Transcriptome analysis reveals SALL4 as a prognostic key gene in gastric adenocarcinoma

Background Stomach adenocarcinoma (STAD) dominates 80-90% of gastric cancer (GC). Over the years, it has been realized that the identification of the genes responsible for gastric carcinogenesis is essential to understand the biomarker discovery. Methods This study aims to identify candidate genes f...

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Bibliographic Details
Published in:Journal of Egyptian National Cancer Institute 2022-03, Vol.34 (1), p.1-8
Main Authors: Sarma, Ranjan Jyoti, Subbarayan, Sarathbabu, Zohmingthanga, John, Chenkual, Saia, Zomuana, Thomas, Lalruatfela, Sailo Tlau, Pautu, Jeremy L
Format: Article
Language:English
Subjects:
Adenocarcinoma
Biomarker
Biomarkers
Biotechnology industry
Cancer
Cell adhesion & migration
Comparative analysis
Data processing
Datasets
Development and progression
Differentially expressed genes
Gastric cancer
Gene expression
Genes
Genetic aspects
Homeostasis
Hypotheses
Hypothesis testing
Ligands
Medical prognosis
Medical research
Medicine, Experimental
Ontology
Poor survival
Potassium
Principal components analysis
RNA
RNA sequencing
RNA-Seq
Stomach adenocarcinoma
Stomach cancer
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Summary:Background Stomach adenocarcinoma (STAD) dominates 80-90% of gastric cancer (GC). Over the years, it has been realized that the identification of the genes responsible for gastric carcinogenesis is essential to understand the biomarker discovery. Methods This study aims to identify candidate genes for biomarker discovery in STAD. RNA-Seq was performed on three paired tumor-normal and one unpaired tumor samples from four GC patients and investigated for differentially expressed genes (DEGs) using DESeq2. Gene set enrichment analysis were performed. The DEGs were compared with two STAD microarray datasets available on Gene Expression Omnibus (GEO) database. Survival study (OS) were performed using KM-Plotter on the common genes between all the datasets. Results Totally, 148 DEGs were identified, wherein 55 genes were upregulated and 93 genes were downregulated with |log2foldchange| > 1 and Benjamini-Hochberg (BH) Adjusted P value < 0.01. Cell adhesion molecule (CAM) Pathway was found to be the most significant among the upregulated genes. Gastric acid secretion and mineral absorption pathways were the most significant pathways among the downregulated genes. Comparison with two GEO datasets followed by OS analysis revealed two upregulating genes, APOC1 and SALL4 with prognostic significance. Conclusion Upregulation of APOC1 is associated with marginal overall survival (OS) and SALL4 over-expression was associated with the poor OS using KM-Plotter during 5 years data period. Our study suggests that SALL4 could be a promising biomarker candidate in STAD.
ISSN:1110-0362
2589-0409
DOI:10.1186/s43046-022-00108-5