J Cancer 2020; 11(13):3783-3793. doi:10.7150/jca.40850

Research Paper

Analysis of Differentially Expressed Genes in a Chinese Cohort of Esophageal Squamous Cell Carcinoma

Gang Liu1,2*, Yuan Zhao3*, Huili Chen1, Jinru Jia1, Xiaomin Cheng2, Fengjie Wang2, Qiang Ji2, Rick F. Thorne1, Song Chen1,4✉, Xiaoying Liu1,2✉

1. Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450003, China
2. Biology Department, School of Life Sciences, Anhui Medical University, Hefei, 230032, China
3. Department of Thoracic Surgery, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, China
4. Institute of Medicinal Biotechnology, Jiangsu College of Nursing, Huai'an, 223005, China
*These authors contribute equally to this work.

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Citation:
Liu G, Zhao Y, Chen H, Jia J, Cheng X, Wang F, Ji Q, Thorne RF, Chen S, Liu X. Analysis of Differentially Expressed Genes in a Chinese Cohort of Esophageal Squamous Cell Carcinoma. J Cancer 2020; 11(13):3783-3793. doi:10.7150/jca.40850. Available from https://www.jcancer.org/v11p3783.htm

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Abstract

Esophageal squamous cell carcinoma (ESCC) is a leading malignancy in China with both high incidence and mortality. Towards improving outcomes, clinically-relevant biomarkers are urgently needed for use as prognostic and treatment targets. Herein we applied RNA-seq for deep sequencing of ten matched pairs of ESCC and adjacent non-cancerous tissues (NT) from Chinese patients. Transcriptomic data mapped to approximately 64% of all annotated genes with 2,047 and 708 unigenes being differentially up-regulated and down-regulated, respectively, between ESCCs and NT samples (p<0.05). Dividing cases by pathological grade revealed significant differentially expressed genes (DEG) between ESCC and NT in both low and high differentiation cases (p<0.05) whereas gene expression differences were not significantly different between high and low differentiation ESCC tissues (p=0.053). Moreover, the majority of ESCC and NT tissues formed clusters in principal component analyses. The veracity of the DEG list was validated in a larger cohort of 45 patient samples, with down-regulated CLIC3, up-regulated CLIC4 and unchanged expression of CLIC2 confirmed in ESCC using quantitative PCR and Western blotting. Our data reveal both previously identified ESCC biomarkers along with novel candidates and represent a ready resource of DEGs in ESCC for further investigation.

Keywords: ESCC, transcriptome, differentially expressed gene (DEG), RNA-seq, CLIC2, CLIC3, CLIC4