1
|
Zhang Y, Morris R, Brown GJ, Lorenzo AMD, Meng X, Kershaw NJ, Kiridena P, Burgio G, Gross S, Cappello JY, Shen Q, Wang H, Turnbull C, Lea-Henry T, Stanley M, Yu Z, Ballard FD, Chuah A, Lee JC, Hatch AM, Enders A, Masters SL, Headley AP, Trnka P, Mallon D, Fletcher JT, Walters GD, Šestan M, Jelušić M, Cook MC, Athanasopoulos V, Fulcher DA, Babon JJ, Vinuesa CG, Ellyard JI. Rare SH2B3 coding variants in lupus patients impair B cell tolerance and predispose to autoimmunity. J Exp Med 2024; 221:e20221080. [PMID: 38417019 PMCID: PMC10901239 DOI: 10.1084/jem.20221080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 03/14/2023] [Accepted: 01/17/2024] [Indexed: 03/01/2024] Open
Abstract
Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease with a clear genetic component. While most SLE patients carry rare gene variants in lupus risk genes, little is known about their contribution to disease pathogenesis. Amongst them, SH2B3-a negative regulator of cytokine and growth factor receptor signaling-harbors rare coding variants in over 5% of SLE patients. Here, we show that unlike the variant found exclusively in healthy controls, SH2B3 rare variants found in lupus patients are predominantly hypomorphic alleles, failing to suppress IFNGR signaling via JAK2-STAT1. The generation of two mouse lines carrying patients' variants revealed that SH2B3 is important in limiting the number of immature and transitional B cells. Furthermore, hypomorphic SH2B3 was shown to impair the negative selection of immature/transitional self-reactive B cells and accelerate autoimmunity in sensitized mice, at least in part due to increased IL-4R signaling and BAFF-R expression. This work identifies a previously unappreciated role for SH2B3 in human B cell tolerance and lupus risk.
Collapse
Affiliation(s)
- Yaoyuan Zhang
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Rhiannon Morris
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Grant J. Brown
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Ayla May D. Lorenzo
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Xiangpeng Meng
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Nadia J. Kershaw
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Pamudika Kiridena
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Gaétan Burgio
- Division of Genome Sciences and Cancer, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Simon Gross
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Jean Y. Cappello
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Qian Shen
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Francis Crick Institute, London, UK
| | - Hao Wang
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Francis Crick Institute, London, UK
| | - Cynthia Turnbull
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Tom Lea-Henry
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- The Canberra Hospital, Garran, Australia
| | - Maurice Stanley
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Zhijia Yu
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Fiona D. Ballard
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Aaron Chuah
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - James C. Lee
- Francis Crick Institute, London, UK
- Department of Gastroenterology, Division of Medicine, Institute for Liver and Digestive Health, University College London, London, UK
| | - Ann-Maree Hatch
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- The Canberra Hospital, Garran, Australia
| | - Anselm Enders
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Seth L. Masters
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | | | - Peter Trnka
- Queensland Children’s Hospital, South Brisbane, Australia
| | | | | | | | - Mario Šestan
- Department of Pediatrics, University of Zagreb School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Marija Jelušić
- Department of Pediatrics, University of Zagreb School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Matthew C. Cook
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- The Canberra Hospital, Garran, Australia
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Vicki Athanasopoulos
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - David A. Fulcher
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| | - Jeffrey J. Babon
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Carola G. Vinuesa
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Francis Crick Institute, London, UK
| | - Julia I. Ellyard
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Acton, Australia
| |
Collapse
|
2
|
Mescia F, Bayati S, Brouwer E, Heeringa P, Toonen EJM, Beenes M, Ball MJ, Rees AJ, Kain R, Lyons PA, Nilsson P, Pin E. Autoantibody Profiling and Anti-Kinesin Reactivity in ANCA-Associated Vasculitis. Int J Mol Sci 2023; 24:15341. [PMID: 37895021 PMCID: PMC10607136 DOI: 10.3390/ijms242015341] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
ANCA-associated vasculitides (AAV) are rare autoimmune diseases causing inflammation and damage to small blood vessels. New autoantibody biomarkers are needed to improve the diagnosis and treatment of AAV patients. In this study, we aimed to profile the autoantibody repertoire of AAV patients using in-house developed antigen arrays to identify previously unreported antibodies linked to the disease per se, clinical subgroups, or clinical activity. A total of 1743 protein fragments representing 1561 unique proteins were screened in 229 serum samples collected from 137 AAV patients at presentation, remission, and relapse. Additionally, serum samples from healthy individuals and patients with other type of vasculitis and autoimmune-inflammatory conditions were included to evaluate the specificity of the autoantibodies identified in AAV. Autoreactivity against members of the kinesin protein family were identified in AAV patients, healthy volunteers, and disease controls. Anti-KIF4A antibodies were significantly more prevalent in AAV. We also observed possible associations between anti-kinesin antibodies and clinically relevant features within AAV patients. Further verification studies will be needed to confirm these findings.
Collapse
Affiliation(s)
- Federica Mescia
- Department of Medicine, University of Cambridge, Cambridge CB2 0SP, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, 25121 Brescia, Italy
| | - Shaghayegh Bayati
- Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, 171 65 Stockholm, Sweden
| | - Elisabeth Brouwer
- Department of Rheumatology and Clinical Immunology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Peter Heeringa
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Erik J M Toonen
- R&D Department, Hycult Biotech, 5405 PB Uden, The Netherlands
| | - Marijke Beenes
- R&D Department, Hycult Biotech, 5405 PB Uden, The Netherlands
| | - Miriam J Ball
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
| | - Andrew J Rees
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
| | - Renate Kain
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
| | - Paul A Lyons
- Department of Medicine, University of Cambridge, Cambridge CB2 0SP, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| | - Peter Nilsson
- Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, 171 65 Stockholm, Sweden
| | - Elisa Pin
- Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, 171 65 Stockholm, Sweden
| |
Collapse
|
3
|
Esmaeilzadeh H, Chavoshzadeh Z, Nabavizadeh SH, Alyasin S, Amanati A, Askarisarvestani A. Systemic aspergillosis in a patient with interferon gamma receptor 1 deficiency; a case report. BMC Pediatr 2023; 23:278. [PMID: 37277724 DOI: 10.1186/s12887-023-04093-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/25/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Interferon-gamma receptor deficiency is a heterogeneous spectrum of disease which involves mutations in IFNGR1, IFNGR2 genes, and the downstream signaling proteins such as STAT1. These mutations are associated with immunodeficiency 27 A and 27B, making the patient prone to mycobacterial infections. Patients with this condition are also at increased risk for affliction with viral and bacterial infections, such as with the Herpesviridae family, Listeria, and Salmonella. Moreover, SH2B3 mutation is associated with autoimmune and lymphoproliferative conditions. CASE PRESENTATION the patient was a 19-month-old infant girl who presented with a two-week history of fever. She had near-normal flowcytometry with high IgM and IgE. She had pneumonic infiltration in her chest and right hilar and para-aortic lymphadenopathy. PCR of whole blood for Aspergillus fumigatus came back positive. In her Whole Exome Sequencing she had IFNGR1 and SH2B3 mutations. CONCLUSION systemic fungal infections such as Aspergillosis can occur in patients with interferon-gamma receptor one deficiency. This type of immunodeficiency should be considered in treating patients with systemic Aspergillosis.
Collapse
Affiliation(s)
- Hossein Esmaeilzadeh
- Division of Allergy and Clinical Immunology, Department of Pediatrics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Allergy Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Chavoshzadeh
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Mofid Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Hesamedin Nabavizadeh
- Division of Allergy and Clinical Immunology, Department of Pediatrics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Allergy Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Soheila Alyasin
- Division of Allergy and Clinical Immunology, Department of Pediatrics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Allergy Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Amanati
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Askarisarvestani
- Division of Allergy and Clinical Immunology, Department of Pediatrics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
4
|
Narala S, Che Y, Saleem A, Lock CB, Kim YH, Rieger KE. Progression of Mycosis Fungoides After Fingolimod Treatment for Multiple Sclerosis and Targeted Next-Generation Sequencing Demonstrating Potential Links Between the Two Diseases. JCO Precis Oncol 2023; 7:e2200501. [PMID: 36724412 DOI: 10.1200/po.22.00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Saisindhu Narala
- Department of Pathology, Stanford University School of Medicine, Stanford, CA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA
| | - Yonglu Che
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA
| | - Atif Saleem
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Christopher B Lock
- Division of Neuroimmunology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Youn H Kim
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA
| | - Kerri E Rieger
- Department of Pathology, Stanford University School of Medicine, Stanford, CA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA
| |
Collapse
|
5
|
Howarth S, Sneddon G, Allinson KR, Razvi S, Mitchell AL, Pearce SHS. Replication of association at the LPP and UBASH3A loci in a UK autoimmune Addison's disease cohort. Eur J Endocrinol 2023; 188:lvac010. [PMID: 36651163 DOI: 10.1093/ejendo/lvac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/21/2022] [Accepted: 11/30/2022] [Indexed: 01/13/2023]
Abstract
Autoimmune Addison's disease (AAD) arises from a complex interplay between multiple genetic susceptibility polymorphisms and environmental factors. The first genome wide association study (GWAS) with patients from Scandinavian Addison's registries has identified association signals at four novel loci in the genes LPP, SH2B3, SIGLEC5, and UBASH3A. To verify these novel risk loci, we performed a case-control association study in our independent cohort of 420 patients with AAD from the across the UK. We report significant association of alleles of the LPP and UBASH3A genes [odds ratio (95% confidence intervals), 1.46 (1.21-1.75)and 1.40 (1.16-1.68), respectively] with AAD in our UK cohort. In addition, we report nominal association of AAD with SH2B3 [OR 1.18 (1.02-1.35)]. We confirm that variants at the LPP and UBASH3A loci confer susceptibility to AAD in a UK population. Further studies with larger patient cohorts are required to robustly confirm the association of SH2B3 and SIGLEC5/SPACA6 alleles.
Collapse
Affiliation(s)
- Sophie Howarth
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Georgina Sneddon
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Kathleen R Allinson
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Salman Razvi
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Anna L Mitchell
- Department of Endocrinology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Simon H S Pearce
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
- Department of Endocrinology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| |
Collapse
|
6
|
Yao M, Qu H, Han Y, Cheng CY, Xiao X. Kinesins in Mammalian Spermatogenesis and Germ Cell Transport. Front Cell Dev Biol 2022; 10:837542. [PMID: 35547823 PMCID: PMC9083010 DOI: 10.3389/fcell.2022.837542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
In mammalian testes, the apical cytoplasm of each Sertoli cell holds up to several dozens of germ cells, especially spermatids that are transported up and down the seminiferous epithelium. The blood-testis barrier (BTB) established by neighboring Sertoli cells in the basal compartment restructures on a regular basis to allow preleptotene/leptotene spermatocytes to pass through. The timely transfer of germ cells and other cellular organelles such as residual bodies, phagosomes, and lysosomes across the epithelium to facilitate spermatogenesis is important and requires the microtubule-based cytoskeleton in Sertoli cells. Kinesins, a superfamily of the microtubule-dependent motor proteins, are abundantly and preferentially expressed in the testis, but their functions are poorly understood. This review summarizes recent findings on kinesins in mammalian spermatogenesis, highlighting their potential role in germ cell traversing through the BTB and the remodeling of Sertoli cell-spermatid junctions to advance spermatid transport. The possibility of kinesins acting as a mediator and/or synchronizer for cell cycle progression, germ cell transit, and junctional rearrangement and turnover is also discussed. We mostly cover findings in rodents, but we also make special remarks regarding humans. We anticipate that this information will provide a framework for future research in the field.
