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Guthrie J, Ko¨stel Bal S, Lombardo SD, Mu¨ller F, Sin C, Hu¨tter CV, Menche J, Boztug K. AutoCore: A network-based definition of the core module of human autoimmunity and autoinflammation. SCIENCE ADVANCES 2023; 9:eadg6375. [PMID: 37656781 PMCID: PMC10848965 DOI: 10.1126/sciadv.adg6375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
Although research on rare autoimmune and autoinflammatory diseases has enabled definition of nonredundant regulators of homeostasis in human immunity, because of the single gene-single disease nature of many of these diseases, contributing factors were mostly unveiled in sequential and noncoordinated individual studies. We used a network-based approach for integrating a set of 186 inborn errors of immunity with predominant autoimmunity/autoinflammation into a comprehensive map of human immune dysregulation, which we termed "AutoCore." The AutoCore is located centrally within the interactome of all protein-protein interactions, connecting and pinpointing multidisease markers for a range of common, polygenic autoimmune/autoinflammatory diseases. The AutoCore can be subdivided into 19 endotypes that correspond to molecularly and phenotypically cohesive disease subgroups, providing a molecular mechanism-based disease classification and rationale toward systematic targeting for therapeutic purposes. Our study provides a proof of concept for using network-based methods to systematically investigate the molecular relationships between individual rare diseases and address a range of conceptual, diagnostic, and therapeutic challenges.
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Affiliation(s)
- Julia Guthrie
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Zimmermannplatz 10, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
| | - Sevgi Ko¨stel Bal
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Zimmermannplatz 10, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Zimmermannplatz 10, A-1090 Vienna, Austria
| | - Salvo Danilo Lombardo
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
| | - Felix Mu¨ller
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
| | - Celine Sin
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
| | - Christiane V. R. Hu¨tter
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter, A-1030 Vienna, Austria
| | - Jo¨rg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
- Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, A-1090 Vienna, Austria
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Zimmermannplatz 10, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Zimmermannplatz 10, A-1090 Vienna, Austria
- St. Anna Children’s Hospital, Kinderspitalgasse 6, A-1090, Vienna, Austria
- Medical University of Vienna, Department of Pediatrics and Adolescent Medicine, Währinger Gürtel 18-20, A-1090 Vienna, Austria
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Cui J, Li H, Wang T, Shen Q, Yang Y, Yu X, Hu H. Novel Immune-Related Genetic Expression for Primary Sjögren's Syndrome. Front Med (Lausanne) 2022; 8:719958. [PMID: 35047519 PMCID: PMC8761677 DOI: 10.3389/fmed.2021.719958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: To identify novel immune-related genes expressed in primary Sjögren's syndrome (pSS). Methods: Gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) were screened. The differences in immune cell proportion between normal and diseased tissues were compared, weighted gene co-expression network analysis was conducted to identify key modules, followed by a protein–protein interaction (PPI) network generation and enrichment analysis. The feature genes were screened and verified using the GEO datasets and quantitative real-time PCR (RT-qPCR). Results: A total of 345 DEGs were identified, and the proportions of gamma delta T cells, memory B cells, regulatory T cells (Tregs), and activated dendritic cells differed significantly between the control and pSS groups. The turquoise module indicated the highest correlation with pSS, and 252 key genes were identified. The PPI network of key genes showed that RPL9, RBX1, and RPL31 had a relatively higher degree. In addition, the key genes were mainly enriched in coronavirus disease-COVID-2019, hepatitis C, and influenza A. Fourteen feature genes were obtained using the support vector machine model, and two subtypes were identified. The genes in the two subtypes were mainly enriched in the JAK-STAT, p53, and toll-like receptor signaling pathways. The majority of the feature genes were upregulated in the pSS group, verified using the GEO datasets and RT-qPCR analysis. Conclusions: Memory B cells, gamma delta T cells, Tregs, activated dendritic cells, RPL9, RBX1, RPL31, and the feature genes possible play vital roles in the development of pSS.
