Analysis of immune-related genes in idiopathic pulmonary fibrosis based on bioinformatics and experimental verification

Li, Xiaoyan; Huang, Yuanyuan; Ye, Naixi; He, Jie

doi:10.21037/apm-21-2676

Cited by 4 publications

(2 citation statements)

References 55 publications

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“…Several studies have shown that IPF patients have increased plasmablasts compared to controls (4,37,38). Furthermore, proteomic analysis on IPF lung tissue demonstrated an accumulation of MZB-1 positive B cells that were characterised as CD20 -CD138 + CD38 + CD27 + (39), which share a number of phenotypic properties with conventional PCs.…”

Section: Discussionmentioning

confidence: 99%

Plasma cell but not CD20-mediated B-cell depletion protects from bleomycin-induced lung fibrosis

et al. 2022

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Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease associated with chronic inflammation and tissue remodelling leading to fibrosis, reduced pulmonary function, respiratory failure and death. Bleomycin (Blm)-induced lung fibrosis in mice replicates several clinical features of human IPF, including prominent lymphoid aggregates of predominantly B cells that accumulate in the lung adjacent to areas of active fibrosis. We have previously shown a requirement for B cells in the development of Blm-induced lung fibrosis in mice. To determine the therapeutic potential of inhibiting B cell function in pulmonary fibrosis, we examined the effects of anti-CD20 B-cell ablation therapy to selectively remove mature B cells from the immune system and inhibit Blm-induced lung fibrosis. Anti-CD20-B cell ablation did not reduce fibrosis in this model, however immune phenotyping of peripheral blood and lung resident cells revealed that anti-CD20 treated mice retained a high frequency of CD19+ CD138+ plasma cells (PCs). Interestingly, high levels of CD138+ cells were also identified in the lung tissue of patients with IPF, consistent with the mouse model. Treatment of mice with bortezomib, which depletes PCs, reduced the level of Blm-induced lung fibrosis, implicating PCs as important effector cells in the development and progression of pulmonary fibrosis.

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Section: Discussionmentioning

confidence: 99%

Plasma cell but not CD20-mediated B-cell depletion protects from bleomycin-induced lung fibrosis

et al. 2022

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“…The percentage of infiltrating immune cells that can be found in malignant tumors has a direct bearing on the growth and spread of tumors, as well as the development of cancer and the patients' overall prognoses [ 30 , 31 ]. CIBERSORT is a bioinformatics analysis tool that can evaluate the proportions of immune cells [ 32 ]. The content of immune cell infiltration can be obtained from each sample, and then the correlations between immune cells can be analyzed.…”

Section: Methodsmentioning

confidence: 99%

Identification of the Diagnostic Biomarker VIPR1 in Hepatocellular Carcinoma Based on Machine Learning Algorithm

Song

Liu

et al. 2022

Journal of Oncology

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The purpose of this study was to identify the potential diagnostic biomarkers in hepatocellular carcinoma (HCC) by machine learning (ML) and to explore the significance of immune cell infiltration in HCC. From GEO datasets, the microarray datasets of HCC patients were obtained and downloaded. Differentially expressed genes (DEGs) were screened from five datasets of GSE57957, GSE84402, GSE112790, GSE113996, and GSE121248, totalling 125 normal liver tissues and 326 HCC tissues. In order to find the diagnostic indicators of HCC, the LASSO regression and the SVM-RFE algorithms were utilized. The prognostic value of VIPR1 was analyzed. Finally, the difference of immune cell infiltration between HCC tissues and normal liver tissues was evaluated by CIBERSORT algorithm. In this study, a total of 232 DEGs were identified in 125 normal liver tissues and 326 HCC tissues. 11 diagnostic markers were identified by LASSO regression and SVM-RFE algorithms. FCN2, ECM1, VIRP1, IGFALS, and ASPG genes with AUC>0.85 were regarded as candidate biomarkers with high diagnostic value, and the above results were verified in GSE36376. Survival analyses showed that VIPR1 and IGFALS were significantly correlated with the OS, while ASPG, ECM1, and FCN2 had no statistical significance with the OS. Multivariate assays indicated that VIPR1 gene could be used as an independent prognostic factor for HCC, while FCN2, ECM1, IGFALS, and ASPG could not be used as independent prognostic factors for HCC. Immune cell infiltration analyses showed that the expression of VIPR1 in HCC was positively correlated with the levels of several immune cells. Overall, VIPR1 gene can be used as a diagnostic feature marker of HCC and may be a potential target for the diagnosis and treatment of liver cancer in the future.

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Influence of the irradiated pulmonary microenvironment on macrophage and T cell dynamics

Groves

Misra

Clair

et al. 2023

Radiotherapy and Oncology

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Analysis of immune-related genes in idiopathic pulmonary fibrosis based on bioinformatics and experimental verification

Cited by 4 publications

References 55 publications

Plasma cell but not CD20-mediated B-cell depletion protects from bleomycin-induced lung fibrosis

Plasma cell but not CD20-mediated B-cell depletion protects from bleomycin-induced lung fibrosis

Identification of the Diagnostic Biomarker VIPR1 in Hepatocellular Carcinoma Based on Machine Learning Algorithm

Influence of the irradiated pulmonary microenvironment on macrophage and T cell dynamics

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