Collapse
Affiliation(s)
- Mingxia Yao
- Center for Reproductive Health, School of Pharmaceutical Sciences, Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, China
| | - Haoyang Qu
- Center for Reproductive Health, School of Pharmaceutical Sciences, Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, China
| | - Yating Han
- Center for Reproductive Health, School of Pharmaceutical Sciences, Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, China
| | - C Yan Cheng
- Department of Urology and Andrology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiang Xiao
- Center for Reproductive Health, School of Pharmaceutical Sciences, Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, China.,Zhejiang Provincial Laboratory of Experimental Animal's & Nonclinical Laboratory Studies, Hangzhou Medical College, Hangzhou, China
| |
Collapse
|
7
|
Beliën J, Goris A, Matthys P. Natural Killer Cells in Multiple Sclerosis: Entering the Stage. Front Immunol 2022; 13:869447. [PMID: 35464427 PMCID: PMC9019710 DOI: 10.3389/fimmu.2022.869447] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/14/2022] [Indexed: 11/14/2022] Open
Abstract
Studies investigating the immunopathology of multiple sclerosis (MS) have largely focused on adaptive T and B lymphocytes. However, in recent years there has been an increased interest in the contribution of innate immune cells, amongst which the natural killer (NK) cells. Apart from their canonical role of controlling viral infections, cell stress and malignancies, NK cells are increasingly being recognized for their modulating effect on the adaptive immune system, both in health and autoimmune disease. From different lines of research there is now evidence that NK cells contribute to MS immunopathology. In this review, we provide an overview of studies that have investigated the role of NK cells in the pathogenesis of MS by use of the experimental autoimmune encephalomyelitis (EAE) animal model, MS genetics or through ex vivo and in vitro work into the immunology of MS patients. With the advent of modern hypothesis-free technologies such as single-cell transcriptomics, we are exposing an unexpected NK cell heterogeneity, increasingly blurring the boundaries between adaptive and innate immunity. We conclude that unravelling this heterogeneity, as well as the mechanistic link between innate and adaptive immune cell functions will lay the foundation for the use of NK cells as prognostic tools and therapeutic targets in MS and a myriad of other currently uncurable autoimmune disorders.
Collapse
Affiliation(s)
- Jarne Beliën
- Department of Neurosciences, Laboratory for Neuroimmunology, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - An Goris
- Department of Neurosciences, Laboratory for Neuroimmunology, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Patrick Matthys
- Department of Microbiology, Immunology and Transplantation, Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| |
Collapse
|
8
|
The Missing LNK: Evolution from Cytosis to Chronic Myelomonocytic Leukemia in a Patient with Multiple Sclerosis and Germline SH2B3 Mutation. Case Rep Genet 2022; 2022:6977041. [PMID: 35281324 PMCID: PMC8904908 DOI: 10.1155/2022/6977041] [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: 10/27/2021] [Accepted: 01/27/2022] [Indexed: 11/18/2022] Open
Abstract
Chronic myelomonocytic leukemia (CMML) is a rare but distinct hematological neoplasm with overlapping features of myelodysplastic syndrome (MDS) and myeloproliferative neoplasm (MPN). Individuals with CMML have persistent monocytosis and bone marrow dyspoiesis associated with various constitutional symptoms like fevers, unintentional weight loss, or night sweats. It is established that there is a strong association of CMML with preceding or coexisting autoimmune diseases and systemic inflammatory syndromes affecting around 20% of patients. Various molecular abnormalities like TET2, SRSF2, ASXL1, and RAS are reported in the pathogenesis of CMML, but no such mutations have been described to explain the strong association of autoimmune diseases and severe inflammatory phenotype seen in CMML. Germline mutation in SH2B adaptor protein 3 (SH2B3) had been reported before to affect a family with autoimmune disorders and acute lymphoblastic leukemia. In this report, we describe the first case of a female subject with many years of preceding history of multiple sclerosis before the diagnosis of CMML. We outline the evidence supporting the pathogenic role of SH2B3 p.E395K germline mutation, connecting the dots of association between autoimmune diseases and CMML genesis.
Collapse
|
9
|
Morris R, Butler L, Perkins A, Kershaw NJ, Babon JJ. The Role of LNK (SH2B3) in the Regulation of JAK-STAT Signalling in Haematopoiesis. Pharmaceuticals (Basel) 2021; 15:ph15010024. [PMID: 35056081 PMCID: PMC8781068 DOI: 10.3390/ph15010024] [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: 11/25/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 01/05/2023] Open
Abstract
LNK is a member of the SH2B family of adaptor proteins and is a non-redundant regulator of cytokine signalling. Cytokines are secreted intercellular messengers that bind to specific receptors on the surface of target cells to activate the Janus Kinase-Signal Transducer and Activator of Transcription (JAK-STAT) signalling pathway. Activation of the JAK-STAT pathway leads to proliferative and often inflammatory effects, and so the amplitude and duration of signalling are tightly controlled. LNK binds phosphotyrosine residues to signalling proteins downstream of cytokines and constrains JAK-STAT signalling. Mutations in LNK have been identified in a range of haematological and inflammatory diseases due to increased signalling following the loss of LNK function. Here, we review the regulation of JAK-STAT signalling via the adaptor protein LNK and discuss the role of LNK in haematological diseases.
Collapse
Affiliation(s)
- Rhiannon Morris
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (R.M.); (N.J.K.)
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Liesl Butler
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3001, Australia; (L.B.); (A.P.)
- Alfred Health, Melbourne, VIC 3001, Australia
| | - Andrew Perkins
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3001, Australia; (L.B.); (A.P.)
- Alfred Health, Melbourne, VIC 3001, Australia
| | - Nadia J. Kershaw
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (R.M.); (N.J.K.)
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Jeffrey J. Babon
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (R.M.); (N.J.K.)
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
- Correspondence: ; Tel.: +61-3-9345-2960; Fax: +61-3-9347-0852
| |
Collapse
|
10
|
Morris R, Zhang Y, Ellyard JI, Vinuesa CG, Murphy JM, Laktyushin A, Kershaw NJ, Babon JJ. Structural and functional analysis of target recognition by the lymphocyte adaptor protein LNK. Nat Commun 2021; 12:6110. [PMID: 34671038 PMCID: PMC8528861 DOI: 10.1038/s41467-021-26394-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/30/2021] [Indexed: 01/17/2023] Open
Abstract
The SH2B family of adaptor proteins, SH2-B, APS, and LNK are key modulators of cellular signalling pathways. Whilst SH2-B and APS have been partially structurally and biochemically characterised, to date there has been no such characterisation of LNK. Here we present two crystal structures of the LNK substrate recognition domain, the SH2 domain, bound to phosphorylated motifs from JAK2 and EPOR, and biochemically define the basis for target recognition. The LNK SH2 domain adopts a canonical SH2 domain fold with an additional N-terminal helix. Targeted analysis of binding to phosphosites in signalling pathways indicated that specificity is conferred by amino acids one- and three-residues downstream of the phosphotyrosine. Several mutations in LNK showed impaired target binding in vitro and a reduced ability to inhibit signalling, allowing an understanding of the molecular basis of LNK dysfunction in variants identified in patients with myeloproliferative disease.
Collapse
Affiliation(s)
- Rhiannon Morris
- grid.1042.7Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Royal Parade, Parkville, VIC 3052 Australia
| | - Yaoyuan Zhang
- grid.1001.00000 0001 2180 7477Australia Department of Immunology and Infectious Diseases, Australian National University, Canberra, ACT Australia ,grid.1001.00000 0001 2180 7477Australia Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, ACT Australia
| | - Julia I. Ellyard
- grid.1001.00000 0001 2180 7477Australia Department of Immunology and Infectious Diseases, Australian National University, Canberra, ACT Australia ,grid.1001.00000 0001 2180 7477Australia Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, ACT Australia
| | - Carola G. Vinuesa
- grid.1001.00000 0001 2180 7477Australia Department of Immunology and Infectious Diseases, Australian National University, Canberra, ACT Australia ,grid.1001.00000 0001 2180 7477Australia Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, ACT Australia
| | - James M. Murphy
- grid.1042.7Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Royal Parade, Parkville, VIC 3052 Australia
| | - Artem Laktyushin
- grid.1042.7Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Royal Parade, Parkville, VIC 3052 Australia
| | - Nadia J. Kershaw
- grid.1042.7Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Royal Parade, Parkville, VIC 3052 Australia
| | - Jeffrey J. Babon
- grid.1042.7Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Royal Parade, Parkville, VIC 3052 Australia
| |
Collapse
|
11
|
Engel B, Laschtowitz A, Janik MK, Junge N, Baumann U, Milkiewicz P, Taubert R, Sebode M. Genetic aspects of adult and pediatric autoimmune hepatitis: A concise review. Eur J Med Genet 2021; 64:104214. [PMID: 33812046 DOI: 10.1016/j.ejmg.2021.104214] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/25/2021] [Accepted: 03/28/2021] [Indexed: 02/06/2023]
Abstract
Autoimmune Hepatitis (AIH) is a heterogenous, mostly chronic liver disease that affects people of all age groups, women more often than men. The aim of therapy is to prevent cirrhosis, as it mainly accounts for liver-related mortality in patients with AIH. Rates of remission are high in patients with AIH, but life-long immunosuppressive therapy is required. AIH is hypothesized to originate from immunologic reactivity targeted against mostly unknown self-antigens, potentially triggered by viral infections among other factors. While AIH does not follow a Mendelian inheritance pattern, part of the risk of developing AIH or worse disease course, is attributed to specific genetic risk factors. Major associations for the risk of development of AIH were found for HLA-DRB1*03:01 and HLA-DRB1*04:01 in adult AIH in the only genome-wide association study on AIH. However, other potential risk loci in SH2B3, CARD10 and KIR genes were described. This review covers the current knowledge on genetic risk factors in adult and pediatric AIH.
Collapse
Affiliation(s)
- Bastian Engel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Germany.
| | - Alena Laschtowitz
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Germany
| | - Maciej K Janik
- Liver and Internal Medicine Unit, Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Germany
| | - Norman Junge
- Pediatric Gastroenterology and Hepatology, Department of Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Germany
| | - Ulrich Baumann
- Pediatric Gastroenterology and Hepatology, Department of Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Germany
| | - Piotr Milkiewicz
- Liver and Internal Medicine Unit, Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland; Translational Medicine Group, Pomeranian Medical University, Szczecin, Poland; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Germany
| | - Richard Taubert
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Germany
| | - Marcial Sebode
- I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Germany
| |
Collapse
|
12
|
Chen XQ, Das U, Park G, Mobley WC. Normal levels of KIF5 but reduced KLC1 levels in both Alzheimer disease and Alzheimer disease in Down syndrome: evidence suggesting defects in anterograde transport. Alzheimers Res Ther 2021; 13:59. [PMID: 33691783 PMCID: PMC7945332 DOI: 10.1186/s13195-021-00796-6] [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: 11/24/2020] [Accepted: 02/22/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Impaired axonal transport may contribute to the pathogenesis of neurodegenerative diseases, including Alzheimer's disease (AD) and Down syndrome (DS). Axonal transport is a complex process in which specific motor proteins move cargoes to and from neuronal cell bodies and their processes. Inconsistent reports point to the changes in AD in the levels of the classical anterograde motor protein kinesin family member 5 (KIF5) and the primary neuronal KIF regulator kinesin light chain 1 (KLC1), raising the possibility that anterograde transport is compromised in AD. METHODS AND MATERIALS To address inconsistencies and determine if the shared pathologies in AD and elderly DS subjects with dementia (AD in DS; AD-DS) extend to the changes in KIF5 and KLC1, we measured the levels of all the three KIF5 family members and KLC1 in the AD and AD-DS frontal cortex and AD temporal cortex and cerebellum in samples taken with a short postmortem interval. To support future studies to explore the cell biological basis for any changes detected, we also examined the levels of these proteins in the brains of young and aged adult mice in the Dp (16)1Yey/+ (Dp16) mouse model of DS and J20 mouse model of AD. RESULTS There were no changes in comparison with controls in KIF5 family members in either the AD or AD-DS samples when normalized to either β-actin or glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Interestingly, however, samples from control brains as well as from AD and AD-DS demonstrated strong positive correlations between the levels of KIF5 family members, suggesting positive co-regulated expression. Importantly, while earlier reports pointed to a negative correlation between the levels of the amyloid precursor protein (APP) and KIF5A levels, we found the opposite to be true in AD-DS; this was especially striking given triplication of the APP gene, with increased APP protein levels. AD and control samples showed positive correlations between fl-hAPP and KIF5 members, but they were less consistent. In contrast to the findings for KIF5, the levels of KLC1 were downregulated in the frontal cortex of both AD and AD-DS brains; interestingly, this change was not seen in the AD temporal cortex or cerebellum. As postmortem interval has a negative effect on the levels of KLC1, but not KIF5 members, we analyzed a subset of samples with a very short postmortem interval (PMI) (≤ 6 h), a PMI that was not significantly correlated with the levels of KLC1 in either AD or AD-DS samples; we confirmed the presence of a statistically significant reduction of KLC1 in AD and AD-DS brains as compared with control brains. Studies comparing Dp16 to its euploid control recapitulated human studies in demonstrating no change in KIF5 levels and a positive correlation between the levels of KIF5 family members. J20 mice also showed normal KIF5 levels. However, unlike the AD and AD-DS frontal cortex, KLC1 levels were not reduced in the brains of Dp16 or J20 mice. CONCLUSION These data point to significant reductions in KLC1 in AD and AD-DS. In so doing, they raise the possibility of compromised KLC1-mediated axonal transport in these conditions, a posit that can now be pursued in model systems in which KLC1 expression is reduced.