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Affiliation(s)
- Jiajia Cui
- Department of Rheumatology and Immunology, East Hospital of the Second People's Hospital of Lianyungang City, Lianyungang, China
| | - Hui Li
- Department of Rheumatology and Immunology, East Hospital of the Second People's Hospital of Lianyungang City, Lianyungang, China
| | - Tianling Wang
- Department of Rheumatology and Immunology, East Hospital of the Second People's Hospital of Lianyungang City, Lianyungang, China
| | - Qin Shen
- Department of Rheumatology and Immunology, East Hospital of the Second People's Hospital of Lianyungang City, Lianyungang, China
| | - Yuanhao Yang
- Department of Rheumatology and Immunology, East Hospital of the Second People's Hospital of Lianyungang City, Lianyungang, China
| | - Xiujuan Yu
- Department of Rheumatology and Immunology, East Hospital of the Second People's Hospital of Lianyungang City, Lianyungang, China
| | - Huaixia Hu
- Department of Rheumatology and Immunology, East Hospital of the Second People's Hospital of Lianyungang City, Lianyungang, China
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Rastmanesh R. Aquaporin5-Targeted Treatment for Dry Eye Through Bioactive Compounds and Gut Microbiota. J Ocul Pharmacol Ther 2021; 37:464-471. [PMID: 34328795 DOI: 10.1089/jop.2021.0029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Dry eye and dry mouth are the principal sources of morbidity for patients with Sjögren's syndrome (SS). There are few effective treatments, particularly systemic ones. Targeting aquaprin-5 (AQP5)-mediated tear secretion has been tested as a novel ancillary strategy and has proved promising. Patients have a great interest in using complementary medicine, including nutraceuticals and bioactive compounds to alleviate their symptoms. Potential mechanisms by which phytocompounds and bioactive compounds may benefit SS ocular and mouth symptoms through modulation of AQP5 activity are presented within this review. Supplementation with prebiotics (such as polyphenols with high bioavailability) in SS patients with lower Firmicutes/Bacteroides (F/B) community ratio phenotype, through administration of butyrate-producing diets, is proposed as ancillary strategy for dry eye and mouth. The potential use of natural bioactive compounds to treat dry eye could also apply to dry mouth occurring in the context of aging and SS. This novel hypothesis could have implications with respect to planning a successful dietary regimen for achieving and maintaining a normal gut microbiota in SS patients. This regimen would include augmenting butyrate-producing foodstuffs and/or polyphenol-rich syrups, and high amounts of some specific probiotic-rich foodstuffs such as yogurt, soy yogurt, or as probiotic supplements. There are applications for pharmaceutical and nutraceutical products aiming to relieve dry eye and mouth.
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Vitali C, Minniti A, Pignataro F, Maglione W, Del Papa N. Management of Sjögren's Syndrome: Present Issues and Future Perspectives. Front Med (Lausanne) 2021; 8:676885. [PMID: 34164418 PMCID: PMC8215198 DOI: 10.3389/fmed.2021.676885] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
In view of the new possibilities for the treatment of primary Sjögren's syndrome (pSS) given by the availability of new biotechnological agents targeting the various molecular and cellular actors of the pathological process of the disease, classification criteria aimed at selecting patients to be enrolled in therapeutic trials, and validated outcome measures to be used as response criteria to these new therapies, have been developed and validated in the last decades. Unfortunately, the therapeutic trials so far completed with these new treatments have yielded unsatisfactory or only partially positive results. The main issues that have been evoked to justify the poor results of the new therapeutic attempts are: (i) the extreme variability of the disease phenotypes of the patients enrolled in the trials, which are dependent on different underlying patterns of biological mechanisms, (ii) the fact that the disease has a long indolent course, and that most of the enrolled patients might already have irreversible clinical features. The advances in the research of new disease biomarkers that can better distinguish the different clinical phenotypes of patients and diagnose the disease in an earlier phase are also discussed.
