Deciphering Immune-Associated Genes to Predict Survival in Clear Cell Renal Cell Cancer
Joint Authors
Source
Issue
Vol. 2019, Issue 2019 (31 Dec. 2019), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2019-12-07
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
Background.
To elucidate the correlations between tumor microenvironment and clinical characteristics as well as prognosis in clear cell renal cell cancer (ccRCC) and investigate the immune-associated genes by a comprehensive analysis of The Cancer Genome Atlas (TCGA) database.
Methods.
We collected mRNA expression profiles of 537 ccRCC samples from the TCGA database.
Immune scores and stromal scores were calculated by applying the ESTIMATE algorithm.
We evaluated the correlation between immune/stromal scores and clinical characteristics as well as prognosis.
The differentially expressed genes (DEGs) were screened between high immune/stromal score and low immune/stromal score groups by the cutoff of |log (fold change)| > 1, P value <0.05 by using package “limma” in R.
Functional enrichment analysis was performed by DAVID, and the protein-protein interaction network of intersected DEGs between stromal score and immune score groups was conducted using the STRING database.
The Kaplan–Meier method was used to explore DEGs with predictive values in overall survival, and the prognostic DEGs were further validated in a Gene Expression Omnibus (GEO) dataset GSE29609.
Results.
A higher immune score was associated with T3/4 (vs.
T1/2, P<0.001), N1 (vs.
N0, P=0.05), M1 (vs.
M0, P=0.004), G3/4 (vs.
G1/2, P<0.001), advanced AJCC stage (P<0.001), and shorter overall survival (P=0.04).
Intersected DEGs between immune and stromal score groups were 48 upregulated and 47 downregulated genes, with 43 DEGs associated with overall survival in ccRCC.
After validation by a cohort of 39 ccRCC cases with detailed follow-up information from GSE29609, six immune-associated DEGs including CASP5, HSD11B1, VSIG4, HMGCS2, HSD11B2, and OGDHL were demonstrated to be predictive of prognosis in ccRCC.
Conclusions.
Our study elucidated tight associations between immune score and clinical characteristics as well as prognosis in ccRCC.
Moreover, six DEGs were explored and validated to exert predictive values in overall survival of ccRCC.
American Psychological Association (APA)
Hu, Daixing& Zhou, Mi& Zhu, Xin. 2019. Deciphering Immune-Associated Genes to Predict Survival in Clear Cell Renal Cell Cancer. BioMed Research International،Vol. 2019, no. 2019, pp.1-10.
https://search.emarefa.net/detail/BIM-1123881
Modern Language Association (MLA)
Hu, Daixing…[et al.]. Deciphering Immune-Associated Genes to Predict Survival in Clear Cell Renal Cell Cancer. BioMed Research International No. 2019 (2019), pp.1-10.
https://search.emarefa.net/detail/BIM-1123881
American Medical Association (AMA)
Hu, Daixing& Zhou, Mi& Zhu, Xin. Deciphering Immune-Associated Genes to Predict Survival in Clear Cell Renal Cell Cancer. BioMed Research International. 2019. Vol. 2019, no. 2019, pp.1-10.
https://search.emarefa.net/detail/BIM-1123881
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1123881