Collapse
Affiliation(s)
- Xu-Qiao Chen
- grid.266100.30000 0001 2107 4242Department of Neurosciences, University of California San Diego, La Jolla, CA 92093 USA
| | - Utpal Das
- grid.266100.30000 0001 2107 4242Department of Neurosciences, University of California San Diego, La Jolla, CA 92093 USA
| | - Gooho Park
- grid.266100.30000 0001 2107 4242Department of Neurosciences, University of California San Diego, La Jolla, CA 92093 USA
| | - William C. Mobley
- grid.266100.30000 0001 2107 4242Department of Neurosciences, University of California San Diego, La Jolla, CA 92093 USA
| |
Collapse
|
13
|
The Relationship of the Mechanisms of the Pathogenesis of Multiple Sclerosis and the Expression of Endogenous Retroviruses. BIOLOGY 2020; 9:biology9120464. [PMID: 33322628 PMCID: PMC7764762 DOI: 10.3390/biology9120464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022]
Abstract
Simple Summary Multiple sclerosis is a neurodegenerative disease of the central nervous system, develops at an early age and often leads to a disability. The etiological cause of the disease has not been fully elucidated, and as a result, no effective treatment is available. This review summarizes the current knowledge about the relationship between the expression of human endogenous retroviruses and the pathogenesis of multiple sclerosis. The epigenetic mechanisms of transcriptional regulation, the role of transcription factors, cytokines, and exogenous viruses are also addressed in this review. The elucidation of the mechanisms of an increase in endogenous retrovirus expression in multiple sclerosis could help to develop therapeutic strategies and novel methods for early diagnosis and treatment of the disease. Abstract Two human endogenous retroviruses of the HERV-W family can act as cofactors triggering multiple sclerosis (MS): MS-associated retrovirus (MSRV) and ERVWE1. Endogenous retroviral elements are believed to have integrated in our ancestors’ DNA millions of years ago. Their involvement in the pathogenesis of various diseases, including neurodegenerative pathologies, has been demonstrated. Numerous studies have shown a correlation between the deterioration of patients’ health and increased expression of endogenous retroviruses. The exact causes and mechanisms of endogenous retroviruses activation remains unknown, which hampers development of therapeutics. In this review, we will summarize the main characteristics of human endogenous W retroviruses and describe the putative mechanisms of activation, including epigenetic mechanisms, humoral factors as well as the role of the exogenous viral infections.
Collapse
|
14
|
Defective negative regulation of Toll-like receptor signaling leads to excessive TNF-α in myeloproliferative neoplasm. Blood Adv 2020; 3:122-131. [PMID: 30647074 PMCID: PMC6341195 DOI: 10.1182/bloodadvances.2018026450] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/12/2018] [Indexed: 12/12/2022] Open
Abstract
Patients with myeloproliferative neoplasms (MPN) have high levels of inflammatory cytokines, some of which drive many of the debilitating constitutional symptoms associated with the disease and may also promote expansion of the neoplastic clone. We report here that monocytes from patients with MPN have defective negative regulation of Toll-like receptor (TLR) signaling that leads to unrestrained production of the inflammatory cytokine tumor necrosis factor α (TNF-α) after TLR activation. Specifically, monocytes of patients with MPN are insensitive to the anti-inflammatory cytokine interleukin 10 (IL-10) that negatively regulates TLR-induced TNF-α production. This inability to respond to IL-10 is a not a direct consequence of JAK2 V617F , as the phenotype of persistent TNF-α production is a feature of JAK2 V617F and wild-type monocytes alike from JAK2 V617F -positive patients. Moreover, persistent TNF-α production was also discovered in the unaffected identical twin of a patient with MPN, suggesting it could be an intrinsic feature of those predisposed to acquire MPN. This work implicates sustained TLR signaling as not only a contributor to the chronic inflammatory state of MPN patients but also a potential predisposition to acquire MPN.
Collapse
|
15
|
Bai L, Jiang J, Li H, Zhang R. Role of CD226 Rs763361 Polymorphism in Susceptibility to Multiple Autoimmune Diseases. Immunol Invest 2019; 49:926-942. [PMID: 31854233 DOI: 10.1080/08820139.2019.1703737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background: Gly307Ser (rs763361) polymorphism in Cluster of Differentiation 226 (CD226) gene has been implicated in susceptibility to autoimmune diseases (ADs) with controversial results. This study aimed to conduct a meta-analysis for examining the relationship between CD226 rs763361 polymorphism and ADs risk. Methods: a literature search was performed to identify relevant studies published in Embase, PubMed, Wanfang, and China National Knowledge Infrastructure. In the most appropriate genetic models, pooled odds ratio (OR) with 95% confidence interval (CI) was calculated for evaluating the strength of the associations. Besides standard meta-analysis, cumulative meta-analysis was also conducted to assess the trend in OR over time. Also, we performed subgroup and sensitivity analysis, and checked for the heterogeneity and publication bias. Results: Twenty-nine reports with 51 independent studies, comprising 18157 cases and 29904 controls, were enrolled in this meta-analysis. Among overall and various ethnic populations (Europeans, Asians, Africans, and South Americans), CD226 rs763361 polymorphism was significantly associated with ADs susceptibility; in the subgroup analysis by disease type, rs763361 polymorphism revealed significant associations with the risk of RA, SLE, T1D, and MS. The sensitivity analysis and cumulative meta-analysis confirmed the stability and robustness of these significant results. However, no evidence of stable significant association emerged in the subgroup analysis of SSc. Conclusion: These findings demonstrate that CD226 rs763361 polymorphism confers susceptibility to ADs in the overall population, Europeans, Asians, Africans, and South Americans. rs763361 polymorphism in CD226 gene may be a potential susceptible predictor of ADs especially RA, SLE, T1D, and MS.
Collapse
Affiliation(s)
- Linfu Bai
- Department of Respiratory Medicine, The First Affiliated Hospital of Chongqing Medical University , Chongqing, China
| | - Jinyue Jiang
- Department of Respiratory Medicine, The First Affiliated Hospital of Chongqing Medical University , Chongqing, China
| | - He Li
- Department of Respiratory Medicine, The Second Affiliated Hospital of Chongqing Medical University , Chongqing, China
| | - Rui Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Chongqing Medical University , Chongqing, China
| |
Collapse
|
16
|
Elkjaer ML, Frisch T, Reynolds R, Kacprowski T, Burton M, Kruse TA, Thomassen M, Baumbach J, Illes Z. Molecular signature of different lesion types in the brain white matter of patients with progressive multiple sclerosis. Acta Neuropathol Commun 2019; 7:205. [PMID: 31829262 PMCID: PMC6907342 DOI: 10.1186/s40478-019-0855-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/25/2019] [Indexed: 12/21/2022] Open
Abstract
To identify pathogenetic markers and potential drivers of different lesion types in the white matter (WM) of patients with progressive multiple sclerosis (PMS), we sequenced RNA from 73 different WM areas. Compared to 25 WM controls, 6713 out of 18,609 genes were significantly differentially expressed in MS tissues (FDR < 0.05). A computational systems medicine analysis was performed to describe the MS lesion endophenotypes. The cellular source of specific molecules was examined by RNAscope, immunohistochemistry, and immunofluorescence. To examine common lesion specific mechanisms, we performed de novo network enrichment based on shared differentially expressed genes (DEGs), and found TGFβ-R2 as a central hub. RNAscope revealed astrocytes as the cellular source of TGFβ-R2 in remyelinating lesions. Since lesion-specific unique DEGs were more common than shared signatures, we examined lesion-specific pathways and de novo networks enriched with unique DEGs. Such network analysis indicated classic inflammatory responses in active lesions; catabolic and heat shock protein responses in inactive lesions; neuronal/axonal specific processes in chronic active lesions. In remyelinating lesions, de novo analyses identified axonal transport responses and adaptive immune markers, which was also supported by the most heterogeneous immunoglobulin gene expression. The signature of the normal-appearing white matter (NAWM) was more similar to control WM than to lesions: only 465 DEGs differentiated NAWM from controls, and 16 were unique. The upregulated marker CD26/DPP4 was expressed by microglia in the NAWM but by mononuclear cells in active lesions, which may indicate a special subset of microglia before the lesion develops, but also emphasizes that omics related to MS lesions should be interpreted in the context of different lesions types. While chronic active lesions were the most distinct from control WM based on the highest number of unique DEGs (n = 2213), remyelinating lesions had the highest gene expression levels, and the most different molecular map from chronic active lesions. This may suggest that these two lesion types represent two ends of the spectrum of lesion evolution in PMS. The profound changes in chronic active lesions, the predominance of synaptic/neural/axonal signatures coupled with minor inflammation may indicate end-stage irreversible molecular events responsible for this less treatable phase.
Collapse
|
17
|
Cabrera CP, Ng FL, Nicholls HL, Gupta A, Barnes MR, Munroe PB, Caulfield MJ. Over 1000 genetic loci influencing blood pressure with multiple systems and tissues implicated. Hum Mol Genet 2019; 28:R151-R161. [PMID: 31411675 PMCID: PMC6872427 DOI: 10.1093/hmg/ddz197] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/26/2019] [Accepted: 08/05/2019] [Indexed: 12/12/2022] Open
Abstract
High blood pressure (BP) remains the major heritable and modifiable risk factor for cardiovascular disease. Persistent high BP, or hypertension, is a complex trait with both genetic and environmental interactions. Despite swift advances in genomics, translating new discoveries to further our understanding of the underlying molecular mechanisms remains a challenge. More than 500 loci implicated in the regulation of BP have been revealed by genome-wide association studies (GWAS) in 2018 alone, taking the total number of BP genetic loci to over 1000. Even with the large number of loci now associated to BP, the genetic variance explained by all loci together remains low (~5.7%). These genetic associations have elucidated mechanisms and pathways regulating BP, highlighting potential new therapeutic and drug repurposing targets. A large proportion of the BP loci were discovered and reported simultaneously by multiple research groups, creating a knowledge gap, where the reported loci to date have not been investigated in a harmonious way. Here, we review the BP-associated genetic variants reported across GWAS studies and investigate their potential impact on the biological systems using in silico enrichment analyses for pathways, tissues, gene ontology and genetic pleiotropy.
Collapse
Affiliation(s)
- Claudia P Cabrera
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Fu Liang Ng
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Hannah L Nicholls
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Ajay Gupta
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Michael R Barnes
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Patricia B Munroe
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Mark J Caulfield
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| |
Collapse
|
18
|
Hasan A, Afzal M. Gene and environment interplay in cognition: Evidence from twin and molecular studies, future directions and suggestions for effective candidate gene x environment (cGxE) research. Mult Scler Relat Disord 2019; 33:121-130. [PMID: 31185373 DOI: 10.1016/j.msard.2019.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/20/2019] [Accepted: 05/13/2019] [Indexed: 12/17/2022]
Abstract
Last decade of molecular research in the field of cognitive science has shown that no single approach can give satisfactory results as far as gene hunt is concerned. Cohesive theory of gene-environment interaction seems to be a rational idea for bridging the gap in our knowledge of disorders involving cognitive deficit. It may even be helpful to some extent in resolving issues of missing heritability. We review the current state of play in the area of cognition at genetic and environmental fronts. Evidence of apparent gene-environment (GxE) interactions from various studies has been mentioned with the aim of redirecting the focus of research community towards studying such interactions with the help of sensitive designs and molecular techniques. We re-evaluate candidate gene-environment research in order to emphasize its potential if carried out strategically.
