Ranjan Jyoti Sarma1, Sarathbabu Subbarayan1, John Zohmingthanga2, Saia Chenkual3, Thomas Zomuana3, Sailo Tlau Lalruatfela3, Jeremy L Pautu4, Arindam Maitra5, Nachimuthu Senthil Kumar6. 1. Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796 004, India. 2. Director, Zoram Medical College, Falkawn, Mizoram, 796005, India. 3. Department of Surgery, Civil Hospital Aizawl, Aizawl, Mizoram, 796 001, India. 4. Department of Medical Oncology, Mizoram State Cancer Institute, Aizawl, Mizoram, 796017, India. 5. National Institute of Biomedical Genomics, Kalyani, West Bengal, 741251, India. am1@nibmg.ac.in. 6. Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796 004, India. nskmzu@gmail.com.
Abstract
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.
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.
Authors: Alexander Dobin; Carrie A Davis; Felix Schlesinger; Jorg Drenkow; Chris Zaleski; Sonali Jha; Philippe Batut; Mark Chaisson; Thomas R Gingeras Journal: Bioinformatics Date: 2012-10-25 Impact factor: 6.937
Authors: Maxim Sorokin; Elena Poddubskaya; Madina Baranova; Alex Glusker; Lali Kogoniya; Ekaterina Markarova; Daria Allina; Maria Suntsova; Victor Tkachev; Andrew Garazha; Marina Sekacheva; Anton Buzdin Journal: Cold Spring Harb Mol Case Stud Date: 2020-04-01