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Screening of prognostic biomarkers for gastric cancer based on bioinformatics

Published on Mar. 15, 2023Total Views: 1271 times Total Downloads: 459 times Download Mobile

Author: Zi-Lin HUANG # Ke-Shu LIU # Xiong CHEN

Affiliation: Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China

Keywords: Gastric cancer TCGA database Biomarkers Bioinformatics COL1A1 COMPD

DOI: 10.12173/j.issn.1004-4337.202101045

Reference: Huang ZL, Liu KS, Chen X. Screening of prognostic biomarkers for gastric cancer based on bioinformatics[J]. Journal of Mathematical Medicine, 2023, 36(2): 95-103. DOI: 10.12173/j.issn.1004-5511.202101045[Article in Chinese]

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Abstract

Objective  To screen biomarkers for the clinical diagnosis and prognosis of gastric cancer.

Methods  Download the clinical information and mRNA expression data of gastirc cancer from the TCGA database and screen differentially expressed genes by R software and Bioconductor sofware. Using GO analysis, KEGG enrichment analysis and protein interaction network analysis to further determine the core dif-ferential genes. Analyze the survival analysis of core genes in gastric cancer and their role in survival time and clinical staging. Volcano map and heat map further determine the degree of COL1A1, COMP's influence on the transcriptome.

Results  It is found that the suivival prognosis of gastic cancer patients with low expression of COL1A1 and COMP gene was significantly better than that of the high expression group. In a subgroup analysis based on the staging of gastric cancer, although the transcript levels of COL1A1 and COMP were not significantly different in stages 1 and 2, the transcript levels of COL1A1 in stage 3 and 4 GC patients were higher than that in healthy people. Fur-thermore, the main enrichment of volcano plots and heat map suggested positive as-sociation with COL1A1 and COMP genes is in terms of cell aggregation function. Conclu-sion  This research reveals that the expression and potential regulatory network of COL1A1 and COMP in gastric cancer lays the foundation for further research on the role of COL1A1 and COMP in the process of carcinogenesis. The expression of COL1A1, COMP is expected to be a potential diagnostic index for gastric cancer.

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References

1.Erratum: Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries[J]. CA Cancer J Clin, 2020, 70(4): 313. DOI: 10.3322/caac.21609.

2.Rosenbaum MW, Gonzalez RS. Targeted therapy for upper gastrointestinal tract cancer: current and future prospects[J]. Histopathology, 2021, 78(1): 148-161. DOI: 10.1111/his.14244.

3.Hsu A, Chudasama R, Almhanna K, et al. Targeted therapies for gastroesophageal cancers[J]. Ann Transl Med, 2020, 8(17): 1104. DOI: 10.21037/atm-20-3265.

4.Ning S, Wei W, Li J, et al. Clinical significance and diagnostic capacity of serum TK1, CEA, CA 19-9 and CA 72-4 levels in gastric and colorectal cancer patients[J]. J Cancer, 2018, 9(3): 494-501. DOI: 10.7150/jca.21562.

5.Mereiter S, Balmaña M, Gomes J, et al. Glycomic approaches for the discovery of targets in gastrointes-tinal cancer[J]. Front Oncol, 2016, 6: 55. DOI: 10.3389/fonc.2016.00055.

6.何磊. 生物标记物在胃癌诊断及预后中作用的研究进展[J]. 医学研究生学报, 2020, 33(9): 1004-1008. [He L. Re-search prowess on the role of biomarkers in the diagnosis and prognosis of gastric cancer[J]. Journal of Medical Postgraduates, 2020, 33(9): 1004-1008.] DOI: 10.16571/j.cnki.1008-8199.2020.09.022.

7.Karimi P, Islami F, Anandasabapathy S, et al. Gastric cancer: descriptive epidemiology, risk factors, screening, and prevention[J]. Cancer Epidemiol Biomarkers Prev, 2014, 23(5): 700-713. DOI: 10.1158/1055-9965.EPI-13-1057.

8.Razzak M. Gastrointestinal cancer: is now the time to extend biomarker stratification to other RAS-family genes?[J]. Nat Rev Clin Oncol, 2013, 10(11): 605. DOI: 10.1038/nrclinonc.2013.176.

9.Paull EO, Aytes A, Jones SJ, et al. A modular master regulator landscape controls cancer transcriptional identity[J]. Cell, 2021, 184(2): 334-351. DOI: 10.1016/j.cell.2020.11.045.

10.Lan Q, Wang P, Tian S, et al. Mining TCGA database for genes of prognostic value in gastric cancer mi-croenvironment[J]. J Cell Mol Med, 2020, 24(19): 11120-11132. DOI: 10.1111/jcmm.15595.

11.Vasaikar SV, Straub P, Wang J, et al. LinkedOmics: analyzing multi-omics data within and across 32 can-cer types[J]. Nucleic Acids Res, 2018, 46(D1): D956-D963. DOI: 10.1093/nar/gkx1090.

