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Investigating regulatory patterns of NLRP3 Inflammasome features and association with immune microenvironment in Crohn’s disease
INTRODUCTION: Crohn’s disease is characterized of dysregulated inflammatory and immune reactions. The role of the NOD-like receptor family, pyrin domain-containing 3 (NLRP3) inflammasome in Crohn’s disease remains largely unknown. METHODS: The microarray-based transcriptomic data and corresponding c...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9849378/ https://www.ncbi.nlm.nih.gov/pubmed/36685554 http://dx.doi.org/10.3389/fimmu.2022.1096587 |
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author | Wu, Huihuan Zeng, Ruijie Qiu, Xinqi Chen, Kequan Zhuo, Zewei Guo, Kehang Xiang, Yawen Yang, Qi Jiang, Rui Leung, Felix W. Lian, Qizhou Sha, Weihong Chen, Hao |
author_facet | Wu, Huihuan Zeng, Ruijie Qiu, Xinqi Chen, Kequan Zhuo, Zewei Guo, Kehang Xiang, Yawen Yang, Qi Jiang, Rui Leung, Felix W. Lian, Qizhou Sha, Weihong Chen, Hao |
author_sort | Wu, Huihuan |
collection | PubMed |
description | INTRODUCTION: Crohn’s disease is characterized of dysregulated inflammatory and immune reactions. The role of the NOD-like receptor family, pyrin domain-containing 3 (NLRP3) inflammasome in Crohn’s disease remains largely unknown. METHODS: The microarray-based transcriptomic data and corresponding clinical information of GSE100833 and GSE16879 were obtained from the Gene Expression Omnibus (GEO) database. Identification of in the NLRP3 inflammasome-related genes and construction of LASSO regression model. Immune landscape analysis was evaluated with ssGSEA. Classification of Crohn’s-disease samples based on NLRP3 inflammasome-related genes with ConsensusClusterPlus. Functional enrichment analysis, gene set variation analysis (GSVA) and drug-gene interaction network. RESULTS: The expressions of NLRP3 inflammasome-related genes were increased in diseased tissues, and higher expressions of NLRP3 inflammasome-related genes were correlated with generally enhanced immune cell infiltration, immune-related pathways and human leukocyte antigen (HLA)-gene expressions. The gene-based signature showed well performance in the diagnosis of Crohn’s disease. Moreover, consensus clustering identified two Crohn’s disease clusters based on NLRP3 inflammasome-related genes, and cluster 2 was with higher expressions of the genes. Cluster 2 demonstrated upregulated activities of immune environment in Crohn’s disease. Furthermore, four key hub genes were identified and potential drugs were explored for the treatment of Crohn’s disease. CONCLUSIONS: Our findings indicate that NLRP3 inflammasome and its related genes could regulate immune cells and responses, as well as involve in the pathogenesis of Crohn’s disease from transcriptomic aspects. These findings provide in silico insights into the diagnosis and treatment of Crohn’s disease and might assist in the clinical decision-making process. |
format | Online Article Text |
id | pubmed-9849378 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-98493782023-01-20 Investigating regulatory patterns of NLRP3 Inflammasome features and association with immune microenvironment in Crohn’s disease Wu, Huihuan Zeng, Ruijie Qiu, Xinqi Chen, Kequan Zhuo, Zewei Guo, Kehang Xiang, Yawen Yang, Qi Jiang, Rui Leung, Felix W. Lian, Qizhou Sha, Weihong Chen, Hao Front Immunol Immunology INTRODUCTION: Crohn’s disease is characterized of dysregulated inflammatory and immune reactions. The role of the NOD-like receptor family, pyrin domain-containing 3 (NLRP3) inflammasome in Crohn’s disease remains largely unknown. METHODS: The microarray-based transcriptomic data and corresponding clinical information of GSE100833 and GSE16879 were obtained from the Gene Expression Omnibus (GEO) database. Identification of in the NLRP3 inflammasome-related genes and construction of LASSO regression model. Immune landscape analysis was evaluated with ssGSEA. Classification of Crohn’s-disease samples based on NLRP3 inflammasome-related genes with ConsensusClusterPlus. Functional enrichment analysis, gene set variation analysis (GSVA) and drug-gene interaction network. RESULTS: The expressions of NLRP3 inflammasome-related genes were increased in diseased tissues, and higher expressions of NLRP3 inflammasome-related genes were correlated with generally enhanced immune cell infiltration, immune-related pathways and human leukocyte antigen (HLA)-gene expressions. The gene-based signature showed well performance in the diagnosis of Crohn’s disease. Moreover, consensus clustering identified two Crohn’s disease clusters based on NLRP3 inflammasome-related genes, and cluster 2 was with higher expressions of the genes. Cluster 2 demonstrated upregulated activities of immune environment in Crohn’s disease. Furthermore, four key hub genes were identified and potential drugs were explored for the treatment of Crohn’s disease. CONCLUSIONS: Our findings indicate that NLRP3 inflammasome and its related genes could regulate immune cells and responses, as well as involve in the pathogenesis of Crohn’s disease from transcriptomic aspects. These findings provide in silico insights into the diagnosis and treatment of Crohn’s disease and might assist in the clinical decision-making process. Frontiers Media S.A. 2023-01-05 /pmc/articles/PMC9849378/ /pubmed/36685554 http://dx.doi.org/10.3389/fimmu.2022.1096587 Text en Copyright © 2023 Wu, Zeng, Qiu, Chen, Zhuo, Guo, Xiang, Yang, Jiang, Leung, Lian, Sha and Chen https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Immunology Wu, Huihuan Zeng, Ruijie Qiu, Xinqi Chen, Kequan Zhuo, Zewei Guo, Kehang Xiang, Yawen Yang, Qi Jiang, Rui Leung, Felix W. Lian, Qizhou Sha, Weihong Chen, Hao Investigating regulatory patterns of NLRP3 Inflammasome features and association with immune microenvironment in Crohn’s disease |
title | Investigating regulatory patterns of NLRP3 Inflammasome features and association with immune microenvironment in Crohn’s disease |
title_full | Investigating regulatory patterns of NLRP3 Inflammasome features and association with immune microenvironment in Crohn’s disease |
title_fullStr | Investigating regulatory patterns of NLRP3 Inflammasome features and association with immune microenvironment in Crohn’s disease |
title_full_unstemmed | Investigating regulatory patterns of NLRP3 Inflammasome features and association with immune microenvironment in Crohn’s disease |
title_short | Investigating regulatory patterns of NLRP3 Inflammasome features and association with immune microenvironment in Crohn’s disease |
title_sort | investigating regulatory patterns of nlrp3 inflammasome features and association with immune microenvironment in crohn’s disease |
topic | Immunology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9849378/ https://www.ncbi.nlm.nih.gov/pubmed/36685554 http://dx.doi.org/10.3389/fimmu.2022.1096587 |
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