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Immune-related genes in tumor-specific CD4(+) and CD8(+) T cells in colon cancer
BACKGROUND: Immune escape is an immunological mechanism underlying tumorigenesis, and T cells play an important role in this process. In this study, immune-related genes were evaluated in tumor-infiltrating CD4(+) and CD8(+) T cells in colon cancer. METHODS: ESTIMATE was used to calculate stromal an...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310260/ https://www.ncbi.nlm.nih.gov/pubmed/32571262 http://dx.doi.org/10.1186/s12885-020-07075-x |
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author | Yang, Xi Wu, Wei Pan, Yuefen Zhou, Qing Xu, Jiamin Han, Shuwen |
author_facet | Yang, Xi Wu, Wei Pan, Yuefen Zhou, Qing Xu, Jiamin Han, Shuwen |
author_sort | Yang, Xi |
collection | PubMed |
description | BACKGROUND: Immune escape is an immunological mechanism underlying tumorigenesis, and T cells play an important role in this process. In this study, immune-related genes were evaluated in tumor-infiltrating CD4(+) and CD8(+) T cells in colon cancer. METHODS: ESTIMATE was used to calculate stromal and immune scores for tumor datasets downloaded from The Cancer Genome Atlas–Colon Cancer (COAD). Differentially expressed genes (DEGs) between samples with high and low stromal and immune scores were screened, followed by a functional enrichment analysis of the overlapping DEGs. The DEGs related to CD4(+) and the CD8(+) T cells were then screened. Predicted miRNA–mRNA and lncRNA–miRNA pairs were used to construct a competing endogenous RNA (ceRNA) network. Furthermore, chemical–gene interactions were predicted for genes in the ceRNA network. Kaplan–Meier survival curves were also plotted. RESULTS: In total, 83 stromal-related DEGs (5 up-regulated and 78 down-regulated) and 1270 immune-related DEGs (807 up-regulated and 293 down-regulated genes) were detected. The 79 overlapping DEGs were enriched for 39 biological process terms. Furthermore, 79 CD4(+) T cell-related genes and 8 CD8(+) T cell-related genes, such as ELK3, were screened. Additionally, ADAD1 and DLG3, related to CD4(+) T cells, were significantly associated with the prognosis of patients with colon cancer. The chr22-38_28785274–29,006,793.1–miR-106a-5p-DDHD1 and chr22-38_28785274–29,006,793.1–miR-4319-GRHL1 axes obtained from CD4(+) and CD8(+) T cell-related ceRNAs were identified as candidates for further studies. CONCLUSION: ELK3 is a candidate immune-related gene in colon cancer. The chr22-38_28785274–29,006,793.1–miR-106a-5p-DDHD1 and chr22-38_28785274–29,006,793.1–miR-4319-GRHL1 axes may be related to CD4(+) and CD8(+) T cell infiltration in colon cancer. |
format | Online Article Text |
id | pubmed-7310260 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-73102602020-06-23 Immune-related genes in tumor-specific CD4(+) and CD8(+) T cells in colon cancer Yang, Xi Wu, Wei Pan, Yuefen Zhou, Qing Xu, Jiamin Han, Shuwen BMC Cancer Research Article BACKGROUND: Immune escape is an immunological mechanism underlying tumorigenesis, and T cells play an important role in this process. In this study, immune-related genes were evaluated in tumor-infiltrating CD4(+) and CD8(+) T cells in colon cancer. METHODS: ESTIMATE was used to calculate stromal and immune scores for tumor datasets downloaded from The Cancer Genome Atlas–Colon Cancer (COAD). Differentially expressed genes (DEGs) between samples with high and low stromal and immune scores were screened, followed by a functional enrichment analysis of the overlapping DEGs. The DEGs related to CD4(+) and the CD8(+) T cells were then screened. Predicted miRNA–mRNA and lncRNA–miRNA pairs were used to construct a competing endogenous RNA (ceRNA) network. Furthermore, chemical–gene interactions were predicted for genes in the ceRNA network. Kaplan–Meier survival curves were also plotted. RESULTS: In total, 83 stromal-related DEGs (5 up-regulated and 78 down-regulated) and 1270 immune-related DEGs (807 up-regulated and 293 down-regulated genes) were detected. The 79 overlapping DEGs were enriched for 39 biological process terms. Furthermore, 79 CD4(+) T cell-related genes and 8 CD8(+) T cell-related genes, such as ELK3, were screened. Additionally, ADAD1 and DLG3, related to CD4(+) T cells, were significantly associated with the prognosis of patients with colon cancer. The chr22-38_28785274–29,006,793.1–miR-106a-5p-DDHD1 and chr22-38_28785274–29,006,793.1–miR-4319-GRHL1 axes obtained from CD4(+) and CD8(+) T cell-related ceRNAs were identified as candidates for further studies. CONCLUSION: ELK3 is a candidate immune-related gene in colon cancer. The chr22-38_28785274–29,006,793.1–miR-106a-5p-DDHD1 and chr22-38_28785274–29,006,793.1–miR-4319-GRHL1 axes may be related to CD4(+) and CD8(+) T cell infiltration in colon cancer. BioMed Central 2020-06-22 /pmc/articles/PMC7310260/ /pubmed/32571262 http://dx.doi.org/10.1186/s12885-020-07075-x Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Yang, Xi Wu, Wei Pan, Yuefen Zhou, Qing Xu, Jiamin Han, Shuwen Immune-related genes in tumor-specific CD4(+) and CD8(+) T cells in colon cancer |
title | Immune-related genes in tumor-specific CD4(+) and CD8(+) T cells in colon cancer |
title_full | Immune-related genes in tumor-specific CD4(+) and CD8(+) T cells in colon cancer |
title_fullStr | Immune-related genes in tumor-specific CD4(+) and CD8(+) T cells in colon cancer |
title_full_unstemmed | Immune-related genes in tumor-specific CD4(+) and CD8(+) T cells in colon cancer |
title_short | Immune-related genes in tumor-specific CD4(+) and CD8(+) T cells in colon cancer |
title_sort | immune-related genes in tumor-specific cd4(+) and cd8(+) t cells in colon cancer |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310260/ https://www.ncbi.nlm.nih.gov/pubmed/32571262 http://dx.doi.org/10.1186/s12885-020-07075-x |
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