1
|
Granja T, Köhler D, Tang L, Burkard P, Eggstein C, Hemmen K, Heinze KG, Heck-Swain KL, Koeppen M, Günther S, Blaha M, Magunia H, Bamberg M, Konrad F, Ngamsri KC, Fuhr A, Keller M, Bernard AM, Haeberle HA, Bakchoul T, Zarbock A, Nieswandt B, Rosenberger P. Semaphorin 7A coordinates neutrophil response during pulmonary inflammation and sepsis. Blood Adv 2024; 8:2660-2674. [PMID: 38489236 PMCID: PMC11157222 DOI: 10.1182/bloodadvances.2023011778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/17/2024] Open
Abstract
ABSTRACT Pulmonary defense mechanisms are critical for host integrity during pneumonia and sepsis. This defense is fundamentally dependent on the activation of neutrophils during the innate immune response. Recent work has shown that semaphorin 7A (Sema7A) holds significant impact on platelet function, yet its role on neutrophil function within the lung is not well understood. This study aimed to identify the role of Sema7A during pulmonary inflammation and sepsis. In patients with acute respiratory distress syndrome (ARDS), we were able to show a correlation between Sema7A and oxygenation levels. During subsequent workup, we found that Sema7A binds to the neutrophil PlexinC1 receptor, increasing integrins, and L-selectin on neutrophils. Sema7A prompted neutrophil chemotaxis in vitro and the formation of platelet-neutrophil complexes in vivo. We also observed altered adhesion and transmigration of neutrophils in Sema7A-/-animals in the lung during pulmonary inflammation. This effect resulted in increased number of neutrophils in the interstitial space of Sema7A-/- animals but reduced numbers of neutrophils in the alveolar space during pulmonary sepsis. This finding was associated with significantly worse outcome of Sema7A-/- animals in a model of pulmonary sepsis. Sema7A has an immunomodulatory effect in the lung, affecting pulmonary sepsis and ARDS. This effect influences the response of neutrophils to external aggression and might influence patient outcome. This trial was registered at www.ClinicalTrials.gov as #NCT02692118.
Collapse
Affiliation(s)
- Tiago Granja
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
- Lusofona's Research Center for Biosciences & Health Technologies, CBIOS-Universidade, Lisboa, Portugal
| | - David Köhler
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| | - Linyan Tang
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
- Department of Intensive Care Medicine, Shenzhen University General Hospital, Shenzhen, China
| | - Philipp Burkard
- Institute of Experimental Biomedicine, University Hospital, University of Würzburg, Würzburg, Germany
| | - Claudia Eggstein
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| | - Katherina Hemmen
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Katrin G. Heinze
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Ka-Lin Heck-Swain
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| | - Michael Koeppen
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| | - Sven Günther
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| | - Maximilian Blaha
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| | - Harry Magunia
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| | - Maximilian Bamberg
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| | - Franziska Konrad
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| | | | - Anika Fuhr
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| | - Marius Keller
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| | - Alice M. Bernard
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| | - Helene A. Haeberle
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| | - Tamam Bakchoul
- Center for Clinical Transfusion Medicine, University Hospital of Tübingen, Tübingen, Germany
| | - Alexander Zarbock
- Department of Anesthesiology and Intensive Care Medicine and Pain Medicine, University Hospital, Münster, Germany
| | - Bernhard Nieswandt
- Department of Intensive Care Medicine, Shenzhen University General Hospital, Shenzhen, China
| | - Peter Rosenberger
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Tübingen, Germany
| |
Collapse
|
2
|
Wang Y, Wang X, Yuan Z, Liu F, Luo X, Yang J. Identifying potential drug targets for keloid: A Mendelian randomization study. J Invest Dermatol 2024:S0022-202X(24)00388-9. [PMID: 38797322 DOI: 10.1016/j.jid.2024.04.023] [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: 12/06/2023] [Revised: 04/03/2024] [Accepted: 04/19/2024] [Indexed: 05/29/2024]
Abstract
Keloids are a skin fibrosis disease characterized by troublesome symptoms, a varying degree of recurrence and inevitable side effects from treatments. Thus, identifying their drug targets is necessary. A two-sample MR analysis was conducted using proteins from the intersection of the deCODE database and "The Druggable Genome and Support for Target Identification and Validation in Drug Development" as the exposure variable. The outcome variable was based on recently published GWAS of keloids. SMR and colocalization analysis was employed to distinguish pleiotropy from linkage. Candidate targets underwent drug target analysis. The primary findings were validated through scRNA-seq data, Western Blot and immunofluorescence staining on keloids. Seven proteins were identified as potential drug targets for keloids. Among these proteins, HHIP, NTM, KLKB1, and CRIPTO showed positive correlations with keloids, while PLXNC1, SCG3 and PDGF-D exhibited negative correlations. Combined with the scRNA-seq data, NTM, PLXNC1, and PDGF-D were found highly expressed in the fibroblasts. NTM showed a significant increase in keloids as compared to normal scars. In accordance with the analysis, higher levels of protein expression of NTM in keloids compared to normal skin was observed. The identified proteins may be appealing drug targets for keloids treatment with a special emphasis on NTM.
Collapse
Affiliation(s)
- Yinmin Wang
- Department of plastic and reconstructive surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Xiuxia Wang
- Department of plastic and reconstructive surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Zhaoqi Yuan
- Department of plastic and reconstructive surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Fei Liu
- Department of plastic and reconstructive surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China; The First People's Hospital of the Lancang Lahu Autonomous County, Yunnan, China
| | - Xusong Luo
- Department of plastic and reconstructive surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
| | - Jun Yang
- Department of plastic and reconstructive surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
| |
Collapse
|
3
|
Jacob TV, Doshi GM. New Promising Routes in Peptic Ulcers: Toll-like Receptors and Semaphorins. Endocr Metab Immune Disord Drug Targets 2024; 24:865-878. [PMID: 37605412 DOI: 10.2174/1871530323666230821102718] [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: 12/03/2022] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 08/23/2023]
Abstract
Peptic ulcers (PU) are one of the commonest yet problematic diseases found to be existing in the majority of the population. Today, drugs from a wide range of therapeutic classes are available for the management of the disease. Still, the complications of the condition are difficult to tackle and the side effect profile is quite a concern. The literature indicates that Toll-like receptors (TLRs) and Semaphorins (SEMAs) have been under study for their various pharmacological actions over the past few decades. Both these signalling pathways are found to regulate immunological and inflammatory responses. Moreover, receptors and signalling molecules from the family of TLRs and SEMAs are found to have bacterial recognition and antibacterial properties which are essential in eradicating Helicobacter pylori (H. pylori), one of the major causative agents of PU. Our understanding of SEMAs, a class of proteins involved in cell signalling, is relatively less developed compared to TLRs, another class of proteins involved in the immune response. SEMAs and TLRs play different roles in biological processes, with SEMAs primarily involved in guiding cell migration and axon guidance during development, while TLRs are responsible for recognizing pathogens and initiating an immune response. Here, in this review, we will discuss in detail the signalling cascade of TLRs and SEMAs and thereby understand its association with PU for future therapeutic targeting. The review also aims at providing an overview of the study that has been into exploring the role of these signalling pathways in the management of PU.
Collapse
Affiliation(s)
- Teresa V Jacob
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, V.M. Road, Vile Parle (W), Mumbai, 400056, India
| | - Gaurav M Doshi
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, V.M. Road, Vile Parle (W), Mumbai, 400056, India
| |
Collapse
|
4
|
Liu X, Li R, Chen X, Yao J, Wang Q, Zhang J, Jiang Y, Qu Y. SYT7 is a key player in increasing exosome secretion and promoting angiogenesis in non-small-cell lung cancer. Cancer Lett 2023; 577:216400. [PMID: 37774826 DOI: 10.1016/j.canlet.2023.216400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 10/01/2023]
Abstract
Lung cancer is the leading cause of cancer-related mortality, and non-small cell lung cancer (NSCLC) accounts for approximately 85% of all lung cancer cases. Our previous study confirmed that synaptotagmin 7 (SYT7) promoted NSCLC metastasis in vivo and in vitro. Studies have shown that SYT7 is an important regulatory molecule of exocytosis in various cells. However, the characteristics of SYT7 across cancers and the function of SYT7 in tumor exosome secretion remain unclear. In this study, we conducted systematic pancancer analyses of SYT7, namely, analyses of expression patterns, diagnostic and prognostic values, genetic alterations, methylation, immune infiltration, and potential biological pathways. Furthermore, we demonstrated that SYT7 increased the secretion of exosomes from A549 and H1299 cells, promoting the migration, proliferation, and tube formation of human umbilical vein endothelial cells (HUVECs). Notably, SYT7 promoted angiogenesis by transferring exosomes containing the molecule centrosomal protein of 55 kDa (CEP55) protein to HUVECs. The CEP55 protein levels was downregulated in STAT1 inhibitor-treating SYT7-overexpresion NSCLC cells. We further found that SYT7 activated the mTOR signaling pathway through the downstream molecule CEP55, thereby promoting the invasion and metastasis of NSCLC cells. SYT7 promoted exosome secretion by NSCLC cells through upregulating syntaxin-1a and syntaxin-3. In vivo, SYT7 promoted the tumorigenesis, angiogenesis and metastasis of A549 cells through the exosome pathway. Our study is of great importance for understanding the mechanism of tumor exosome secretion and the role of exosomes in tumor progression.
Collapse
Affiliation(s)
- Xiao Liu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Rui Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xiao Chen
- Department of Respiratory Medicine, Tai'an City Central Hospital, Tai'an, China
| | - Jie Yao
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Qingxiang Wang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Jinghong Zhang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Yuanyuan Jiang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China.
| | - Yiqing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China.
| |
Collapse
|
5
|
Tseng CC, Sung YW, Chen KY, Wang PY, Yen CY, Sung WY, Wu CC, Ou TT, Tsai WC, Liao WT, Chen CJ, Lee SC, Chang SJ, Yen JH. The Role of Macrophages in Connective Tissue Disease-Associated Interstitial Lung Disease: Focusing on Molecular Mechanisms and Potential Treatment Strategies. Int J Mol Sci 2023; 24:11995. [PMID: 37569370 PMCID: PMC10419312 DOI: 10.3390/ijms241511995] [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: 04/20/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Connective tissue disease-associated interstitial lung disease (CTD-ILD) is a severe manifestation of CTD that leads to significant morbidity and mortality. Clinically, ILD can occur in diverse CTDs. Pathologically, CTD-ILD is characterized by various histologic patterns, such as nonspecific interstitial pneumonia, organizing pneumonia, and usual interstitial pneumonia. Abnormal immune system responses have traditionally been instrumental in its pathophysiology, and various changes in immune cells have been described, especially in macrophages. This article first briefly overviews the epidemiology, clinical characteristics, impacts, and histopathologic changes associated with CTD-ILD. Next, it summarizes the roles of various signaling pathways in macrophages or products of macrophages in ILD, helped by insights gained from animal models. In the following sections, this review returns to studies of macrophages in CTD-ILD in humans for an overall picture of the current understanding. Finally, we direct attention to potential therapies targeting macrophages in CTD-ILD in investigation or in clinical trials, as well as the future directions regarding macrophages in the context of CTD-ILD. Although the field of macrophages in CTD-ILD is still in its infancy, several lines of evidence suggest the potential of this area.
