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Li Z, Zhang W, Li S, Tao X, Xu H, Wu Y, Chen Q, Ning A, Tian T, Zhang L, Cui J, Wang W, Chu M. Integration of apaQTL and eQTL analysis reveals novel SNPs associated with occupational pulmonary fibrosis risk. Arch Toxicol 2024; 98:2117-2129. [PMID: 38538875 DOI: 10.1007/s00204-024-03734-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/07/2024] [Indexed: 06/13/2024]
Abstract
To explore the association between apaQTL/eQTL-SNPs and the susceptibility to silicosis. A silicosis-related GWAS was initially conducted to screen for single nucleotide polymorphisms (SNPs) associated with the risk of silicosis. Candidate SNPs with apaQTL and eQTL functions were then obtained from the 3'aQTL-atlas and GTEx databases. Subsequently, additional case-control studies were performed to validate the relationship between the candidate apaQTL/eQTL-SNPs and the risk of silicosis. Finally, experiments were conducted to illustrate APA events occurring at different alleles of the identified apaQTL/eQTL-SNPs. The combined results of the GWAS and iMLDR validations indicate that the variant T allele of the rs2974341 located on SMIM19 (additive model: OR = 0.66, the 95% CI = 0.53-0.84, P = 0.001) and the variant T allele of the rs2390488 located on TMTC4 (additive model: OR = 0.72, 95% CI = 0.57-0.90, P = 0.005) were significantly associated with decreased risk of developing silicosis susceptibility. Furthermore, 3'RACE experiments verified the presence of two poly (A) sites (proximal and distal) in SMIM19, rs2974341 may remotely regulate the binding between miRNA-3646 and SMIM19 with its high LD locus rs2974353 to affect the expression level of SMIM19. The rs2974341 variant T allele may contribute to the generation of the shorter 3'UTR transcript of SMIM19 and affect the binding of miRNA-3646 to the target gene SMIM19. The apaQTL/eQTL-SNPs may provide new perspectives for evaluating the regulatory function of SNPs in the development of silicosis.
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Affiliation(s)
- Zhenyu Li
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Wendi Zhang
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Siqi Li
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Xiaobo Tao
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Huiwen Xu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yutong Wu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Qiong Chen
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Anhui Ning
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Tian Tian
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Lei Zhang
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Jiahua Cui
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Wei Wang
- Department of Occupational Health, Center for Disease Control and Prevention of Wuxi, Wuxi, China
| | - Minjie Chu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China.
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Ahmad S, Singh AP, Bano N, Raza K, Singh J, Medigeshi GR, Pandey R, Gautam HK. Integrative analysis discovers Imidurea as dual multitargeted inhibitor of CD69, CD40, SHP2, lysozyme, GATA3, cCBL, and S-cysteinase from SARS-CoV-2 and M. tuberculosis. Int J Biol Macromol 2024; 270:132332. [PMID: 38768914 DOI: 10.1016/j.ijbiomac.2024.132332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/30/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024]
Abstract
Two of the deadliest infectious diseases, COVID-19 and tuberculosis (TB), have combined to establish a worldwide pandemic, wreaking havoc on economies and claiming countless lives. The optimised, multitargeted medications may diminish resistance and counter them together. Based on computational expression studies, 183 genes were co-expressed in COVID-19 and TB blood samples. We used the multisampling screening algorithms on the top ten co-expressed genes (CD40, SHP2, Lysozyme, GATA3, cCBL, SIVmac239 Nef, CD69, S-adenosylhomocysteinase, Chemokine Receptor-7, and Membrane Protein). Imidurea is a multitargeted inhibitor for COVID-19 and TB, as confirmed by extensive screening and post-filtering utilising MM\GBSA algorithms. Imidurea has shown docking and MM\GBSA scores of -8.21 to -4.75 Kcal/mol and -64.16 to -29.38 Kcal/mol, respectively. The DFT, pharmacokinetics, and interaction patterns suggest that Imidurea may be a drug candidate, and all ten complexes were tested for stability and bond strength using 100 ns for all MD atoms. The modelling findings showed the complex's repurposing potential, with a cumulative deviation and fluctuation of <2 Å and significant intermolecular interaction, which validated the possibilities. Finally, an inhibition test was performed to confirm our in-silico findings on SARS-CoV-2 Delta variant infection, which was suppressed by adding imidurea to Vero E6 cells after infection.
