Construction and Comprehensive Prognostic Analysis of a lncRNA–miRNA–mRNA Regulatory Network and Tumor Immune Cell Infiltration in Colorectal Cancer

Colorectal cancer (CRC) is a malignant tumor with high morbidity and mortality worldwide. Recent studies have shown that long noncoding RNAs (lncRNAs) play an important role in almost all human tumors, including CRC. Competitive endogenous RNA (ceRNA) regulatory networks have become hot topics in ca...

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Main Authors: Xiong Guo, Xiaolong Liang, Yujun Wang, Anqi Cheng, Chuan Qin, Han Zhang, Ziwei Wang
Format: Article
Language:English
Published: Frontiers Media S.A. 2021-07-01
Series:Frontiers in Genetics
Subjects:
Online Access:https://www.frontiersin.org/articles/10.3389/fgene.2021.652601/full
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spelling doaj-79d1e1f6ec474fcdadb6f8d562a372762021-07-01T15:23:21ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-07-011210.3389/fgene.2021.652601652601Construction and Comprehensive Prognostic Analysis of a lncRNA–miRNA–mRNA Regulatory Network and Tumor Immune Cell Infiltration in Colorectal CancerXiong Guo0Xiaolong Liang1Yujun Wang2Anqi Cheng3Chuan Qin4Han Zhang5Ziwei Wang6Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, ChinaDepartment of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, ChinaDepartment of Pathology, Daping Hospital, Army Military Medical University, Chongqing, ChinaDepartment of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, ChinaDepartment of Gastrointestinal Surgery, Three Gorges Hospital, Chongqing University, Chongqing, ChinaDepartment of Digestive Oncology, Three Gorges Hospital, Chongqing University, Chongqing, ChinaDepartment of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, ChinaColorectal cancer (CRC) is a malignant tumor with high morbidity and mortality worldwide. Recent studies have shown that long noncoding RNAs (lncRNAs) play an important role in almost all human tumors, including CRC. Competitive endogenous RNA (ceRNA) regulatory networks have become hot topics in cancer research. Tumor-infiltrating immune cells (TICs) have also been reported to be closely related to the survival and prognosis of CRC patients. In this study, we used the lncRNA–miRNA–mRNA regulatory network combined with tumor immune cell infiltration to predict the survival and prognosis of 598 CRC patients. First, we downloaded the lncRNA, mRNA, and miRNA transcriptome data of CRC patients from The Cancer Genome Atlas (TCGA) database and identified differentially expressed genes through “limma” package of R software. The ceRNA regulatory network was established by using the “GDCRNATools” R package. Then, univariate Cox analysis and least absolute shrinkage and selection operator analysis were performed to identify the optimal prognostic network nodes, including SRPX, UST, H19, SNHG7, hsa-miR-29b-3p, and TTYH3. Next, we analyzed the differences in 22 types of TICs between 58 normal subjects and 206 CRC patients and included memory CD4 T cells, dendritic cells and neutrophils in the construction of a prognostic model. Finally, we identified the relationship between the ceRNA prognostic model and the infiltrating immune cell prognostic model. In conclusion, we constructed two prognostic models that provide insights on the prognosis and treatment strategy of CRC.https://www.frontiersin.org/articles/10.3389/fgene.2021.652601/fullcolorectal cancerceRNA networkinfiltrating immune cellsprognostic modelbioinformatics analysis
collection DOAJ
language English
format Article
sources DOAJ
author Xiong Guo
Xiaolong Liang
Yujun Wang
Anqi Cheng
Chuan Qin
Han Zhang
Ziwei Wang
spellingShingle Xiong Guo
Xiaolong Liang
Yujun Wang
Anqi Cheng
Chuan Qin
Han Zhang
Ziwei Wang
Construction and Comprehensive Prognostic Analysis of a lncRNA–miRNA–mRNA Regulatory Network and Tumor Immune Cell Infiltration in Colorectal Cancer
Frontiers in Genetics
colorectal cancer
ceRNA network
infiltrating immune cells
prognostic model
bioinformatics analysis
author_facet Xiong Guo
Xiaolong Liang
Yujun Wang
Anqi Cheng
Chuan Qin
Han Zhang
Ziwei Wang
author_sort Xiong Guo
title Construction and Comprehensive Prognostic Analysis of a lncRNA–miRNA–mRNA Regulatory Network and Tumor Immune Cell Infiltration in Colorectal Cancer
title_short Construction and Comprehensive Prognostic Analysis of a lncRNA–miRNA–mRNA Regulatory Network and Tumor Immune Cell Infiltration in Colorectal Cancer
title_full Construction and Comprehensive Prognostic Analysis of a lncRNA–miRNA–mRNA Regulatory Network and Tumor Immune Cell Infiltration in Colorectal Cancer
title_fullStr Construction and Comprehensive Prognostic Analysis of a lncRNA–miRNA–mRNA Regulatory Network and Tumor Immune Cell Infiltration in Colorectal Cancer
title_full_unstemmed Construction and Comprehensive Prognostic Analysis of a lncRNA–miRNA–mRNA Regulatory Network and Tumor Immune Cell Infiltration in Colorectal Cancer
title_sort construction and comprehensive prognostic analysis of a lncrna–mirna–mrna regulatory network and tumor immune cell infiltration in colorectal cancer
publisher Frontiers Media S.A.
series Frontiers in Genetics
issn 1664-8021
publishDate 2021-07-01
description Colorectal cancer (CRC) is a malignant tumor with high morbidity and mortality worldwide. Recent studies have shown that long noncoding RNAs (lncRNAs) play an important role in almost all human tumors, including CRC. Competitive endogenous RNA (ceRNA) regulatory networks have become hot topics in cancer research. Tumor-infiltrating immune cells (TICs) have also been reported to be closely related to the survival and prognosis of CRC patients. In this study, we used the lncRNA–miRNA–mRNA regulatory network combined with tumor immune cell infiltration to predict the survival and prognosis of 598 CRC patients. First, we downloaded the lncRNA, mRNA, and miRNA transcriptome data of CRC patients from The Cancer Genome Atlas (TCGA) database and identified differentially expressed genes through “limma” package of R software. The ceRNA regulatory network was established by using the “GDCRNATools” R package. Then, univariate Cox analysis and least absolute shrinkage and selection operator analysis were performed to identify the optimal prognostic network nodes, including SRPX, UST, H19, SNHG7, hsa-miR-29b-3p, and TTYH3. Next, we analyzed the differences in 22 types of TICs between 58 normal subjects and 206 CRC patients and included memory CD4 T cells, dendritic cells and neutrophils in the construction of a prognostic model. Finally, we identified the relationship between the ceRNA prognostic model and the infiltrating immune cell prognostic model. In conclusion, we constructed two prognostic models that provide insights on the prognosis and treatment strategy of CRC.
topic colorectal cancer
ceRNA network
infiltrating immune cells
prognostic model
bioinformatics analysis
url https://www.frontiersin.org/articles/10.3389/fgene.2021.652601/full
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