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Liman N, Lanasa D, Meylan F, Park JH. The ever-expanding role of cytokine receptor DR3 in T cells. Cytokine 2024; 176:156540. [PMID: 38359559 PMCID: PMC10895922 DOI: 10.1016/j.cyto.2024.156540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/17/2024]
Abstract
Death Receptor 3 (DR3) is a cytokine receptor of the Tumor Necrosis Factor receptor superfamily that plays a multifaceted role in both innate and adaptive immunity. Based on the death domain motif in its cytosolic tail, DR3 had been proposed and functionally affirmed as a trigger of apoptosis. Further studies, however, also revealed roles of DR3 in other cellular pathways, including inflammation, survival, and proliferation. DR3 is expressed in various cell types, including T cells, B cells, innate lymphocytes, myeloid cells, fibroblasts, and even outside the immune system. Because DR3 is mainly expressed on T cells, DR3-mediated immune perturbations leading to autoimmunity and other diseases were mostly attributed to DR3 activation of T cells. However, which T cell subset and what T effector functions are controlled by DR3 to drive these processes remain incompletely understood. DR3 engagement was previously found to alter CD4 T helper subset differentiation, expand the Foxp3+ Treg cell pool, and maintain intraepithelial γδ T cells in the gut. Recent studies further unveiled a previously unacknowledged aspect of DR3 in regulating innate-like invariant NKT (iNKT) cell activation, expanding the scope of DR3-mediated immunity in T lineage cells. Importantly, in the context of iNKT cells, DR3 ligation exerted costimulatory effects in agonistic TCR signaling, unveiling a new regulatory framework in T cell activation and proliferation. The current review is aimed at summarizing such recent findings on the role of DR3 on conventional T cells and innate-like T cells and discussing them in the context of immunopathogenesis.
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Affiliation(s)
- Nurcin Liman
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Dominic Lanasa
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Françoise Meylan
- Office of Science and Technology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, NIH, Bethesda, MD 20892, United States
| | - Jung-Hyun Park
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, United States.
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2
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Liu Y, Lyons CJ, Ayu C, O'Brien T. Recent advances in endothelial colony-forming cells: from the transcriptomic perspective. J Transl Med 2024; 22:313. [PMID: 38532420 PMCID: PMC10967123 DOI: 10.1186/s12967-024-05108-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Endothelial colony-forming cells (ECFCs) are progenitors of endothelial cells with significant proliferative and angiogenic ability. ECFCs are a promising treatment option for various diseases, such as ischemic heart disease and peripheral artery disease. However, some barriers hinder the clinical application of ECFC therapeutics. One of the current obstacles is that ECFCs are dysfunctional due to the underlying disease states. ECFCs exhibit dysfunctional phenotypes in pathologic states, which include but are not limited to the following: premature neonates and pregnancy-related diseases, diabetes mellitus, cancers, haematological system diseases, hypoxia, pulmonary arterial hypertension, coronary artery diseases, and other vascular diseases. Besides, ECFCs are heterogeneous among donors, tissue sources, and within cell subpopulations. Therefore, it is important to elucidate the underlying mechanisms of ECFC dysfunction and characterize their heterogeneity to enable clinical application. In this review, we summarize the current and potential application of transcriptomic analysis in the field of ECFC biology. Transcriptomic analysis is a powerful tool for exploring the key molecules and pathways involved in health and disease and can be used to characterize ECFC heterogeneity.
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Affiliation(s)
- Yaqiong Liu
- Regenerative Medicine Institute (REMEDI), Biomedical Sciences Building, University of Galway, Galway, Ireland
| | - Caomhán J Lyons
- Regenerative Medicine Institute (REMEDI), Biomedical Sciences Building, University of Galway, Galway, Ireland
| | - Christine Ayu
- Regenerative Medicine Institute (REMEDI), Biomedical Sciences Building, University of Galway, Galway, Ireland
| | - Timothy O'Brien
- Regenerative Medicine Institute (REMEDI), Biomedical Sciences Building, University of Galway, Galway, Ireland.