Collapse
Affiliation(s)
- Anam Hasan
- Human Genetics and Toxicology Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
| | - Mohammad Afzal
- Human Genetics and Toxicology Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India.
| |
Collapse
|
19
|
Olkhovskiy IA, Gorbenko AS, Stolyar MA, Vasiliev EV, Mikhalev MA, Tabakova KA. T784C LNK gene polymorphism and the risk of myeloproliferative disorders. Leuk Lymphoma 2018; 60:277-278. [PMID: 29749755 DOI: 10.1080/10428194.2018.1459604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Igor A Olkhovskiy
- a Krasnoyarsk Branch of the "National Research Center for Hematology" , Krasnoyarsk , Russian Federation.,b Federal Research Center Krasnoyarsk Scientific Center of the Siberian Branch of the Russian Academy of Sciences , Krasnoyarsk , Russian Federation
| | - Aleksey S Gorbenko
- a Krasnoyarsk Branch of the "National Research Center for Hematology" , Krasnoyarsk , Russian Federation
| | - Marina A Stolyar
- a Krasnoyarsk Branch of the "National Research Center for Hematology" , Krasnoyarsk , Russian Federation
| | - Evgeniy V Vasiliev
- c Krasnoyarsk Regional Clinic Hospital , Krasnoyarsk , Russian Federation
| | - Mikhail A Mikhalev
- d Krasnoyarsk City Clinical Hospital №7 , Krasnoyarsk , Russian Federation
| | | |
Collapse
|
20
|
Blood Eosinophil Count and Metabolic, Cardiac and Pulmonary Outcomes: A Mendelian Randomization Study. Twin Res Hum Genet 2018; 21:89-100. [PMID: 29506594 DOI: 10.1017/thg.2018.6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Blood eosinophil count is associated with a variety of common complex outcomes in epidemiological observation. The aim of this study was to explore the causal association between determined blood eosinophil count and 20 common complex outcomes (10 metabolic, 6 cardiac, and 4 pulmonary). Through Mendelian randomization, we investigated genetic evidence for the genetically determined eosinophil in association with each outcomes using individual-level LifeLines cohort data (n = 13,301), where a weighted eosinophil genetic risk score comprising five eosinophil associated variants was created. We further examined the associations of the genetically determined eosinophil with those outcomes using summary statistics obtained from genome-wide association study consortia (6 consortia and 14 outcomes). Blood eosinophil count, by a 1-SD genetically increased, was not statistically associated with common complex outcomes in the LifeLines. Using the summary statistics, we showed that a higher genetically determined eosinophil count had a significant association with lower odds of obesity (odds ratio (OR) 0.81, 95% confidence interval (CI) [0.74, 0.89]) but not with the other traits and diseases. To conclude, an elevated eosinophil count is unlikely to be causally associated to higher risk of metabolic, cardiac, and pulmonary outcomes. Further studies with a stronger genetic risk score for eosinophil count may support these results.
Collapse
|
21
|
Christiansen MK, Larsen SB, Nyegaard M, Neergaard-Petersen S, Würtz M, Grove EL, Hvas AM, Jensen HK, Kristensen SD. The SH2B3 and KCNK5 loci may be implicated in regulation of platelet count, volume, and maturity. Thromb Res 2017; 158:86-92. [PMID: 28865245 DOI: 10.1016/j.thromres.2017.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/21/2017] [Accepted: 08/17/2017] [Indexed: 01/11/2023]
Abstract
INTRODUCTION In recent genome-wide association studies, coronary artery disease (CAD) and myocardial infarction (MI) have been linked to a number of genetic variants, but their role in thrombopoiesis is largely unknown. AIM We investigated the association between CAD and MI-associated genetic variants and five thrombopoiesis-related indices: platelet count (PC), mean platelet volume (MPV), immature platelet count (IPC), immature platelet fraction (IPF), and serum thrombopoietin (TPO). METHODS We genotyped 45 genome-wide significant CAD/MI-markers in 879 stable CAD patients. A genetic risk score was calculated to assess the combined risk associated with all the genetic variants. Platelet indices were analysed using the Sysmex XE-2100 haematology analyser. TPO was measured by ELISA. RESULTS Two variants were nominally associated with several indices; for rs10947789 (KCNK5), the adjusted geometric mean was 2% higher for MPV (95% confidence interval: 1-2%, p=0.002), 6% for IPC (0-12%, p=0.033), and 9% for IPF (3-16%, p=0.004) per CAD risk allele. Moreover, an 11% lower TPO (3-19%, p=0.010) was observed. Rs3184504 (SH2B3) was associated with a higher adjusted geometric mean of 3% (1-6%, p=0.003) per CAD risk allele for PC, and an 11% (5-17%, p<0.001) lower TPO. Furthermore, the adjusted IPC was 5% (0-9%, p=0.037) lower per CAD risk allele for PC, whereas IPF levels did not vary across genotypes. CONCLUSION As a novel finding, our study suggests a role for KCNK5 in the regulation of platelet size and maturity. Furthermore, our findings confirm an association between the SH2B3-locus and platelet count.
Collapse
Affiliation(s)
- Morten K Christiansen
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark; Faculty of Health, Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Sanne B Larsen
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark.
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Morten Würtz
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark
| | - Erik L Grove
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark; Faculty of Health, Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Anne-Mette Hvas
- Faculty of Health, Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
| | - Henrik K Jensen
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark; Faculty of Health, Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Steen D Kristensen
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark; Faculty of Health, Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| |
Collapse
|
22
|
Axonal transport deficits in multiple sclerosis: spiraling into the abyss. Acta Neuropathol 2017; 134:1-14. [PMID: 28315956 PMCID: PMC5486629 DOI: 10.1007/s00401-017-1697-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 12/16/2022]
Abstract
The transport of mitochondria and other cellular components along the axonal microtubule cytoskeleton plays an essential role in neuronal survival. Defects in this system have been linked to a large number of neurological disorders. In multiple sclerosis (MS) and associated models such as experimental autoimmune encephalomyelitis (EAE), alterations in axonal transport have been shown to exist before neurodegeneration occurs. Genome-wide association (GWA) studies have linked several motor proteins to MS susceptibility, while neuropathological studies have shown accumulations of proteins and organelles suggestive for transport deficits. A reduced effectiveness of axonal transport can lead to neurodegeneration through inhibition of mitochondrial motility, disruption of axoglial interaction or prevention of remyelination. In MS, demyelination leads to dysregulation of axonal transport, aggravated by the effects of TNF-alpha, nitric oxide and glutamate on the cytoskeleton. The combined effect of all these pathways is a vicious cycle in which a defective axonal transport system leads to an increase in ATP consumption through loss of membrane organization and a reduction in available ATP through inhibition of mitochondrial transport, resulting in even further inhibition of transport. The persistent activity of this positive feedback loop contributes to neurodegeneration in MS.
Collapse
|
23
|
Maslah N, Cassinat B, Verger E, Kiladjian JJ, Velazquez L. The role of LNK/SH2B3 genetic alterations in myeloproliferative neoplasms and other hematological disorders. Leukemia 2017; 31:1661-1670. [PMID: 28484264 DOI: 10.1038/leu.2017.139] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/10/2017] [Accepted: 04/24/2017] [Indexed: 12/11/2022]
Abstract
Malignant hematological diseases are mainly because of the occurrence of molecular abnormalities leading to the deregulation of signaling pathways essential for precise cell behavior. High-resolution genome analysis using microarray and large-scale sequencing have helped identify several important acquired gene mutations that are responsible for such signaling deregulations across different hematological malignancies. In particular, the genetic landscape of classical myeloproliferative neoplasms (MPNs) has been in large part completed with the identification of driver mutations (targeting the cytokine receptor/Janus-activated kinase 2 (JAK2) pathway) that determine MPN phenotype, as well as additional mutations mainly affecting the regulation of gene expression (epigenetics or splicing regulators) and signaling. At present, most efforts concentrate in understanding how all these genetic alterations intertwine together to influence disease evolution and/or dictate clinical phenotype in order to use them to personalize diagnostic and clinical care. However, it is now evident that factors other than somatic mutations also play an important role in MPN disease initiation and progression, among which germline predisposition (single-nucleotide polymorphisms and haplotypes) may strongly influence the occurrence of MPNs. In this context, the LNK inhibitory adaptor protein encoded by the LNK/SH2B adaptor protein 3 (SH2B3) gene is the target of several genetic variations, acquired or inherited in MPNs, lymphoid leukemia and nonmalignant hematological diseases, underlying its importance in these pathological processes. As LNK adaptor is a key regulator of normal hematopoiesis, understanding the consequences of LNK variants on its protein functions and on driver or other mutations could be helpful to correlate genotype and phenotype of patients and to develop therapeutic strategies to target this molecule. In this review we summarize the current knowledge of LNK function in normal hematopoiesis, the different SH2B3 mutations reported to date and discuss how these genetic variations may influence the development of hematological malignancies.
Collapse
Affiliation(s)
- N Maslah
- APHP, Laboratoire de Biologie Cellulaire, Hôpital Saint-Louis, Paris, France.,Inserm UMRS 1131, IUH, Université Paris-Diderot, Paris, France
| | - B Cassinat
- APHP, Laboratoire de Biologie Cellulaire, Hôpital Saint-Louis, Paris, France.,Inserm UMRS 1131, IUH, Université Paris-Diderot, Paris, France
| | - E Verger
- APHP, Laboratoire de Biologie Cellulaire, Hôpital Saint-Louis, Paris, France.,Inserm UMRS 1131, IUH, Université Paris-Diderot, Paris, France
| | - J-J Kiladjian
- Inserm UMRS 1131, IUH, Université Paris-Diderot, Paris, France.,APHP, Centre d'investigations Cliniques, Hôpital Saint-Louis, Paris, France
| | - L Velazquez
- INSERM UMRS-MD1197, Institut André Lwoff/Université Paris XI, Hôpital Paul Brousse, Villejuif, France
| |
Collapse
|
24
|
Reply to Liu et al.: Haplotype matters: CD226 polymorphism as a potential trigger for impaired immune regulation in multiple sclerosis. Proc Natl Acad Sci U S A 2017; 114:E908-E909. [PMID: 28137888 DOI: 10.1073/pnas.1619059114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
25
|
Impaired NK-mediated regulation of T-cell activity in multiple sclerosis is reconstituted by IL-2 receptor modulation. Proc Natl Acad Sci U S A 2016; 113:E2973-82. [PMID: 27162345 DOI: 10.1073/pnas.1524924113] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory autoimmune disease of the central nervous system (CNS) resulting from a breakdown in peripheral immune tolerance. Although a beneficial role of natural killer (NK)-cell immune-regulatory function has been proposed, it still needs to be elucidated whether NK cells are functionally impaired as part of the disease. We observed NK cells in active MS lesions in close proximity to T cells. In accordance with a higher migratory capacity across the blood-brain barrier, CD56(bright) NK cells represent the major intrathecal NK-cell subset in both MS patients and healthy individuals. Investigating the peripheral blood and cerebrospinal fluid of MS patients treated with natalizumab revealed that transmigration of this subset depends on the α4β1 integrin very late antigen (VLA)-4. Although no MS-related changes in the migratory capacity of NK cells were observed, NK cells derived from patients with MS exhibit a reduced cytolytic activity in response to antigen-activated CD4(+) T cells. Defective NK-mediated immune regulation in MS is mainly attributable to a CD4(+) T-cell evasion caused by an impaired DNAX accessory molecule (DNAM)-1/CD155 interaction. Both the expression of the activating NK-cell receptor DNAM-1, a genetic alteration consistently found in MS-association studies, and up-regulation of the receptor's ligand CD155 on CD4(+) T cells are reduced in MS. Therapeutic immune modulation of IL-2 receptor restores impaired immune regulation in MS by increasing the proportion of CD155-expressing CD4(+) T cells and the cytolytic activity of NK cells.
