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Brownlie RJ, Salmond RJ. Regulation of T Cell Signaling and Immune Responses by PTPN22. Mol Cell Biol 2024:1-10. [PMID: 39039893 DOI: 10.1080/10985549.2024.2378810] [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: 06/06/2024] [Accepted: 07/07/2024] [Indexed: 07/24/2024] Open
Abstract
Protein tyrosine phosphatases (PTPs) play central roles in the regulation of cell signaling, organismal development, cellular differentiation and proliferation, and cancer. In the immune system, PTPs regulate the activation, differentiation and effector function of lymphocytes and myeloid cells whilst single-nucleotide polymorphisms (SNPs) in PTP-encoding genes have been identified as risk factors for the development of autoimmunity. In this review we describe the roles for PTP nonreceptor type 22 (PTPN22) in the regulation of T lymphocyte signaling and activation in autoimmunity, infection and cancer. We summarize recent progress in our understanding of the regulation of PTPN22 activity, the impact of autoimmune disease-associated PTPN22 SNPs on T cell responses and describe approaches to harness PTPN22 as a target to improve T cell-based immunotherapies in cancer.
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Zhuang C, Yang S, Gonzalez CG, Ainsworth RI, Li S, Kobayashi MT, Wierzbicki I, Rossitto LAM, Wen Y, Peti W, Stanford SM, Gonzalez DJ, Murali R, Santelli E, Bottini N. A novel gain-of-function phosphorylation site modulates PTPN22 inhibition of TCR signaling. J Biol Chem 2024; 300:107393. [PMID: 38777143 PMCID: PMC11237943 DOI: 10.1016/j.jbc.2024.107393] [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: 02/22/2024] [Revised: 04/20/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Protein tyrosine phosphatase nonreceptor type 22 (PTPN22) is encoded by a major autoimmunity gene and is a known inhibitor of T cell receptor (TCR) signaling and drug target for cancer immunotherapy. However, little is known about PTPN22 posttranslational regulation. Here, we characterize a phosphorylation site at Ser325 situated C terminal to the catalytic domain of PTPN22 and its roles in altering protein function. In human T cells, Ser325 is phosphorylated by glycogen synthase kinase-3 (GSK3) following TCR stimulation, which promotes its TCR-inhibitory activity. Signaling through the major TCR-dependent pathway under PTPN22 control was enhanced by CRISPR/Cas9-mediated suppression of Ser325 phosphorylation and inhibited by mimicking it via glutamic acid substitution. Global phospho-mass spectrometry showed Ser325 phosphorylation state alters downstream transcriptional activity through enrichment of Swi3p, Rsc8p, and Moira domain binding proteins, and next-generation sequencing revealed it differentially regulates the expression of chemokines and T cell activation pathways. Moreover, in vitro kinetic data suggest the modulation of activity depends on a cellular context. Finally, we begin to address the structural and mechanistic basis for the influence of Ser325 phosphorylation on the protein's properties by deuterium exchange mass spectrometry and NMR spectroscopy. In conclusion, this study explores the function of a novel phosphorylation site of PTPN22 that is involved in complex regulation of TCR signaling and provides details that might inform the future development of allosteric modulators of PTPN22.
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Affiliation(s)
- Chuling Zhuang
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA
| | - Shen Yang
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA; Department of Medicine, Kao Autoimmunity Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Carlos G Gonzalez
- Department of Pharmacology, University of California, San Diego, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Richard I Ainsworth
- Department of Medicine, Kao Autoimmunity Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, California, USA
| | - Masumi Takayama Kobayashi
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut, USA
| | - Igor Wierzbicki
- Department of Pharmacology, University of California, San Diego, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Leigh-Ana M Rossitto
- Department of Pharmacology, University of California, San Diego, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Yutao Wen
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut, USA
| | - Stephanie M Stanford
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Eugenio Santelli
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA; Department of Medicine, Kao Autoimmunity Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nunzio Bottini
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA; Department of Medicine, Kao Autoimmunity Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA.