Collapse
Affiliation(s)
- Chia-Chun Tseng
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Ya-Wen Sung
- Department of Nursing, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Kuan-Yu Chen
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Pin-Yi Wang
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Chang-Yi Yen
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Wan-Yu Sung
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Cheng-Chin Wu
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Tsan-Teng Ou
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Wen-Chan Tsai
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Wei-Ting Liao
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Chung-Jen Chen
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 801, Taiwan
| | - Su-Chen Lee
- Laboratory Diagnosis of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shun-Jen Chang
- Department of Kinesiology, Health and Leisure Studies, National University of Kaohsiung, Kaohsiung 811, Taiwan
| | - Jeng-Hsien Yen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| |
Collapse
|
6
|
Wang R, Yang YM. Identification of potential biomarkers for idiopathic pulmonary fibrosis and validation of TDO2 as a potential therapeutic target. World J Cardiol 2023; 15:293-308. [PMID: 37397828 PMCID: PMC10308271 DOI: 10.4330/wjc.v15.i6.293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/01/2023] [Accepted: 06/13/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease with a high mortality rate. On this basis, exploring potential therapeutic targets to meet the unmet needs of IPF patients is important.
AIM To explore novel hub genes for IPF therapy.
METHODS Here, we used public datasets to identify differentially expressed genes between IPF patients and healthy donors. Potential targets were considered based on multiple bioinformatics analyses, especially the correlation between hub genes and carbon monoxide diffusing capacity of carbon monoxide, forced vital capacity, and patient survival rate. The mRNA levels of the hub genes were determined through quantitative real-time polymerase chain reaction.
RESULTS We found that TDO2 was upregulated in IPF patients and predicted poor prognosis. Surprisingly, single-cell RNA sequencing data analysis revealed significant enrichment of TDO2 in alveolar fibroblasts, indicating that TDO2 may participate in the regulation of proliferation and survival. Therefore, we verified the upregulated expression of TDO2 in an experimental mouse model of transforming growth factor-β (TGF-β)-induced pulmonary fibrosis. Furthermore, the results showed that a TDO2 inhibitor effectively suppressed TGF-β-induced fibroblast activation. These findings suggest that TDO2 may be a potential target for IPF treatment. Based on transcription factors-microRNA prediction and scRNA-seq analysis, elevated TDO2 promoted the IPF proliferation of fibroblasts and may be involved in the P53 pathway and aggravate ageing and persistent pulmonary fibrosis.
CONCLUSION We provided new target genes prediction and proposed blocking TGF-β production as a potential treatment for IPF.
Collapse
Affiliation(s)
- Ru Wang
- Henan University of Chinese Medicine, Collaborative Innovation Centre for Chinese Medicine and Respiratory Diseases, Zhengzhou 450046, Henan Province, China
| | - Yan-Mei Yang
- Zhengzhou University, Research Centre of Basic Medicine, Academy of Medical Sciences, Zhengzhou 450000, Henan Province, China
| |
Collapse
|
7
|
Targeting the Semaphorin3E-plexinD1 complex in allergic asthma. Pharmacol Ther 2023; 242:108351. [PMID: 36706796 DOI: 10.1016/j.pharmthera.2023.108351] [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: 03/31/2022] [Revised: 01/09/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
Asthma is a heterogenous airway disease characterized by airway inflammation and remodeling. It affects more than 300 million people worldwide and poses a significant burden on society. Semaphorins, discovered initially as neural guidance molecules, are ubiquitously expressed in various organs and regulate multiple signaling pathways. Interestingly, Semaphorin3E is a critical molecule in lung pathophysiology through its role in both lung development and homeostasis. Semaphorin3E binds to plexinD1, mediating regulatory effects on cell migration, proliferation, and angiogenesis. Recent in vitro and in vivo studies have demonstrated that the Semaphorin3E-plexinD1 axis is implicated in asthma, impacting inflammatory and structural cells associated with airway inflammation, tissue remodeling, and airway hyperresponsiveness. This review details the Semaphorin3E-plexinD1 axis in various aspects of asthma and highlights future directions in research including its potential role as a therapeutic target in airway allergic diseases.
Collapse
|
8
|
Zhang J, Zhang Y, Wang Z, Zhao J, Li Z, Wang K, Tian L, Yao B, Wu Q, Wang T, Wang J. Genes related to N6-methyladenosine in the diagnosis and prognosis of idiopathic pulmonary fibrosis. Front Genet 2023; 13:1102422. [PMID: 36685949 PMCID: PMC9846232 DOI: 10.3389/fgene.2022.1102422] [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: 11/18/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023] Open
Abstract
Introduction: Idiopathic pulmonary fibrosis (IPF) is a chronic progressive pulmonary fibrotic disease with unknown etiology and poor outcomes. It severely affects the quality of life. In this study, we comprehensively analyzed the expression of N6-methyladenosine (m6A) RNA methylation regulators using gene expression data from various tissue sources in IPF patients and healthy volunteers. Methods: The gene expression matrix and clinical characteristics of IPF patients were retrieved from the Gene Expression Omnibus database. A random forest model was used to construct diagnosis signature m6A regulators. Regression analysis and correlation analysis were used to identify prognosis m6A regulators. Consensus cluster analysis was used to construct different m6A prognosis risk groups, then functional enrichment, immune infiltration and drug sensitivity analysis were performed. Result: Five candidate m6A genes from lung tissue were used to predict the incidence, and the incidence was validated using datasets from bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells. Subsequently, the BALF dataset containing outcomes data was used for the prognosis analysis of m6A regulators. METTL14, G3BP2, and ZC3H13 were independent protective factors. Using correlation analysis with lung function in the lung tissue-derived dataset, METTL14 was a protective factor in IPF. Based on METTL14 and G3BP2, a consensus cluster analysis was applied to distinguish the prognostic m6A regulation patterns. The low-risk group's prognosis was significantly better than the high-risk group. Biological processes regulated by various risk groups included fibrogenesis and cell adhesion. Analysis of immune cell infiltration showed upregulation of neutrophils in the m6A high-risk group. Subsequently, five m6A high-risk group sensitive drugs and one m6A low-risk group sensitive drug were identified. Discussion: These findings suggest that m6A regulators are involved in the diagnosis and prognosis of IPF, and m6A patterns are a method to identify IPF outcomes.
Collapse
Affiliation(s)
- Jingcheng Zhang
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Ying Zhang
- Department of Respiratory, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Ziyuan Wang
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Jiachao Zhao
- College of Integrated Traditional Chinese and Western Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Zhenyu Li
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Keju Wang
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Lin Tian
- Department of Respiratory, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Baojin Yao
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Qibiao Wu
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, China,Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong University of Technology, Guangzhou, China,Zhuhai MUST Science and Technology Research Institute, Zhuhai, China,*Correspondence: Qibiao Wu, ; Tan Wang, ; Jing Wang,
| | - Tan Wang
- Department of Respiratory, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China,*Correspondence: Qibiao Wu, ; Tan Wang, ; Jing Wang,
| | - Jing Wang
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China,Department of Respiratory, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China,*Correspondence: Qibiao Wu, ; Tan Wang, ; Jing Wang,
| |
Collapse
|
9
|
Wan X, Xiao Y, Tian X, Lu Y, Chu H. Selective depletion of CD11b-positive monocytes/macrophages potently suppresses bleomycin-induced pulmonary fibrosis. Int Immunopharmacol 2023; 114:109570. [PMID: 36700767 DOI: 10.1016/j.intimp.2022.109570] [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: 10/07/2022] [Revised: 11/09/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
The understanding of pathogenesis underlying idiopathic pulmonary fibrosis (IPF) is still limited presently. Monocytes or macrophages are involved in progression of the pulmonary injury and repair. The aim of this study is to investigate the roles of CD11b+ monocytes/macrophages in the progression of pulmonary fibrosis. In this study, the expression levels of CD11B gene and inflammatory genes in the IPF patients are evaluated using the available datasets. CD11b cells are conditionally depleted in a CD11b-diptheria toxin receptor (CD11b-DTR) mouse by administration of diptheria toxin (DT). Pulmonary fibrosis in mice is induced using intranasalbleomycin. The mRNAs and proteins expression in lung tissues are determined by quantitative real-time polymerase chain reaction (qRT-PCR), immunofluorescence (IF) staining and Western-blot assays. It shows that the expression of CD11B mRNA is up-regulated in fibrotic lungs and alveolar macrophages of IPF patients and bleomycin-treated rodents. Selective depletion of CD11b+ monocytes/macrophages in CD11b-DTR mice potently halts bleomycin-induced pulmonary fibrosis progression. CD11b depletion inhibits the polarization of macrophages in the fibrotic lungs. Mechanically, CD11b deficiency represses the activation of sphingosine 1-phosphate receptor 2 (S1PR2)/sphingosine kinase 2 (SphK2) signaling during pulmonary fibrosis. In conclusion, our data suggest that CD11b+ monocytes/macrophages contribute to pulmonary fibrosis and represent a potential therapeutic target for IPF.
Collapse
Affiliation(s)
- Xiaoyu Wan
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yongtao Xiao
- Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xinbei Tian
- Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Lu
- Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haiqing Chu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.
| |
Collapse
|
10
|
Shen J, Zhao C, Zhang H, Zhou P, Li Z. Classification of tuberculosis-related programmed cell death-related patient subgroups and associated immune cell profiling. Front Immunol 2023; 14:1159713. [PMID: 37205113 PMCID: PMC10185908 DOI: 10.3389/fimmu.2023.1159713] [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: 02/06/2023] [Accepted: 04/12/2023] [Indexed: 05/21/2023] Open
Abstract
Background Tuberculosis (TB) is the deadliest communicable disease in the world with the exception of the ongoing COVID-19 pandemic. Programmed cell death (PCD) patterns play key roles in the development and progression of many disease states such that they may offer value as effective biomarkers or therapeutic targets that can aid in identifying and treating TB patients. Materials and methods The Gene Expression Omnibus (GEO) was used to gather TB-related datasets after which immune cell profiles in these data were analyzed to examine the potential TB-related loss of immune homeostasis. Profiling of differentially expressed PCD-related genes was performed, after which candidate hub PCD-associated genes were selected via a machine learning approach. TB patients were then stratified into two subsets based on the expression of PCD-related genes via consensus clustering. The potential roles of these PCD-associated genes in other TB-related diseases were further examined. Results In total, 14 PCD-related differentially expressed genes (DEGs) were identified and highly expressed in TB patient samples and significantly correlated with the abundance of many immune cell types. Machine learning algorithms enabled the selection of seven hub PCD-related genes that were used to establish PCD-associated patient subgroups, followed by the validation of these subgroups in independent datasets. These findings, together with GSVA results, indicated that immune-related pathways were significantly enriched in TB patients exhibiting high levels of PCD-related gene expression, whereas metabolic pathways were significantly enriched in the other patient group. Single cell RNA-seq (scRNA-seq) further highlighted significant differences in the immune status of these different TB patient samples. Furthermore, we used CMap to predict five potential drugs for TB-related diseases. Conclusion These results highlight clear enrichment of PCD-related gene expression in TB patients and suggest that this PCD activity is closely associated with immune cell abundance. This thus indicates that PCD may play a role in TB progression through the induction or dysregulation of an immune response. These findings provide a foundation for further research aimed at clarifying the molecular drivers of TB, the selection of appropriate diagnostic biomarkers, and the design of novel therapeutic interventions aimed at treating this deadly infectious disease.