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Affiliation(s)
- Shaban Ahmad
- Computational Intelligence and Bioinformatics Lab, Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India.
| | - Akash Pratap Singh
- Division of Immunology and Infectious Disease Biology, Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India; Academy of Innovative and Scientific Research (AcSIR), Ghaziabad 201002, India; Department of Botany, Maitreyi College, University of Delhi, New Delhi 110021, India.
| | - Nagmi Bano
- Computational Intelligence and Bioinformatics Lab, Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India.
| | - Khalid Raza
- Computational Intelligence and Bioinformatics Lab, Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India.
| | - Janmejay Singh
- Bioassay Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India.
| | - Guruprasad R Medigeshi
- Bioassay Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India.
| | - Rajesh Pandey
- Academy of Innovative and Scientific Research (AcSIR), Ghaziabad 201002, India; Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE), Institute of Genomics and Integrative Biology (IGIB), Mall Road, New Delhi 110007, India.
| | - Hemant K Gautam
- Division of Immunology and Infectious Disease Biology, Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India; Academy of Innovative and Scientific Research (AcSIR), Ghaziabad 201002, India.
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3
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Liu C, Wu H, Li K, Chi Y, Wu Z, Xing C. Identification of biomarkers for abdominal aortic aneurysm in Behçet's disease via mendelian randomization and integrated bioinformatics analyses. J Cell Mol Med 2024; 28:e18398. [PMID: 38785203 PMCID: PMC11117452 DOI: 10.1111/jcmm.18398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/03/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Behçet's disease (BD) is a complex autoimmune disorder impacting several organ systems. Although the involvement of abdominal aortic aneurysm (AAA) in BD is rare, it can be associated with severe consequences. In the present study, we identified diagnostic biomarkers in patients with BD having AAA. Mendelian randomization (MR) analysis was initially used to explore the potential causal association between BD and AAA. The Limma package, WGCNA, PPI and machine learning algorithms were employed to identify potential diagnostic genes. A receiver operating characteristic curve (ROC) for the nomogram was constructed to ascertain the diagnostic value of AAA in patients with BD. Finally, immune cell infiltration analyses and single-sample gene set enrichment analysis (ssGSEA) were conducted. The MR analysis indicated a suggestive association between BD and the risk of AAA (odds ratio [OR]: 1.0384, 95% confidence interval [CI]: 1.0081-1.0696, p = 0.0126). Three hub genes (CD247, CD2 and CCR7) were identified using the integrated bioinformatics analyses, which were subsequently utilised to construct a nomogram (area under the curve [AUC]: 0.982, 95% CI: 0.944-1.000). Finally, the immune cell infiltration assay revealed that dysregulation immune cells were positively correlated with the three hub genes. Our MR analyses revealed a higher susceptibility of patients with BD to AAA. We used a systematic approach to identify three potential hub genes (CD247, CD2 and CCR7) and developed a nomogram to assist in the diagnosis of AAA among patients with BD. In addition, immune cell infiltration analysis indicated the dysregulation in immune cell proportions.
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Affiliation(s)
- Chunjiang Liu
- Department of General SurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Huadong Wu
- Department of vascular surgeryFirst affiliated Hospital of Huzhou UniversityHuzhouChina
| | - Kuan Li
- Department of General SurgeryKunshan Hospital of Traditional Chinese MedicineKunshanChina
| | - Yongxing Chi
- Department of General SurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Zhaoying Wu
- Department of General SurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Chungen Xing
- Department of General SurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouChina
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Tan ZY, Lou Y, Qin YC, Lin W, Liang BB, Sooranna SR, Ma YL, Zhou SF. Novel kinase 1 regulates CD8+T cells as a potential therapeutic mechanism for idiopathic pulmonary fibrosis. Int J Med Sci 2024; 21:1079-1090. [PMID: 38774751 PMCID: PMC11103402 DOI: 10.7150/ijms.93510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/11/2024] [Indexed: 05/24/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a rare, chronic and progressively worsening lung disease that poses a significant threat to patient prognosis, with a mortality rate exceeding that of some common malignancies. Effective methods for early diagnosis and treatment remain for this condition are elusive. In our study, we used the GEO database to access second-generation sequencing data and associated clinical information from IPF patients. By utilizing bioinformatics techniques, we identified crucial disease-related genes and their biological functions, and characterized their expression patterns. Furthermore, we mapped out the immune landscape of IPF, which revealed potential roles for novel kinase 1 and CD8+T cells in disease progression and outcome. These findings can aid the development of new strategies for the clinical diagnosis and treatment of IPF.
