Three-gene Prognostic Biomarkers for Seminoma Identified by Weighted Gene Co-expression Network Analysis

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2020 Oct 26

PMID 33104706

Citations 2

Authors

Hualin Chen

Gang Chen

Yang Pan

Xiaoxiang Jin

Affiliations

Soon will be listed here.

Abstract

Testicular germ cell tumors (TGCTs) are common in young males, and seminoma accounts for a large proportion of TGCTs. However, there are limited records on the exploration of novel biomarkers for seminoma. Hence, we aimed to identify new biomarkers associated with overall survival in seminoma. mRNA-seq and clinical traits of TGCTs were downloaded from UCSC XENA and analyzed by weighted gene co-expression network analysis. After intersection with differentially expressed genes in GSE8607, common genes were subjected to protein-protein interaction (PPI) network construction and enrichment analyses. Then, the top 10 common genes were investigated by Kaplan-Meier (KM) survival analyses and univariate Cox regression analyses. Ultimately, TYROBP, CD68, and ITGAM were considered three prognostic biomarkers in seminoma. Based on correlation analysis between these genes and immune infiltrates, we suggest that the three biomarkers influence the survival of seminoma patients, possibly through regulating the infiltration of immune cells. In conclusion, our study demonstrated that TYROBP, CD68, and ITGAM could be regarded as prognostic biomarkers and therapeutic targets for seminoma patients.

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References

Li T, Fan J, Wang B, Traugh N, Chen Q, Liu J . TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells. Cancer Res. 2017; 77(21):e108-e110. PMC: 6042652. DOI: 10.1158/0008-5472.CAN-17-0307. View

Regouc M, Belge G, Lorch A, Dieckmann K, Pichler M . Non-Coding microRNAs as Novel Potential Tumor Markers in Testicular Cancer. Cancers (Basel). 2020; 12(3). PMC: 7140096. DOI: 10.3390/cancers12030749. View

Chen X, Sun L, Zhao Y . NCMCMDA: miRNA-disease association prediction through neighborhood constraint matrix completion. Brief Bioinform. 2020; 22(1):485-496. DOI: 10.1093/bib/bbz159. View

Ohtani H . Focus on TILs: prognostic significance of tumor infiltrating lymphocytes in human colorectal cancer. Cancer Immun. 2007; 7:4. PMC: 2935759. View

Harley J, Alarcon-Riquelme M, Criswell L, Jacob C, Kimberly R, Moser K . Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet. 2008; 40(2):204-10. PMC: 3712260. DOI: 10.1038/ng.81. View

Sfakianakis S, Bei E, Zervakis M, Vassou D, Kafetzopoulos D . On the identification of circulating tumor cells in breast cancer. IEEE J Biomed Health Inform. 2014; 18(3):773-82. DOI: 10.1109/JBHI.2013.2295262. View

Hom G, Graham R, Modrek B, Taylor K, Ortmann W, Garnier S . Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. N Engl J Med. 2008; 358(9):900-9. DOI: 10.1056/NEJMoa0707865. View

Sadigh S, Farahani S, Shah A, Vaughn D, Lal P . Differences in PD-L1-Expressing Macrophages and Immune Microenvironment in Testicular Germ Cell Tumors. Am J Clin Pathol. 2019; 153(3):387-395. DOI: 10.1093/ajcp/aqz184. View

Langfelder P, Horvath S . WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008; 9:559. PMC: 2631488. DOI: 10.1186/1471-2105-9-559. View

10.

Chen X, Wang L, Qu J, Guan N, Li J . Predicting miRNA-disease association based on inductive matrix completion. Bioinformatics. 2018; 34(24):4256-4265. DOI: 10.1093/bioinformatics/bty503. View

11.

Chen X, Xie D, Zhao Q, You Z . MicroRNAs and complex diseases: from experimental results to computational models. Brief Bioinform. 2017; 20(2):515-539. DOI: 10.1093/bib/bbx130. View

12.

Tomasello E, Vivier E . KARAP/DAP12/TYROBP: three names and a multiplicity of biological functions. Eur J Immunol. 2005; 35(6):1670-7. DOI: 10.1002/eji.200425932. View

13.

Okada K, Katagiri T, Tsunoda T, Mizutani Y, Suzuki Y, Kamada M . Analysis of gene-expression profiles in testicular seminomas using a genome-wide cDNA microarray. Int J Oncol. 2003; 23(6):1615-35. View

14.

Kirkley A, Barbosa H, Barthelemy M, Ghoshal G . From the betweenness centrality in street networks to structural invariants in random planar graphs. Nat Commun. 2018; 9(1):2501. PMC: 6021391. DOI: 10.1038/s41467-018-04978-z. View

15.

Ruf C, Isbarn H, Wagner W, Fisch M, Matthies C, Dieckmann K . Changes in epidemiologic features of testicular germ cell cancer: age at diagnosis and relative frequency of seminoma are constantly and significantly increasing. Urol Oncol. 2013; 32(1):33.e1-6. DOI: 10.1016/j.urolonc.2012.12.002. View

16.

Uhlen M, Fagerberg L, Hallstrom B, Lindskog C, Oksvold P, Mardinoglu A . Proteomics. Tissue-based map of the human proteome. Science. 2015; 347(6220):1260419. DOI: 10.1126/science.1260419. View

17.

Wei J, Yin Y, Deng Q, Zhou J, Wang Y, Yin G . Integrative Analysis of MicroRNA and Gene Interactions for Revealing Candidate Signatures in Prostate Cancer. Front Genet. 2020; 11:176. PMC: 7057858. DOI: 10.3389/fgene.2020.00176. View

18.

Capocaccia R, Gatta G, Dal Maso L . Life expectancy of colon, breast, and testicular cancer patients: an analysis of US-SEER population-based data. Ann Oncol. 2015; 26(6):1263-1268. DOI: 10.1093/annonc/mdv131. View

19.

Tang Z, Li C, Kang B, Gao G, Li C, Zhang Z . GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017; 45(W1):W98-W102. PMC: 5570223. DOI: 10.1093/nar/gkx247. View

20.

Chin C, Chen S, Wu H, Ho C, Ko M, Lin C . cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014; 8 Suppl 4:S11. PMC: 4290687. DOI: 10.1186/1752-0509-8-S4-S11. View