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Giriyappagoudar M, Vastrad B, Horakeri R, Vastrad C. Study on Potential Differentially Expressed Genes in Idiopathic Pulmonary Fibrosis by Bioinformatics and Next-Generation Sequencing Data Analysis. Biomedicines 2023; 11:3109. [PMID: 38137330 PMCID: PMC10740779 DOI: 10.3390/biomedicines11123109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/24/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the potential molecular pathogenesis of IPF and provide guidance for clinical treatment. Next-generation sequencing dataset GSE213001 was obtained from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified between IPF and normal control group. The DEGs between IPF and normal control group were screened with the DESeq2 package of R language. The Gene Ontology (GO) and REACTOME pathway enrichment analyses of the DEGs were performed. Using the g:Profiler, the function and pathway enrichment analyses of DEGs were performed. Then, a protein-protein interaction (PPI) network was constructed via the Integrated Interactions Database (IID) database. Cytoscape with Network Analyzer was used to identify the hub genes. miRNet and NetworkAnalyst databaseswereused to construct the targeted microRNAs (miRNAs), transcription factors (TFs), and small drug molecules. Finally, receiver operating characteristic (ROC) curve analysis was used to validate the hub genes. A total of 958 DEGs were screened out in this study, including 479 up regulated genes and 479 down regulated genes. Most of the DEGs were significantly enriched in response to stimulus, GPCR ligand binding, microtubule-based process, and defective GALNT3 causes HFTC. In combination with the results of the PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network, hub genes including LRRK2, BMI1, EBP, MNDA, KBTBD7, KRT15, OTX1, TEKT4, SPAG8, and EFHC2 were selected. Cyclothiazide and rotigotinethe are predicted small drug molecules for IPF treatment. Our findings will contribute to identification of potential biomarkers and novel strategies for the treatment of IPF, and provide a novel strategy for clinical therapy.
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Affiliation(s)
- Muttanagouda Giriyappagoudar
- Department of Radiation Oncology, Karnataka Institute of Medical Sciences (KIMS), Hubballi 580022, Karnataka, India;
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. Socitey’s College of Pharmacy, Gadag 582101, Karnataka, India;
| | - Rajeshwari Horakeri
- Department of Computer Science, Govt First Grade College, Hubballi 580032, Karnataka, India;
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karnataka, India
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Hu M, Li T, Ma X, Liu S, Li C, Huang Z, Lin Y, Wu R, Wang S, Lu D, Lu T, Men X, Shen S, Huang H, Liu Y, Song K, Jian B, Jiang Y, Qiu W, Liu Q, Lu Z, Cai W. Macrophage lineage cells-derived migrasomes activate complement-dependent blood-brain barrier damage in cerebral amyloid angiopathy mouse model. Nat Commun 2023; 14:3945. [PMID: 37402721 DOI: 10.1038/s41467-023-39693-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 06/16/2023] [Indexed: 07/06/2023] Open
Abstract
Accumulation of amyloid beta protein (Aβ) in brain vessels damages blood brain barrier (BBB) integrity in cerebral amyloid angiopathy (CAA). Macrophage lineage cells scavenge Aβ and produce disease-modifying mediators. Herein, we report that Aβ40-induced macrophage-derived migrasomes are sticky to blood vessels in skin biopsy samples from CAA patients and brain tissue from CAA mouse models (Tg-SwDI/B and 5xFAD mice). We show that CD5L is packed in migrasomes and docked to blood vessels, and that enrichment of CD5L impairs the resistance to complement activation. Increased migrasome-producing capacity of macrophages and membrane attack complex (MAC) in blood are associated with disease severity in both patients and Tg-SwDI/B mice. Of note, complement inhibitory treatment protects against migrasomes-mediated blood-brain barrier injury in Tg-SwDI/B mice. We thus propose that macrophage-derived migrasomes and the consequent complement activation are potential biomarkers and therapeutic targets in CAA.
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Affiliation(s)
- Mengyan Hu
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, 510630, China
- Center of Clinical Immunology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Tiemei Li
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Xiaomeng Ma
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Sanxin Liu
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Chunyi Li
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Zhenchao Huang
- Department of Neurosurgery, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Yinyao Lin
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Ruizhen Wu
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Shisi Wang
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Danli Lu
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Tingting Lu
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Xuejiao Men
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Shishi Shen
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Huipeng Huang
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Yuxin Liu
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Kangyu Song
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Banghao Jian
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Yuxuan Jiang
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Wei Qiu
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Quentin Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, 510060, China.
| | - Zhengqi Lu
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
| | - Wei Cai
- Department of Neurology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, 510630, China.