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Affiliation(s)
- Zhen-Yuan Tan
- School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Yuan Lou
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, Guangxi 530021, China
| | - Yu-Cui Qin
- School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Wei Lin
- School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Bin-Bin Liang
- School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Suren R. Sooranna
- Department of Metabolism, Digestion and Reproduction Faculty of Medicine Imperial College London Chelsea & Westminster Hospital, London SW10 9NH, UK
- Life Science and Clinical Research Center, Youjiang Medical University for Nationalities,18 Zhongshan Road II, Baise 533000, Guangxi, China
| | - Yi-Li Ma
- School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Su-Fang Zhou
- School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
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Li L, Hu Y, Li X, Ju B. A comprehensive analysis of the KLRB1 expression and its clinical implication in testicular germ cell tumors: A review. Medicine (Baltimore) 2024; 103:e37688. [PMID: 38608099 PMCID: PMC11018193 DOI: 10.1097/md.0000000000037688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 03/01/2024] [Indexed: 04/14/2024] Open
Abstract
Testicular germ cell tumors (TGCT) are the most common testicular malignancies. KLRB1 is considered to influence the development and progression of a number of cancers. However, it is unclear how the KLRB1 gene functions in TGCT. First, it was determined the expression level of KLRB1 in TGCT using The Cancer Genome Atlas (TCGA) (The Cancer Genome Atlas) dataset and GTEx (Genotype-Tissue Expression) dataset. The clinical significance and biological functions of KLRB1 were explored using the TCGA dataset, and we analyzed the correlation of the KLRB1 gene with tumor immunity and infiltrating immune cells using gene set variation analysis and the TIMER database. We found that the expression level of KLRB1 was upregulated in TGCT malignant tissues with the corresponding normal tissues as controls, and KLRB1 expression correlated with clinicopathologic features of TGCT. Functional enrichment analysis suggested that KLRB1 might be involved in immune response and inflammatory response. KLRB1 was highly positively correlated with natural killer cell activation in immune response and positively correlated with tumor-infiltrating immune cells. This study demonstrated for the first time the role of KLRB1 in TGCT, which may serve as a new biomarker associated with immune infiltration and provide a potential therapeutic target for the treatment of TGCT.
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Affiliation(s)
- Luyu Li
- The First Clinical School of Medicine Henan University of Chinese Medicine, Zhengzhou, Henan 450000, China
| | - Yaorui Hu
- Department of Neurobiology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- Institute of Neurobiology, Health and Rehabilitation Sciences of University, Qingdao, Shandong 266000, China
| | - Xiao Li
- Department of Andrology, the First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan 450000, China
| | - Baojun Ju
- Department of Andrology, the First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan 450000, China
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Zhou Y, Hu Z, Sun Q, Dong Y. 5-methyladenosine regulators play a crucial role in development of chronic hypersensitivity pneumonitis and idiopathic pulmonary fibrosis. Sci Rep 2023; 13:5941. [PMID: 37045913 PMCID: PMC10097674 DOI: 10.1038/s41598-023-32452-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
5-methyladenosine (m5C) modification regulates gene expression and biological functions in oncologic areas. However, the effect of m5C modification in chronic hypersensitivity pneumonitis (CHP) and idiopathic pulmonary fibrosis (IPF) remains unknown. Expression data for 12 significant m5C regulators were obtained from the interstitial lung disease dataset. Five candidate m5C regulators, namely tet methylcytosine dioxygenase 2, NOP2/Sun RNA methyltransferase 5, Y-box binding protein 1, tRNA aspartic acid methyltransferase 1, and NOP2/Sun RNA methyltransferase 3 were screened using random forest and nomogram models to predict risks of pulmonary fibrosis. Next, we applied the consensus clustering method to stratify the samples with different m5C patterns into two groups (cluster A and B). Finally, we calculated immune cell infiltration scores via single-sample gene set enrichment analysis, then compared immune cell infiltration, related functions as well as the expression of programmed cell death 1 (PD-1, PDCD1) and programmed death protein ligand-1 (PD-L1, CD274) between the two clusters. Principal component analysis of m5C-related scores across the 288 samples revealed that cluster A had higher immune-related expression than B. Notably, T helper cell (Th) 2 type cytokines and Th1 signatures were more abundant in clusters A and B, respectively. Our results suggest that m5C is associated with and plays a crucial role in development of pulmonary fibrosis. These m5C patterns could be potential biomarkers for identification of CHP and IPF, and guide future development of immunotherapy or other new drugs strategies for pulmonary fibrosis.