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Bai B, Li T, Zhao J, Zhao Y, Zhang X, Wang T, Zhang N, Wang X, Ba X, Xu J, Yu Y, Wang B. The Tyrosine Phosphatase Activity of PTPN22 Is Involved in T Cell Development via the Regulation of TCR Expression. Int J Mol Sci 2023; 24:14505. [PMID: 37833951 PMCID: PMC10572452 DOI: 10.3390/ijms241914505] [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: 08/24/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The protein tyrosine phosphatase PTPN22 inhibits T cell activation by dephosphorylating some essential proteins in the T cell receptor (TCR)-mediated signaling pathway, such as the lymphocyte-specific protein tyrosine kinase (Lck), Src family tyrosine kinases Fyn, and the phosphorylation levels of Zeta-chain-associated protein kinase-70 (ZAP70). For the first time, we have successfully produced PTPN22 CS transgenic mice in which the tyrosine phosphatase activity of PTPN22 is suppressed. Notably, the number of thymocytes in the PTPN22 CS mice was significantly reduced, and the expression of cytokines in the spleen and lymph nodes was changed significantly. Furthermore, PTPN22 CS facilitated the positive and negative selection of developing thymocytes, increased the expression of the TCRαβ-CD3 complex on the thymus cell surface, and regulated their internalization and recycling. ZAP70, Lck, Phospholipase C gamma1(PLCγ1), and other proteins were observed to be reduced in PTPN22 CS mouse thymocytes. In summary, PTPN22 regulates TCR internalization and recycling via the modulation of the TCR signaling pathway and affects TCR expression on the T cell surface to regulate negative and positive selection. PTPN22 affected the development of the thymus, spleen, lymph nodes, and other peripheral immune organs in mice. Our study demonstrated that PTPN22 plays a crucial role in T cell development and provides a theoretical basis for immune system construction.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Yang Yu
- Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life Science and Health, Northeastern University, #195 Chuangxin Road, Hunnan Xinqu, Shenyang 110169, China; (B.B.); (T.L.); (J.Z.); (Y.Z.); (X.Z.); (T.W.); (N.Z.); (X.W.); (X.B.); (J.X.)
| | - Bing Wang
- Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life Science and Health, Northeastern University, #195 Chuangxin Road, Hunnan Xinqu, Shenyang 110169, China; (B.B.); (T.L.); (J.Z.); (Y.Z.); (X.Z.); (T.W.); (N.Z.); (X.W.); (X.B.); (J.X.)
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Dudley MZ, Gerber JE, Budigan Ni H, Blunt M, Holroyd TA, Carleton BC, Poland GA, Salmon DA. Vaccinomics: A scoping review. Vaccine 2023; 41:2357-2367. [PMID: 36803903 PMCID: PMC10065969 DOI: 10.1016/j.vaccine.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 12/24/2022] [Accepted: 02/03/2023] [Indexed: 02/21/2023]
Abstract
BACKGROUND This scoping review summarizes a key aspect of vaccinomics by collating known associations between heterogeneity in human genetics and vaccine immunogenicity and safety. METHODS We searched PubMed for articles in English using terms covering vaccines routinely recommended to the general US population, their effects, and genetics/genomics. Included studies were controlled and demonstrated statistically significant associations with vaccine immunogenicity or safety. Studies of Pandemrix®, an influenza vaccine previously used in Europe, were also included, due to its widely publicized genetically mediated association with narcolepsy. FINDINGS Of the 2,300 articles manually screened, 214 were included for data extraction. Six included articles examined genetic influences on vaccine safety; the rest examined vaccine immunogenicity. Hepatitis B vaccine immunogenicity was reported in 92 articles and associated with 277 genetic determinants across 117 genes. Thirty-three articles identified 291 genetic determinants across 118 genes associated with measles vaccine immunogenicity, 22 articles identified 311 genetic determinants across 110 genes associated with rubella vaccine immunogenicity, and 25 articles identified 48 genetic determinants across 34 genes associated with influenza vaccine immunogenicity. Other vaccines had fewer than 10 studies each identifying genetic determinants of their immunogenicity. Genetic associations were reported with 4 adverse events following influenza vaccination (narcolepsy, GBS, GCA/PMR, high temperature) and 2 adverse events following measles vaccination (fever, febrile seizure). CONCLUSION This scoping review identified numerous genetic associations with vaccine immunogenicity and several genetic associations with vaccine safety. Most associations were only reported in one study. This illustrates both the potential of and need for investment in vaccinomics. Current research in this field is focused on systems and genetic-based studies designed to identify risk signatures for serious vaccine reactions or diminished vaccine immunogenicity. Such research could bolster our ability to develop safer and more effective vaccines.