Collapse
|
26
|
Borné Y, Smith JG, Nilsson PM, Melander O, Hedblad B, Engström G. Total and Differential Leukocyte Counts in Relation to Incidence of Diabetes Mellitus: A Prospective Population-Based Cohort Study. PLoS One 2016; 11:e0148963. [PMID: 26891449 PMCID: PMC4758613 DOI: 10.1371/journal.pone.0148963] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 01/26/2016] [Indexed: 01/04/2023] Open
Abstract
Objective High concentrations of leukocytes in blood have been associated with diabetes mellitus. This prospective study aimed to explore whether total and differential leukocyte counts are associated with incidence of diabetes. A missense variant R262W in the SH2B3 (SH2B adaptor protein 3) gene, coding for a protein that negatively regulates hematopoietic cell proliferation, was also studied in relation to incidence of diabetes. Methods and Results Leukocyte count and its subtypes (neutrophils, lymphocytes and mixed cells) were analyzed in 26,667 men and women, 45–73 years old, from the population-based Malmö Diet and Cancer study. Information about the R262W polymorphism (rs3184504) in SH2B3 was genotyped in 24,489 subjects. Incidence of diabetes was studied during a mean follow-up of 14 years. Cox proportional hazards regression was used to examine incidence of diabetes by total and differential leukocyte counts. Mendelian randomization analysis using R262W as an instrumental variable was performed with two-stage least squares regression. A total of 2,946 subjects developed diabetes during the follow-up period. After taking several possible confounders into account, concentrations of total leukocyte count, neutrophils and lymphocytes were all significantly associated with incidence of diabetes. The adjusted hazard ratios (95% confidence interval; quartile 4 vs quartile 1) were 1.37 (1.22–1.53) for total leukocytes, 1.33 (1.19–1.49) for neutrophils and 1.29 (1.15–1.44) for lymphocytes. The R262W polymorphism was strongly associated with leukocytes (0.11x109 cells/l per T allele, p = 1.14 x10-12), lymphocytes (p = 4.3 x10-16), neutrophils (p = 8.0 x10-6) and mixed cells (p = 3.0 x10-6). However, there was no significant association between R262W and fasting glucose, HbA1c or incidence of diabetes. Conclusions Concentrations of total leukocytes, neutrophils and lymphocytes are associated with incidence of diabetes. However, the lack of association with the R262W polymorphism suggests that the associations may not be causal, although limitations in statistical power and balancing pleiotropic effects cannot be excluded.
Collapse
Affiliation(s)
- Yan Borné
- Department of Clinical Sciences, Malmö, Lund University, Malmö, Sweden
- * E-mail:
| | - J. Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program of Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Peter M. Nilsson
- Department of Clinical Sciences, Malmö, Lund University, Malmö, Sweden
- Department of Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | - Olle Melander
- Department of Clinical Sciences, Malmö, Lund University, Malmö, Sweden
- Department of Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | - Bo Hedblad
- Department of Clinical Sciences, Malmö, Lund University, Malmö, Sweden
| | - Gunnar Engström
- Department of Clinical Sciences, Malmö, Lund University, Malmö, Sweden
| |
Collapse
|
27
|
High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry. Nat Genet 2016; 48:323-30. [PMID: 26808113 PMCID: PMC4767573 DOI: 10.1038/ng.3496] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 12/23/2015] [Indexed: 01/04/2023]
Abstract
Systemic lupus erythematosus (SLE) has a strong but incompletely understood genetic architecture. We conducted an association study with replication in 4,478 SLE cases and 12,656 controls from six East Asian cohorts to identify new SLE susceptibility loci and better localize known loci. We identified ten new loci and confirmed 20 known loci with genome-wide significance. Among the new loci, the most significant locus was GTF2IRD1-GTF2I at 7q11.23 (rs73366469, Pmeta = 3.75 × 10(-117), odds ratio (OR) = 2.38), followed by DEF6, IL12B, TCF7, TERT, CD226, PCNXL3, RASGRP1, SYNGR1 and SIGLEC6. We identified the most likely functional variants at each locus by analyzing epigenetic marks and gene expression data. Ten candidate variants are known to alter gene expression in cis or in trans. Enrichment analysis highlights the importance of these loci in B cell and T cell biology. The new loci, together with previously known loci, increase the explained heritability of SLE to 24%. The new loci share functional and ontological characteristics with previously reported loci and are possible drug targets for SLE therapeutics.
Collapse
|
28
|
Nakagome S, Alkorta-Aranburu G, Amato R, Howie B, Peter BM, Hudson RR, Di Rienzo A. Estimating the Ages of Selection Signals from Different Epochs in Human History. Mol Biol Evol 2015; 33:657-69. [PMID: 26545921 DOI: 10.1093/molbev/msv256] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genetic variation harbors signatures of natural selection driven by selective pressures that are often unknown. Estimating the ages of selection signals may allow reconstructing the history of environmental changes that shaped human phenotypes and diseases. We have developed an approximate Bayesian computation (ABC) approach to estimate allele ages under a model of selection on new mutations and under demographic models appropriate for human populations. We have applied it to two resequencing data sets: An ultra-high depth data set from a relatively small sample of unrelated individuals and a lower depth data set in a larger sample with transmission information. In addition to evaluating the accuracy of our method based on simulations, for each SNP, we assessed the consistency between the posterior probabilities estimated by the ABC approach and the ancient DNA record, finding good agreement between the two types of data and methods. Applying this ABC approach to data for eight single nucleotide polymorphisms (SNPs), we were able to rule out an onset of selection prior to the dispersal out-of-Africa for three of them and more recent than the spread of agriculture for an additional three SNPs.
Collapse
Affiliation(s)
| | | | - Roberto Amato
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, United Kingdom
| | - Bryan Howie
- Department of Human Genetics, University of Chicago
| | | | - Richard R Hudson
- Department of Human Genetics, University of Chicago Department of Ecology and Evolution, University of Chicago
| | | |
Collapse
|
29
|
Kuś A, Szymański K, Peeters RP, Miśkiewicz P, Porcu E, Pistis G, Sanna S, Naitza S, Płoski R, Medici M, Bednarczuk T. The association of thyroid peroxidase antibody risk loci with susceptibility to and phenotype of Graves' disease. Clin Endocrinol (Oxf) 2015; 83:556-62. [PMID: 25345847 DOI: 10.1111/cen.12640] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/19/2014] [Accepted: 10/17/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND Despite great progress, the genetic basis of Graves' disease (GD) remains poorly understood. Recently, a population-based genomewide association study (GWAS) identified five novel loci (ATXN2/SH2B3, MAGI3, BACH2, TPO and KALRN) as significantly associated with the presence of thyroid peroxidase autoantibodies (TPOAbs), whereas several other loci showed suggestive association. METHODS In this study, we investigated 16 single nucleotide polymorphisms (SNPs) associated with TPOAbs for the association with susceptibility to and phenotype of GD in a cohort of 647 patients with GD and 769 controls from a Polish Caucasian population. RESULTS SNPs within/near HCP5 (rs3094228, P = 1·6 × 10(-12) , OR = 1·88), MAGI3 (rs1230666, P = 1·9 × 10(-5) , OR = 1·51) and ATXN2/SH2B3 (rs653178, P = 0·0015, OR = 1·28) loci were significantly associated with susceptibility to GD. Allele frequencies differed significantly in subgroups of patients with GD stratified by age of GD onset for HCP5 (P = 0·0014, OR = 1·50) and showed a suggestive difference for MAGI3 (P = 0·0035, OR = 1·50) SNPs. Although rs11675434 located near TPO showed no association with GD susceptibility, it was significantly associated with the presence of clinically evident Graves' ophthalmopathy (GO, P = 5·2 × 10(-5) , OR = 1·64), and this effect was independent from smoking status, age of GD onset and gender. CONCLUSIONS This is the first study showing an association of the ATXN2/SH2B3 locus with susceptibility to GD. Furthermore, we observed a novel significant association within the HLA region at a SNP located near HCP5 and confirmed the association of the MAGI3 locus with GD susceptibility. HCP5 and MAGI3 SNPs were further correlated with age of GD onset. Finally, we identified TPO as a new susceptibility locus for GO.
Collapse
Affiliation(s)
- Aleksander Kuś
- Department of Internal Medicine and Endocrinology, Medical University of Warsaw, Warsaw, Poland
| | - Konrad Szymański
- Department of Medical Genetics, Centre for Biostructure, Medical University of Warsaw, Warsaw, Poland
| | - Robin P Peeters
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Piotr Miśkiewicz
- Department of Internal Medicine and Endocrinology, Medical University of Warsaw, Warsaw, Poland
| | - Eleonora Porcu
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche, c/o Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
- Dipartimento di Scienze Biomediche, Universita di Sassari, Sassari, Italy
| | - Giorgio Pistis
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche, c/o Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
- Dipartimento di Scienze Biomediche, Universita di Sassari, Sassari, Italy
| | - Serena Sanna
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche, c/o Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Silvia Naitza
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche, c/o Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Rafał Płoski
- Department of Medical Genetics, Centre for Biostructure, Medical University of Warsaw, Warsaw, Poland
| | - Marco Medici
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Tomasz Bednarczuk
- Department of Internal Medicine and Endocrinology, Medical University of Warsaw, Warsaw, Poland
| |
Collapse
|
30
|
IRF5, PTPN22, CD28, IL2RA, KIF5A, BLK and TNFAIP3 genes polymorphisms and lupus susceptibility in a cohort from the Egypt Delta; relation to other ethnic groups. Hum Immunol 2015; 76:525-31. [DOI: 10.1016/j.humimm.2015.06.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 01/28/2015] [Accepted: 06/02/2015] [Indexed: 01/28/2023]
|
31
|
Cabrera CP, Ng FL, Warren HR, Barnes MR, Munroe PB, Caulfield MJ. Exploring hypertension genome-wide association studies findings and impact on pathophysiology, pathways, and pharmacogenetics. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:73-90. [DOI: 10.1002/wsbm.1290] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/25/2014] [Accepted: 01/05/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Claudia P Cabrera
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London UK
- NIHR Barts Cardiovascular Biomedical Research Unit; Queen Mary University of London; London UK
| | - Fu Liang Ng
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London UK
| | - Helen R Warren
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London UK
- NIHR Barts Cardiovascular Biomedical Research Unit; Queen Mary University of London; London UK
| | - Michael R Barnes
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London UK
- NIHR Barts Cardiovascular Biomedical Research Unit; Queen Mary University of London; London UK
| | - Patricia B Munroe
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London UK
- NIHR Barts Cardiovascular Biomedical Research Unit; Queen Mary University of London; London UK
| | - Mark J Caulfield
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London UK
- NIHR Barts Cardiovascular Biomedical Research Unit; Queen Mary University of London; London UK
| |
Collapse
|
32
|
Flister MJ, Hoffman MJ, Lemke A, Prisco SZ, Rudemiller N, O'Meara CC, Tsaih SW, Moreno C, Geurts AM, Lazar J, Adhikari N, Hall JL, Jacob HJ. SH2B3 Is a Genetic Determinant of Cardiac Inflammation and Fibrosis. ACTA ACUST UNITED AC 2015; 8:294-304. [PMID: 25628389 DOI: 10.1161/circgenetics.114.000527] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 01/14/2015] [Indexed: 01/11/2023]
Abstract
BACKGROUND Genome-wide association studies are powerful tools for nominating pathogenic variants, but offer little insight as to how candidate genes affect disease outcome. Such is the case for SH2B adaptor protein 3 (SH2B3), which is a negative regulator of multiple cytokine signaling pathways and is associated with increased risk of myocardial infarction (MI), but its role in post-MI inflammation and fibrosis is completely unknown. METHODS AND RESULTS Using an experimental model of MI (left anterior descending artery occlusion/reperfusion injury) in wild-type and Sh2b3 knockout rats (Sh2b3(em2Mcwi)), we assessed the role of Sh2b3 in post-MI fibrosis, leukocyte infiltration, angiogenesis, left ventricle contractility, and inflammatory gene expression. Compared with wild-type, Sh2b3(em2Mcwi) rats had significantly increased fibrosis (2.2-fold; P<0.05) and elevated leukocyte infiltration (>2-fold; P<0.05), which coincided with decreased left ventricle fractional shortening (-Δ11%; P<0.05) at 7 days post left anterior descending artery occlusion/reperfusion injury. Despite an increased angiogenic potential in Sh2b3(em2Mcwi) rats (1.7-fold; P<0.05), we observed no significant differences in left ventricle capillary density between wild-type and Sh2b3(em2Mcwi) rats. In total, 12 genes were significantly elevated in the post left anterior descending artery occluded/reperfused hearts of Sh2b3(em2Mcwi) rats relative to wild-type, of which 3 (NLRP12, CCR2, and IFNγ) were significantly elevated in the left ventricle of heart failure patients carrying the MI-associated rs3184504 [T] SH2B3 risk allele. CONCLUSIONS These data demonstrate for the first time that SH2B3 is a crucial mediator of post-MI inflammation and fibrosis.