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Ratajczak F, Joblin M, Hildebrandt M, Ringsquandl M, Falter-Braun P, Heinig M. Speos: an ensemble graph representation learning framework to predict core gene candidates for complex diseases. Nat Commun 2023; 14:7206. [PMID: 37938585 PMCID: PMC10632370 DOI: 10.1038/s41467-023-42975-z] [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: 03/27/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
Understanding phenotype-to-genotype relationships is a grand challenge of 21st century biology with translational implications. The recently proposed "omnigenic" model postulates that effects of genetic variation on traits are mediated by core-genes and -proteins whose activities mechanistically influence the phenotype, whereas peripheral genes encode a regulatory network that indirectly affects phenotypes via core gene products. Here, we develop a positive-unlabeled graph representation-learning ensemble-approach based on a nested cross-validation to predict core-like genes for diverse diseases using Mendelian disorder genes for training. Employing mouse knockout phenotypes for external validations, we demonstrate that core-like genes display several key properties of core genes: Mouse knockouts of genes corresponding to our most confident predictions give rise to relevant mouse phenotypes at rates on par with the Mendelian disorder genes, and all candidates exhibit core gene properties like transcriptional deregulation in disease and loss-of-function intolerance. Moreover, as predicted for core genes, our candidates are enriched for drug targets and druggable proteins. In contrast to Mendelian disorder genes the new core-like genes are enriched for druggable yet untargeted gene products, which are therefore attractive targets for drug development. Interpretation of the underlying deep learning model suggests plausible explanations for our core gene predictions in form of molecular mechanisms and physical interactions. Our results demonstrate the potential of graph representation learning for the interpretation of biological complexity and pave the way for studying core gene properties and future drug development.
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Affiliation(s)
- Florin Ratajczak
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Munich, Neuherberg, Germany
| | | | | | | | - Pascal Falter-Braun
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Munich, Neuherberg, Germany.
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| | - Matthias Heinig
- Institute of Computational Biology (ICB), Helmholtz Munich, Neuherberg, Germany.
- Department of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- German Centre for Cardiovascular Research (DZHK), Munich Heart Association, Partner Site Munich, Berlin, Germany.
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Bacci M, Cancellara A, Ciceri R, Romualdi E, Pessi V, Tumminello F, Fantuzzi M, Donadini MP, Lodigiani C, Della Bella S, Calcaterra F, Mavilio D. Development of Personalized Thrombogenesis and Thrombin Generation Assays to Assess Endothelial Dysfunction in Cardiovascular Diseases. Biomedicines 2023; 11:1669. [PMID: 37371764 DOI: 10.3390/biomedicines11061669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/25/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
The study of endothelial dysfunction (ED) is crucial to identify the pathogenetic mechanism(s) and provide indications for patient management in cardiovascular diseases. It is currently hindered by the limited availability of patient-specific primary endothelial cells (ECs). Endothelial colony-forming cells (ECFCs) represent an optimal non-invasive tool to overcome this issue. Therefore, we investigated the use of ECFCs as a substrate in thrombogenesis and thrombin generation assay (TGA) to assess ED. Both assays were set up on human umbilical vein endothelial cells (HUVECs) and then tested on ECFCs obtained from healthy donors. To prove the ability of the assays to detect endothelial activation, ECs stimulated with TNFα were compared with unstimulated ECs. EC activation was confirmed by the upregulation of VCAM-1 and Tissue Factor expression. Both assays discriminated between unstimulated and activated HUVECs and ECFCs, as significantly higher platelet deposition and fibrin formation in thrombogenesis assay, and thrombin generation in TGA, were observed when TNFα-activated ECs were used as a substrate. The amount of fibrin and thrombin measured in the two assays were directly correlated. Our results support the combined use of a thrombogenesis assay and TGA performed on patient-derived ECFCs to provide a personalized global assessment of ED relevant to the patient's hemostatic profile.