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Affiliation(s)
- Matthew Z Dudley
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Institute for Vaccine Safety, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Jennifer E Gerber
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Survey Research Division, RTI International, Washington, DC, USA
| | - Haley Budigan Ni
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Office of Health Equity, California Department of Public Health, Richmond, CA, USA
| | - Madeleine Blunt
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Taylor A Holroyd
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; International Vaccine Access Center, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Bruce C Carleton
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada; Pharmaceutical Outcomes Programme, BC Children's Hospital, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Gregory A Poland
- Division of General Internal Medicine, Mayo Clinic, Rochester, MN, USA; Mayo Vaccine Research Group, Mayo Clinic, Rochester, MN, USA
| | - Daniel A Salmon
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Institute for Vaccine Safety, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Department of Health, Behavior & Society, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
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Zhou L, Bao L, Wang Y, Chen M, Zhang Y, Geng Z, Zhao R, Sun J, Bao Y, Shi Y, Yao R, Guo S, Cui X. An Integrated Analysis Reveals Geniposide Extracted From Gardenia jasminoides J.Ellis Regulates Calcium Signaling Pathway Essential for Influenza A Virus Replication. Front Pharmacol 2021; 12:755796. [PMID: 34867371 PMCID: PMC8640456 DOI: 10.3389/fphar.2021.755796] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Geniposide, an iridoid glycoside purified from the fruit of Gardenia jasminoides J.Ellis, has been reported to possess pleiotropic activity against different diseases. In particular, geniposide possesses a variety of biological activities and exerts good therapeutic effects in the treatment of several strains of the influenza virus. However, the molecular mechanism for the therapeutic effect has not been well defined. This study aimed to investigate the mechanism of geniposide on influenza A virus (IAV). The potential targets and signaling pathways of geniposide in the IAV infection were predicted using network pharmacology analysis. According to the result of network pharmacology analysis, we validated the calcium signaling pathway induced by IAV and investigated the effect of geniposide extracted from Gardenia jasminoides J.Ellis on this pathway. The primary Gene Ontology (GO) biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways KEGG enrichment analysis indicated that geniposide has a multi-target and multi-pathway inhibitory effect against influenza, and one of the mechanisms involves calcium signaling pathway. In the current study, geniposide treatment greatly decreased the levels of RNA polymerase in HEK-293T cells infected with IAV. Knocking down CAMKII in IAV-infected HEK-293T cells enhanced virus RNA (vRNA) production. Geniposide treatment increased CAMKII expression after IAV infection. Meanwhile, the CREB and c-Fos expressions were inhibited by geniposide after IAV infection. The experimental validation data showed that the geniposide was able to alleviate extracellular Ca2+ influx, dramatically decreased neuraminidase activity, and suppressed IAV replication in vitro via regulating the calcium signaling pathway. These anti-IAV effects might be related to the disrupted interplay between IAV RNA polymerase and CAMKII and the regulation of the downstream calcium signaling pathway essential for IAV replication. Taken together, the findings reveal a new facet of the mechanism by which geniposide fights IAV in a way that depends on CAMKII replication.
