Transcriptome-wide analysis of alternative RNA splicing events in Epstein-Barr virus-associated gastric carcinomas

Abstract

Multiple human diseases including cancer have been associated with a dysregulation in RNA splicing patterns. In the current study, modifications to the global RNA splicing landscape of cellular genes were investigated in the context of Epstein-Barr virus-associated gastric cancer. Global alterations to the RNA splicing landscape of cellular genes was examined in a large-scale screen from 295 primary gastric adenocarcinomas using high-throughput RNA sequencing data. RT-PCR analysis, mass spectrometry, and co-immunoprecipitation studies were also used to experimentally validate and investigate the differential alternative splicing (AS) events that were observed through RNA-seq studies. Our study identifies alterations in the AS patterns of approximately 900 genes such as tumor suppressor genes, transcription factors, splicing factors, and kinases. These findings allowed the identification of unique gene signatures for which AS is misregulated in both Epstein-Barr virus-associated gastric cancer and EBV-negative gastric cancer. Moreover, we show that the expression of Epstein–Barr nuclear antigen 1 (EBNA1) leads to modifications in the AS profile of cellular genes and that the EBNA1 protein interacts with cellular splicing factors. These findings provide insights into the molecular differences between various types of gastric cancer and suggest a role for the EBNA1 protein in the dysregulation of cellular AS.

A novel splice variant of LOXL2 promotes progression of human papillomavirus–negative head and neck squamous cell carcinoma

“…31 Independent of DNA-level genetic mutations and alterations, alternative splicing represents another process by which a single gene can produce various Cancer February 15, 2020 mRNA and protein isoforms with related, distinct, or even opposing functional differences that can have profound biological consequences. 12,32,33 Using microarray analysis, we confirmed several tumor-specific splice variants of the LAMA3, DST, and TP63 genes in HNSCC, 34 and used RNA sequencing analysis to identify the oncogenic splice variant of AKT3 and DOCK5 in HPV-positive HNSCC and HPV-negative HNSCC, respectively. Alternative RNA splicing is one of the main cellular engines that expands the complexity and diversity of the eukaryotic proteome.…”

“…9 The genome-wide mapping of alternative splicing variants also has been identified in a variety of tumors, including gastric, prostate, and breast cancer as well as other tumors. 12,32,33 Using microarray analysis, we confirmed several tumor-specific splice variants of the LAMA3, DST, and TP63 genes in HNSCC, 34 and used RNA sequencing analysis to identify the oncogenic splice variant of AKT3 and DOCK5 in HPV-positive HNSCC and HPV-negative HNSCC, respectively. 15,16 In addition to a specific DOCK5 variant, a total of 580 ASEs associated with HPV-negative HNSCC were determined using outlier analysis, including the specific LOXL2 variant with a novel inserted exon.…”

“…7,8 Given the importance of ASEs in regulating gene expression, the role of alternative splicing in tumorigenesis has attracted considerable interest, 9,10 and many cancer-related genes are considered to have functional diversity due to alternative splicing. [12][13][14] Through analysis of The Cancer Genome Atlas (TCGA) RNA sequencing data, we previously identified hundreds of differential expressed ASEs in HPV-positive and HPV-negative HNSCC, and found that the novel functional splice variants of AKT3 and DOCK5 played oncogenic roles in HPV-positive and HPV-negative HNSCC, respectively. 11 In lymphoma and hepatocellular carcinoma, 2 splice variants of BCL2L1 with proangiogenic and antiapoptotic effects also have been identified.…”

“…10 With the development of next-generation sequencing technologies and computational analysis, more cancer-specific ASEs have been proposed by large-scale screening and confirmed to Cancer February 15, 2020 play critical roles in the initiation and progression of cancer. [12][13][14] Through analysis of The Cancer Genome Atlas (TCGA) RNA sequencing data, we previously identified hundreds of differential expressed ASEs in HPV-positive and HPV-negative HNSCC, and found that the novel functional splice variants of AKT3 and DOCK5 played oncogenic roles in HPV-positive and HPV-negative HNSCC, respectively. 15,16 These differential expression patterns of ASEs greatly broaden and deepen our knowledge of the role of alternative spicing in regulating the initiation and progression of HNSCC.…”

Viral modulation of cellular RNA alternative splicing: A new key player in virus–host interactions?

“…Oncogenic viruses have a special relationship with host‐cell AS, as cancer cells present dysregulated AS profiles (David & Manley, ). In the context of cancer, it was demonstrated that EBV‐positive gastric carcinomas showed specific alteration in AS compared to EBV‐negative gastric carcinomas (Armero et al, ). The same conclusion was drawn with hepatitis B (HBV) and hepatitis C virus in hepatocellular carcinomas (Tremblay et al, ).…”