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Affiliation(s)
- Yiyi Zhou
- Department of Respiratory and Critical Care Medicine, Changhai Hospital, Shanghai, China
| | - Zhenli Hu
- Department of Respiratory and Critical Care Medicine, Changhai Hospital, Shanghai, China
| | - Qinying Sun
- Department of Respiratory and Critical Care Medicine, Changhai Hospital, Shanghai, China
| | - Yuchao Dong
- Department of Respiratory and Critical Care Medicine, Changhai Hospital, Shanghai, China.
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Saito S, Deskin B, Rehan M, Yadav S, Matsunaga Y, Lasky JA, Thannickal VJ. Novel mediators of idiopathic pulmonary fibrosis. Clin Sci (Lond) 2022; 136:1229-1240. [PMID: 36043396 DOI: 10.1042/cs20210878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022]
Abstract
Fibrosis involving the lung may occur in many settings, including in association with known environmental agents, connective tissue diseases, and exposure to drugs or radiation therapy. The most common form is referred to as 'idiopathic' since a causal agent or specific association has not been determined; the strongest risk factor for idiopathic pulmonary fibrosis is aging. Emerging studies indicate that targeting certain components of aging biology may be effective in mitigating age-associated fibrosis. While transforming growth factor-β1 (TGF-β1) is a central mediator of fibrosis in almost all contexts, and across multiple organs, it is not feasible to target this canonical pathway at the ligand-receptor level due to the pleiotropic nature of its actions; importantly, its homeostatic roles as a tumor-suppressor and immune-modulator make this an imprudent strategy. However, defining targets downstream of its receptor(s) that mediate fibrogenesis, while relatively dispenable for tumor- and immune-suppressive functions may aid in developing safer and more effective therapies. In this review, we explore molecular targets that, although TGF-β1 induced/activated, may be relatively more selective in mediating tissue fibrosis. Additionally, we explore epigenetic mechanisms with global effects on the fibrogenic process, as well as metabolic pathways that regulate aging and fibrosis.