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Affiliation(s)
- Lirun Zhou
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lei Bao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yaxin Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mengping Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yingying Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Zihan Geng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ronghua Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jing Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanyan Bao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yujing Shi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Rongmei Yao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shanshan Guo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaolan Cui
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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6
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Ho D, Nyaga DM, Schierding W, Saffery R, Perry JK, Taylor JA, Vickers MH, Kempa-Liehr AW, O'Sullivan JM. Identifying the lungs as a susceptible site for allele-specific regulatory changes associated with type 1 diabetes risk. Commun Biol 2021; 4:1072. [PMID: 34521982 PMCID: PMC8440780 DOI: 10.1038/s42003-021-02594-0] [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: 07/23/2020] [Accepted: 08/20/2021] [Indexed: 02/08/2023] Open
Abstract
Type 1 diabetes (T1D) etiology is complex. We developed a machine learning approach that ranked the tissue-specific transcription regulatory effects for T1D SNPs and estimated their relative contributions to conversion to T1D by integrating case and control genotypes (Wellcome Trust Case Control Consortium and UK Biobank) with tissue-specific expression quantitative trait loci (eQTL) data. Here we show an eQTL (rs6679677) associated with changes to AP4B1-AS1 transcript levels in lung tissue makes the largest gene regulatory contribution to the risk of T1D development. Luciferase reporter assays confirmed allele-specific enhancer activity for the rs6679677 tagged locus in lung epithelial cells (i.e. A549 cells; C > A reduces expression, p = 0.005). Our results identify tissue-specific eQTLs for SNPs associated with T1D. The strongest tissue-specific eQTL effects were in the lung and may help explain associations between respiratory infections and risk of islet autoantibody seroconversion in young children.
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Affiliation(s)
- Daniel Ho
- Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Denis M Nyaga
- Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Richard Saffery
- Murdoch Children Research Institute, The University of Melbourne, Melbourne, Australia
| | - Jo K Perry
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - John A Taylor
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Mark H Vickers
- Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Andreas W Kempa-Liehr
- Department of Engineering Science, The University of Auckland, Auckland, New Zealand
| | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.
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7
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Isaacs SR, Foskett DB, Maxwell AJ, Ward EJ, Faulkner CL, Luo JYX, Rawlinson WD, Craig ME, Kim KW. Viruses and Type 1 Diabetes: From Enteroviruses to the Virome. Microorganisms 2021; 9:microorganisms9071519. [PMID: 34361954 PMCID: PMC8306446 DOI: 10.3390/microorganisms9071519] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
For over a century, viruses have left a long trail of evidence implicating them as frequent suspects in the development of type 1 diabetes. Through vigorous interrogation of viral infections in individuals with islet autoimmunity and type 1 diabetes using serological and molecular virus detection methods, as well as mechanistic studies of virus-infected human pancreatic β-cells, the prime suspects have been narrowed down to predominantly human enteroviruses. Here, we provide a comprehensive overview of evidence supporting the hypothesised role of enteroviruses in the development of islet autoimmunity and type 1 diabetes. We also discuss concerns over the historical focus and investigation bias toward enteroviruses and summarise current unbiased efforts aimed at characterising the complete population of viruses (the “virome”) contributing early in life to the development of islet autoimmunity and type 1 diabetes. Finally, we review the range of vaccine and antiviral drug candidates currently being evaluated in clinical trials for the prevention and potential treatment of type 1 diabetes.
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Affiliation(s)
- Sonia R. Isaacs
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Dylan B. Foskett
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Anna J. Maxwell
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Emily J. Ward
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Faculty of Medicine and Health, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Clare L. Faulkner
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Jessica Y. X. Luo
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - William D. Rawlinson
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Faculty of Medicine and Health, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Maria E. Craig
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Institute of Endocrinology and Diabetes, Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Faculty of Medicine and Health, Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Ki Wook Kim
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Correspondence: ; Tel.: +61-2-9382-9096
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8
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Armitage LH, Wallet MA, Mathews CE. Influence of PTPN22 Allotypes on Innate and Adaptive Immune Function in Health and Disease. Front Immunol 2021; 12:636618. [PMID: 33717184 PMCID: PMC7946861 DOI: 10.3389/fimmu.2021.636618] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/18/2021] [Indexed: 01/18/2023] Open
Abstract
Protein tyrosine phosphatase, non-receptor type 22 (PTPN22) regulates a panoply of leukocyte signaling pathways. A single nucleotide polymorphism (SNP) in PTPN22, rs2476601, is associated with increased risk of Type 1 Diabetes (T1D) and other autoimmune diseases. Over the past decade PTPN22 has been studied intensely in T cell receptor (TCR) and B cell receptor (BCR) signaling. However, the effect of the minor allele on PTPN22 function in TCR signaling is controversial with some reports concluding it has enhanced function and blunts TCR signaling and others reporting it has reduced function and increases TCR signaling. More recently, the core function of PTPN22 as well as functional derangements imparted by the autoimmunity-associated variant allele of PTPN22 have been examined in monocytes, macrophages, dendritic cells, and neutrophils. In this review we will discuss the known functions of PTPN22 in human cells, and we will elaborate on how autoimmunity-associated variants influence these functions across the panoply of immune cells that express PTPN22. Further, we consider currently unresolved questions that require clarification on the role of PTPN22 in immune cell function.