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Affiliation(s)
- Monica Bacci
- Center for Thrombosis and Hemorrhagic Diseases, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Assunta Cancellara
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, 20089 Rozzano, Italy
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Roberta Ciceri
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, 20089 Rozzano, Italy
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Erica Romualdi
- Centro Trombosi ed Emostasi, Ospedale di Circolo e Fondazione Macchi, ASST Sette Laghi, 21100 Varese, Italy
- UO Medicina 2, Ospedale di Circolo e Fondazione Macchi, ASST Sette Laghi, 21100 Varese, Italy
| | - Valentina Pessi
- Dipartimento di Medicina e Chirurgia, Università Dell'Insubria, 21100 Varese, Italy
| | - Fabio Tumminello
- Center for Thrombosis and Hemorrhagic Diseases, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Italy
| | - Martina Fantuzzi
- Dipartimento di Medicina e Chirurgia, Università Dell'Insubria, 21100 Varese, Italy
| | - Marco Paolo Donadini
- Centro Trombosi ed Emostasi, Ospedale di Circolo e Fondazione Macchi, ASST Sette Laghi, 21100 Varese, Italy
- Dipartimento di Medicina e Chirurgia, Università Dell'Insubria, 21100 Varese, Italy
| | - Corrado Lodigiani
- Center for Thrombosis and Hemorrhagic Diseases, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Silvia Della Bella
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, 20089 Rozzano, Italy
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Francesca Calcaterra
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, 20089 Rozzano, Italy
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Domenico Mavilio
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, 20089 Rozzano, Italy
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
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Moreno-Lorenzana D, Torres-Barrera P, Flores-Lopez G, Chávez-González MA, Isordia-Salas I, Yoder MC, Majluf-Cruz A, Alvarado-Moreno JA. Self-regulation of TNF-α Induces Dysfunction of Endothelial Colony-forming Cells from Patients with Venous Thromboembolic Disease. Arch Med Res 2022; 53:680-687. [DOI: 10.1016/j.arcmed.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/09/2022] [Accepted: 10/05/2022] [Indexed: 11/30/2022]
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Su Y, Li Q, Zheng Z, Wei X, Hou P. Identification of genes, pathways and transcription factor-miRNA-target gene networks and experimental verification in venous thromboembolism. Sci Rep 2021; 11:16352. [PMID: 34381164 PMCID: PMC8357955 DOI: 10.1038/s41598-021-95909-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 08/02/2021] [Indexed: 12/17/2022] Open
Abstract
Venous thromboembolism (VTE) is a complex, multifactorial life-threatening disease that involves vascular endothelial cell (VEC) dysfunction. However, the exact pathogenesis and underlying mechanisms of VTE are not completely clear. The aim of this study was to identify the core genes and pathways in VECs that are involved in the development and progression of unprovoked VTE (uVTE). The microarray dataset GSE118259 was downloaded from the Gene Expression Omnibus database, and 341 up-regulated and 8 down-regulated genes were identified in the VTE patients relative to the healthy controls, including CREB1, HIF1α, CBL, ILK, ESM1 and the ribosomal protein family genes. The protein-protein interaction (PPI) network and the transcription factor (TF)-miRNA-target gene network were constructed with these differentially expressed genes (DEGs), and visualized using Cytoscape software 3.6.1. Eighty-nine miRNAs were predicted as the targeting miRNAs of the DEGs, and 197 TFs were predicted as regulators of these miRNAs. In addition, 237 node genes and 4 modules were identified in the PPI network. The significantly enriched pathways included metabolic, cell adhesion, cell proliferation and cellular response to growth factor stimulus pathways. CREB1 was a differentially expressed TF in the TF-miRNA-target gene network, which regulated six miRNA-target gene pairs. The up-regulation of ESM1, HIF1α and CREB1 was confirmed at the mRNA and protein level in the plasma of uVTE patients. Taken together, ESM1, HIF1α and the CREB1-miRNA-target genes axis play potential mechanistic roles in uVTE development.
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Affiliation(s)
- Yiming Su
- Department of Vascular Surgery, LiuzhouWorker's Hospital, Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545005, Guangxi Province, China
| | - Qiyi Li
- Department of Vascular Surgery, LiuzhouWorker's Hospital, Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545005, Guangxi Province, China
| | - Zhiyong Zheng
- Department of Vascular Surgery, LiuzhouWorker's Hospital, Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545005, Guangxi Province, China
| | - Xiaomin Wei
- Department of Vascular Surgery, LiuzhouWorker's Hospital, Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545005, Guangxi Province, China
| | - Peiyong Hou
- Department of Vascular Surgery, LiuzhouWorker's Hospital, Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545005, Guangxi Province, China.