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Affiliation(s)
- Shigeki Saito
- Section of Pulmonary Diseases, Critical Care and Environmental Medicine, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
| | - Brian Deskin
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
| | - Mohammad Rehan
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
| | - Santosh Yadav
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
| | - Yasuka Matsunaga
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
| | - Joseph A Lasky
- Section of Pulmonary Diseases, Critical Care and Environmental Medicine, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
| | - Victor J Thannickal
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
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Deng LF. Identification of Immune-Related Hub Genes in Thymoma: Defects in CD247 and Characteristics of Paraneoplastic Syndrome. Front Genet 2022; 13:895587. [PMID: 35774508 PMCID: PMC9237438 DOI: 10.3389/fgene.2022.895587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Thymomas (Ts) and thymic carcinomas (TCs) are rare primary tumors of the mediastinum. Paraneoplastic syndrome (PNS) is an important feature of thymoma, which presents great challenges to clinicians.Methods: The present study uses the weighted gene co-expression network analysis (WGCNA) to identify possible immunologic mechanisms of thymoma. RNA sequencing data from thymoma samples were downloaded from the TCGA. Core genes were taken from the module that is closely related to the WHO’s stage of classification. Enhanced analysis using the online database “Metascape” and an overall survival (OS) analysis were carried out via the Kaplan–Meier method. The hub genes were obtained from the protein–protein interaction (PPI) network. In addition, we jointly analyzed multiple sets of PNS data related to thymomas from other sources to verify the correlation between thymomas and PNS. The impact of hub genes on the prognosis of PNS was evaluated via the ROC curve, with simultaneous analysis of immune infiltration by CIBERSORT.Findings: The 14 immune hub genes closely related to thymomas were found to be jointly involved in the T-cell receptor signaling pathway. Compared to the normal thymus and type B1/B2 thymoma, there is a lower number of T-cells in type A/B3 thymoma and thymic carcinoma. The expression of genes related to the T-cell receptor signaling pathway appeared defective. The low expression of CD247 and the decrease in the number of mature T-cells are common features among thymomas, specific pulmonary fibrosis, rheumatoid arthritis, and systemic lupus erythematosus.
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Affiliation(s)
- Lin-Fang Deng
- College of Sciences, Shanghai University, Shanghai, China
- College of Medicine, Shanghai University, Shanghai, China
- *Correspondence: Lin-Fang Deng,
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Zhang B, Zhong W, Yang B, Li Y, Duan S, Huang J, Mao Y. Gene expression profiling reveals candidate biomarkers and probable molecular mechanisms in chronic stress. Bioengineered 2022; 13:6048-6060. [PMID: 35184642 PMCID: PMC8973686 DOI: 10.1080/21655979.2022.2040872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Chronic stress refers to nonspecific systemic reactions under the over-stimulation of different external and internal factors for a long time. Previous studies confirmed that chronic psychological stress had a negative effect on almost all tissues and organs. We intended to further identify potential gene targets related to the pathogenesis of chronic stress-induced consequences involved in different diseases. In our study, mice in the model group lived under the condition of chronic unpredictable mild stress (CUMS) until they expressed behaviors like depression which were supposed to undergo chronic stress. We applied high-throughput RNA sequencing to assess mRNA expression and obtained transcription profiles in lung tissue from CUMS mice and control mice for analysis. In view of the prediction of high-throughput RNA sequences and bioinformatics software, and mRNA regulatory network was constructed. First, we conducted differentially expressed genes (DEGs) and obtained 282 DEGs between CUMS (group A) and the control model (group B). Then, we conducted functional and pathway enrichment analyses. In general, the function of upregulated regulated DEGs is related to immune and inflammatory responses. PPI network identified several essential genes, of which ten hub genes were related to the T cell receptor signaling pathway. qRT-PCR results verified the regulatory network of mRNA. The expressions of CD28, CD3e, and CD247 increased in mice with CUMS compared with that in control. This illustrated immune pathways are related to the pathological molecular mechanism of chronic stress and may provide information for identifying potential biomarkers and early detection of chronic stress.