Collapse
Affiliation(s)
- Jie Shen
- School of Medical Laboratory, Weifang Medical University, Weifang, China
| | - Chao Zhao
- Office of Academic Affairs, Weifang Medical University, Weifang, China
| | - Hong Zhang
- School of Public Health, Weifang Medical University, Weifang, China
| | - Peipei Zhou
- School of Medical Laboratory, Weifang Medical University, Weifang, China
| | - Zhenpeng Li
- School of Medical Laboratory, Weifang Medical University, Weifang, China
- *Correspondence: Zhenpeng Li,
| |
Collapse
|
11
|
Elitist random swapped particle swarm optimization embedded with variable k-nearest neighbour classification: a new PSO variant applied to gene identification. Soft comput 2022. [DOI: 10.1007/s00500-022-07515-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
|
12
|
Mostafaei S, Borna H, Emamvirdizadeh A, Arabfard M, Ahmadi A, Salimian J, Salesi M, Azimzadeh Jamalkandi S. Causal Path of COPD Progression-Associated Genes in Different Biological Samples. COPD 2022; 19:290-299. [PMID: 35696265 DOI: 10.1080/15412555.2022.2081541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory disease with pulmonary and extra-pulmonary complications. Due to the disease's systemic nature, many investigations investigated the genetic alterations in various biological samples. We aimed to infer causal genes in COPD's pathogenesis in different biological samples using elastic-net logistic regression and the Structural Equation Model. Samples of small airway epithelial cells, bronchoalveolar lavage macrophages, lung tissue biopsy, sputum, and blood samples were selected (135, 70, 235, 143, and 226 samples, respectively). Elastic-net Logistic Regression analysis was implemented to identify the most important genes involved in COPD progression. Thirty-three candidate genes were identified as essential factors in the pathogenesis of COPD and regulation of lung function. Recognized candidate genes in small airway epithelial (SAE) cells have the highest area under the ROC curve (AUC = 97%, SD = 3.9%). Our analysis indicates that macrophages and epithelial cells are more influential in COPD progression at the transcriptome level.
Collapse
Affiliation(s)
- Shayan Mostafaei
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Department of Biostatistics, Faculty of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hojat Borna
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Alireza Emamvirdizadeh
- Department of Molecular Genetics, Faculty of Bio Sciences, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Masoud Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Jafar Salimian
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahmood Salesi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Sadegh Azimzadeh Jamalkandi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| |
Collapse
|
13
|
Li Y, Chen S, Li X, Wang X, Li H, Ning S, Chen H. CD247, a Potential T Cell-Derived Disease Severity and Prognostic Biomarker in Patients With Idiopathic Pulmonary Fibrosis. Front Immunol 2021; 12:762594. [PMID: 34880861 PMCID: PMC8645971 DOI: 10.3389/fimmu.2021.762594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) has high mortality worldwide. The CD247 molecule (CD247, as known as T-cell surface glycoprotein CD3 zeta chain) has been reported as a susceptibility locus in systemic sclerosis, but its correlation with IPF remains unclear. Methods Datasets were acquired by researching the Gene Expression Omnibus (GEO). CD247 was identified as the hub gene associated with percent predicted diffusion capacity of the lung for carbon monoxide (Dlco% predicted) and prognosis according to Pearson correlation, logistic regression, and survival analysis. Results CD247 is significantly downregulated in patients with IPF compared with controls in both blood and lung tissue samples. Moreover, CD247 is significantly positively associated with Dlco% predicted in blood and lung tissue samples. Patients with low-expression CD247 had shorter transplant-free survival (TFS) time and more composite end-point events (CEP, death, or decline in FVC >10% over a 6-month period) compared with patients with high-expression CD247 (blood). Moreover, in the follow-up 1st, 3rd, 6th, and 12th months, low expression of CD247 was still the risk factor of CEP in the GSE93606 dataset (blood). Thirteen genes were found to interact with CD247 according to the protein-protein interaction network, and the 14 genes including CD247 were associated with the functions of T cells and natural killer (NK) cells such as PD-L1 expression and PD-1 checkpoint pathway and NK cell-mediated cytotoxicity. Furthermore, we also found that a low expression of CD247 might be associated with a lower activity of TIL (tumor-infiltrating lymphocytes), checkpoint, and cytolytic activity and a higher activity of macrophages and neutrophils. Conclusion These results imply that CD247 may be a potential T cell-derived disease severity and prognostic biomarker for IPF.
Collapse
Affiliation(s)
- Yupeng Li
- Department of Respiratory 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
| | - Xincheng Li
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xue Wang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Huiwen Li
- Department of Respiratory 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
| | - Hong Chen
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| |
Collapse
|
14
|
Ishikawa G, Liu A, Herzog EL. Evolving Perspectives on Innate Immune Mechanisms of IPF. Front Mol Biosci 2021; 8:676569. [PMID: 34434962 PMCID: PMC8381017 DOI: 10.3389/fmolb.2021.676569] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/29/2021] [Indexed: 12/29/2022] Open
Abstract
While epithelial-fibroblast interactions are viewed as the primary drivers of Idiopathic Pulmonary Fibrosis (IPF), evidence gleaned from animal modeling and human studies implicates innate immunity as well. To provide perspective on this topic, this review synthesizes the available data regarding the complex role of innate immunity in IPF. The role of substances present in the fibrotic microenvironment including pathogen associated molecular patterns (PAMPs) derived from invading or commensal microbes, and danger associated molecular patterns (DAMPs) derived from injured cells and tissues will be discussed along with the proposed contribution of innate immune populations such as macrophages, neutrophils, fibrocytes, myeloid suppressor cells, and innate lymphoid cells. Each component will be considered in the context of its relationship to environmental and genetic factors, disease outcomes, and potential therapies. We conclude with discussion of unanswered questions and opportunities for future study in this area.
Collapse
Affiliation(s)
- Genta Ishikawa
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Angela Liu
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Erica L. Herzog
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States,Department of Pathology, Yale School of Medicine, New Haven, CT, United States,*Correspondence: Erica L. Herzog,
| |
Collapse
|
15
|
Plexin C1: A novel screening test for lung cancer. JOURNAL OF SURGERY AND MEDICINE 2021. [DOI: 10.28982/josam.955975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
16
|
Ni Z, Huang C, Zhao H, Zhou J, Hu M, Chen Q, Ge B, Huang Q. PLXNC1: A Novel Potential Immune-Related Target for Stomach Adenocarcinoma. Front Cell Dev Biol 2021; 9:662707. [PMID: 34277610 PMCID: PMC8283001 DOI: 10.3389/fcell.2021.662707] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/09/2021] [Indexed: 12/26/2022] Open
Abstract
Background Gastric cancer is associated with tumor microenvironment and chronic inflammation, but the underlying tumor-promoting mechanisms still remain unknown. Methods The ATAC-seq was used to identify genes with chromatin accessibilities in promoter regions. The RNA-seq datasets were performed to identify differentially expressed genes (DEGs). Pearson correlation analysis with the mRNA expression of three families of tumor-related inflammation TFs was used to filter downstream DEGs. Cox univariate survival analysis was performed to identify the prognostic value. The ImmPort database and CIBERSORTx algorithm were used to investigate the regulatory relationship between hub DEGs and immune cells. Immunohistochemistry (IHC) and multidimensional database were performed to verification. Results In this case, we require 2,454 genes with chromatin accessibility in promoter regions by ATAC-seq. Based on the gene expression profiles (RNA-seq), we identified 365 genes with chromatin accessibility and differential expression. Combined with the Cox univariate survival analysis, we identified 32 survival-related DEGs with chromatin accessibility. According to ImmPort database, CXCL3, PLXNC1, and EDN2 were identified as immune- related genes in STAD. By applying the CIBERSORTx algorithm and Pearson correlation, PLXNC1 was the only gene correlated with various immune cells, significantly associated with M2 macrophages. Furthermore, gene set variation analysis (GSVA) suggests the "hallmark_interferon_gamma_response" pathway was most significantly correlated with PLXNC1. Immunohistochemistry results revealed that PLXNC1 protein level was significantly higher in STAD tissues than in normal tissues (p < 0.001). Conclusion PLXNC1, regulated by IRF5, is an immune-related gene that was significantly associated with M2 macrophages and poor outcome in stomach adenocarcinoma.
Collapse
Affiliation(s)
- Zhizhan Ni
- Department of General Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Chenshen Huang
- Department of General Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hongmei Zhao
- Department of VIP Clinic, East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jinzhe Zhou
- Department of General Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Muren Hu
- Department of General Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qing Chen
- Department of General Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bujun Ge
- Department of General Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qi Huang
- Department of General Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| |
Collapse
|
17
|
Viral fibrotic scoring and drug screen based on MAPK activity uncovers EGFR as a key regulator of COVID-19 fibrosis. Sci Rep 2021; 11:11234. [PMID: 34045585 PMCID: PMC8160348 DOI: 10.1038/s41598-021-90701-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/05/2021] [Indexed: 02/07/2023] Open
Abstract
Understanding the molecular basis of fibrosis, the lethal complication of COVID-19, is urgent. By the analysis of RNA-sequencing data of SARS-CoV-2-infected cells combined with data mining we identified genes involved in COVID-19 progression. To characterize their implication in the fibrosis development we established a correlation matrix based on the transcriptomic data of patients with idiopathic pulmonary fibrosis. With this method, we have identified a cluster of genes responsible for SARS-CoV-2-fibrosis including its entry receptor ACE2 and epidermal growth factor EGF. Then, we developed Vi-Fi scoring—a novel drug repurposing approach and simultaneously quantified antiviral and antifibrotic activities of the drugs based on their transcriptomic signatures. We revealed the strong dual antifibrotic and antiviral activity of EGFR/ErbB inhibitors. Before the in vitro validation, we have clustered 277 cell lines and revealed distinct COVID-19 transcriptomic signatures of the cells with similar phenotypes that defines their suitability for COVID-19 research. By ERK activity monitoring in living lung cells, we show that the drugs with predicted antifibrotic activity downregulate ERK in the host lung cells. Overall, our study provides novel insights on SARS-CoV-2 dependence on EGFR/ERK signaling and demonstrates the utility of EGFR/ErbB inhibitors for COVID-19 treatment.
Collapse
|
18
|
Kanth SM, Gairhe S, Torabi-Parizi P. The Role of Semaphorins and Their Receptors in Innate Immune Responses and Clinical Diseases of Acute Inflammation. Front Immunol 2021; 12:672441. [PMID: 34012455 PMCID: PMC8126651 DOI: 10.3389/fimmu.2021.672441] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/20/2021] [Indexed: 12/16/2022] Open
Abstract
Semaphorins are a group of proteins that have been studied extensively for their critical function in neuronal development. They have been shown to regulate airway development, tumorigenesis, autoimmune diseases, and the adaptive immune response. Notably, emerging literature describes the role of immunoregulatory semaphorins and their receptors, plexins and neuropilins, as modulators of innate immunity and diseases defined by acute injury to the kidneys, abdomen, heart and lungs. In this review we discuss the pathogenic functions of semaphorins in clinical conditions of acute inflammation, including sepsis and acute lung injury, with a focus on regulation of the innate immune response as well as potential future therapeutic targeting.