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Affiliation(s)
- Lucas H Armitage
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Mark A Wallet
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States.,Immuno-Oncology at Century Therapeutics, LLC, Philadelphia, PA, United States
| | - Clayton E Mathews
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
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9
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Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. GENE REPORTS 2020; 21:100956. [PMID: 33553808 PMCID: PMC7854084 DOI: 10.1016/j.genrep.2020.100956] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/31/2020] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection is a leading cause of pneumonia and death. The aim of this investigation is to identify the key genes in SARS-CoV-2 infection and uncover their potential functions. We downloaded the expression profiling by high throughput sequencing of GSE152075 from the Gene Expression Omnibus database. Normalization of the data from primary SARS-CoV-2 infected samples and negative control samples in the database was conducted using R software. Then, joint analysis of the data was performed. Pathway and Gene ontology (GO) enrichment analyses were performed, and the protein-protein interaction (PPI) network, target gene - miRNA regulatory network, target gene - TF regulatory network of the differentially expressed genes (DEGs) were constructed using Cytoscape software. Identification of diagnostic biomarkers was conducted using receiver operating characteristic (ROC) curve analysis. 994 DEGs (496 up regulated and 498 down regulated genes) were identified. Pathway and GO enrichment analysis showed up and down regulated genes mainly enriched in the NOD-like receptor signaling pathway, Ribosome, response to external biotic stimulus and viral transcription in SARS-CoV-2 infection. Down and up regulated genes were selected to establish the PPI network, modules, target gene - miRNA regulatory network, target gene - TF regulatory network revealed that these genes were involved in adaptive immune system, fluid shear stress and atherosclerosis, influenza A and protein processing in endoplasmic reticulum. In total, ten genes (CBL, ISG15, NEDD4, PML, REL, CTNNB1, ERBB2, JUN, RPS8 and STUB1) were identified as good diagnostic biomarkers. In conclusion, the identified DEGs, hub genes and target genes contribute to the understanding of the molecular mechanisms underlying the advancement of SARS-CoV-2 infection and they may be used as diagnostic and molecular targets for the treatment of patients with SARS-CoV-2 infection in the future.