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Affiliation(s)
- Bohan Zhang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, SH, China
| | - Weijie Zhong
- Department of Neurosurgery, Ninth People Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, SH, China
| | - Biao Yang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, SH, China
| | - Yi Li
- Department of Neurosurgery, Ninth People Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, SH, China
| | - Shuxian Duan
- Department of Neurosurgery, Ninth People Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, SH, China
| | - Junlong Huang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, SH, China
| | - Yanfei Mao
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, SH, China
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Li Y, He Y, Chen S, Wang Q, Yang Y, Shen D, Ma J, Wen Z, Ning S, Chen H. S100A12 as Biomarker of Disease Severity and Prognosis in Patients With Idiopathic Pulmonary Fibrosis. Front Immunol 2022; 13:810338. [PMID: 35185901 PMCID: PMC8854978 DOI: 10.3389/fimmu.2022.810338] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/13/2022] [Indexed: 02/06/2023] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is one of interstitial lung diseases (ILDs) with poor prognosis. S100 calcium binding protein A12 (S100A12) has been reported as a prognostic serum biomarker in the IPF, but its correlation with IPF remains unclear in the lung tissue and bronchoalveolar lavage fluids (BALF). Methods Datasets were collected from the Gene Expression Omnibus (GEO) database. Person correlation coefficient, Kaplan–Meier analysis, Cox regression analysis, functional enrichment analysis and so on were used. And single cell RNA-sequencing (scRNA-seq) analysis was also used to explore the role of S100A12 and related genes in the IPF. Results S100A12 was mainly and highly expressed in the monocytes, and its expression was downregulated in the lung of patients with IPF according to scRNA-seq and the transcriptome analysis. However, S100A12 expression was upregulated both in blood and BALF of patients with IPF. In addition, 10 genes were found to interact with S100A12 according to protein–protein interaction (PPI) network, and the first four transcription factors (TF) targeted these genes were found according to hTFtarget database. Two most significant co-expression genes of S100A12 were S100A8 and S100A9. The 3 genes were significantly negatively associated with lung function and positively associated with the St. George’s Respiratory Questionnaire (SGRQ) scores in the lung of patients with IPF. And, high expression of the 3 genes was associated with higher mortality in the BALF, and shorter transplant-free survival (TFS) and progression-free survival (PFS) time in the blood. Prognostic predictive value of S100A12 was more superior to S100A8 and S100A9 in patients with IPF, and the composited variable [S100A12 + GAP index (gender, age, and physiological index)] may be a more effective predictive index. Conclusion These results imply that S100A12 might be an efficient disease severity and prognostic biomarker in patients with IPF.
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Affiliation(s)
- Yupeng Li
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yaowu He
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shibin Chen
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Qi Wang
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yi Yang
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Danting Shen
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jing Ma
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhe Wen
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- *Correspondence: Hong Chen, ; Shangwei Ning,
| | - Hong Chen
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Hong Chen, ; Shangwei Ning,
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He Y, Shang Y, Li Y, Wang M, Yu D, Yang Y, Ning S, Chen H. An 8-ferroptosis-related genes signature from Bronchoalveolar Lavage Fluid for prognosis in patients with idiopathic pulmonary fibrosis. BMC Pulm Med 2022; 22:15. [PMID: 34983465 PMCID: PMC8728942 DOI: 10.1186/s12890-021-01799-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022] Open
Abstract
Background With the rapid advances of genetic and genomic technologies, the pathophysiological mechanisms of idiopathic pulmonary fibrosis (IPF) were gradually becoming clear, however, the prognosis of IPF was still poor. This study aimed to systematically explore the ferroptosis-related genes model associated with prognosis in IPF patients. Methods Datasets were collected from the Gene Expression Omnibus (GEO). The least absolute shrinkage and selection operator (LASSO) Cox regression analysis was applied to create a multi-gene predicted model from patients with IPF in the Freiburg cohort of the GSE70866 dataset. The Siena cohort and the Leuven cohort were used for validation. Results Nineteen differentially expressed genes (DEGs) between the patients with IPF and control were associated with poor prognosis based on the univariate Cox regression analysis (all P < 0.05). According to the median value of the risk score derived from an 8-ferroptosis-related genes signature, the three cohorts’ patients were stratified into two risk groups. Prognosis of high-risk group (high risk score) was significantly poorer compared with low-risk group in the three cohorts. According to multivariate Cox regression analyses, the risk score was an independently predictor for poor prognosis in the three cohorts. Receiver operating characteristic (ROC) curve analysis and decision curve analysis (DCA) confirmed the signature's predictive value in the three cohorts. According to functional analysis, inflammation- and immune-related pathways and biological process could participate in the progression of IPF. Conclusions These results imply that the 8-ferroptosis-related genes signature in the bronchoalveolar lavage samples might be an effective model to predict the poor prognosis of IPF. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01799-7.
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Affiliation(s)
- Yaowu He
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Yu Shang
- Department of Respiration, The First Hospital of Harbin, Harbin, 150010, China
| | - Yupeng Li
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Menghan Wang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Dongping Yu
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Yi Yang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China.
| | - Hong Chen
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
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