Collapse
Affiliation(s)
- Shreya M Kanth
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Salina Gairhe
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Parizad Torabi-Parizi
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
19
|
Merino GA, Raad J, Bugnon LA, Yones C, Kamenetzky L, Claus J, Ariel F, Milone DH, Stegmayer G. Novel SARS-CoV-2 encoded small RNAs in the passage to humans. Bioinformatics 2021; 36:5571-5581. [PMID: 33244583 PMCID: PMC7717134 DOI: 10.1093/bioinformatics/btaa1002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/15/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
Motivation The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has recently emerged as the responsible for the pandemic outbreak of the coronavirus disease (COVID-19). This virus is closely related to coronaviruses infecting bats and Malayan pangolins, species suspected to be an intermediate host in the passage to humans. Several genomic mutations affecting viral proteins have been identified, contributing to the understanding of the recent animal-to-human transmission. However, the capacity of SARS-CoV-2 to encode functional putative microRNAs (miRNAs) remains largely unexplored. Results We have used deep learning to discover 12 candidate stem-loop structures hidden in the viral protein-coding genome. Among the precursors, the expression of eight mature miRNAs-like sequences was confirmed in small RNA-seq data from SARS-CoV-2 infected human cells. Predicted miRNAs are likely to target a subset of human genes of which 109 are transcriptionally deregulated upon infection. Remarkably, 28 of those genes potentially targeted by SARS-CoV-2 miRNAs are down-regulated in infected human cells. Interestingly, most of them have been related to respiratory diseases and viral infection, including several afflictions previously associated with SARS-CoV-1 and SARS-CoV-2. The comparison of SARS-CoV-2 pre-miRNA sequences with those from bat and pangolin coronaviruses suggests that single nucleotide mutations could have helped its progenitors jumping inter-species boundaries, allowing the gain of novel mature miRNAs targeting human mRNAs. Our results suggest that the recent acquisition of novel miRNAs-like sequences in the SARS-CoV-2 genome may have contributed to modulate the transcriptional reprogramming of the new host upon infection.
Collapse
Affiliation(s)
- Gabriela A Merino
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina.,Bioengineering and Bioinformatics Research and Development Institute (IBB), FI-UNER, CONICET, Entre Ríos 3100, Argentina.,European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridgeshire CB101SD, UK
| | - Jonathan Raad
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Leandro A Bugnon
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Cristian Yones
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, UBA-CONICET, Ciudad Autónoma de Buenos Aires 1121, Argentina.,Laboratorio de Genómica y Bioinformática de Patógenos, iB3, Instituto de Biociencias, Biotecnología y Biología traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1121, Argentina
| | - Juan Claus
- Laboratorio de Virología, FBCB, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral (IAL), CONICET, FBCB, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Diego H Milone
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Georgina Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| |
Collapse
|
20
|
Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms. PLoS One 2021; 16:e0248889. [PMID: 33755690 PMCID: PMC7987152 DOI: 10.1371/journal.pone.0248889] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/07/2021] [Indexed: 12/13/2022] Open
Abstract
Idiopathic pulmonary fibrosis is a progressive and debilitating lung disease with large unmet medical need and few treatment options. We describe an analysis connecting single cell gene expression with bulk gene expression-based subsetting of patient cohorts to identify IPF patient subsets with different underlying pathogenesis and cellular changes. We reproduced earlier findings indicating the existence of two major subsets in IPF and showed that these subsets display different alterations in cellular composition of the lung. We developed classifiers based on the cellular changes in disease to distinguish subsets. Specifically, we showed that one subset of IPF patients had significant increases in gene signature scores for myeloid cells versus a second subset that had significantly increased gene signature scores for ciliated epithelial cells, suggesting a differential pathogenesis among IPF subsets. Ligand-receptor analyses suggested there was a monocyte-macrophage chemoattractant axis (including potentially CCL2-CCR2 and CCL17-CCR4) among the myeloid-enriched IPF subset and a ciliated epithelium-derived chemokine axis (e.g. CCL15) among the ciliated epithelium-enriched IPF subset. We also found that these IPF subsets had differential expression of pirfenidone-responsive genes suggesting that our findings may provide an approach to identify patients with differential responses to pirfenidone and other drugs. We believe this work is an important step towards targeted therapies and biomarkers of response.
Collapse
|
21
|
Gao R, Peng X, Perry C, Sun H, Ntokou A, Ryu C, Gomez JL, Reeves BC, Walia A, Kaminski N, Neumark N, Ishikawa G, Black KE, Hariri LP, Moore MW, Gulati M, Homer RJ, Greif DM, Eltzschig HK, Herzog EL. Macrophage-derived netrin-1 drives adrenergic nerve-associated lung fibrosis. J Clin Invest 2021; 131:136542. [PMID: 33393489 PMCID: PMC7773383 DOI: 10.1172/jci136542] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/10/2020] [Indexed: 12/12/2022] Open
Abstract
Fibrosis is a macrophage-driven process of uncontrolled extracellular matrix accumulation. Neuronal guidance proteins such as netrin-1 promote inflammatory scarring. We found that macrophage-derived netrin-1 stimulates fibrosis through its neuronal guidance functions. In mice, fibrosis due to inhaled bleomycin engendered netrin-1-expressing macrophages and fibroblasts, remodeled adrenergic nerves, and augmented noradrenaline. Cell-specific knockout mice showed that collagen accumulation, fibrotic histology, and nerve-associated endpoints required netrin-1 of macrophage but not fibroblast origin. Adrenergic denervation; haploinsufficiency of netrin-1's receptor, deleted in colorectal carcinoma; and therapeutic α1 adrenoreceptor antagonism improved collagen content and histology. An idiopathic pulmonary fibrosis (IPF) lung microarray data set showed increased netrin-1 expression. IPF lung tissues were enriched for netrin-1+ macrophages and noradrenaline. A longitudinal IPF cohort showed improved survival in patients prescribed α1 adrenoreceptor blockade. This work showed that macrophages stimulate lung fibrosis via netrin-1-driven adrenergic processes and introduced α1 blockers as a potentially new fibrotic therapy.
Collapse
Affiliation(s)
- Ruijuan Gao
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Oncology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xueyan Peng
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Carrighan Perry
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Huanxing Sun
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Aglaia Ntokou
- Section of Cardiology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Changwan Ryu
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jose L. Gomez
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Benjamin C. Reeves
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Anjali Walia
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Nir Neumark
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Genta Ishikawa
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Lida P. Hariri
- Division of Pulmonary and Critical Care Medicine, and
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Meagan W. Moore
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Mridu Gulati
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Robert J. Homer
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, and
| | - Daniel M. Greif
- Section of Cardiology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Holger K. Eltzschig
- Department of Anesthesiology, University of Texas at Houston Medical School, Houston, Texas, USA
| | - Erica L. Herzog
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, and
| |
Collapse
|
22
|
Wan X, Tian X, Du J, Lu Y, Xiao Y. Long non-coding RNA H19 deficiency ameliorates bleomycin-induced pulmonary inflammation and fibrosis. Respir Res 2020; 21:290. [PMID: 33138822 PMCID: PMC7607673 DOI: 10.1186/s12931-020-01534-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
Background The poor understanding of pathogenesis in idiopathic pulmonary fibrosis (IPF) impaired development of effective therapeutic strategies. The aim of the current study is to investigate the roles of long non-coding RNA H19 (lncRNA H19) in the pulmonary inflammation and fibrosis of IPF. Methods Bleomycin was used to induce pulmonary inflammation and fibrosis in mice. The mRNAs and proteins expression in lung tissues was determined by quantitative real-time polymerase chain reaction (qRT-PCR) and western blot. H19 knockout (H19−/−) mice were generated by CRISPR/Cas9. Results The expression of H19 mRNA was up-regulated in fibrotic lungs patients with IPF as well as in lungs tissues that obtained from bleomycin-treated mice. H19−/− mice suppressed bleomycin-mediated pulmonary inflammation and inhibited the Il6/Stat3 signaling. H19 deficiency ameliorated bleomycin-induced pulmonary fibrosis and repressed the activation of TGF-β/Smad and S1pr2/Sphk2 in the lungs of bleomycin-treated mice. Conclusions Our data suggests that H19 is a profibrotic lncRNA and a potential therapeutic target for IPF.
Collapse
Affiliation(s)
- Xiaoyu Wan
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xinbei Tian
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Jun Du
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Ying Lu
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yongtao Xiao
- Shanghai Institute for Pediatric Research, Shanghai, China. .,Department of Pediatric Surgery, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, No. 1665, Kong Jiang Road, Shanghai, China.
| |
Collapse
|
23
|
Jin H, Pang Q, Fang M, Wang Y, Man Z, Tan Y, Liu H. Syt-7 overexpression predicts poor prognosis and promotes cell proliferation in hepatocellular carcinoma. Future Oncol 2020; 16:2809-2819. [PMID: 33052751 DOI: 10.2217/fon-2020-0262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Aim: To explore the prognostic significance of Syt-7 in hepatocellular carcinoma (HCC) and the potential mechanisms. Methods: Immunohistochemistry was used to examine the expression of Syt-7. Overall survival and disease-free survival were compared between Syt-7 positive and negative groups. The effects of Syt-7 knockdown on BEL-7404 cells were further evaluated. Results: Syt-7 expression was significantly higher in HCC tumorous tissues compared with paracancerous tissues. Syt-7 was closely associated with α-fetoprotein tumor size, vascular invasion, tumor node metastasis stage and tumor differentiation. Syt-7 was an independent risk factor for overall survival and disease-free survival. Additionally, Syt-7 knockdown inhibited proliferation and colony formation and induced cell cycle arrest in HCC cells. Conclusion: Syt-7 overexpression forecasts unfavorable prognosis and promotes cell proliferation in HCC.