Collapse
Affiliation(s)
- Michael J Flister
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Matthew J Hoffman
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Angela Lemke
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Sasha Z Prisco
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Nathan Rudemiller
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Caitlin C O'Meara
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Shirng-Wern Tsaih
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Carol Moreno
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Aron M Geurts
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Jozef Lazar
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Neeta Adhikari
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Jennifer L Hall
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Howard J Jacob
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.).
| |
Collapse
|
33
|
Yu RY, Brazaitis J, Gallagher G. The human IL-23 receptor rs11209026 A allele promotes the expression of a soluble IL-23R-encoding mRNA species. THE JOURNAL OF IMMUNOLOGY 2014; 194:1062-8. [PMID: 25552541 DOI: 10.4049/jimmunol.1401850] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The human IL23R gene single nucleotide polymorphism rs11209026 A allele confers protection against inflammatory diseases. However, although this difference has been associated with reductions in IL-23-induced IL-17A production and STAT3 phosphorylation, the molecular mechanism underlying these changes remains undefined. Th17 cell maturation depends on IL-23 signaling. Multiple splice forms of the human IL23R transcript exist, and one, Δ9, encodes a soluble form of the receptor. In this study, we asked whether this protective allele was associated with mRNA splicing. Using mini-gene constructs and competitive oligonucleotide binding, we showed that the A allele alters IL-23R α-chain mRNA splicing and favors exon 9 skipping by reducing the binding of the splicing enhancer SF2. This enhances expression of the Δ9 mRNA and consequently diminishes IL-23 signaling. Thus, the presence of the A allele increases expression of the soluble form of IL23R mRNA (which then functions as a decoy receptor) and lowers the ability to develop a Th17 phenotype upon IL-23 stimulation. We further showed that antisense oligonucleotides targeting the SF2 binding site could efficiently induce exon 9 skipping in the presence of the G allele, and thereby replicate the effect of the A allele. Antisense oligonucleotide treatment caused dose-responsive induction of the IL23RΔ9 mRNA and interfered with in vitro differentiation of human Th17 cells, reducing their expression of the signature Th17 cytokines IL-17A and IL-17F. This may represent a novel approach to therapy of Th17-mediated diseases by elevating soluble IL-23R while simultaneously reducing the remaining cell surface receptor density.
Collapse
Affiliation(s)
- Raymond Y Yu
- Genetic Immunology Laboratory, HUMIGEN, The Institute for Genetic Immunology, Genesis Biotechnology Group, Hamilton, NJ 08690
| | - Jonathan Brazaitis
- Genetic Immunology Laboratory, HUMIGEN, The Institute for Genetic Immunology, Genesis Biotechnology Group, Hamilton, NJ 08690
| | - Grant Gallagher
- Genetic Immunology Laboratory, HUMIGEN, The Institute for Genetic Immunology, Genesis Biotechnology Group, Hamilton, NJ 08690
| |
Collapse
|
34
|
Zhang Z, Xiang LF. Genetic susceptibility to vitiligo: Recent progress from genome-wide association studies. DERMATOL SIN 2014. [DOI: 10.1016/j.dsi.2014.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
35
|
Kreft KL, van Meurs M, Wierenga-Wolf AF, Melief MJ, van Strien ME, Hol EM, Oostra BA, Laman JD, Hintzen RQ. Abundant kif21b is associated with accelerated progression in neurodegenerative diseases. Acta Neuropathol Commun 2014; 2:144. [PMID: 25274010 PMCID: PMC4207309 DOI: 10.1186/s40478-014-0144-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 09/14/2014] [Indexed: 01/29/2023] Open
Abstract
Kinesin family member 21b (kif21b) is one of the few multiple sclerosis (MS) risk genes with a presumed central nervous system function. Kif21b belongs to the kinesin family, proteins involved in intracellular transport of proteins and organelles. We hypothesised that kif21b is involved in the neurodegenerative component of MS and Alzheimer's (AD) disease. Post-mortem kinesin expression was assessed in 50 MS, 58 age and gender matched non-demented controls (NDC) and 50 AD. Kif21b expression was five-fold increased in AD compared to MS and NDC aged below 62 years (p = 8*10(-5)), three-fold between 62-72 years (p = 0.005) and not different above 72 years. No significant differences were observed between MS and NDC. In AD, kif21b expression was two-fold increased in Braak stage 6 (scoring for density of neurofibrillary tangles) compared with stage 5 (p = 0.003). In MS patients, kif21b correlated with the extent of grey matter demyelination (Spearman's rho = 0.31, p = 0.03). Abundant kif21b, defined as expression above the median, was associated with a two-fold accelerated development of the Kurtzke Expanded Disability Status Scale (EDSS) 6.0 (median time in low kif21b group 16 years vs. high kif21b 7.5 years, log-rank test p = 0.04) in MS. Given the genetic association of kif21b with MS, the results were stratified according to rs12122721[A] single nucleotide polymorphism (SNP). No association was found between kif21b expression or the time to EDSS 6 in kif21b risk SNP carriers compared to non-risk carriers. Kif21b was expressed in astrocytes in addition to neurons. Upon astrocyte activation, kif21b increased nine-fold. Abundant kif21b expression is associated with severe MS and AD pathology and with accelerated neurodegeneration independent of the kif21b risk SNP.
Collapse
Affiliation(s)
- Karim L Kreft
- Department Neurology Erasmus MC, University Medical Center, Room Ba 4.92, Rotterdam, 3000 CA The Netherlands
- Department Immunology Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department MS Center ErasMS Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Marjan van Meurs
- Department Immunology Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department MS Center ErasMS Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Annet F Wierenga-Wolf
- Department Immunology Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department MS Center ErasMS Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Marie-Jose Melief
- Department Immunology Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department MS Center ErasMS Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Miriam E van Strien
- Astrocyte Biology & Neurodegeneration, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and Sciences, Amsterdam, The Netherlands
- Department Translational Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elly M Hol
- Astrocyte Biology & Neurodegeneration, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and Sciences, Amsterdam, The Netherlands
- Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
- Department Translational Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ben A Oostra
- Department Clinical Genetics Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Jon D Laman
- Department Immunology Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department MS Center ErasMS Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Rogier Q Hintzen
- Department Neurology Erasmus MC, University Medical Center, Room Ba 4.92, Rotterdam, 3000 CA The Netherlands
- Department MS Center ErasMS Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
36
|
Byström S, Ayoglu B, Häggmark A, Mitsios N, Hong MG, Drobin K, Forsström B, Fredolini C, Khademi M, Amor S, Uhlén M, Olsson T, Mulder J, Nilsson P, Schwenk JM. Affinity proteomic profiling of plasma, cerebrospinal fluid, and brain tissue within multiple sclerosis. J Proteome Res 2014; 13:4607-19. [PMID: 25231264 DOI: 10.1021/pr500609e] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The brain is a vital organ and because it is well shielded from the outside environment, possibilities for noninvasive analysis are often limited. Instead, fluids taken from the spinal cord or circulatory system are preferred sources for the discovery of candidate markers within neurological diseases. In the context of multiple sclerosis (MS), we applied an affinity proteomic strategy and screened 22 plasma samples with 4595 antibodies (3450 genes) on bead arrays, then defined 375 antibodies (334 genes) for targeted analysis in a set of 172 samples and finally used 101 antibodies (43 genes) on 443 plasma as well as 573 cerebrospinal spinal fluid (CSF) samples. This revealed alteration of protein profiles in relation to MS subtypes for IRF8, IL7, METTL14, SLC30A7, and GAP43. Respective antibodies were subsequently used for immunofluorescence on human post-mortem brain tissue with MS pathology for expression and association analysis. There, antibodies for IRF8, IL7, and METTL14 stained neurons in proximity of lesions, which highlighted these candidate protein targets for further studies within MS and brain tissue. The affinity proteomic translation of profiles discovered by profiling human body fluids and tissue provides a powerful strategy to suggest additional candidates to studies of neurological disorders.
Collapse
Affiliation(s)
- Sanna Byström
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology , Stockholm 171 21, Sweden
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Current aspects of vitiligo genetics. Postepy Dermatol Alergol 2014; 31:247-55. [PMID: 25254010 PMCID: PMC4171675 DOI: 10.5114/pdia.2014.43497] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 05/17/2014] [Accepted: 05/27/2014] [Indexed: 12/24/2022] Open
Abstract
Vitiligo is a common acquired depigmentation disorder of the skin manifested by the presence of white macules. The disease occurs at a frequency of approximately 1–4% of the world population. Currently, the most popular theory of vitiligo development is a multifactorial hypothesis according to which genetic conditions predispose vitiligo macules to occur as a result of specific environmental factors. According to the genetic hypothesis, vitiligo inheritance is multigenic. Genetic studies conducted so far concern patients with non-segmental vitiligo. There are three basic techniques of genetic studies: candidate gene association studies, genomewide linkage studies and genome-wide association studies (GWAS). The GWAS are the “gold standard” for detecting susceptibility genes. Up to now, approximately 36 convincing non-segmental vitiligo susceptibility loci have been identified. Approximately 90% of them encode immunoregulatory proteins, while approximately 10% encode melanocyte proteins. The existence of various associations between vitiligo and other autoimmune diseases may provide new knowledge on the causes of many disorders. Examples include the inverse relationship between vitiligo and melanoma and association of vitiligo with other autoimmune diseases. The main goal of all researches is to find new, optimal therapeutic strategies for vitiligo and other autoimmune diseases.
Collapse
|
38
|
Auburger G, Gispert S, Lahut S, Ömür &O, Damrath E, Heck M, Başak N. 12q24 locus association with type 1 diabetes: SH2B3 or ATXN2? World J Diabetes 2014; 5:316-327. [PMID: 24936253 PMCID: PMC4058736 DOI: 10.4239/wjd.v5.i3.316] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/13/2014] [Accepted: 04/11/2014] [Indexed: 02/05/2023] Open
Abstract
Genetic linkage analyses, genome-wide association studies of single nucleotide polymorphisms, copy number variation surveys, and mutation screenings found the human chromosomal 12q24 locus, with the genes SH2B3 and ATXN2 in its core, to be associated with an exceptionally wide spectrum of disease susceptibilities. Hematopoietic traits of red and white blood cells (like erythrocytosis and myeloproliferative disease), autoimmune disorders (like type 1 diabetes, coeliac disease, juvenile idiopathic arthritis, rheumatoid arthritis, thrombotic antiphospholipid syndrome, lupus erythematosus, multiple sclerosis, hypothyroidism and vitiligo), also vascular pathology (like kidney glomerular filtration rate deficits, serum urate levels, plasma beta-2-microglobulin levels, retinal microcirculation problems, diastolic and systolic blood pressure and hypertension, cardiovascular infarction), furthermore obesity, neurodegenerative conditions (like the polyglutamine-expansion disorder spinocerebellar ataxia type 2, Parkinson’s disease, the motor-neuron disease amyotrophic lateral sclerosis, and progressive supranuclear palsy), and finally longevity were reported. Now it is important to clarify, in which ways the loss or gain of function of the locally encoded proteins SH2B3/LNK and ataxin-2, respectively, contribute to these polygenic health problems. SH2B3/LNK is known to repress the JAK2/ABL1 dependent proliferation of white blood cells. Its null mutations in human and mouse are triggers of autoimmune traits and leukemia (acute lymphoblastic leukemia or chronic myeloid leukemia-like), while missense mutations were found in erythrocytosis-1 patients. Ataxin-2 is known to act on RNA-processing and trophic receptor internalization. While its polyglutamine-expansion mediated gain-of-function causes neuronal atrophy in human and mouse, its deletion leads to obesity and insulin resistance in mice. Thus, it is conceivable that the polygenic pathogenesis of type 1 diabetes is enhanced by an SH2B3-dysregulation-mediated predisposition to autoimmune diseases that conspires with an ATXN2-deficiency-mediated predisposition to lipid and glucose metabolism pathology.