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Key Words
- Bioinformatics
- CBL, Cbl proto-oncogene
- DEGs, differentially expressed genes
- Diagnosis
- GO, Gene ontology
- ISG15, ISG15 ubiquitin like modifier
- Key genes
- NEDD4, NEDD4 E3 ubiquitin protein ligase
- PML, promyelocyticleukemia
- PPI, protein-protein interaction
- Pathways
- REL, REL proto-oncogene, NF-kB subunit
- ROC, receiver operating characteristic
- SARS-CoV-2 infection
- SARS-CoV-2, Severe acute respiratory syndrome corona virus 2
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10
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Identification of potential mRNA panels for severe acute respiratory syndrome coronavirus 2 (COVID-19) diagnosis and treatment using microarray dataset and bioinformatics methods. 3 Biotech 2020; 10:422. [PMID: 33251083 PMCID: PMC7679428 DOI: 10.1007/s13205-020-02406-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/20/2020] [Indexed: 12/15/2022] Open
Abstract
The goal of the present investigation is to identify the differentially expressed genes (DEGs) between SARS-CoV-2 infected and normal control samples to investigate the molecular mechanisms of infection with SARS-CoV-2. The microarray data of the dataset E-MTAB-8871 were retrieved from the ArrayExpress database. Pathway and Gene Ontology (GO) enrichment study, protein–protein interaction (PPI) network, modules, target gene–miRNA regulatory network, and target gene–TF regulatory network have been performed. Subsequently, the key genes were validated using an analysis of the receiver operating characteristic (ROC) curve. In SARS-CoV-2 infection, a total of 324 DEGs (76 up- and 248 down-regulated genes) were identified and enriched in a number of associated SARS-CoV-2 infection pathways and GO terms. Hub and target genes such as TP53, HRAS, MAPK11, RELA, IKZF3, IFNAR2, SKI, TNFRSF13C, JAK1, TRAF6, KLRF2, CD1A were identified from PPI network, target gene–miRNA regulatory network, and target gene–TF regulatory network. Study of the ROC showed that ten genes (CCL5, IFNAR2, JAK2, MX1, STAT1, BID, CD55, CD80, HAL-B, and HLA-DMA) were substantially involved in SARS-CoV-2 patients. The present investigation identified key genes and pathways that deepen our understanding of the molecular mechanisms of SARS-CoV-2 infection, and could be used for SARS-CoV-2 infection as diagnostic and therapeutic biomarkers.
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11
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Blanter M, Sork H, Tuomela S, Flodström-Tullberg M. Genetic and Environmental Interaction in Type 1 Diabetes: a Relationship Between Genetic Risk Alleles and Molecular Traits of Enterovirus Infection? Curr Diab Rep 2019; 19:82. [PMID: 31401790 PMCID: PMC6689284 DOI: 10.1007/s11892-019-1192-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW We provide an overview of the current knowledge regarding the natural history of human type 1 diabetes (T1D) and the documented associations between virus infections (in particular the enteroviruses) and disease development. We review studies that examine whether T1D-specific risk alleles in genes involved in the function of the immune system can alter susceptibility to virus infections or affect the magnitude of the host antiviral response. We also highlight where the major gaps in our knowledge exist and consider possible implications that new insights gained from the discussed gene-environment interaction studies may bring. RECENT FINDINGS A commonality between several of the studied T1D risk variants studied is their role in modulating the host immune response to viral infection. Generally, little support exists indicating that the risk variants increase susceptibility to infection and moreover, they usually appear to predispose the immune system towards a hyper-reactive state, decrease the risk of infection, and/or favor the establishment of viral persistence. In conclusion, although the current number of studies is limited, this type of research can provide important insights into the mechanisms that are central to disease pathogenesis and further describe how genetic and environmental factors jointly influence the risk of T1D development. The latter may provide genetic markers that could be used for patient stratification and for the selection of method(s) for disease prevention.
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Affiliation(s)
- Marfa Blanter
- 0000 0000 9241 5705grid.24381.3cCenter for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- 0000 0001 0668 7884grid.5596.fLaboratory of Molecular Immunology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, EU Belgium
| | - Helena Sork
- 0000 0000 9241 5705grid.24381.3cCenter for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Soile Tuomela
- 0000 0000 9241 5705grid.24381.3cCenter for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Malin Flodström-Tullberg
- 0000 0000 9241 5705grid.24381.3cCenter for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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12
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Hellesen A, Bratland E. The potential role for infections in the pathogenesis of autoimmune Addison's disease. Clin Exp Immunol 2018; 195:52-63. [PMID: 30144040 DOI: 10.1111/cei.13207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/02/2018] [Accepted: 08/10/2018] [Indexed: 12/21/2022] Open
Abstract
Autoimmune Addison's disease (AAD), or primary adrenocortical insufficiency, is a classical organ-specific autoimmune disease with 160 years of history. AAD is remarkably homogeneous with one major dominant self-antigen, the cytochrome P450 21-hydroxylase enzyme, which is targeted by both autoantibodies and autoreactive T cells. Like most autoimmune diseases, AAD is thought to be caused by an unfortunate combination of genetic and environmental factors. While the number of genetic associations with AAD is increasing, almost nothing is known about environmental factors. A major environmental factor commonly proposed for autoimmune diseases, based partly on experimental and clinical data and partly on shared pathways between anti-viral immunity and autoimmunity, is viral infections. However, there are few reports associating viral infections to AAD, and it has proved difficult to establish which immunological processes that could link any viral infection with the initiation or progression of AAD. In this review, we will summarize the current knowledge on the underlying mechanisms of AAD and take a closer look on the potential involvement of viruses.