12.Liu F, Wu H. Identification of prognostic biomarkers and molecular targets among JAK family in breast cancer[J]. J Inflamm Res, 2021, 14: 97-114. DOI: 10.2147/JIR.S284889.

13.Boguslawska J, Kedzierska H, Poplawski P, et al. Expression of genes involved in cellular adhesion and extracellular matrix remodeling correlates with poor survival of patients with renal cancer[J]. J Urol, 2016, 195(6): 1892-1902. DOI: 10.1016/j.juro.2015.11.050.

14.Liu T, Ye P, Ye Y, et al. Circular RNA hsa_circRNA_002178 silencing retards breast cancer progression via mi-croRNA-328-3p-mediated inhibition of COL1A1[J]. J Cell Mol Med, 2020, 24(3): 2189-2201. DOI: 10.1111/jcmm.14875.

15.Wang Y, Xu H, Zhu B, et al. Systematic identification of the key candidate genes in breast cancer stro-ma[J]. Cell Mol Biol Lett, 2018, 23: 44. DOI: 10.1186/s11658-018-0110-4.

16.Gumpenberger M, Wessner B, Graf A, et al. Remodeling the skeletal muscle extracellular matrix in older age-effects of acute  exercise stimuli on gene expression[J]. Int J Mol Sci, 2020, 21(19): 7089. DOI: 10.3390/ijms21197089.

17.Geng Q, Shen Z, Li L, et al. COL1A1 is a prognostic biomarker and correlated with immune infiltrates in lung cancer[J]. PeerJ, 2021, 9: e11145. DOI: 10.7717/peerj.11145.

18.Shao ZM, Nguyen M. Tumor-specific DNA in plasma of breast cancer patients[J]. Anticancer Drugs, 2002, 13(4): 353-357. DOI: 10.1097/00001813-200204000-00003.

19.Zhang C, Liu S, Wang X, et al. COL1A1 is a potential prognostic biomarker and correlated with immune infiltration in mesothelioma[J]. Biomed Res Int, 2021, 2021: 5320941. DOI: 10.1155/2021/5320941.

20.Liu X, Wu J, Zhang D, et al. Identification of potential key genes associated with the pathogenesis and prognosis of gastric cancer based on integrated bioinformatics analysis[J]. Front Genet, 2018, 9: 265. DOI: 10.3389/fgene.2018.00265.

21.Posey KL, Coustry F, Hecht JT. Cartilage oligomeric matrix protein: COMPopathies and beyond[J]. Ma-trix Biol, 2018, 71-72: 161-173. DOI: 10.1016/j.matbio.2018.02.023.

22.Liu TT, Liu XS, Zhang M, et al. Cartilage oligomeric matrix protein is a prognostic factor and biomarker of colon cancer and promotes cell proliferation by activating the Akt pathway[J]. J Cancer Res Clin Oncol, 2018, 144(6): 1049-1063. DOI: 10.1007/s00432-018-2626-4.

23.Englund E, Bartoschek M, Reitsma B, et al. Cartilage oligomeric matrix protein contributes to the de-velopment and metastasis of breast cancer[J]. Oncogene, 2016, 35(43): 5585-5596. DOI: 10.1038/onc.2016.98.

24.Norman GL, Gatselis NK, Shums Z, et al. Cartilage oligomeric matrix protein: A novel non-invasive mark-er for assessing cirrhosis and risk of hepatocellular carcinoma[J]. World J Hepatol, 2015, 7(14): 1875-1883. DOI: 10.4254/wjh.v7.i14.1875.

25.Li Q, Wang C, Wang Y, et al. HSCs-derived COMP drives hepatocellular carcinoma progression by acti-vating MEK/ERK and PI3K/AKT signaling pathways[J]. J Exp Clin Cancer Res, 2018, 37(1): 231. DOI: 10.1186/s13046-018-0908-y.

26.Gagarina V, Carlberg AL, Pereira-Mouries L, et al. Cartilage oligomeric matrix protein protects cells against death by elevating members of the IAP family of survival proteins[J]. J Biol Chem, 2008, 283(1): 648-659. DOI: 10.1074/jbc.M704035200.

27.Zhao X, Wu S, Jing J. Identifying diagnostic and prognostic biomarkers and candidate therapeutic drugs of gastric cancer based on transcriptomics and single-cell sequencing[J]. Pathol Oncol Res, 2021, 27: 1609955.DOI: 10.3389/pore.2021.1609955.

28.Zhao Q, Xie J, Xie J, et al. Weighted correlation network analysis identifies FN1, COL1A1 and SERPINE1 associated with the progression and prognosis of gastric cancer[J]. Cancer Biomark, 2021, 31(1): 59-75. DOI: 10.3233/CBM-200594.

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