Collapse
|
39
|
Association of a single-nucleotide polymorphism in the SH2B3 gene with JAK2V617F-positive myeloproliferative neoplasms. Blood 2014; 123:794-6. [PMID: 24482502 DOI: 10.1182/blood-2013-10-532622] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
|
40
|
Shameer K, Denny JC, Ding K, Jouni H, Crosslin DR, de Andrade M, Chute CG, Peissig P, Pacheco JA, Li R, Bastarache L, Kho AN, Ritchie MD, Masys DR, Chisholm RL, Larson EB, McCarty CA, Roden DM, Jarvik GP, Kullo IJ. A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. Hum Genet 2014; 133:95-109. [PMID: 24026423 PMCID: PMC3880605 DOI: 10.1007/s00439-013-1355-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 08/22/2013] [Indexed: 12/21/2022]
Abstract
Platelets are enucleated cell fragments derived from megakaryocytes that play key roles in hemostasis and in the pathogenesis of atherothrombosis and cancer. Platelet traits are highly heritable and identification of genetic variants associated with platelet traits and assessing their pleiotropic effects may help to understand the role of underlying biological pathways. We conducted an electronic medical record (EMR)-based study to identify common variants that influence inter-individual variation in the number of circulating platelets (PLT) and mean platelet volume (MPV), by performing a genome-wide association study (GWAS). We characterized genetic variants associated with MPV and PLT using functional, pathway and disease enrichment analyses; we assessed pleiotropic effects of such variants by performing a phenome-wide association study (PheWAS) with a wide range of EMR-derived phenotypes. A total of 13,582 participants in the electronic MEdical Records and GEnomic network had data for PLT and 6,291 participants had data for MPV. We identified five chromosomal regions associated with PLT and eight associated with MPV at genome-wide significance (P < 5E-8). In addition, we replicated 20 SNPs [out of 56 SNPs (α: 0.05/56 = 9E-4)] influencing PLT and 22 SNPs [out of 29 SNPs (α: 0.05/29 = 2E-3)] influencing MPV in a published meta-analysis of GWAS of PLT and MPV. While our GWAS did not find any new associations, our functional analyses revealed that genes in these regions influence thrombopoiesis and encode kinases, membrane proteins, proteins involved in cellular trafficking, transcription factors, proteasome complex subunits, proteins of signal transduction pathways, proteins involved in megakaryocyte development, and platelet production and hemostasis. PheWAS using a single-SNP Bonferroni correction for 1,368 diagnoses (0.05/1368 = 3.6E-5) revealed that several variants in these genes have pleiotropic associations with myocardial infarction, autoimmune, and hematologic disorders. We conclude that multiple genetic loci influence interindividual variation in platelet traits and also have significant pleiotropic effects; the related genes are in multiple functional pathways including those relevant to thrombopoiesis.
Collapse
Affiliation(s)
- Khader Shameer
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Joshua C. Denny
- Departments of Medicine and Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA
| | - Keyue Ding
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Hayan Jouni
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - David R. Crosslin
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Christopher G. Chute
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Peggy Peissig
- Biomedical Informatics Research Center, Marshfield Clinic, Marshfield, WI, 54449, USA
| | - Jennifer A. Pacheco
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rongling Li
- Office of Population Genomics, National Human Genome Research Institute, 5635 Fishers Lane, Suite 3058, MSC 9307, Bethesda, MD, 20892, USA
| | - Lisa Bastarache
- Departments of Medicine and Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA
| | - Abel N. Kho
- Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Marylyn D Ritchie
- Center for Systems Genomics, Pennsylvania State University, Eberly College of Science, The Huck Institutes of the Life Sciences, 512 Wartik Laboratory, University Park, PA 16802 USA
| | - Daniel R. Masys
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Room 416 Eskind Medical Library, Nashville, TN, 37232, USA
| | - Rex L. Chisholm
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eric B. Larson
- Group Health Research Institute, 1730 Minor Avenue, Suite 1600, Seattle, WA, 98101, USA
| | | | - Dan M. Roden
- Department of Pharmacology, Vanderbilt University School of Medicine, 1285 Medical Research Building IV, Nashville, TN, 37232, USA
| | - Gail P. Jarvik
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle WA 98195, USA
| | - Iftikhar J. Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| |
Collapse
|
41
|
Zhang G, Muglia LJ, Chakraborty R, Akey JM, Williams SM. Signatures of natural selection on genetic variants affecting complex human traits. Appl Transl Genom 2013; 2:78-94. [PMID: 27896059 PMCID: PMC5121263 DOI: 10.1016/j.atg.2013.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/14/2013] [Indexed: 01/04/2023]
Abstract
It has recently been hypothesized that polygenic adaptation, resulting in modest allele frequency changes at many loci, could be a major mechanism behind the adaptation of complex phenotypes in human populations. Here we leverage the large number of variants that have been identified through genome-wide association (GWA) studies to comprehensively study signatures of natural selection on genetic variants associated with complex traits. Using population differentiation based methods, such as FST and phylogenetic branch length analyses, we systematically examined nearly 1300 SNPs associated with 38 complex phenotypes. Instead of detecting selection signatures at individual variants, we aimed to identify combined evidence of natural selection by aggregating signals across many trait associated SNPs. Our results have revealed some general features of polygenic selection on complex traits associated variants. First, natural selection acting on standing variants associated with complex traits is a common phenomenon. Second, characteristics of selection for different polygenic traits vary both temporarily and geographically. Third, some studied traits (e.g. height and urate level) could have been the primary targets of selection, as indicated by the significant correlation between the effect sizes and the estimated strength of selection in the trait associated variants; however, for most traits, the allele frequency changes in trait associated variants might have been driven by the selection on other correlated phenotypes. Fourth, the changes in allele frequencies as a result of selection can be highly stochastic, such that, polygenic adaptation may accelerate differentiation in allele frequencies among populations, but generally does not produce predictable directional changes. Fifth, multiple mechanisms (pleiotropy, hitchhiking, etc) may act together to govern the changes in allele frequencies of genetic variants associated with complex traits.
Collapse
Affiliation(s)
- Ge Zhang
- Human Genetics Division, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Louis J. Muglia
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
| | - Ranajit Chakraborty
- Center for Computational Genomics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Scott M. Williams
- Department of Genetics and Institute for Quantitative Biomedical Sciences, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| |
Collapse
|
42
|
Abstract
The SH2B adaptor protein 3 (SH2B3) gene encodes a negative regulator of cytokine signaling with a critical role in the homeostasis of hematopoietic stem cells and lymphoid progenitors. Here, we report the identification of germline homozygous SH2B3 mutations in 2 siblings affected with developmental delay and autoimmunity, one in whom B-precursor acute lymphoblastic leukemia (ALL) developed. Mechanistically, loss of SH2B3 increases Janus kinase-signal transducer and activator of transcription signaling, promotes lymphoid cell proliferation, and accelerates leukemia development in a mouse model of NOTCH1-induced ALL. Moreover, extended mutation analysis showed homozygous somatic mutations in SH2B3 in 2 of 167 ALLs analyzed. Overall, these results demonstrate a Knudson tumor suppressor role for SH2B3 in the pathogenesis of ALL and highlight a possible link between genetic predisposition factors in the pathogenesis of autoimmunity and leukemogenesis.
Collapse
|
43
|
Ochoa E, Iriondo M, Bielsa A, Ruiz-Irastorza G, Estonba A, Zubiaga AM. Thrombotic antiphospholipid syndrome shows strong haplotypic association with SH2B3-ATXN2 locus. PLoS One 2013; 8:e67897. [PMID: 23844121 PMCID: PMC3701057 DOI: 10.1371/journal.pone.0067897] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 05/22/2013] [Indexed: 01/11/2023] Open
Abstract
Background Thrombotic antiphospholipid syndrome is defined as a complex form of thrombophilia that is developed by a fraction of antiphospholipid antibody (aPLA) carriers. Little is known about the genetic risk factors involved in thrombosis development among aPLA carriers. Methods To identify new loci conferring susceptibility to thrombotic antiphospholipid syndrome, a two-stage genotyping strategy was performed. In stage one, 19,000 CNV loci were genotyped in 14 thrombotic aPLA+ patients and 14 healthy controls by array-CGH. In stage two, significant CNV loci were fine-mapped in a larger cohort (85 thrombotic aPLA+, 100 non-thrombotic aPLA+ and 569 healthy controls). Results Array-CGH and fine-mapping analysis led to the identification of 12q24.12 locus as a new susceptibility locus for thrombotic APS. Within this region, a TAC risk haplotype comprising one SNP in SH2B3 gene (rs3184504) and two SNPs in ATXN2 gene (rs10774625 and rs653178) exhibited the strongest association with thrombotic antiphospholipid syndrome (p-value = 5,9 × 10−4 OR 95% CI 1.84 (1.32–2.55)). Conclusion The presence of a TAC risk haplotype in ATXN2-SH2B3 locus may contribute to increased thrombotic risk in aPLA carriers.
Collapse
Affiliation(s)
- Eguzkine Ochoa
- Department of Genetics, Physical Anthropology and Animal Physiology. School of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Mikel Iriondo
- Department of Genetics, Physical Anthropology and Animal Physiology. School of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ana Bielsa
- Autoimmune Disease Research Unit, Service of Internal Medicine, Hospital de Cruces, University of the Basque Country (UPV/EHU), Barakaldo, Spain
| | - Guillermo Ruiz-Irastorza
- Autoimmune Disease Research Unit, Service of Internal Medicine, Hospital de Cruces, University of the Basque Country (UPV/EHU), Barakaldo, Spain
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology. School of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ana M. Zubiaga
- Department of Genetics, Physical Anthropology and Animal Physiology. School of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
- * E-mail:
| |
Collapse
|
44
|
Hinks A, Cobb J, Marion MC, Prahalad S, Sudman M, Bowes J, Martin P, Comeau ME, Sajuthi S, Andrews R, Brown M, Chen WM, Concannon P, Deloukas P, Edkins S, Eyre S, Gaffney PM, Guthery SL, Guthridge JM, Hunt SE, James JA, Keddache M, Moser KL, Nigrovic PA, Onengut-Gumuscu S, Onslow ML, Rosé CD, Rich SS, Steel KJA, Wakeland EK, Wallace CA, Wedderburn LR, Woo P, Bohnsack JF, Haas JP, Glass DN, Langefeld CD, Thomson W, Thompson SD. Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis. Nat Genet 2013; 45:664-9. [PMID: 23603761 PMCID: PMC3673707 DOI: 10.1038/ng.2614] [Citation(s) in RCA: 269] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 03/25/2013] [Indexed: 12/15/2022]
Abstract
We used the Immunochip array to analyze 2,816 individuals with juvenile idiopathic arthritis (JIA), comprising the most common subtypes (oligoarticular and rheumatoid factor-negative polyarticular JIA), and 13,056 controls. We confirmed association of 3 known JIA risk loci (the human leukocyte antigen (HLA) region, PTPN22 and PTPN2) and identified 14 loci reaching genome-wide significance (P < 5 × 10(-8)) for the first time. Eleven additional new regions showed suggestive evidence of association with JIA (P < 1 × 10(-6)). Dense mapping of loci along with bioinformatics analysis refined the associations to one gene in each of eight regions, highlighting crucial pathways, including the interleukin (IL)-2 pathway, in JIA disease pathogenesis. The entire Immunochip content, the HLA region and the top 27 loci (P < 1 × 10(-6)) explain an estimated 18, 13 and 6% of the risk of JIA, respectively. In summary, this is the largest collection of JIA cases investigated so far and provides new insight into the genetic basis of this childhood autoimmune disease.
Collapse
Affiliation(s)
- Anne Hinks
- Arthritis Research UK Epidemiology Unit, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Genome-wide association study identified the human leukocyte antigen region as a novel locus for plasma beta-2 microglobulin. Hum Genet 2013. [PMID: 23417110 DOI: 10.1007/s00439‐013‐1274‐7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Beta-2 microglobulin (B2M) is a component of the major histocompatibility complex (MHC) class I molecule and has been studied as a biomarker of kidney function, cardiovascular diseases and mortality. Little is known about the genes influencing its levels directly or through glomerular filtration rate (GFR). We conducted a genome-wide association study of plasma B2M levels in 6738 European Americans from the Atherosclerosis Risk in Communities study to identify novel loci for B2M and assessed its association with known estimated GFR (eGFR) loci. We identified 2 genome-wide significant loci. One was in the human leukocyte antigen (HLA) region on chromosome 6 (lowest p value = 1.8 × 10(-23) for rs9264638). At this locus, 6 index SNPs accounted for 3.2 % of log(B2M) variance, and their association with B2M could largely be explained by imputed classical alleles of the MHC class I genes: HLA-A, HLA-B, or HLA-C. The index SNPs at this locus were not associated with eGFR based on serum creatinine (eGFRcr). The other locus of B2M was on chromosome 12 (rs3184504 at SH2B3, beta = 0.02, p value = 3.1 × 10(-8)), which was previously implicated as an eGFR locus. In conclusion, although B2M is known to be a component of MHC class I molecule, the association between HLA class I alleles and plasma B2M levels in a community-based population is novel. The identification of the two novel loci for B2M extends our understanding of its metabolism and informs its use as a kidney filtration biomarker.
