Construction of prediction model of inflammation related genes in idiopathic pulmonary fibrosis and its correlation with immune microenvironment
BackgroundThe role of inflammation in the formation of idiopathic pulmonary fibrosis (IPF) has gained a lot of attention recently. However, the involvement of genes related to inflammation and immune exchange environment status in the prognosis of IPF remains to be further clarified. The objective o...
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| Format: | Article |
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Frontiers Media S.A.
2022-12-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2022.1010345/full |
| _version_ | 1811291467257217024 |
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| author | Ying-Qiu Yin Feng Peng Hui-Jing Situ Jun-Ling Xie Liming Tan Jie Wei Fang-fang Jiang Shan-Qiang Zhang Jun Liu |
| author_facet | Ying-Qiu Yin Feng Peng Hui-Jing Situ Jun-Ling Xie Liming Tan Jie Wei Fang-fang Jiang Shan-Qiang Zhang Jun Liu |
| author_sort | Ying-Qiu Yin |
| collection | DOAJ |
| description | BackgroundThe role of inflammation in the formation of idiopathic pulmonary fibrosis (IPF) has gained a lot of attention recently. However, the involvement of genes related to inflammation and immune exchange environment status in the prognosis of IPF remains to be further clarified. The objective of this research is to establish a new model for the prediction of the overall survival (OS) rate of inflammation-related IPF.MethodsGene Expression Omnibus (GEO) was employed to obtain the three expression microarrays of IPF, including two from alveolar lavage fluid cells and one from peripheral blood mononuclear cells. To construct the risk assessment model of inflammation-linked genes, least absolute shrinkage and selection operator (lasso), univariate cox and multivariate stepwise regression, and random forest method were used. The proportion of immune cell infiltration was evaluated by single sample Gene Set Enrichment Analysis (ssGSEA) algorithm.ResultsThe value of genes linked with inflammation in the prognosis of IPF was analyzed, and a four-genes risk model was constructed, including tpbg, Myc, ffar2, and CCL2. It was highlighted by Kaplan Meier (K-M) survival analysis that patients with high-risk scores had worse overall survival time in all training and validation sets, and univariate and multivariate analysis highlighted that it has the potential to act as an independent risk indicator for poor prognosis. ROC analysis showed that the prediction efficiency of 1-, 3-, and 5-year OS time in the training set reached 0.784, 0.835, and 0.921, respectively. Immune infiltration analysis showed that Myeloid-Derived Suppressor Cells (MDSC), macrophages, regulatory T cells, cd4+ t cells, neutrophils, and dendritic cells were more infiltrated in the high-risk group than in the low-risk group.ConclusionInflammation-related genes can be well used to evaluate the IPF prognosis and impart a new idea for the treatment and follow-up management of IPF patients. |
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| id | doaj.art-a75d1e2420a04755bc17dd9521d6f1d3 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-13T04:29:49Z |
| publishDate | 2022-12-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Immunology |
| spelling | doaj.art-a75d1e2420a04755bc17dd9521d6f1d32022-12-22T03:02:22ZengFrontiers Media S.A.Frontiers in Immunology1664-32242022-12-011310.3389/fimmu.2022.10103451010345Construction of prediction model of inflammation related genes in idiopathic pulmonary fibrosis and its correlation with immune microenvironmentYing-Qiu Yin0Feng Peng1Hui-Jing Situ2Jun-Ling Xie3Liming Tan4Jie Wei5Fang-fang Jiang6Shan-Qiang Zhang7Jun Liu8Department of Respiratory Medicine, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, Guangdong, ChinaDepartment of Respiratory Medicine, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, Guangdong, ChinaDepartment of Radiotherapy, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, Guangdong, ChinaDepartment of Respiratory Medicine, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, Guangdong, ChinaDepartment of Respiratory Medicine, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, Guangdong, ChinaDepartment of Respiratory Medicine, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, Guangdong, ChinaDepartment of Respiratory Medicine, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, Guangdong, ChinaMedical Research Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, Guangdong, ChinaMedical Research Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, Guangdong, ChinaBackgroundThe role of inflammation in the formation of idiopathic pulmonary fibrosis (IPF) has gained a lot of attention recently. However, the involvement of genes related to inflammation and immune exchange environment status in the prognosis of IPF remains to be further clarified. The objective of this research is to establish a new model for the prediction of the overall survival (OS) rate of inflammation-related IPF.MethodsGene Expression Omnibus (GEO) was employed to obtain the three expression microarrays of IPF, including two from alveolar lavage fluid cells and one from peripheral blood mononuclear cells. To construct the risk assessment model of inflammation-linked genes, least absolute shrinkage and selection operator (lasso), univariate cox and multivariate stepwise regression, and random forest method were used. The proportion of immune cell infiltration was evaluated by single sample Gene Set Enrichment Analysis (ssGSEA) algorithm.ResultsThe value of genes linked with inflammation in the prognosis of IPF was analyzed, and a four-genes risk model was constructed, including tpbg, Myc, ffar2, and CCL2. It was highlighted by Kaplan Meier (K-M) survival analysis that patients with high-risk scores had worse overall survival time in all training and validation sets, and univariate and multivariate analysis highlighted that it has the potential to act as an independent risk indicator for poor prognosis. ROC analysis showed that the prediction efficiency of 1-, 3-, and 5-year OS time in the training set reached 0.784, 0.835, and 0.921, respectively. Immune infiltration analysis showed that Myeloid-Derived Suppressor Cells (MDSC), macrophages, regulatory T cells, cd4+ t cells, neutrophils, and dendritic cells were more infiltrated in the high-risk group than in the low-risk group.ConclusionInflammation-related genes can be well used to evaluate the IPF prognosis and impart a new idea for the treatment and follow-up management of IPF patients.https://www.frontiersin.org/articles/10.3389/fimmu.2022.1010345/fullidiopathic pulmonary fibrosisinflammationimmune microenvironmentprognosisssGSEA |
| spellingShingle | Ying-Qiu Yin Feng Peng Hui-Jing Situ Jun-Ling Xie Liming Tan Jie Wei Fang-fang Jiang Shan-Qiang Zhang Jun Liu Construction of prediction model of inflammation related genes in idiopathic pulmonary fibrosis and its correlation with immune microenvironment Frontiers in Immunology idiopathic pulmonary fibrosis inflammation immune microenvironment prognosis ssGSEA |
| title | Construction of prediction model of inflammation related genes in idiopathic pulmonary fibrosis and its correlation with immune microenvironment |
| title_full | Construction of prediction model of inflammation related genes in idiopathic pulmonary fibrosis and its correlation with immune microenvironment |
| title_fullStr | Construction of prediction model of inflammation related genes in idiopathic pulmonary fibrosis and its correlation with immune microenvironment |
| title_full_unstemmed | Construction of prediction model of inflammation related genes in idiopathic pulmonary fibrosis and its correlation with immune microenvironment |
| title_short | Construction of prediction model of inflammation related genes in idiopathic pulmonary fibrosis and its correlation with immune microenvironment |
| title_sort | construction of prediction model of inflammation related genes in idiopathic pulmonary fibrosis and its correlation with immune microenvironment |
| topic | idiopathic pulmonary fibrosis inflammation immune microenvironment prognosis ssGSEA |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2022.1010345/full |
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