Collapse
Affiliation(s)
- Hao Jin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, PR China
| | - Qing Pang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, PR China
| | - Meifang Fang
- Department of Radiotherapy, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, PR China
| | - Yong Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, PR China
| | - Zhongran Man
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, PR China
| | - Yi Tan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, PR China
| | - Huichun Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, PR China
| |
Collapse
|
24
|
Luthert PJ, Kiel C. Combining Gene-Disease Associations with Single-Cell Gene Expression Data Provides Anatomy-Specific Subnetworks in Age-Related Macular Degeneration. NETWORK AND SYSTEMS MEDICINE 2020; 3:105-121. [PMID: 32789304 PMCID: PMC7416628 DOI: 10.1089/nsm.2020.0005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Age-related macular degeneration (AMD) is the most common cause of visual impairment in the developed world. Despite some treatment options for late AMD, there is no intervention that blocks early AMD proceeding to the late and blinding forms. This is partly due to the lack of precise drug targets, despite great advances in genetics, epidemiology, and protein-protein interaction (PPI) networks proposed to be driving the disease pathology. A systems approach to narrow down PPI networks to specific protein drug targets would provide new therapeutic options. Materials and Methods: In this study we analyzed single cell RNAseq (RNA sequencing) datasets of 17 cell types present in choroidal, retinal pigment epithelium (RPE), and neural retina (NR) tissues to explore if a more granular analysis incorporating different cell types exposes more specific pathways and relationships. Furthermore, we developed a novel and systematic gene ontology database (SysGO) to explore if a subcellular classification of processes will further enhance the understanding of the pathogenesis of this complex disorder and its comorbidities with other age-related diseases. Results: We found that 57% of the AMD (risk) genes are among the top 25% expressed genes in ∼1 of the 17 choroidal/RPE/NR cell types, and 9% were among the top 1% of expressed genes. Using SysGO, we identified an enrichment of AMD genes in cell membrane and extracellular anatomical locations, and we found both functional enrichments (e.g., cell adhesion) and cell types (e.g., fibroblasts, microglia) not previously associated with AMD pathogenesis. We reconstructed PPI networks among the top expressed AMD genes for all 17 choroidal/RPE/NR cell types, which provides molecular and anatomical definitions of AMD phenotypes that can guide therapeutic approaches to target this complex disease. Conclusion: We provide mechanism-based AMD endophenotypes that can be exploited in vitro, using computational models and for drug discovery/repurposing.
Collapse
Affiliation(s)
- Philip J. Luthert
- UCL Institute of Ophthalmology, and NIHR Moorfields Biomedical Research Centre, University College London, London, United Kingdom
| | - Christina Kiel
- Systems Biology Ireland and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin, Ireland
| |
Collapse
|
25
|
Maghsoudloo M, Azimzadeh Jamalkandi S, Najafi A, Masoudi-Nejad A. An efficient hybrid feature selection method to identify potential biomarkers in common chronic lung inflammatory diseases. Genomics 2020; 112:3284-3293. [PMID: 32540493 DOI: 10.1016/j.ygeno.2020.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/21/2020] [Accepted: 06/04/2020] [Indexed: 12/13/2022]
Abstract
Asthma, chronic obstructive pulmonary disease (COPD), and idiopathic pulmonary fibrosis (IPF) are three serious lung inflammatory diseases. The understanding of the pathogenesis mechanism and the identification of potential prognostic biomarkers of these diseases can provide the patients with more efficient treatments. In this study, an efficient hybrid feature selection method was introduced in order to extract informative genes. We implemented an ontology-based ranking approach on differentially expressed genes following a wrapper method. The examination of the different gene ontologies and their combinations motivated us to propose a biological functional-based method to improve the performance of further wrapper methods. The results identified: TOM1L1, SRSF1, and GIT2 in asthma; CHCHD4, PAIP2, CRLF3, UBQLN4, TRAK1, PRELID1, VAMP4, CCM2, and APBB1IP in COPD; and TUFT1, GAB2, B4GALNT1, TNFRSF17, PRDM8, and SETDB2 in IPF as the potential biomarkers. The proposed method can be used to identify hub genes in other high-throughput datasets.
Collapse
Affiliation(s)
- Mazaher Maghsoudloo
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran; Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran; Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| |
Collapse
|
26
|
Ulke HM, Mutze K, Lehmann M, Wagner DE, Heinzelmann K, Günther A, Eickelberg O, Königshoff M. The Oncogene ECT2 Contributes to a Hyperplastic, Proliferative Lung Epithelial Cell Phenotype in Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2020; 61:713-726. [PMID: 31145635 DOI: 10.1165/rcmb.2019-0047oc] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) and lung cancer are progressive lung diseases with a poor prognosis. IPF is a risk factor for the development of lung cancer, and the incidence of lung cancer is increased in patients with IPF. The disease pathogenesis of IPF and lung cancer involves common genetic alterations, dysregulated pathways, and the emergence of hyperplastic and metaplastic epithelial cells. Here, we aimed to identify novel, common mediators that might contribute to epithelial cell reprogramming in IPF. Gene set enrichment analysis of publicly available non-small cell lung cancer and IPF datasets revealed a common pattern of misregulated genes linked to cell proliferation and transformation. The oncogene ECT2 (epithelial cell transforming sequence 2), a guanine nucleotide exchange factor for Rho GTPases, was highly enriched in both IPF and non-small cell lung cancer compared with nondiseased controls. Increased expression of ECT2 was verified by qPCR and Western blotting in bleomycin-induced lung fibrosis and human IPF tissue. Immunohistochemistry demonstrated strong expression of ECT2 staining in hyperplastic alveolar epithelial type II (ATII) cells in IPF, as well as its colocalization with proliferating cell nuclear antigen, a well-known proliferation marker. Increased ECT2 expression coincided with enhanced proliferation of primary mouse ATII cells as analyzed by flow cytometry. ECT2 knockdown in ATII cells resulted in decreased proliferation and collagen I expression in vitro. These data suggest that the oncogene ECT2 contributes to epithelial cell reprogramming in IPF, and further emphasize the hyperplastic, proliferative ATII cell as a potential target in patients with IPF and lung cancer.
Collapse
Affiliation(s)
- Henrik M Ulke
- Lung Repair and Regeneration, Comprehensive Pneumology Center, Ludwig Maximilians University, University Hospital Großhadern, and Helmholtz Zentrum München, Member of the German Center for Lung Research, Munich, Germany
| | - Kathrin Mutze
- Lung Repair and Regeneration, Comprehensive Pneumology Center, Ludwig Maximilians University, University Hospital Großhadern, and Helmholtz Zentrum München, Member of the German Center for Lung Research, Munich, Germany
| | - Mareike Lehmann
- Lung Repair and Regeneration, Comprehensive Pneumology Center, Ludwig Maximilians University, University Hospital Großhadern, and Helmholtz Zentrum München, Member of the German Center for Lung Research, Munich, Germany
| | - Darcy E Wagner
- Lung Repair and Regeneration, Comprehensive Pneumology Center, Ludwig Maximilians University, University Hospital Großhadern, and Helmholtz Zentrum München, Member of the German Center for Lung Research, Munich, Germany.,Lung Bioengineering and Regeneration, Lund University, Lund, Sweden
| | - Katharina Heinzelmann
- Lung Repair and Regeneration, Comprehensive Pneumology Center, Ludwig Maximilians University, University Hospital Großhadern, and Helmholtz Zentrum München, Member of the German Center for Lung Research, Munich, Germany
| | - Andreas Günther
- Department of Internal Medicine, Universities of Giessen and Marburg Lung Center, Justus Liebig University Giessen, Member of the German Center for Lung Research, Giessen, Germany; and
| | - Oliver Eickelberg
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Denver, Aurora, Colorado
| | - Melanie Königshoff
- Lung Repair and Regeneration, Comprehensive Pneumology Center, Ludwig Maximilians University, University Hospital Großhadern, and Helmholtz Zentrum München, Member of the German Center for Lung Research, Munich, Germany.,Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Denver, Aurora, Colorado
| |
Collapse
|
27
|
Maghsoudloo M, Azimzadeh Jamalkandi S, Najafi A, Masoudi-Nejad A. Identification of biomarkers in common chronic lung diseases by co-expression networks and drug-target interactions analysis. Mol Med 2020; 26:9. [PMID: 31952466 PMCID: PMC6969427 DOI: 10.1186/s10020-019-0135-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/30/2019] [Indexed: 02/07/2023] Open
Abstract
Background asthma, chronic obstructive pulmonary disease (COPD), and idiopathic pulmonary fibrosis (IPF) are three serious pulmonary diseases that contain common and unique characteristics. Therefore, the identification of biomarkers that differentiate these diseases is of importance for preventing misdiagnosis. In this regard, the present study aimed to identify the disorders at the early stages, based on lung transcriptomics data and drug-target interactions. Methods To this end, the differentially expressed genes were found in each disease. Then, WGCNA was utilized to find specific and consensus gene modules among the three diseases. Finally, the disease-disease similarity was analyzed, followed by determining candidate drug-target interactions. Results The results confirmed that the asthma lung transcriptome was more similar to COPD than IPF. In addition, the biomarkers were found in each disease and thus were proposed for further clinical validations. These genes included RBM42, STX5, and TRIM41 in asthma, CYP27A1, GM2A, LGALS9, SPI1, and NLRC4 in COPD, ATF3, PPP1R15A, ZFP36, SOCS3, NAMPT, and GADD45B in IPF, LRRC48 and CETN2 in asthma-COPD, COL15A1, GIMAP6, and JAM2 in asthma-IPF and LMO7, TSPAN13, LAMA3, and ANXA3 in COPD-IPF. Finally, analyzing drug-target networks suggested anti-inflammatory candidate drugs for treating the above mentioned diseases. Conclusion In general, the results revealed the unique and common biomarkers among three chronic lung diseases. Eventually, some drugs were suggested for treatment purposes.
Collapse
Affiliation(s)
- Mazaher Maghsoudloo
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran.,Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran. .,Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| |
Collapse
|
28
|
Yao Y, Gu Y, Yang M, Cao D, Wu F. The Gene Expression Biomarkers for Chronic Obstructive Pulmonary Disease and Interstitial Lung Disease. Front Genet 2019; 10:1154. [PMID: 31824564 PMCID: PMC6879656 DOI: 10.3389/fgene.2019.01154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 01/01/2023] Open
Abstract
COPD (chronic obstructive pulmonary disease) and ILD (interstitial lung disease) are two common respiratory diseases. They share similar clinical traits but require different therapeutic treatments. Identifying the biomarkers that are differentially expressed between them will not only help the diagnosis of COPD and ILD, but also provide candidate drug targets that may facilitate the development of new treatment for COPD and ILD. Due to the irreversible complex pathological changes of COPD, there are very limited therapeutic options for COPD patients. In this study, we analyzed the gene expression profiles of two datasets: one training dataset that includes 144 COPD patients and 194 ILD patients, and one test dataset that includes 75 COPD patients and 61 ILD patients. Advanced feature selection methods, mRMR (minimal Redundancy Maximal Relevance) and incremental feature selection (IFS), were applied to identify the 38-gene biomarker. An SVM (support vector machine) classifier was built based on the 38-gene biomarker. Its accuracy, sensitivity, and specificity on training dataset evaluated by leave one out cross-validation were 0.905, 0.896, and 0.912, respectively. And on independent test dataset, the accuracy, sensitivity, and specificity on were as great as and were 0.904, 0.933, and 0.869, respectively. The biological function analysis of the 38 genes indicated that many of them can be potential treatment targets that may benefit COPD and ILD patients.
