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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Published inJournal of Egyptian National Cancer Institute Vol. 34; no. 1; pp. 11 - 8
Main Authors Sarma, Ranjan Jyoti, Subbarayan, Sarathbabu, Zohmingthanga, John, Chenkual, Saia, Zomuana, Thomas, Lalruatfela, Sailo Tlau, Pautu, Jeremy L., Maitra, Arindam, Kumar, Nachimuthu Senthil
Format Journal Article
LanguageEnglish
Published Berlin/Heidelberg Springer Berlin Heidelberg 14.03.2022
Springer
Springer Nature B.V
SpringerOpen
Subjects
Adenocarcinoma
Adenocarcinoma - pathology
Biomarker
Biomarkers
Biotechnology industry
Cancer
Cell adhesion & migration
Comparative analysis
Data processing
Datasets
Development and progression
Differentially expressed genes
Gastric cancer
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Genes
Genetic aspects
Homeostasis
Humans
Hypotheses
Hypothesis testing
Ligands
Medical prognosis
Medical research
Medicine
Medicine & Public Health
Medicine, Experimental
Oncology
Ontology
Poor survival
Potassium
Principal components analysis
Prognosis
RNA
RNA sequencing
RNA-Seq
Stomach adenocarcinoma
Stomach cancer
Stomach Neoplasms - pathology
Transcription Factors - genetics
United States
India
United States > US
Poor survival
Differentially expressed genes
Biomarker
Stomach adenocarcinoma
RNA-Seq
Online AccessGet full text

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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.
AbstractList BackgroundStomach 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.MethodsThis 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.ResultsTotally, 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.ConclusionUpregulation 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.
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. 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. 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. 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.
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.
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.
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. 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. 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. 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.
Audience Academic
Author Chenkual, Saia
Zomuana, Thomas
Kumar, Nachimuthu Senthil
Pautu, Jeremy L.
Sarma, Ranjan Jyoti
Maitra, Arindam
Subbarayan, Sarathbabu
Lalruatfela, Sailo Tlau
Zohmingthanga, John
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  organization: Department of Biotechnology, Mizoram University
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CitedBy_id crossref_primary_10_1080_1354750X_2024_2361796
crossref_primary_10_1515_biol_2022_0528
crossref_primary_10_1016_j_tranon_2023_101731
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Keywords Poor survival
Differentially expressed genes
Biomarker
Stomach adenocarcinoma
RNA-Seq
Language English
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Snippet Background Stomach adenocarcinoma (STAD) dominates 80–90% of gastric cancer (GC). Over the years, it has been realized that the identification of the genes...
Stomach adenocarcinoma (STAD) dominates 80-90% of gastric cancer (GC). Over the years, it has been realized that the identification of the genes responsible...
Background Stomach adenocarcinoma (STAD) dominates 80-90% of gastric cancer (GC). Over the years, it has been realized that the identification of the genes...
BackgroundStomach adenocarcinoma (STAD) dominates 80–90% of gastric cancer (GC). Over the years, it has been realized that the identification of the genes...
Abstract Background Stomach adenocarcinoma (STAD) dominates 80–90% of gastric cancer (GC). Over the years, it has been realized that the identification of the...
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SubjectTerms Adenocarcinoma
Adenocarcinoma - pathology
Biomarker
Biomarkers
Biotechnology industry
Cancer
Cell adhesion & migration
Comparative analysis
Data processing
Datasets
Development and progression
Differentially expressed genes
Gastric cancer
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Genes
Genetic aspects
Homeostasis
Humans
Hypotheses
Hypothesis testing
Ligands
Medical prognosis
Medical research
Medicine
Medicine & Public Health
Medicine, Experimental
Oncology
Ontology
Poor survival
Potassium
Principal components analysis
Prognosis
RNA
RNA sequencing
RNA-Seq
Stomach adenocarcinoma
Stomach cancer
Stomach Neoplasms - pathology
Transcription Factors - genetics
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Title Transcriptome analysis reveals SALL4 as a prognostic key gene in gastric adenocarcinoma
URI https://link.springer.com/article/10.1186/s43046-022-00108-5
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Volume 34
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