Identification of genes of prognostic value in the ccRCC microenvironment from TCGA database
Abstract Background Clear cell renal cell carcinoma (ccRCC) is the most common pathological subtype of renal cell carcinoma. Bioinformatics analyses were used to screen candidate genes associated with the prognosis and microenvironment of ccRCC and elucidate the underlying molecular mechanisms of ac...
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doaj-db34d6cd84ab4933851db34328e8156c2020-11-25T02:54:23ZengWileyMolecular Genetics & Genomic Medicine2324-92692020-04-0184n/an/a10.1002/mgg3.1159Identification of genes of prognostic value in the ccRCC microenvironment from TCGA databaseBangbei Wan0Bo Liu1Yuan Huang2Cai Lv3Department of Urology Central South University Xiangya School of Medicine Affiliated Haikou Hospital Haikou Hainan ChinaLaboratory of Developmental Cell Biology and Disease School of Ophthalmology and Optometry and Eye Hospital Wenzhou Medical University Wenzhou Zhejiang ChinaDepartment of Neurology Central South University Xiangya School of Medicine Affiliated Haikou Hospital Haikou Hainan ChinaDepartment of Urology Central South University Xiangya School of Medicine Affiliated Haikou Hospital Haikou Hainan ChinaAbstract Background Clear cell renal cell carcinoma (ccRCC) is the most common pathological subtype of renal cell carcinoma. Bioinformatics analyses were used to screen candidate genes associated with the prognosis and microenvironment of ccRCC and elucidate the underlying molecular mechanisms of action. Methods The gene expression profiles and clinical data of ccRCC patients were downloaded from The Cancer Genome Atlas database. The ESTIMATE algorithm was used to compute the immune and stromal scores of patients. Based on the median immune/stromal scores, all patients were sorted into low‐ and high‐immune/stromal score groups. Differentially expressed genes (DEGs) were extracted from high‐ versus low‐immune/stromal score groups and were described using functional annotations and protein‒protein interaction (PPI) network. Results Patients in the high‐immune/stromal score group had poorer survival outcome. In total, 95 DEGs (48 upregulated and 47 downregulated genes) were screened from the gene expression profiles of patients with high immune and stromal scores. The genes were primarily involved in six signaling pathways. Among the 95 DEGs, 43 were markedly related to overall survival of patients. The PPI network identified the top 10 hub genes—CD19, CD79A, IL10, IGLL5, POU2AF1, CCL19, AMBP, CCL18, CCL21, and IGJ—and four modules. Enrichment analyses revealed that the genes in the most important module were involved in the B‐cell receptor signaling pathway. Conclusion This study mainly revealed the relationship between the ccRCC microenvironment and prognosis of patients. These results also increase the understanding of how gene expression patterns can impact the prognosis and development of ccRCC by modulating the tumor microenvironment. The results could contribute to the search for ccRCC biomarkers and therapeutic targets.https://doi.org/10.1002/mgg3.1159ccRCCimmune scoresmicroenvironmentstromal scoresTCGA database |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Bangbei Wan Bo Liu Yuan Huang Cai Lv |
spellingShingle |
Bangbei Wan Bo Liu Yuan Huang Cai Lv Identification of genes of prognostic value in the ccRCC microenvironment from TCGA database Molecular Genetics & Genomic Medicine ccRCC immune scores microenvironment stromal scores TCGA database |
author_facet |
Bangbei Wan Bo Liu Yuan Huang Cai Lv |
author_sort |
Bangbei Wan |
title |
Identification of genes of prognostic value in the ccRCC microenvironment from TCGA database |
title_short |
Identification of genes of prognostic value in the ccRCC microenvironment from TCGA database |
title_full |
Identification of genes of prognostic value in the ccRCC microenvironment from TCGA database |
title_fullStr |
Identification of genes of prognostic value in the ccRCC microenvironment from TCGA database |
title_full_unstemmed |
Identification of genes of prognostic value in the ccRCC microenvironment from TCGA database |
title_sort |
identification of genes of prognostic value in the ccrcc microenvironment from tcga database |
publisher |
Wiley |
series |
Molecular Genetics & Genomic Medicine |
issn |
2324-9269 |
publishDate |
2020-04-01 |
description |
Abstract Background Clear cell renal cell carcinoma (ccRCC) is the most common pathological subtype of renal cell carcinoma. Bioinformatics analyses were used to screen candidate genes associated with the prognosis and microenvironment of ccRCC and elucidate the underlying molecular mechanisms of action. Methods The gene expression profiles and clinical data of ccRCC patients were downloaded from The Cancer Genome Atlas database. The ESTIMATE algorithm was used to compute the immune and stromal scores of patients. Based on the median immune/stromal scores, all patients were sorted into low‐ and high‐immune/stromal score groups. Differentially expressed genes (DEGs) were extracted from high‐ versus low‐immune/stromal score groups and were described using functional annotations and protein‒protein interaction (PPI) network. Results Patients in the high‐immune/stromal score group had poorer survival outcome. In total, 95 DEGs (48 upregulated and 47 downregulated genes) were screened from the gene expression profiles of patients with high immune and stromal scores. The genes were primarily involved in six signaling pathways. Among the 95 DEGs, 43 were markedly related to overall survival of patients. The PPI network identified the top 10 hub genes—CD19, CD79A, IL10, IGLL5, POU2AF1, CCL19, AMBP, CCL18, CCL21, and IGJ—and four modules. Enrichment analyses revealed that the genes in the most important module were involved in the B‐cell receptor signaling pathway. Conclusion This study mainly revealed the relationship between the ccRCC microenvironment and prognosis of patients. These results also increase the understanding of how gene expression patterns can impact the prognosis and development of ccRCC by modulating the tumor microenvironment. The results could contribute to the search for ccRCC biomarkers and therapeutic targets. |
topic |
ccRCC immune scores microenvironment stromal scores TCGA database |
url |
https://doi.org/10.1002/mgg3.1159 |
work_keys_str_mv |
AT bangbeiwan identificationofgenesofprognosticvalueintheccrccmicroenvironmentfromtcgadatabase AT boliu identificationofgenesofprognosticvalueintheccrccmicroenvironmentfromtcgadatabase AT yuanhuang identificationofgenesofprognosticvalueintheccrccmicroenvironmentfromtcgadatabase AT cailv identificationofgenesofprognosticvalueintheccrccmicroenvironmentfromtcgadatabase |
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