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Affiliation(s)
- Claudio Vitali
- Rheumatology Outpatient Clinics, "Mater Domini" Humanitas Hospital, Castellanza, Italy
| | | | | | - Wanda Maglione
- Department of Rheumatology, ASST G. Pini-CTO, Milan, Italy
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Del Papa N, Minniti A, Lorini M, Carbonelli V, Maglione W, Pignataro F, Montano N, Caporali R, Vitali C. The Role of Interferons in the Pathogenesis of Sjögren's Syndrome and Future Therapeutic Perspectives. Biomolecules 2021; 11:biom11020251. [PMID: 33572487 PMCID: PMC7916411 DOI: 10.3390/biom11020251] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/16/2022] Open
Abstract
There is a great deal of evidence pointing to interferons (IFNs) as being key cytokines in the pathogenesis of different systemic autoimmune diseases, including primary Sjögren’s syndrome (pSS). In this disease, a large number of studies have shown that an overexpression of type I IFN, the ‘so-called’ type I IFN signature, is present in peripheral blood mononuclear cells, and that this finding is associated with the development of systemic extra-glandular manifestations, and a substantial production of autoantibodies and inflammatory cytokines. In contrast, the absence or a milder expression of type I IFN signature and low level of inflammatory cytokines characterizes patients with a different clinical phenotype, where the disease is limited to glandular involvement and often marked by the presence of widespread pain and depression. The role of type II (IFNγ) in this subset of pSS patients, together with the potentially related activation of completely different immunological and metabolic pathways, are emerging issues. Expression of both types of IFNs has also been shown in target tissues, namely in minor salivary glands where a predominance of type II IFN signature appeared to have a certain association with the development of lymphoma. In view of the role played by IFN overexpression in the development and progression of pSS, inhibition or modulation of IFN signaling has been regarded as a potential target for the therapeutic approach. A number of therapeutic compounds with variable mechanisms of action have been tested or are under consideration for the treatment of patients with pSS.
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Affiliation(s)
- Nicoletta Del Papa
- Department of Rheumatology, ASST G. Pini-CTO, 20122 Milano, Italy; (A.M.); (W.M.); (F.P.); (R.C.)
- Correspondence:
| | - Antonina Minniti
- Department of Rheumatology, ASST G. Pini-CTO, 20122 Milano, Italy; (A.M.); (W.M.); (F.P.); (R.C.)
| | - Maurizio Lorini
- Department of Clinical Sciences and Community Health, Ca’ Granda IRCCS Foundation, Ospedale Maggiore Policlinico, Università degli Studi di Milano, 20122 Milano, Italy; (M.L.); (V.C.); (N.M.)
| | - Vincenzo Carbonelli
- Department of Clinical Sciences and Community Health, Ca’ Granda IRCCS Foundation, Ospedale Maggiore Policlinico, Università degli Studi di Milano, 20122 Milano, Italy; (M.L.); (V.C.); (N.M.)
| | - Wanda Maglione
- Department of Rheumatology, ASST G. Pini-CTO, 20122 Milano, Italy; (A.M.); (W.M.); (F.P.); (R.C.)
| | - Francesca Pignataro
- Department of Rheumatology, ASST G. Pini-CTO, 20122 Milano, Italy; (A.M.); (W.M.); (F.P.); (R.C.)
| | - Nicola Montano
- Department of Clinical Sciences and Community Health, Ca’ Granda IRCCS Foundation, Ospedale Maggiore Policlinico, Università degli Studi di Milano, 20122 Milano, Italy; (M.L.); (V.C.); (N.M.)
| | - Roberto Caporali
- Department of Rheumatology, ASST G. Pini-CTO, 20122 Milano, Italy; (A.M.); (W.M.); (F.P.); (R.C.)
- Research Center for Adult and Pediatric Rheumatic Diseases, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20122 Milano, Italy
| | - Claudio Vitali
- Mater Domini Humanitas Hospital, Rheumatology Outpatient Clinics, 21053 Castellanza, Italy;
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