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Chen X, Cao J, Ge Z, Xia Z. Correlation and integration of circulating miRNA and peripheral whole blood gene expression profiles in patients with venous thromboembolism. Bioengineered 2021; 12:2352-2363. [PMID: 34077299 PMCID: PMC8806583 DOI: 10.1080/21655979.2021.1935401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The main aim of this work was to evaluate differential expression and biological functions of circulating miRNA and whole peripheral blood (PB) genes in patients affected by venous thromboembolism (VTE) and in healthy subjects. Circulating miRNA sequences and PB expression profiles were obtained from GEO datasets. Ten miRNAs with the most significant differential expression rate (dif-miRNA) were subjected to miRbase to confirm their identity. Dif-miRNA targets were predicted by TargetScan and aligned with differentially expressed genes to obtain overlapping co-genes. Biological functions of co-genes were analyzed by Gene Ontology and KEGG analysis. Interaction network of dif-miRNAs, co-genes, and their downstream pathways were studied by analyzing protein-protein interaction (PPI) clusters (STRING) and determining the crucial hubs (Cytoscape).MiR-522-3p and miR-134 dif-miRNAs are involved in protein translation and apoptosis by regulating their respective co-genes in PB. Co-genes are present in nucleolus and extracellular exosomes and are involved in oxidative phosphorylation and ribosome/poly(A)-RNA organization. The predicted PPI network covered 107 clustered genes and 220 marginal joints, where ten hub genes participating in PPIs were found. All these hub genes were down-regulated in VTE patients. Our study identifies new miRNAs as potential biological markers and therapeutic targets for VTE.
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Affiliation(s)
- Xiaonan Chen
- Emergency and Acute Critical Care Department, Huashan Hospital North, Fudan University, Shanghai, China
| | - Jun Cao
- Emergency and Acute Critical Care Department, Huashan Hospital North, Fudan University, Shanghai, China
| | - Zi Ge
- Emergency and Acute Critical Care Department, Huashan Hospital North, Fudan University, Shanghai, China
| | - Zhijie Xia
- Emergency and Acute Critical Care Department, Huashan Hospital North, Fudan University, Shanghai, China
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Yu Y, Jiang P, Sun P, Su N, Lin F. Analysis of therapeutic potential of preclinical models based on DR3/TL1A pathway modulation (Review). Exp Ther Med 2021; 22:693. [PMID: 33986858 PMCID: PMC8111866 DOI: 10.3892/etm.2021.10125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/11/2020] [Indexed: 12/13/2022] Open
Abstract
Death receptor 3 (DR3) and its corresponding ligand, tumor necrosis factor-like ligand 1A (TL1A), belong to the tumor necrosis factor superfamily. Signaling via this receptor-ligand pair results in pro-inflammatory and anti-inflammatory effects. Effector lymphocytes can be activated to exert pro-inflammatory activity by triggering the DR3/TL1A pathway. By contrast, DR3/TL1A signaling also induces expansion of the suppressive function of regulatory T cells, which serve an important role in exerting anti-inflammatory functions and maintaining immune homeostasis. Preclinical evidence indicates that neutralizing and agonistic antibodies, as well as ligand-based approaches targeting the DR3/TL1A pathway, may be used to treat diseases, including inflammatory and immune-mediated diseases. Accumulating evidence has suggested that modulating the DR3/TL1A pathway is a promising therapeutic approach for patients with these diseases. This review discusses preclinical models to gauge the progress of therapeutic strategies for diseases involving the DR3/TL1A pathway to aid in drug development.
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Affiliation(s)
- Yunhong Yu
- Institute of Blood Transfusion, Chinese Academy of Medical Science and Peking Union Medical College, Chengdu, Sichuan 610052, P.R. China
| | - Peng Jiang
- Institute of Blood Transfusion, Chinese Academy of Medical Science and Peking Union Medical College, Chengdu, Sichuan 610052, P.R. China
| | - Pan Sun
- Institute of Blood Transfusion, Chinese Academy of Medical Science and Peking Union Medical College, Chengdu, Sichuan 610052, P.R. China
| | - Na Su
- Institute of Blood Transfusion, Chinese Academy of Medical Science and Peking Union Medical College, Chengdu, Sichuan 610052, P.R. China
| | - Fangzhao Lin
- Institute of Blood Transfusion, Chinese Academy of Medical Science and Peking Union Medical College, Chengdu, Sichuan 610052, P.R. China
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