Mutations, Differential Gene Expression, and Chimeric Transcripts in Esophageal Squamous Cell Carcinoma Show High Heterogeneity

Translational Oncology
Paulo Thiago de Souza-SantosLuis Felipe Ribeiro Pinto

Abstract

Esophageal squamous cell carcinoma (ESCC) is a frequent and lethal neoplasia. As recent advances in targeted therapy have not improved ESCC prognosis, characterization of molecular alterations associated to this tumor is of foremost relevance. In this study, we analyze, for the first time, the complete genomic profile of ESCC by RNA-seq. TP53 was the most frequently mutated gene in the investigation and validation sets (78.6% and 67.4%, respectively). Differential expression analysis between tumor and nontumor adjacent mucosa showed 6698 differentially expressed genes, most of which were overexpressed (74%). Enrichment analysis identified overrepresentation of Wnt pathway, with overexpressed activators and underexpressed inactivators, suggesting activation of canonical and noncanonical Wnt signaling pathways. Higher WNT7B expression was associated with poor prognosis. Twenty-one gene fusions were identified in 50% of tumors, none of which involving the same genes in different patients; 71% of fusions involved syntenic genes. Comparisons with TCGA data showed co-amplification of seven gene pairs involved in fusions in the present study (~33%), suggesting that these rearrangements might have been driven by chromoanagenesis. In co...Continue Reading

Citations

Jun 22, 2019·Journal of Cellular and Molecular Medicine·Guiqin SongGang Feng
Sep 14, 2020·Cellular and Molecular Life Sciences : CMLS·Nathalia Meireles Da CostaLuiz Eurico Nasciutti
Mar 31, 2019·Nature Communications·Paul KrimpenfortAnton Berns
Mar 27, 2021·Expert Opinion on Drug Discovery·Ruth NussinovHyunbum Jang
Jan 7, 2022·Clinical & Translational Oncology : Official Publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico·L K KadianS S Chauhan

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Methods Mentioned

BETA
biopsies
chip
PCR
RNA-seq
DNA-seq

Software Mentioned

. db
RefSeq
Prinseq
FusionMap
BWA aligner
Genome Analyses Toolkit ( GATK )
R package KEGG
HTSeq Python package
Samtools
ANNOVAR

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