Co-occurrence of mutations and related signal pathway analysis of CCND1 amplification in esophageal squamous cell cancer.

Abstract

e16044 Background: Profiling molecular subtypes was usually necessary for cancer patients to facilitate better treatment strategy. Esophageal squamous cell cancer (ESCC) has four subtypes including cell cycle pathway activation (CCA), NRF2 oncogenic activation (NRFA), immune suppression (IS), and immune modulation (IM). CCND1 amplification is one of the important molecular biomarkers for CCA subtype. Previous research showed that CCND1 amplification was associated with immune resistance in ESCC. The co-occurred mutations and related signaling pathways are of great interest to study molecular mechanism in ESCC. Methods: This study enrolled 50 ESCC patient samples comprising 19 whole exome sequencing (WES) samples, 18 whole genome sequencing (WGS) samples and 13 NGS panel (667 genes) samples. To use all the samples, the minimal set of 667 genes was analyzed in detail for gene amplifications and mutations. Kaplan-Meier (KM) survival analysis was applied to study the prognosis associations with the frequently occurred amplifications including CCND1, FGF3, FGF4 and FGF19, etc. Gene expression profiles were then investigated by RNA-Seq sequencing on ESCC cell lines with CCND1 (K30-N) and without CCND1 gene (K30-S, knocked out). PCA analysis was applied to explore the differences between K30-S and K30-N, and KEGG and GO enrichment analysis were performed on the differential expressed genes (DEGs). All analyses were carried out through R4.1.0. Results: The mutational profiles showed that TP53, CCND1, FGF4, FGF19, FGF3, and CDKN2A/B were the most frequently mutated genes in ESCC patients, with the mutation frequencies of 62%, 58%, 56%, 50%, 48% and 40%, respectively. Among those genes, CCND1 and FGF3/4/19 co-occurred amplifications presented in almost all the samples and no other co-existent gene amplifications were identified. The CCND1 and FGF3/4/19 amplification patients were associated with worse prognosis. A total of 1494 differential expressed genes were identified between K30-N and K30-S cell lines, including 998 up-regulated genes and 496 down-regulated gene in K30-S cell line. KEGG enrichment analysis showed that these DEGs were mainly enriched in MAPK signaling pathway, p53 signaling pathway, mTOR signaling pathway and etc. GO enrichment analysis revealed that these differential genes are mainly enriched in cell growth, developmental cell growth, Ras protein signal transmission. Those results were consistent with CCA molecular subtype and highlighted the important role of CCND1 in ESCC subtype classification. Conclusions: This study demonstrated that CCND1 and FGF3/4/19 amplifications frequently co-occurred in ESCC and they were associated with worse prognosis. Signal pathway analysis showed CCND1 play important roles in subtype classification of ESCC.