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Affiliation(s)
- A Hellesen
- Department of Clinical Science, University of Bergen, Bergen, Norway.,K.G. Jebsen Senter for Autoimmune Sykdommer, University of Bergen, Bergen, Norway
| | - E Bratland
- Department of Clinical Science, University of Bergen, Bergen, Norway.,K.G. Jebsen Senter for Autoimmune Sykdommer, University of Bergen, Bergen, Norway
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13
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Stacey HD, Barjesteh N, Mapletoft JP, Miller MS. "Gnothi Seauton": Leveraging the Host Response to Improve Influenza Virus Vaccine Efficacy. Vaccines (Basel) 2018; 6:vaccines6020023. [PMID: 29649134 PMCID: PMC6027147 DOI: 10.3390/vaccines6020023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 02/07/2023] Open
Abstract
Vaccination against the seasonal influenza virus is the best way to prevent infection. Nevertheless, vaccine efficacy remains far from optimal especially in high-risk populations such as the elderly. Recent technological advancements have facilitated rapid and precise identification of the B and T cell epitopes that are targets for protective responses. While these discoveries have undoubtedly brought the field closer to "universal" influenza virus vaccines, choosing the correct antigen is only one piece of the equation. Achieving efficacy and durability requires a detailed understanding of the diverse host factors and pathways that are required for attaining optimal responses. Sequencing technologies, systems biology, and immunological studies have recently advanced our understanding of the diverse aspects of the host response required for vaccine efficacy. In this paper, we review the critical role of the host response in determining efficacious responses and discuss the gaps in knowledge that will need to be addressed if the field is to be successful in developing new and more effective influenza virus vaccines.
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Affiliation(s)
- Hannah D Stacey
- Michael G. DeGroote Institute for Infectious Diseases Research, McMaster Immunology Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Neda Barjesteh
- Michael G. DeGroote Institute for Infectious Diseases Research, McMaster Immunology Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Jonathan P Mapletoft
- Michael G. DeGroote Institute for Infectious Diseases Research, McMaster Immunology Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Matthew S Miller
- Michael G. DeGroote Institute for Infectious Diseases Research, McMaster Immunology Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada.
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14
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Immunologic response to vaccine challenge in pregnant PTPN22 R620W carriers and non-carriers. PLoS One 2017; 12:e0181338. [PMID: 28723925 PMCID: PMC5517002 DOI: 10.1371/journal.pone.0181338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/29/2017] [Indexed: 11/21/2022] Open
Abstract
Objectives Influenza infection is a significant cause of respiratory morbidity among pregnant women. Seasonal influenza vaccination engages innate immune receptors to promote protective immunity. A coding polymorphism (R620W) in PTPN22 imparts elevated risk for human infection and autoimmune disease, predisposes to diminished innate immune responses, and associates with reduced immunization responses. We sought to quantify the effects of PTPN22-R620W on humoral and cell-mediated immune responses to the inactivated influenza vaccine among healthy pregnant women. Study Design Immune responses were measured in healthy pregnant R620W carrier (n = 17) and non-carrier (n = 33) women receiving the 2013 quadrivalent inactivated influenza vaccine (Fluzone). Hemagglutination inhibition assays were performed to quantify neutralizing antibodies; functional influenza-reactive CD4 T cells were quantified by flow cytometry, and influenza-specific CD8 T cells were enumerated with MHC Class I tetramers. Antibody seroconversion data were evaluated by Chi-square analysis, and the Mann-Whitney or Wilcoxon signed-rank tests were applied to T cell response data. Results PTPN22 R620W carrier (n = 17) and non-carrier (n = 33) groups did not differ in age, parity, BMI, gestational age at time of vaccine, or history of prior influenza vaccination. After Fluzone exposure, 51.5% of non-carriers met criteria for antibody seroconversion to H1N1 influenza, compared with 23.5% of R620W carriers (p = 0.06). Influenza-reactive CD4 T cells showed modest increase at days 9–15 after vaccination in both R620W carriers and non-carriers (p = 0.02 and p = 0.04, respectively). However, there was no difference in overall response between the two groups (p = 0.6). The vaccine did not result in significant induction of influenza-specific CD8 T cells in either group. Conclusions There was no significant difference among healthy pregnant R620W carriers and non-carriers in H1N1 antibody seroconversion rates after influenza vaccination. Studies of larger cohorts will be needed to define the effect of PTPN22 risk allele carriage on antibody and T cell responses to influenza vaccination during pregnancy.