Collapse
Affiliation(s)
- Yangwei Yao
- Department of Pulmonary and Critical Care Medicine, The Second Hospital of Jiaxing, Jiaxing, China
| | - Yangyang Gu
- Department of Pulmonary and Critical Care Medicine, The Second Hospital of Jiaxing, Jiaxing, China
| | - Meng Yang
- Department of Pulmonary and Critical Care Medicine, The Second Hospital of Jiaxing, Jiaxing, China
| | - Dakui Cao
- Department of Pulmonary and Critical Care Medicine, The Second Hospital of Jiaxing, Jiaxing, China
| | - Fengjie Wu
- Department of Pulmonary and Critical Care Medicine, The Second Hospital of Jiaxing, Jiaxing, China
| |
Collapse
|
29
|
Ishikawa G, Fujiwara N, Hirschfield H, Varricchio L, Hoshida Y, Barosi G, Rosti V, Padilla M, Mazzarini M, Friedman SL, Hoffman R, Migliaccio AR. Shared and Tissue-Specific Expression Signatures between Bone Marrow from Primary Myelofibrosis and Essential Thrombocythemia. Exp Hematol 2019; 79:16-25.e3. [PMID: 31678370 PMCID: PMC6910948 DOI: 10.1016/j.exphem.2019.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 12/13/2022]
Abstract
Megakaryocytes have been implicated in the micro-environmental abnormalities associated with fibrosis and hematopoietic failure in the bone marrow (BM) of primary myelofibrosis (PMF) patients, the Philadelphia-negative myeloproliferative neoplasm (MPN) associated with the poorest prognosis. To identify possible therapeutic targets for restoring BM functions in PMF, we compared the expression profiling of PMF BM with that of BM from essential thrombocytopenia (ET), a fibrosis-free MPN also associated with BM megakaryocyte hyperplasia. The signature of PMF BM was also compared with published signatures associated with liver and lung fibrosis. Gene set enrichment analysis (GSEA) identified distinctive differences between the expression profiles of PMF and ET. Notch, K-Ras, IL-8, and apoptosis pathways were altered the most in PMF as compared with controls. By contrast, cholesterol homeostasis, unfolded protein response, and hypoxia were the pathways found altered to the greatest degree in ET compared with control specimens. BM from PMF expressed a noncanonical transforming growth factor β (TGF-β) signature, which included activation of ID1, JUN, GADD45b, and genes with binding motifs for the JUN transcriptional complex AP1. By contrast, the expression of ID1 and GADD45b was not altered and there was a modest signal for JUN activation in ET. The similarities among PMF, liver fibrosis, and lung fibrosis were modest and included activation of integrin-α9 and tropomyosin-α1 between PMF and liver fibrosis, and of ectoderm-neural cortex protein 1 and FRAS1-related extracellular matrix protein 1 between PMF and lung fibrosis, but not TGF-β. These data identify TGF-β as a potential target for micro-environmental therapy in PMF.
Collapse
Affiliation(s)
- Genta Ishikawa
- Division of Pulmonary Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Naoto Fujiwara
- Division of Liver Diseases, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Liver Tumor Translational Research Program, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Hadassa Hirschfield
- Division of Liver Diseases, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lilian Varricchio
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yujin Hoshida
- Division of Liver Diseases, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Liver Tumor Translational Research Program, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Giovanni Barosi
- Center for the Study of Myelofibrosis, Laboratory of Biochemistry, Biotechnology and Advanced Diagnostic, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Vittorio Rosti
- Center for the Study of Myelofibrosis, Laboratory of Biochemistry, Biotechnology and Advanced Diagnostic, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Maria Padilla
- Division of Pulmonary Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Maria Mazzarini
- Department of Biomedical and Neuromotorial Sciences, Alma Mater University, Bologna, Italy
| | - Scott L Friedman
- Division of Liver Diseases, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ronald Hoffman
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Anna Rita Migliaccio
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Biomedical and Neuromotorial Sciences, Alma Mater University, Bologna, Italy.
| |
Collapse
|
30
|
Vanderstocken G, Dvorkin-Gheva A, Shen P, Brandsma CA, Obeidat M, Bossé Y, Hassell JA, Stampfli MR. Identification of Drug Candidates to Suppress Cigarette Smoke-induced Inflammation via Connectivity Map Analyses. Am J Respir Cell Mol Biol 2019; 58:727-735. [PMID: 29256623 DOI: 10.1165/rcmb.2017-0202oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cigarette smoking is the main risk factor for chronic obstructive pulmonary disease, and to date, existing pharmacologic interventions have been ineffective at controlling inflammatory processes associated with the disease. To address this issue, we used the Connectivity Map (cMap) database to identify drug candidates with the potential to attenuate cigarette smoke-induced inflammation. We queried cMap using three independent in-house cohorts of healthy nonsmokers and smokers. Potential drug candidates were validated against four publicly available human datasets, as well as six independent datasets from cigarette smoke-exposed mice. Overall, these analyses yielded two potential drug candidates: kaempferol and bethanechol. Subsequently, the efficacy of each drug was validated in vivo in a model of cigarette smoke-induced inflammation. BALB/c mice were exposed to room air or cigarette smoke and treated with each of the two candidate drugs either prophylactically or therapeutically. We found that kaempferol, but not bethanechol, was able to reduce cigarette smoke-induced neutrophilia, both when administered prophylactically and when administered therapeutically. Mechanistically, kaempferol decreased expression of IL-1α and CXCL5 concentrations in the lung. Our data suggest that cMap analyses may serve as a useful tool to identify novel drug candidates against cigarette smoke-induced inflammation.
Collapse
Affiliation(s)
- Gilles Vanderstocken
- 1 Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre
| | - Anna Dvorkin-Gheva
- 1 Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre.,2 Department of Pathology and Molecular Medicine, Centre for Functional Genomics, and
| | - Pamela Shen
- 1 Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre
| | - Corry-Anke Brandsma
- 3 Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Ma'en Obeidat
- 4 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Yohan Bossé
- 5 Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec City, Québec, Canada; and.,6 Department of Molecular Medicine, Laval University, Québec City, Québec, Canada
| | - John A Hassell
- 2 Department of Pathology and Molecular Medicine, Centre for Functional Genomics, and
| | - Martin R Stampfli
- 1 Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre.,7 Department of Medicine, Firestone Institute for Respiratory Health at St. Joseph's Healthcare, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
31
|
Lodyga M, Cambridge E, Karvonen HM, Pakshir P, Wu B, Boo S, Kiebalo M, Kaarteenaho R, Glogauer M, Kapoor M, Ask K, Hinz B. Cadherin-11-mediated adhesion of macrophages to myofibroblasts establishes a profibrotic niche of active TGF-β. Sci Signal 2019; 12:12/564/eaao3469. [PMID: 30647145 DOI: 10.1126/scisignal.aao3469] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Macrophages contribute to the activation of fibroblastic cells into myofibroblasts, which secrete collagen and contract the collagen matrix to acutely repair injured tissue. Persistent myofibroblast activation leads to the accumulation of fibrotic scar tissue that impairs organ function. We investigated the key processes that turn acute beneficial repair into destructive progressive fibrosis. We showed that homotypic cadherin-11 interactions promoted the specific binding of macrophages to and persistent activation of profibrotic myofibroblasts. Cadherin-11 was highly abundant at contacts between macrophages and myofibroblasts in mouse and human fibrotic lung tissues. In attachment assays, cadherin-11 junctions mediated specific recognition and strong adhesion between macrophages and myofibroblasts. One functional outcome of cadherin-11-mediated adhesion was locally restricted activation of latent transforming growth factor-β (TGF-β) between macrophage-myofibroblast pairs that was not observed in cocultures of macrophages and myofibroblasts that were not in contact with one another. Our data suggest that cadherin-11 junctions maintain latent TGF-β-producing macrophages and TGF-β-activating myofibroblasts in close proximity to one another. Inhibition of homotypic cadherin-11 interactions could be used to cause macrophage-myofibroblast separation, thereby destabilizing the profibrotic niche.
Collapse
Affiliation(s)
- Monika Lodyga
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
| | - Elizabeth Cambridge
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
| | - Henna M Karvonen
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada.,Respiratory Medicine, Research Unit of Internal Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, POB 20, 90029, Oulu, Finland
| | - Pardis Pakshir
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Brian Wu
- Department of Surgery and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5T 2S8, Canada.,Arthritis Program, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Stellar Boo
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
| | - Melanie Kiebalo
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
| | - Riitta Kaarteenaho
- Respiratory Medicine, Research Unit of Internal Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, POB 20, 90029, Oulu, Finland
| | - Michael Glogauer
- Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
| | - Mohit Kapoor
- Department of Surgery and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5T 2S8, Canada.,Arthritis Program, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Kjetil Ask
- Department of Medicine, McMaster University, Firestone Institute for Respiratory Health, Hamilton, Ontario L8N 4A6, Canada
| | - Boris Hinz
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada. .,Respiratory Medicine, Research Unit of Internal Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, POB 20, 90029, Oulu, Finland.,Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
| |
Collapse
|
32
|
Sharma A, Kitsak M, Cho MH, Ameli A, Zhou X, Jiang Z, Crapo JD, Beaty TH, Menche J, Bakke PS, Santolini M, Silverman EK. Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease Network Module. Sci Rep 2018; 8:14439. [PMID: 30262855 PMCID: PMC6160419 DOI: 10.1038/s41598-018-32173-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 08/20/2018] [Indexed: 12/21/2022] Open
Abstract
The polygenic nature of complex diseases offers potential opportunities to utilize network-based approaches that leverage the comprehensive set of protein-protein interactions (the human interactome) to identify new genes of interest and relevant biological pathways. However, the incompleteness of the current human interactome prevents it from reaching its full potential to extract network-based knowledge from gene discovery efforts, such as genome-wide association studies, for complex diseases like chronic obstructive pulmonary disease (COPD). Here, we provide a framework that integrates the existing human interactome information with experimental protein-protein interaction data for FAM13A, one of the most highly associated genetic loci to COPD, to find a more comprehensive disease network module. We identified an initial disease network neighborhood by applying a random-walk method. Next, we developed a network-based closeness approach (CAB) that revealed 9 out of 96 FAM13A interacting partners identified by affinity purification assays were significantly close to the initial network neighborhood. Moreover, compared to a similar method (local radiality), the CAB approach predicts low-degree genes as potential candidates. The candidates identified by the network-based closeness approach were combined with the initial network neighborhood to build a comprehensive disease network module (163 genes) that was enriched with genes differentially expressed between controls and COPD subjects in alveolar macrophages, lung tissue, sputum, blood, and bronchial brushing datasets. Overall, we demonstrate an approach to find disease-related network components using new laboratory data to overcome incompleteness of the current interactome.
