expression patterns and mutation signatures. Genes which were over-expressed in subtype I EACs rather than subtype II EAC cases, were enriched in biological processes including epithelial cell differentiation, keratinocyte differentiation, and KEGG pathways including basal cell carcinoma. TP53 and CDKN2A are significantly mutated in both EAC subtypes. 24 genes including SMAD4 were found to be only significantly mutated in subtype I EAC cases, while 30 genes including ARID1A are only significantly mutated in subtype II EACs.

Conclusion: Two EAC molecular subtypes were defined and validated. This finding may offer new opportunities for targeted therapies.

Keywords: Esophageal adenocarcinoma; Gene expression; Molecular subtype; Mutation; Therapy.

Fig. 1

Identification of two molecular subtypes of esophageal adenocarcinoma. a Area under empirical cumulative distribution plots (k = 2 to k = 12) determined the two optimal molecular subtypes of EAC. (k denotes the number of clusters). b Consensus matrix displaying the two robust subgroups of EAC were defined by gene expression. c Significance analysis of subtype classifications in each dataset was determined by SigClust. d Silhouette analysis of EAC samples based on the assignments from Consensus Clustering. e Subclass association (SA) matrix of molecular subtypes between three cohorts. The rainbow bar indicates the FDR-corrected p value

Fig. 2

GSEA gene sets and relative expression heatmap. a. GSEA Enrichment plot for gene set HUPER_BREAST_BASAL_VS_LUMINAL_UP. b GSEA Enrichment plot for gene set WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN. c Heatmap of core enrichment genes for gene set HUPER_BREAST_BASAL_VS_LUMINAL_UP. d Heatmap of core enrichment genes for gene set WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN. Note. “Basal” and “Classic” stand for Subtype I and Subtype II EAC, respectively

Fig. 3

Unsupervised hierarchical clustering of two subtypes of EAC, normal esophagus, and BE. “BARRETT_low” denotes low grade dysplasia in Barrett’s esophagus, while “BARRETT_high” means high grade dysplasia in Barrett’s esophagus. “BARRETT_no” stands for non-dysplastic Barrett’s esophagus (data from GSE13898)

Fig. 4

Unsupervised hierarchical clustering of two subtypes of EAC, gastric and squamous carcinoma. “Gastric” labelled above heatmap denotes gastric adenocarcinoma while “Squamous” stands for squamous cell carcinoma (Data from GSE19417)

Fig. 5

Somatic mutation profiles of EAC across two molecular subtypes

Fig. 6

Heatmap of top50 genes from subtype I and subtype II EAC