- Center of Clinical Immunology, Mental and Neurological Disease Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
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Yang H, Luo Y, Lai X. The comprehensive role of apoptosis inhibitor of macrophage (AIM) in pathological conditions. Clin Exp Immunol 2023; 212:184-198. [PMID: 36427004 PMCID: PMC10243866 DOI: 10.1093/cei/uxac095] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/30/2022] [Accepted: 11/08/2022] [Indexed: 08/19/2023] Open
Abstract
CD5L/AIM (apoptosis inhibitor of macrophage), as an important component in maintaining tissue homeostasis and inflammation, is mainly produced and secreted by macrophages but partially dissociated and released from blood AIM-IgM. AIM plays a regulatory role in intracellular physiological mechanisms, including lipid metabolism and apoptosis. AIM not only increases in autoimmune diseases, directly targets liver cells in liver cancer and promotes cell clearance in acute kidney injury, but also causes arteriosclerosis and cardiovascular events, and aggravates inflammatory reactions in lung diseases and sepsis. Obviously, AIM plays a pleiotropic role in the body. However, to date, studies have failed to decipher the mechanisms behind its different roles (beneficial or harmful) in inflammatory regulation. The inflammatory response is a "double-edged sword," and maintaining balance is critical for effective host defense while minimizing the adverse side effects of acute inflammation. Enhancing the understanding of AIM function could provide the theoretical basis for new therapies in these pathological settings. In this review, we discuss recent studies on the roles of AIM in lipid metabolism, autoimmune diseases and organic tissues, such as liver cancer, myocardial infarction, and kidney disease.
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Affiliation(s)
- Huiqing Yang
- Department of Laboratory Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yan Luo
- Department of Laboratory Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaofei Lai
- Department of Laboratory Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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The Presence of Psoriasis, Metabolic Syndrome and Their Combination Increases the Serum Levels of CRP and CD5L but Not sCD200R1 and sTLR2 in Participants. J Pers Med 2022; 12:jpm12121965. [PMID: 36556186 PMCID: PMC9783034 DOI: 10.3390/jpm12121965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Psoriasis and metabolic syndrome (MetS) are chronic inflammatory conditions associated with the dysregulation of immune system reactivity. The inflammatory processes of both diseases have not yet been fully characterized, and the evaluation of proteins/markers that could be involved in their pathogenesis is of great importance. We selected four markers: CRP, sCD200R1, CD5L, and sTLR2; in particular, sCDR2001 has not yet been measured in the context of psoriasis and metabolic syndrome. Material and methods: In the study, 64 controls and 43 patients with psoriasis with or without a metabolic syndrome were enrolled. The levels of selected markers were measured using ELISA kits. Results: CRP levels were significantly higher in psoriasis patients, especially in the subgroup of patients with MetS compared to nonMetS patients (p < 0.01). sCD200R1 and sTLR2 were not significantly different between groups and subgroups; however, CD200R1 levels were slightly higher in both control groups compared to both groups of patients. CD5L levels were significantly higher in patients with MetS compared to nonMets patients (p < 0.02). We also evaluated the correlations between parameters in controls and patients’ groups, as well as in subgroups. Correlations between BMI and CRP were found in all groups and subgroups. Other correlations were group- and subgroup-specific. For example, in the patients’ group, CD5L correlated with sCD200R1 (p < 0.05) and in MetS controls, with age (p < 0.03). Conclusion: The results show that the presence of systemic inflammation associated with psoriasis and metabolic syndrome and their combination alters the expression of specific molecules, especially CRP and CD5L, which were significantly increased in patients with psoriasis and a metabolic syndrome compared to controls without metabolic syndromes. Correlations between CRP and BMI in all groups suggest that overweight and obesity increase the intensity of inflammation and potentiate CD5L expression. In contrast, levels of molecules that may limit inflammation were not increased in psoriasis and metabolic syndrome subjects (they were non-significantly lower compared with healthy controls), which may reflect the chronic nature of both diseases and the exhaustion of inhibitory mechanisms.
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