Collapse
Affiliation(s)
- Amitabh Sharma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA. .,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA. .,Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, 02115, USA. .,Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
| | - Maksim Kitsak
- Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, 02115, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.,Pulmonary and Critical Care Division, Brigham and Women's Hospital and Harvard Medical School, Boston, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Asher Ameli
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.,Department of Physics, Northeastern University, Boston, MA, 02115, United States
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhiqiang Jiang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA
| | - James D Crapo
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jörg Menche
- Department of Bioinformatics, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090, Vienna, Austria
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marc Santolini
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.,Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, 02115, USA.,Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA. .,Pulmonary and Critical Care Division, Brigham and Women's Hospital and Harvard Medical School, Boston, USA. .,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
33
|
Wang K, Xiao H, Zhang J, Zhu D. Synaptotagmin7 Is Overexpressed In Colorectal Cancer And Regulates Colorectal Cancer Cell Proliferation. J Cancer 2018; 9:2349-2356. [PMID: 30026831 PMCID: PMC6036711 DOI: 10.7150/jca.25098] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/01/2018] [Indexed: 12/25/2022] Open
Abstract
Purpose: Synaptotagmin7 (SYT7) belongs to the synaptotagmin gene family and plays an important role in synaptic transmission. However, the function of this gene in most human cancer especially in colorectal cancer (CRC) remains unknown. In this research, we examined SYT7's role in CRC and tried to reveal its underlying mechanism. Methods: We examined SYT7's expression levels in normal colorectal tissue and CRC tissues from 83 patients and analyzed the possible correlation between the expression level of SYT7 and pathological characteristics. The influences of SYT7 knockdown on cell growth were detected by Celigo image cytometer, colony formation assay, cell cycle analysis and apoptosis assay in vitro. The possible molecular mechanism was assessed using a microarray and Ingenuity Pathway Analysis. Results: Our results show that the expression of SYT7 is upregulated in colorectal cancer tissues in comparison with normal tissues and positively correlated with the pathological stage of colorectal cancer. (P=0.015). We examined SYT7's role in human colorectal cancer cell line RKO by using SYT7-shRNA and revealed that SYT7 knockdown inhibit cell proliferation (P=8.6E-5), clonogenic ability (P=4.5E-6) and promoted G2/M Phase arrest and apoptosis (P=4.6E-7). Multiple cancer-associated pathways regulated by SYT7 were unraveled by microarray and Ingenuity Pathway Analysis. Conclusions: Our study suggests that SYT7 plays an important role in the development of CRC and SYT7 may become a new therapeutic target in CRC.
Collapse
Affiliation(s)
- Kewei Wang
- Department of Gastrointestinal & hernia Surgery, First Hospital of China Medical University, Shenyang, China
| | - Huimin Xiao
- Department of General Surgery, People's Hospital of China Medical University, Shenyang, China
| | - Jiaqi Zhang
- Department of Gastrointestinal & hernia Surgery, First Hospital of China Medical University, Shenyang, China
| | - Dehua Zhu
- Department of Gastrointestinal & hernia Surgery, First Hospital of China Medical University, Shenyang, China
| |
Collapse
|
34
|
Vishweswaraiah S, George L, Purushothaman N, Ganguly K. A candidate gene identification strategy utilizing mouse to human big-data mining: "3R-tenet" in COPD genetic research. Respir Res 2018; 19:92. [PMID: 29871630 PMCID: PMC5989378 DOI: 10.1186/s12931-018-0795-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 04/27/2018] [Indexed: 12/13/2022] Open
Abstract
Background Early life impairments leading to lower lung function by adulthood are considered as risk factors for chronic obstructive pulmonary disease (COPD). Recently, we compared the lung transcriptomic profile between two mouse strains with extreme total lung capacities to identify plausible pulmonary function determining genes using microarray analysis (GSE80078). Advancement of high-throughput techniques like deep sequencing (eg. RNA-seq) and microarray have resulted in an explosion of genomic data in the online public repositories which however remains under-exploited. Strategic curation of publicly available genomic data with a mouse-human translational approach can effectively implement “3R- Tenet” by reducing screening experiments with animals and performing mechanistic studies using physiologically relevant in vitro model systems. Therefore, we sought to analyze the association of functional variations within human orthologs of mouse lung function candidate genes in a publicly available COPD lung RNA-seq data-set. Methods Association of missense single nucleotide polymorphisms, insertions, deletions, and splice junction variants were analyzed for susceptibility to COPD using RNA-seq data of a Korean population (GSE57148). Expression of the associated genes were studied using the Gene Paint (mouse embryo) and Human Protein Atlas (normal adult human lung) databases. The genes were also assessed for replication of the associations and expression in COPD−/mouse cigarette smoke exposed lung tissues using other datasets. Results Significant association (p < 0.05) of variations in 20 genes to higher COPD susceptibility have been detected within the investigated cohort. Association of HJURP, MCRS1 and TLR8 are novel in relation to COPD. The associated ADAM19 and KIT loci have been reported earlier. The remaining 15 genes have also been previously associated to COPD. Differential transcript expression levels of the associated genes in COPD- and/ or mouse emphysematous lung tissues have been detected. Conclusion Our findings suggest strategic mouse-human datamining approaches can identify novel COPD candidate genes using existing datasets in the online repositories. The candidates can be further evaluated for mechanistic role through in vitro studies using appropriate primary cells/cell lines. Functional studies can be limited to transgenic animal models of only well supported candidate genes. This approach will lead to a significant reduction of animal experimentation in respiratory research. Electronic supplementary material The online version of this article (10.1186/s12931-018-0795-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Leema George
- SRM Research Institute, SRM University, Chennai, 603203, India
| | - Natarajan Purushothaman
- Department of Genetic Engineering, School of Bioengineering, Faculty of Engineering and Technology, SRM University, Chennai, 603203, India
| | - Koustav Ganguly
- SRM Research Institute, SRM University, Chennai, 603203, India. .,Work Environment Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 287, SE-171 77, Stockholm, Sweden.
| |
Collapse
|
35
|
MacDougall DD, Lin Z, Chon NL, Jackman SL, Lin H, Knight JD, Anantharam A. The high-affinity calcium sensor synaptotagmin-7 serves multiple roles in regulated exocytosis. J Gen Physiol 2018; 150:783-807. [PMID: 29794152 PMCID: PMC5987875 DOI: 10.1085/jgp.201711944] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/07/2018] [Indexed: 12/19/2022] Open
Abstract
MacDougall et al. review the structure and function of the calcium sensor synaptotagmin-7 in exocytosis. Synaptotagmin (Syt) proteins comprise a 17-member family, many of which trigger exocytosis in response to calcium. Historically, most studies have focused on the isoform Syt-1, which serves as the primary calcium sensor in synchronous neurotransmitter release. Recently, Syt-7 has become a topic of broad interest because of its extreme calcium sensitivity and diversity of roles in a wide range of cell types. Here, we review the known and emerging roles of Syt-7 in various contexts and stress the importance of its actions. Unique functions of Syt-7 are discussed in light of recent imaging, electrophysiological, and computational studies. Particular emphasis is placed on Syt-7–dependent regulation of synaptic transmission and neuroendocrine cell secretion. Finally, based on biochemical and structural data, we propose a mechanism to link Syt-7’s role in membrane fusion with its role in subsequent fusion pore expansion via strong calcium-dependent phospholipid binding.
Collapse
Affiliation(s)
| | - Zesen Lin
- Department of Pharmacology, University of Michigan, Ann Arbor, MI
| | - Nara L Chon
- Department of Chemistry, University of Colorado, Denver, CO
| | - Skyler L Jackman
- Vollum Institute, Oregon Health & Science University, Portland, OR
| | - Hai Lin
- Department of Chemistry, University of Colorado, Denver, CO
| | | | - Arun Anantharam
- Department of Pharmacology, University of Michigan, Ann Arbor, MI
| |
Collapse
|
36
|
Desai O, Winkler J, Minasyan M, Herzog EL. The Role of Immune and Inflammatory Cells in Idiopathic Pulmonary Fibrosis. Front Med (Lausanne) 2018; 5:43. [PMID: 29616220 PMCID: PMC5869935 DOI: 10.3389/fmed.2018.00043] [Citation(s) in RCA: 185] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 02/06/2018] [Indexed: 12/15/2022] Open
Abstract
The contribution of the immune system to idiopathic pulmonary fibrosis (IPF) remains poorly understood. While most sources agree that IPF does not result from a primary immunopathogenic mechanism, evidence gleaned from animal modeling and human studies suggests that innate and adaptive immune processes can orchestrate existing fibrotic responses. This review will synthesize the available data regarding the complex role of professional immune cells in IPF. The role of innate immune populations such as monocytes, macrophages, myeloid suppressor cells, and innate lymphoid cells will be discussed, as will the activation of these cells via pathogen-associated molecular patterns derived from invading or commensural microbes, and danger-associated molecular patterns derived from injured cells and tissues. The contribution of adaptive immune responses driven by T-helper cells and B cells will be reviewed as well. Each form of immune activation will be discussed in the context of its relationship to environmental and genetic factors, disease outcomes, and potential therapies. We conclude with discussion of unanswered questions and opportunities for future study in this area.
Collapse
Affiliation(s)
- Omkar Desai
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Julia Winkler
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Maksym Minasyan
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Erica L Herzog
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| |
Collapse
|
37
|
Movassagh H, Khadem F, Gounni AS. Semaphorins and Their Roles in Airway Biology: Potential as Therapeutic Targets. Am J Respir Cell Mol Biol 2018; 58:21-27. [PMID: 28817310 DOI: 10.1165/rcmb.2017-0171tr] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Semaphorins are a large family of proteins originally identified as axon guidance cues that play a crucial role in neural development. They are also ubiquitously expressed beyond the nervous system and contribute to regulation of essential cell functions, such as cell migration, proliferation, and adhesion. Binding of semaphorins to their receptors, including plexins and neuropilins, triggers diverse signaling pathways, which are involved in the pathogenesis of various diseases, from cancer to autoimmune and allergic disorders. Despite emerging evidence suggestive of nonredundant roles of semaphorins in cellular and molecular mechanisms of the airway biology, their precise expression and function have not been fully addressed. Here, we first provide an overview about the semaphorin family, their receptors, signaling pathways, and their cellular functions. Then, we highlight the novel findings on the role of semaphorins in airway biology under developmental, homeostatic, and pathological conditions. In particular, we discuss the dual roles of semaphorins in respiratory disorders where they can up- or downregulate processes underlying the pathophysiology of the airway diseases. Next, our recent findings on the expression and function of semaphorin 3E in allergic asthma are further emphasized, and its potential mechanism of action in allergic airway inflammation and remodeling is discussed. Finally, we raise some unanswered questions aiming to develop future research directions.
Collapse
Affiliation(s)
- Hesam Movassagh
- Department of Immunology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Forough Khadem
- Department of Immunology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Abdelilah S Gounni
- Department of Immunology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| |
Collapse
|
38
|
Xiao Z, Shu J, Zhou F, Han Y. JQ1 is a potential therapeutic option for COPD patients with agrin overexpression. Am J Physiol Lung Cell Mol Physiol 2017; 314:L690-L694. [PMID: 29351440 DOI: 10.1152/ajplung.00500.2017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is one of the leading causes of morbidity and death worldwide. It is characterized by chronic pulmonary inflammation and obstructed airflow from the lungs. To date, there is no effective treatment for COPD. The activation of the agrin (AGRN-YAP pathway can promote heart regeneration. Because agrin can induce only mild cardiomyocyte proliferation compared with ERBB2 pathway activation, it might exert pleiotropic effects, such as mitigation of innate inflammation, immune response, and fibrosis. Previously, we demonstrated that several common pathological gene regulatory programs such as innate inflammatory and profibrotic transcriptional networks were shared by COPD and heart failure. In this study, we show that agrin is inversely correlated with COPD development and progression and may exert its effects by suppressing innate inflammation and profibrotic signaling pathways. BET inhibitor JQ1, in line with our previous findings, is a promising therapeutic option in the treatment of patients with COPD. Nevertheless, wet laboratory experiments and clinical trials are needed before its application in clinical practice.