Collapse
|
46
|
Tin A, Astor BC, Boerwinkle E, Hoogeveen RC, Coresh J, Kao WHL. Genome-wide association study identified the human leukocyte antigen region as a novel locus for plasma beta-2 microglobulin. Hum Genet 2013; 132:619-27. [PMID: 23417110 DOI: 10.1007/s00439-013-1274-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 02/06/2013] [Indexed: 01/11/2023]
Abstract
Beta-2 microglobulin (B2M) is a component of the major histocompatibility complex (MHC) class I molecule and has been studied as a biomarker of kidney function, cardiovascular diseases and mortality. Little is known about the genes influencing its levels directly or through glomerular filtration rate (GFR). We conducted a genome-wide association study of plasma B2M levels in 6738 European Americans from the Atherosclerosis Risk in Communities study to identify novel loci for B2M and assessed its association with known estimated GFR (eGFR) loci. We identified 2 genome-wide significant loci. One was in the human leukocyte antigen (HLA) region on chromosome 6 (lowest p value = 1.8 × 10(-23) for rs9264638). At this locus, 6 index SNPs accounted for 3.2 % of log(B2M) variance, and their association with B2M could largely be explained by imputed classical alleles of the MHC class I genes: HLA-A, HLA-B, or HLA-C. The index SNPs at this locus were not associated with eGFR based on serum creatinine (eGFRcr). The other locus of B2M was on chromosome 12 (rs3184504 at SH2B3, beta = 0.02, p value = 3.1 × 10(-8)), which was previously implicated as an eGFR locus. In conclusion, although B2M is known to be a component of MHC class I molecule, the association between HLA class I alleles and plasma B2M levels in a community-based population is novel. The identification of the two novel loci for B2M extends our understanding of its metabolism and informs its use as a kidney filtration biomarker.
Collapse
Affiliation(s)
- Adrienne Tin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
| | | | | | | | | | | |
Collapse
|
47
|
Cordell HJ, Töpf A, Mamasoula C, Postma AV, Bentham J, Zelenika D, Heath S, Blue G, Cosgrove C, Granados Riveron J, Darlay R, Soemedi R, Wilson IJ, Ayers KL, Rahman TJ, Hall D, Mulder BJM, Zwinderman AH, van Engelen K, Brook JD, Setchfield K, Bu'Lock FA, Thornborough C, O'Sullivan J, Stuart AG, Parsons J, Bhattacharya S, Winlaw D, Mital S, Gewillig M, Breckpot J, Devriendt K, Moorman AFM, Rauch A, Lathrop GM, Keavney BD, Goodship JA. Genome-wide association study identifies loci on 12q24 and 13q32 associated with tetralogy of Fallot. Hum Mol Genet 2013; 22:1473-81. [PMID: 23297363 PMCID: PMC3596849 DOI: 10.1093/hmg/dds552] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We conducted a genome-wide association study to search for risk alleles associated with Tetralogy of Fallot (TOF), using a northern European discovery set of 835 cases and 5159 controls. A region on chromosome 12q24 was associated (P = 1.4 × 10(-7)) and replicated convincingly (P = 3.9 × 10(-5)) in 798 cases and 2931 controls [per allele odds ratio (OR) = 1.27 in replication cohort, P = 7.7 × 10(-11) in combined populations]. Single nucleotide polymorphisms in the glypican 5 gene on chromosome 13q32 were also associated (P = 1.7 × 10(-7)) and replicated convincingly (P = 1.2 × 10(-5)) in 789 cases and 2927 controls (per allele OR = 1.31 in replication cohort, P = 3.03 × 10(-11) in combined populations). Four additional regions on chromosomes 10, 15 and 16 showed suggestive association accompanied by nominal replication. This study, the first genome-wide association study of a congenital heart malformation phenotype, provides evidence that common genetic variation influences the risk of TOF.
Collapse
Affiliation(s)
- Heather J Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
del Rio R, McAllister RD, Meeker ND, Wall EH, Bond JP, Kyttaris VC, Tsokos GC, Tung KSK, Teuscher C. Identification of Orch3, a locus controlling dominant resistance to autoimmune orchitis, as kinesin family member 1C. PLoS Genet 2012; 8:e1003140. [PMID: 23300462 PMCID: PMC3531464 DOI: 10.1371/journal.pgen.1003140] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Accepted: 10/18/2012] [Indexed: 01/18/2023] Open
Abstract
Experimental autoimmune orchitis (EAO), the principal model of non-infectious testicular inflammatory disease, can be induced in susceptible mouse strains by immunization with autologous testicular homogenate and appropriate adjuvants. As previously established, the genome of DBA/2J mice encodes genes that are capable of conferring dominant resistance to EAO, while the genome of BALB/cByJ mice does not and they are therefore susceptible to EAO. In a genome scan, we previously identified Orch3 as the major quantitative trait locus controlling dominant resistance to EAO and mapped it to chromosome 11. Here, by utilizing a forward genetic approach, we identified kinesin family member 1C (Kif1c) as a positional candidate for Orch3 and, using a transgenic approach, demonstrated that Kif1c is Orch3. Mechanistically, we showed that the resistant Kif1cD2 allele leads to a reduced antigen-specific T cell proliferative response as a consequence of decreased MHC class II expression by antigen presenting cells, and that the L578→P578 and S1027→P1027 polymorphisms distinguishing the BALB/cByJ and DBA/2J alleles, respectively, can play a role in transcriptional regulation. These findings may provide mechanistic insight into how polymorphism in other kinesins such as KIF21B and KIF5A influence susceptibility and resistance to human autoimmune diseases. Although the etiology of autoimmunity is not well known, a variety of studies have demonstrated that genetic predisposition is a major contributor to disease susceptibility and resistance. The major histocompatibility complex (MHC) is the primary genetic determinant of autoimmune disease susceptibility with multiple additional interacting loci required. However, the identification and characterization of non–MHC genes has been problematic, since most autoimmune diseases are polygenic with the individual genes exhibiting only partial or minimal penetrance. We previously identified Orch3 (mouse chromosome 11) as the most important immune-suppressive locus controlling dominant resistance to autoimmune orchitis, the principal animal model of non-infectious testicular inflammatory/autoimmune disease. Here, using congenic mapping, we identified kinesin family member 1C (Kif1c) as a positional candidate for Orch3. Furthermore, over-expression of the Kif1c resistant allele in susceptible mice rendered animals autoimmune orchitis resistant, demonstrating that Kif1c is Orch3. We propose that Kif1c plays an immunoregulatory role by controlling the levels of MHC class II in antigen presenting cells and consequently impacting autoreactive orchitogenic T cell responses. These finding are particularly relevant since polymorphism in other kinesins such as KIF21B and KIF5A have been associated with susceptibility and resistance to human autoimmune disease.
Collapse
Affiliation(s)
- Roxana del Rio
- Department of Medicine/Immunobiology Program, University of Vermont, Burlington, Vermont, United States of America
| | - Ryan D. McAllister
- Department of Microbiology, University of Illinois, Urbana-Champaign, Illinois, United States of America
| | - Nathan D. Meeker
- Mountain States Tumor Institute, Boise, Idaho, United States of America
| | - Emma H. Wall
- Department of Medicine/Immunobiology Program, University of Vermont, Burlington, Vermont, United States of America
| | - Jeffrey P. Bond
- Vermont Genetics Network Bioinformatics Core, University of Vermont, Burlington, Vermont, United States of America
| | - Vasileios C. Kyttaris
- Division of Rheumatology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - George C. Tsokos
- Division of Rheumatology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kenneth S. K. Tung
- Department of Pathology and Beirne B. Carter Center of Immunology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Cory Teuscher
- Department of Medicine/Immunobiology Program, University of Vermont, Burlington, Vermont, United States of America
- Department of Pathology, University of Vermont, Burlington, Vermont, United States of America
- * E-mail:
| |
Collapse
|
49
|
Lindén M, Khademi M, Lima Bomfim I, Piehl F, Jagodic M, Kockum I, Olsson T. Multiple sclerosis risk genotypes correlate with an elevated cerebrospinal fluid level of the suggested prognostic marker CXCL13. Mult Scler 2012; 19:863-70. [DOI: 10.1177/1352458512463482] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background: The mechanisms of multiple sclerosis (MS) pathogenesis are still largely unknown. The heterogeneity of disease manifestations make the prediction of prognosis and choice of appropriate treatment protocols challenging. Recently, increased cerebrospinal fluid (CSF) levels of the B-cell chemokine CXCL13 was proposed as a possible marker for a more severe disease course and conversion from clinically isolated syndrome (CIS) to relapsing–remitting MS (RRMS). Objective: To investigate whether there are genetic susceptibility variants in MS that correlate with the levels of CXCL13 present in the CSF of MS patients. Methods: We genotyped the human leukocyte antigens HLA-DRB1 and HLA-A, plus a panel of single nucleotide polymorphisms (SNPs) that have been associated with susceptibility to MS and then correlated the genotypes with the levels of CXCL13, as measured with ELISA in the CSF of a total of 663 patients with MS, CIS, other neurological diseases (OND) or OND with an inflammatory component (iOND). Results: Presence of the HLA-DRB1*15 and the MS risk genotypes for SNPs in the RGS1, IRF5 and OLIG3/TNFAIP3 gene regions correlated significantly with increased levels of CXCL13. Conclusion: Our results pointed towards a genetic predisposition for increased CXCL13 levels, which in MS patients correlates with the severity of the disease course. These findings encourage further investigation and replication, in an independent patient cohort.
Collapse
Affiliation(s)
- M Lindén
- Department of Clinical Neuroscience, Karolinska Institutet Stockholm, Sweden
| | - M Khademi
- Department of Clinical Neuroscience, Karolinska Institutet Stockholm, Sweden
| | - I Lima Bomfim
- Department of Clinical Neuroscience, Karolinska Institutet Stockholm, Sweden
| | - F Piehl
- Department of Clinical Neuroscience, Karolinska Institutet Stockholm, Sweden
| | - M Jagodic
- Department of Clinical Neuroscience, Karolinska Institutet Stockholm, Sweden
| | - I Kockum
- Department of Clinical Neuroscience, Karolinska Institutet Stockholm, Sweden
| | - T Olsson
- Department of Clinical Neuroscience, Karolinska Institutet Stockholm, Sweden
| |
Collapse
|
50
|
Alcina A, Fedetz M, Fernández O, Saiz A, Izquierdo G, Lucas M, Leyva L, García-León JA, Abad-Grau MDM, Alloza I, Antigüedad A, Garcia-Barcina MJ, Vandenbroeck K, Varadé J, de la Hera B, Arroyo R, Comabella M, Montalban X, Petit-Marty N, Navarro A, Otaegui D, Olascoaga J, Blanco Y, Urcelay E, Matesanz F. Identification of a functional variant in the KIF5A-CYP27B1-METTL1-FAM119B locus associated with multiple sclerosis. J Med Genet 2012; 50:25-33. [PMID: 23160276 PMCID: PMC3538279 DOI: 10.1136/jmedgenet-2012-101085] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background and aim Several studies have highlighted the association of the 12q13.3–12q14.1 region with coeliac disease, type 1 diabetes, rheumatoid arthritis and multiple sclerosis (MS); however, the causal variants underlying diseases are still unclear. The authors sought to identify the functional variant of this region associated with MS. Methods Tag-single nucleotide polymorphism (SNP) analysis of the associated region encoding 15 genes was performed in 2876 MS patients and 2910 healthy Caucasian controls together with expression regulation analyses. Results rs6581155, which tagged 18 variants within a region where 9 genes map, was sufficient to model the association. This SNP was in total linkage disequilibrium (LD) with other polymorphisms that associated with the expression levels of FAM119B, AVIL, TSFM, TSPAN31 and CYP27B1 genes in different expression quantitative trait loci studies. Functional annotations from Encyclopedia of DNA Elements (ENCODE) showed that six out of these rs6581155-tagged-SNPs were located in regions with regulatory potential and only one of them, rs10877013, exhibited allele-dependent (ratio A/G=9.5-fold) and orientation-dependent (forward/reverse=2.7-fold) enhancer activity as determined by luciferase reporter assays. This enhancer is located in a region where a long-range chromatin interaction among the promoters and promoter-enhancer of several genes has been described, possibly affecting their expression simultaneously. Conclusions This study determines a functional variant which alters the enhancer activity of a regulatory element in the locus affecting the expression of several genes and explains the association of the 12q13.3–12q14.1 region with MS.
Collapse
Affiliation(s)
- Antonio Alcina
- Department of Cell Biology and Immunology Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas (IPBLNCSIC), Granada, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|