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SEC24D gene as a biomarker in human cancers and its association with CD8+ T cell immune cell infiltration.

作者信息

Sarwar Sidra, Ashraf Sardar, Shafiq Muhammad, Malik Abdul, Akhtar Suhail, Arshad Rabia, Jamil Muhammad, Gul Hadia, Ullah Naimat

机构信息

Avicenna Medical College Lahore, Pakistan.

Rural Health Centre Chawinda Sialkot, Pakistan.

出版信息

Am J Transl Res. 2023 May 15;15(5):3115-3130. eCollection 2023.


DOI:
PMID:37303662
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10251021/
Abstract

OBJECTIVE: The SEC24D (SEC24 Homolog D, COPII Coat Complex Component) gene belongs to the SEC24 subfamily of genes. The protein encoded by this gene, along with its other binding partners, mediates the transport of newly-synthesized proteins from the endoplasmic reticulum to the Golgi apparatus. METHODS: A pan-cancer analysis of this gene, as well as its diagnostic and prognostic implications, are lacking in the medical literature. First, we analyzed SEC24D gene expression, its prognostic effect, promoter methylation level, genetic alteration landscape, pathways, CD8+ T immune cell infiltration, and gene-drug network in various types of cancer through various online databases and bioinformatic tools. Then, we performed the expression and methylation validation analysis of the SEC24D gene on cell lines using RNA sequencing (RNA-seq) and targeted bisulfite sequencing (bisulfite-seq) techniques. RESULTS: Bioinformatic analysis showed that the SEC24D gene was overexpressed in metastasis across Kidney Renal Clear Cell Carcinoma (KIRC), Lung Squamous Cell Carcinoma (LUSC), and Stomach Adenocarcinoma (STAD) patients and was a prognostic risk factor. Then, using RNA sequencing and targeted bisulfite sequencing analysis, it was validated in cell lines that SEC24D was overexpressed and hypomethylated in KIRC patients. Mutational analysis revealed that SEC24D was mutated less frequently in KIRC, LUSC, and STAD patients. It was further observed that CD8+ T cell infiltration levels were increased in SEC24D-overexpressed KIRC, LUSC, and STAD samples. Pathway enrichment analysis of SEC24D-associated genes revealed their participation in two important pathways. Moreover, we suggested a few valuable drugs for treating KIRC, LUSC, and STAD patients with respect to overexpressed SEC24D. CONCLUSION: This is the first pan-cancer study that details the oncogenic roles of SEC24D among different cancers.

摘要

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SEC24D gene as a biomarker in human cancers and its association with CD8+ T cell immune cell infiltration.

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本文引用的文献

[1]
Infection: Their potential implication in the Etiology of Cervical Cancer.

J Cancer. 2021-6-11

[2]
Analysis of SEC24D Gene in Breast Cancer Based on UALCAN Database.

Open Life Sci. 2019-12-31

[3]
Andrographolide as a Therapeutic Agent Against Breast and Ovarian Cancers.

Open Life Sci. 2019-12-4

[4]
TNMplot.com: A Web Tool for the Comparison of Gene Expression in Normal, Tumor and Metastatic Tissues.

Int J Mol Sci. 2021-3-5

[5]
Does human papillomavirus cause human colorectal cancer? Applying Bradford Hill criteria postulates.

Ecancermedicalscience. 2020-9-21

[6]
Identification of a Novel Immune-Related Prognostic Biomarker and Small-Molecule Drugs in Clear Cell Renal Cell Carcinoma (ccRCC) by a Merged Microarray-Acquired Dataset and TCGA Database.

Front Genet. 2020-8-18

[7]
Screening lncRNAs with diagnostic and prognostic value for human stomach adenocarcinoma based on machine learning and mRNA-lncRNA co-expression network analysis.

Mol Genet Genomic Med. 2020-11

[8]
Analysis of Protein-Targeting in the Nucleus of Host Cells and the Implications in Colon Cancer: An in-silico Approach.

Infect Drug Resist. 2020-7-20

[9]
TIMER2.0 for analysis of tumor-infiltrating immune cells.

Nucleic Acids Res. 2020-7-2

[10]
Computational Proteome-Wide Study for the Prediction of Protein Targeting in Host Cell Organelles and Their Implication in Development of Colon Cancer.

ACS Omega. 2020-3-30

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