Press Release

Integrative genome-wide analyses reveal the transcriptional aberrations in Japanese esophageal squamous cell carcinoma

Published: August 17, 2021

Abstract

Esophageal squamous cell carcinoma (ESCC) is a malignant disease. At present, the genomic profiles of ESCC are known to a considerable extent, and DNA methylation and gene expression profiles have been mainly used for the classification of ESCC subtypes, but integrative genomic, transcriptomic, and epigenomic analyses remain insufficient. Therefore, we performed integrative analyses using whole-exome sequencing, DNA methylation, and RNA sequencing (RNA-seq) analyses of Japanese patients with ESCC. In cancer-related genes, such as NOTCH family genes, RTK/PI3K pathway genes, and NFE2L2 pathway genes, variants and copy number amplification were detected frequently. Japanese ESCC cases were clustered into two mutational signatures: an APOBEC-associated signature and an age-related signature. In imprinted genes, DNA methylation was aberrant in gene promoter regions and correlated well with gene expression profiles. Nonsynonymous single-nucleotide variants and allelic expression imbalance were detected frequently in FAT family genes. Our integrative genome-wide analyses, including DNA methylation and allele-specific gene expression profiles, revealed altered gene regulation of imprinted genes and FAT family genes in ESCC.

Journal Article

JOURNALCancer Science

TITLE:Integrative genome-wide analyses reveal the transcriptional aberrations in Japanese esophageal squamous cell carcinoma


DOIhttps://doi.org/10.1111/cas.15063

Correspondence to

Johji Inazawa, M.D., Ph.D., Professor

Department of Molecular Cytogenetics,
Medical Research Institute,
Tokyo Medical and Dental University(TMDU)
E-mail:johinaz.cgen (at) mri.tmd.ac.jp

 Kousuke Tanimoto, Assistant Professor

Genome Laboratory,
Medical Research Institute,
Tokyo Medical and Dental University(TMDU)
E-mail:ktani.nri (at) mri.tmd.ac.jp


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