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15
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Jofra T, Galvani G, Kuka M, Di Fonte R, Mfarrej BG, Iannacone M, Salek-Ardakani S, Battaglia M, Fousteri G. Extrinsic Protein Tyrosine Phosphatase Non-Receptor 22 Signals Contribute to CD8 T Cell Exhaustion and Promote Persistence of Chronic Lymphocytic Choriomeningitis Virus Infection. Front Immunol 2017; 8:811. [PMID: 28747914 PMCID: PMC5506075 DOI: 10.3389/fimmu.2017.00811] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 06/27/2017] [Indexed: 01/04/2023] Open
Abstract
A genetic variant of the protein tyrosine phosphatase non-receptor 22 (PTPN22) is associated with a wide range of autoimmune diseases; however, the reasons behind its prevalence in the general population remain not completely understood. Recent evidence highlights an important role of autoimmune susceptibility genetic variants in conferring resistance against certain pathogens. In this study, we examined the role of PTPN22 in persistent infection in mice lacking PTPN22 infected with lymphocytic choriomeningitis virus clone 13. We found that lack of PTPN22 in mice resulted in viral clearance 30 days after infection, which was reflected in their reduced weight loss and overall improved health. PTPN22-/- mice exhibited enhanced virus-specific CD8 and CD4 T cell numbers and functionality and reduced exhausted phenotype. Moreover, mixed bone marrow chimera studies demonstrated no differences in virus-specific CD8 T cell accumulation and function between the PTPN22+/+ and PTPN22-/- compartments, showing that the effects of PTPN22 on CD8 T cells are T cell-extrinsic. Together, these findings identify a CD8 T cell-extrinsic role for PTPN22 in weakening early CD8 T cell responses to collectively promote persistence of a chronic viral infection.
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Affiliation(s)
- Tatiana Jofra
- Division of Immunology Transplantation and Infectious Diseases (DITID), Diabetes Research Institute (DRI) IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giuseppe Galvani
- Division of Immunology Transplantation and Infectious Diseases (DITID), Diabetes Research Institute (DRI) IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Mirela Kuka
- Division of Immunology Transplantation and Infectious Diseases (DITID), Diabetes Research Institute (DRI) IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Roberta Di Fonte
- Division of Immunology Transplantation and Infectious Diseases (DITID), Diabetes Research Institute (DRI) IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bechara G Mfarrej
- Division of Immunology Transplantation and Infectious Diseases (DITID), Diabetes Research Institute (DRI) IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Iannacone
- Division of Immunology Transplantation and Infectious Diseases (DITID), Diabetes Research Institute (DRI) IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Shahram Salek-Ardakani
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Manuela Battaglia
- Division of Immunology Transplantation and Infectious Diseases (DITID), Diabetes Research Institute (DRI) IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Georgia Fousteri
- Division of Immunology Transplantation and Infectious Diseases (DITID), Diabetes Research Institute (DRI) IRCCS San Raffaele Scientific Institute, Milan, Italy
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