Collapse
Affiliation(s)
- Zhen Xiao
- Department of Reproductive Endocrinology, Zhejiang Provincial People's Hospital, Hangzhou Medical College , Hangzhou , China
| | - Jing Shu
- Department of Reproductive Endocrinology, Zhejiang Provincial People's Hospital, Hangzhou Medical College , Hangzhou , China
| | - Feng Zhou
- Department of Urology, The First Affiliated Hospital of Soochow University , Suzhou , China
| | - Yong Han
- Clinical Research Institute, Zhejiang Provincial People's Hospital , Zhejiang , China.,People's Hospital of Hangzhou Medical College , Zhejiang , China.,Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province , Zhejiang , China
| |
Collapse
|
39
|
Wang Y, Yella J, Chen J, McCormack FX, Madala SK, Jegga AG. Unsupervised gene expression analyses identify IPF-severity correlated signatures, associated genes and biomarkers. BMC Pulm Med 2017; 17:133. [PMID: 29058630 PMCID: PMC5649521 DOI: 10.1186/s12890-017-0472-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/01/2017] [Indexed: 12/30/2022] Open
Abstract
Background Idiopathic Pulmonary Fibrosis (IPF) is a fatal fibrotic lung disease occurring predominantly in middle-aged and older adults. The traditional diagnostic classification of IPF is based on clinical, radiological, and histopathological features. However, the considerable heterogeneity in IPF presentation suggests that differences in gene expression profiles can help to characterize and distinguish disease severity. Methods We used data-driven unsupervised clustering analysis, combined with a knowledge-based approach to identify and characterize IPF subgroups. Results Using transcriptional profiles on lung tissue from 131 patients with IPF/UIP and 12 non-diseased controls, we identified six subgroups of IPF that generally correlated with the disease severity and lung function decline. Network-informed clustering identified the most severe subgroup of IPF that was enriched with genes regulating inflammatory processes, blood pressure and branching morphogenesis of the lung. The differentially expressed genes in six subgroups of IPF compared to healthy control include transcripts of extracellular matrix, epithelial-mesenchymal cell cross-talk, calcium ion homeostasis, and oxygen transport. Further, we compiled differentially expressed gene signatures to identify unique gene clusters that can segregate IPF from normal, and severe from mild IPF. Additional validations of these signatures were carried out in three independent cohorts of IPF/UIP. Finally, using knowledge-based approaches, we identified several novel candidate genes which may also serve as potential biomarkers of IPF. Conclusions Discovery of unique and redundant gene signatures for subgroups in IPF can be greatly facilitated through unsupervised clustering. Findings derived from such gene signatures may provide insights into pathogenesis of IPF and facilitate the development of clinically useful biomarkers. Electronic supplementary material The online version of this article (10.1186/s12890-017-0472-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yunguan Wang
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jaswanth Yella
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Francis X McCormack
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Satish K Madala
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Anil G Jegga
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Department of Computer Science, University of Cincinnati College of Engineering, Cincinnati, OH, USA.
| |
Collapse
|
40
|
Movassagh H, Shan L, Duke-Cohan JS, Halayko AJ, Uzonna JE, Gounni AS. Semaphorin 3E Alleviates Hallmarks of House Dust Mite-Induced Allergic Airway Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2017. [PMID: 28634005 DOI: 10.1016/j.ajpath.2017.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Semaphorins are an essential family of guidance cues ubiquitously expressed in various organs, which play diverse developmental, homeostatic, and pathological roles. Semaphorin 3E (Sema3E), initially identified as a neuronal chemorepellent, is involved in the regulation of cell migration, proliferation, and angiogenesis. However, expression and function of Sema3E in allergic asthma has not been extensively investigated. We determined the expression of Sema3E in the airways and its effect on airway inflammation, hyperresponsiveness, and remodeling as pathological features of allergic asthma provoked by house dust mite in vivo. Our data indicate that exposure to house dust mite markedly reduces Sema3E expression in mouse airways. More important, replenishment of Sema3E by intranasal administration of exogenous Sema3E protects mice from allergic asthma by reducing eosinophilic inflammation, serum IgE level, and T helper cell 2/T helper cell 17 cytokine response. The regulatory effect of Sema3E on cytokine response was sustained on allergen recall response in the lymph nodes and spleen. Furthermore, goblet cell hyperplasia, collagen deposition, and airway hyperresponsiveness were significantly diminished on Sema3E treatment. The inhibitory effect of Sema3E was associated with a reduction of pulmonary CD11b+ conventional dendritic cells and regulation of CD4+ T-cell cytokine response. Collectively, our data represent a novel approach to treating allergic asthma via regulation of immune response to house dust mite.
Collapse
Affiliation(s)
- Hesam Movassagh
- Department of Immunology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Lianyu Shan
- Department of Immunology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jonathan S Duke-Cohan
- Department of Medical Oncology, Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Andrew J Halayko
- Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jude E Uzonna
- Department of Immunology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Abdelilah S Gounni
- Department of Immunology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada.
| |
Collapse
|
41
|
Du J, Han Y. Letter to the editor: BET inhibitors might target innate inflammatory and profibrotic signaling networks in COPD. Am J Physiol Lung Cell Mol Physiol 2017; 313:L648-L649. [PMID: 28864534 DOI: 10.1152/ajplung.00246.2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 06/08/2017] [Indexed: 11/22/2022] Open
Affiliation(s)
- Jing Du
- Department of Gastroenterology, Zhejiang Provincial People's Hospital, Zhejiang, People's Republic of China
| | - Yong Han
- Clinical Research Institute, Zhejiang Provincial People’s Hospital, Zhejiang, People’s Republic of China
- People's Hospital of Hangzhou Medical College, Zhejiang, People’s Republic of China; and
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang, People’s Republic of China
| |
Collapse
|
42
|
Jin H, Xu G, Zhang Q, Pang Q, Fang M. Synaptotagmin-7 is overexpressed in hepatocellular carcinoma and regulates hepatocellular carcinoma cell proliferation via Chk1-p53 signaling. Onco Targets Ther 2017; 10:4283-4293. [PMID: 28919777 PMCID: PMC5587153 DOI: 10.2147/ott.s143619] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Synaptotagmin-7 (Syt-7) is a member of the synaptotagmin (Syt) family, which plays an important role in many physiological and pathological processes. However, to the best of our knowledge, there is no study describing its function in tumors, particularly in hepatocellular carcinoma (HCC). Therefore, in this study, we examined the role of Syt-7 in HCC and attempted to elucidate its underlying mechanism. Materials and methods We examined the expression levels of Syt-7 in HCC cell lines and normal hepatocytes by real-time quantitative polymerase chain reaction analysis. The effects of Syt-7 knockdown on in vitro cell growth were assessed by Celigo image cytometry, MTT assay, colony formation assay, and cell cycle analysis. In vivo tumorigenesis was evaluated using a nude mouse model. The underlying molecular mechanism was evaluated using a PathScan Stress Signaling Antibody Array. Results Syt-7 mRNA levels were highly expressed in Huh-7 and Hep3B cells; moderately expressed in SMMC-7721, HepG2, and BEL-7402 cells; and lowly expressed in normal hepatocytes L-O2. Functional experiments demonstrated that Syt-7 knockdown significantly suppressed cell proliferation and induced cell cycle arrest by increasing phosphorylation of Chk1 and p53. Furthermore, Syt-7 knockdown remarkably reduced the growth of xenograft tumors in mice. Conclusion The results of this study suggest that Syt-7 plays a vital role in tumorigenesis and in the development of HCC. Syt-7 can be used as a new diagnostic and therapeutic target in HCC.
Collapse
Affiliation(s)
- Hao Jin
- School of Medicine, Shandong University, Jinan.,Department of Hepatic Surgery, Anhui Provincial Hospital, Hefei.,Department of Hepatobiliary Surgery, The First Affiliated Hospital, Bengbu Medical College, Bengbu, Anhui, People's Republic of China
| | - Geliang Xu
- Department of Hepatic Surgery, Anhui Provincial Hospital, Hefei
| | - Qiang Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Bengbu Medical College, Bengbu, Anhui, People's Republic of China
| | - Qing Pang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Bengbu Medical College, Bengbu, Anhui, People's Republic of China
| | - Meifang Fang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Bengbu Medical College, Bengbu, Anhui, People's Republic of China
| |
Collapse
|
43
|
Murray LA, Habiel DM, Hohmann M, Camelo A, Shang H, Zhou Y, Coelho AL, Peng X, Gulati M, Crestani B, Sleeman MA, Mustelin T, Moore MW, Ryu C, Osafo-Addo AD, Elias JA, Lee CG, Hu B, Herazo-Maya JD, Knight DA, Hogaboam CM, Herzog EL. Antifibrotic role of vascular endothelial growth factor in pulmonary fibrosis. JCI Insight 2017; 2:92192. [PMID: 28814671 PMCID: PMC5621899 DOI: 10.1172/jci.insight.92192] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 07/06/2017] [Indexed: 01/07/2023] Open
Abstract
The chronic progressive decline in lung function observed in idiopathic pulmonary fibrosis (IPF) appears to result from persistent nonresolving injury to the epithelium, impaired restitution of the epithelial barrier in the lung, and enhanced fibroblast activation. Thus, understanding these key mechanisms and pathways modulating both is essential to greater understanding of IPF pathogenesis. We examined the association of VEGF with the IPF disease state and preclinical models in vivo and in vitro. Tissue and circulating levels of VEGF were significantly reduced in patients with IPF, particularly in those with a rapidly progressive phenotype, compared with healthy controls. Lung-specific overexpression of VEGF significantly protected mice following intratracheal bleomycin challenge, with a decrease in fibrosis and bleomycin-induced cell death observed in the VEGF transgenic mice. In vitro, apoptotic endothelial cell–derived mediators enhanced epithelial cell injury and reduced epithelial wound closure. This process was rescued by VEGF pretreatment of the endothelial cells via a mechanism involving thrombospondin-1 (TSP1). Taken together, these data indicate beneficial roles for VEGF during lung fibrosis via modulating epithelial homeostasis through a previously unrecognized mechanism involving the endothelium. Elevated VEGF is associated with less severe disease in IPF patients, and VEGF overexpression ameliorates bleomycin-induced lung fibrosis in a murine model.
Collapse
Affiliation(s)
| | - David M Habiel
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Miriam Hohmann
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ana Camelo
- MedImmune Ltd., Cambridge, England, United Kingdom
| | - Huilan Shang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Yang Zhou
- Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ana Lucia Coelho
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Xueyan Peng
- Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mridu Gulati
- Yale University School of Medicine, New Haven, Connecticut, USA
| | - Bruno Crestani
- APHP, Hôpital Bichat, Service de Pneumologie A, Centre de Compétences des Maladies Pulmonaires Rares, Paris, France Université Paris Diderot, Sorbonne Paris Cité, INSERM Unité 1152, Paris
| | | | | | - Meagan W Moore
- Yale University School of Medicine, New Haven, Connecticut, USA
| | - Changwan Ryu
- Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Jack A Elias
- Warren Alpert School of Medicine, Providence, Rhode Island, USA
| | - Chun G Lee
- Warren Alpert School of Medicine, Providence, Rhode Island, USA
| | - Buqu Hu
- Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Darryl A Knight
- Viva program, Hunter Medical Research Institute, Newcastle, NSW, Australia.,Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada.,School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
| | - Cory M Hogaboam
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Erica L Herzog
- Yale University School of Medicine, New Haven, Connecticut, USA
| |
Collapse
|