Alterations of RNA splicing patterns in esophagus squamous cell carcinoma

Jiyu Ding,Bingli Wu,Chao Song,Yinwei Cheng,Qiuyu Wang,Chunquan Li,Zhidong Tang,Ling Lin,Zepeng Du,Enmin Li,Liyan Xu,Wenjing Bai,Wei Liu,Qiaoxi Xia

doi:10.1186/s13578-021-00546-z

Abstract

Alternative splicing (AS) is an important biological process for regulating the expression of various isoforms from a single gene and thus to promote proteome diversity. In this study, RNA-seq data from 15 pairs of matched esophageal squamous cell carcinoma (ESCC) and normal tissue samples as well as two cell lines were analyzed. AS events with significant differences were identified between ESCC and matched normal tissues, which were re-annotated to find protein coding genes or non-coding RNAs. A total of 45,439 AS events were found. Of these, 6019 (13.25%) significant differentially AS events were identified. Exon skipping (SE) events occupied the largest proportion of abnormal splicing events. Fifteen differential splicing events with the same trends of ΔΨ values in ESCC tissues, as well in the two cell lines were found. Four pathways and 20 biological processes related to pro-metastasis cell junction and migration were significantly enriched for the differentially spliced genes. The upregulated splicing factor SF3B4, which regulates 92 gene splicing events, could be a potential prognostic factor of ESCC. Differentially spliced genes, including HNRNPC, VCL, ZNF207, KIAA1217, TPM1 and CALD1 are shown with a sashimi plot. These results suggest that cell junction- and migration-related biological processes are influenced by AS abnormalities, and aberrant splicing events can be affected by splicing factor expression changes. The involved splicing factor SF3B4 was found to be a survival-related gene in ESCC and is presumed to regulate AS in multiple cancers. In summary, we identified significant differentially expressed AS events which may be related to the development of ESCC.

Highlights

Esophageal cancer is mainly classified into two types that differ in epidemiology and pathology: esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC)
6,019 Alternative splicing (AS) events were significantly differently spliced in ESCC tissues as compared to normal tissues, with a cut-off of BF > 5, |ΔΨ|> 0.2
The AS results of ESCC tissue samples showed that the proportion of SE events that could be detected were the most abundant at about 33.6%, RI events at 6.9%, mutually exclusive exon (MXE) 6.8%, alternative 3’ splice site (A3SS) 8.5%, and alternative 5’ splice site (A5SS) 6.4% of the total events

Summary

Introduction

Esophageal cancer is the sixth leading cause of cancer fatalities in the world [1], with a five-year survival of less than 20% [2]. Esophageal cancer is mainly classified into two types that differ in epidemiology and pathology: esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). About 90% of esophageal cancer cases worldwide are ESCC [1]. Pre-mRNA splicing is a biological process, carried out by a spliceosome consisting of five snRNP complexes and more than 200 auxiliary proteins [4], that removes intron lariats and joins exons together to produce mature mRNAs [3]. It has been reported that alternative splicing plays important roles in normal organ development and cell differentiation [6]. Splicing pattern abnormalities caused by mutations of cis-acting sequences and spliceosomal proteins can trigger human diseases, including cancer [7, 8].

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Results

Conclusion