Identifying M1 Macrophage-Related Genes Through a Co-expression Network to Construct a Four-Gene Risk-Scoring Model for Predicting Thyroid Cancer Prognosis

Frontiers in Genetics
Gaojian ZhuangGuoqing Luo

Abstract

Macrophages are key innate immune cells in the tumor microenvironment that regulate primary tumor growth, vascularization, metastatic spread and response to therapies. Macrophages can polarize into two different states (M1 and M2) with distinct phenotypes and functions. To investigate the known tumoricidal effects of M1 macrophages, we obtained RNA expression profiles and clinical data from The Cancer Genome Atlas Thyroid Cancer (TCGA-THCA). The proportions of immune cells in tumor samples were assessed using CIBERSORT, and weighted gene co-expression network analysis (WGCNA) was used to identify M1 macrophage-related modules. Univariate Cox analysis and LASSO-Cox regression analysis were performed, and four genes (SPP1, DHRS3, SLC11A1, and CFB) with significant differential expression were selected through GEPIA. These four genes can be considered hub genes. The four-gene risk-scoring model may be an independent prognostic factor for THCA patients. The validation cohort and the entire cohort confirmed the results. Univariate and multivariate Cox analysis was performed to identify independent prognostic factors for THCA. Finally, a prognostic nomogram was built based on the entire cohort, and the nomogram combining the risk sco...Continue Reading

References

Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Nov 14, 2006·Medical Decision Making : an International Journal of the Society for Medical Decision Making·Andrew J Vickers, Elena B Elkin
Aug 5, 2008·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Gisele OlerJanete M Cerutti
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
Feb 19, 2015·Contemporary Oncology Współczesna Onkologia·Katarzyna TomczakMaciej Wiznerowicz
Mar 31, 2015·Nature Methods·Aaron M NewmanAsh A Alizadeh
Jul 6, 2016·BMC Bioinformatics·Trevor Clancy, Eivind Hovig
Dec 14, 2016·The American Journal of Pathology·Timothy J BaulerKarin E Peterson
Jan 19, 2018·Methods in Molecular Biology·Binbin ChenAsh A Alizadeh
Feb 6, 2019·Endocrinology and Metabolism Clinics of North America·Veronica Valvo, Carmelo Nucera
Feb 8, 2019·Chemico-biological Interactions·Lizhi WuOlga V Belyaeva
Mar 5, 2019·Cancer Biomarkers : Section a of Disease Markers·Sung Hyun KimChang Moo Kang
Jan 23, 2020·International Journal of Molecular Sciences·Leticia Oliveira-FerrerWalter Fiedler
Apr 14, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Luka de VosDimo Dietrich
Apr 23, 2020·International Journal of Oncology·Yoshihito YamakoshiMasaichi Ohira
Apr 24, 2020·Clinical Immunology : the Official Journal of the Clinical Immunology Society·Xia ShanPei Yang
May 12, 2020·Cancer Biomarkers : Section a of Disease Markers·Iulia V IancuCorin Virgil Badiu
Jun 27, 2020·Technology in Cancer Research & Treatment·Yuanbo XueXiubo Lu
Jul 7, 2020·International Journal of Radiation Oncology, Biology, Physics·Jacob Gadwa, Sana D Karam

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Software Mentioned

WGCNA
GEPIA
GSEA
R package “ WGCNA
clusterProfiler
LASSO
survminer
R package “ survminer ”
R package “
R

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