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Arleo T, Tong D, Shabto J, O'Keefe G, Khosroshahi A. Clinical course and outcomes of COVID-19 in rheumatic disease patients: a case cohort study with a diverse population. Clin Rheumatol 2021; 40:2633-2642. [PMID: 33420870 PMCID: PMC7794618 DOI: 10.1007/s10067-021-05578-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To determine clinical course and outcomes in rheumatic disease patients with coronavirus disease 2019 (COVID-19) and compare results to uninfected patients. METHODS We conducted a case cohort study of autoimmune disease patients with COVID-19 (confirmed by severe acute respiratory syndrome coronavirus 2 PCR) from February 1, 2020, to July 31, 2020, and compared them in a 1:3 ratio with uninfected patients who were matched based on race, age, sex, and comorbidity index. Patient demographics, clinical course, and outcomes were compared among these patient groups. RESULTS A total of 70 rheumatic disease patients with COVID-19 (mean age, 56.6 years; 64% African American) were identified. The 34 (49%) patients who were hospitalized used oral glucocorticoids more frequently than those treated as outpatients (p < 0.01). All 10 patients using anti-TNFα medications were treated as outpatients (p < 0.01). Those hospitalized with COVID-19 more often required ICU admission (17 (50%) vs 27 (26%), p = 0.01) and intubation (10 (29%) vs 6 (6%), p < 0.01) than uninfected patients and had higher mortality rates (6 (18%) vs 3 (3%), p < 0.01). Of the six COVID-19 patients who died, only one was of African ancestry (p = 0.03). CONCLUSION Rheumatic disease patients infected with COVID-19 were more likely to require ICU admission, ventilation, and died more frequently versus uninfected patients with autoimmune disease. Patients on anti-TNFα medications were hospitalized less frequently, while those on chronic glucocorticoids were hospitalized more frequently. These findings have important implications for medication choice in rheumatic disease patients during the ongoing spread of COVID-19. Key Points • We show that hospitalized rheumatic disease patients with COVID-19 have poorer outcomes including ICU admission, ventilation, and death compared to hospitalized rheumatic disease patients not infected with COVID-19. • This study adds further support regarding protective effects of anti-TNFα medications in COVID-19 disease course, with 0 of 10 of these patients required hospitalization.
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Affiliation(s)
- Timothy Arleo
- Emory University School of Medicine, Atlanta, GA, USA
| | - David Tong
- Division of Hospital Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Julie Shabto
- Emory University School of Medicine, Atlanta, GA, USA
| | - Ghazala O'Keefe
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, GA, USA
| | - Arezou Khosroshahi
- Division of Rheumatology, Emory University School of Medicine, 244 Whitehead Bldg., 615 Michael Street, Atlanta, GA, 30322, USA.
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Katz M, Gillespie S, Stevens JP, Hall L, Kolachala V, Ford R, Levin K, Gupta NA. African American Pediatric Liver Transplant Recipients Have an Increased Risk of Death After Transferring to Adult Healthcare. J Pediatr 2021; 233:119-125.e1. [PMID: 33667506 DOI: 10.1016/j.jpeds.2021.02.069] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/10/2021] [Accepted: 02/25/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To analyze the long-term outcomes in pediatric liver transplant recipients after they have transferred to an adult provider and assess for racial disparities in health outcomes. STUDY DESIGN This is a single-center, retrospective review of pediatric patients who underwent liver transplantation between July 1990 and August 2015 at a tertiary healthcare system with a large transplant center. Patient mortality and retransplantation were assessed after transfer to adult care. RESULTS There were 120 patients who were transferred, of whom 19 did not meet the inclusion criteria. Of the remaining 101 patients, 64 (63%) transferred care to a nearby affiliated tertiary adult facility, 29 (29%) were followed by other healthcare systems, and 8 (8%) were lost to follow-up. Of the patients followed at our affiliated adult center, 18 of the 64 (28%) died. Of those 18 deaths, 4 (22%) occurred within the first 2 years after transfer, and 10 (55%) within 5 years of transfer. Four patients were retransplanted by an adult provider, of whom 2 eventually received a third transplant. African Americans had higher rates of death after transfer than patients of other races (44% mortality vs 16%, representing 67% of all cases of death; P = .032), with nearly 50% mortality at 20 years from time of transplantation. CONCLUSIONS Death is common in pediatric liver transplant recipients after transfer to adult care, with African Americans having disproportionately higher mortality. This period of transition of care is a vulnerable time, and measures must be taken to ensure the safe transfer of young adults with chronic health care needs.
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Affiliation(s)
- Mikaela Katz
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Scott Gillespie
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - James P Stevens
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA; Transplant services, Children's Healthcare of Atlanta, Atlanta, GA
| | - Lori Hall
- Transplant services, Children's Healthcare of Atlanta, Atlanta, GA
| | - Vasantha Kolachala
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Ryan Ford
- Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Keri Levin
- Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Nitika A Gupta
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA; Transplant services, Children's Healthcare of Atlanta, Atlanta, GA.
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Al Naqbi H, Mawart A, Alshamsi J, Al Safar H, Tay GK. Major histocompatibility complex (MHC) associations with diseases in ethnic groups of the Arabian Peninsula. Immunogenetics 2021; 73:131-152. [PMID: 33528690 PMCID: PMC7946680 DOI: 10.1007/s00251-021-01204-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022]
Abstract
Since the discovery of human leukocyte antigens (HLAs), the function of major histocompatibility complex (MHC) gene families in a wide range of diseases have been the subject of research for decades. In particular, the associations of autoimmune disorders to allelic variants and candidate genes encoding the MHC are well documented. However, despite decades of research, the knowledge of MHC associations with human disease susceptibility have been predominantly studied in European origin, with limited understanding in different populations and ethnic groups. This is particularly evident in countries and ethnic populations of the Arabian Peninsula. Human MHC haplotypes, and its association with diseases, of the variable ethnic groups of this region are poorly studied. This review compiled published manuscripts that have reported a list of autoimmune diseases (insulin-dependent diabetes mellitus, systemic lupus erythematosus, myasthenia gravis, rheumatoid arthritis, psoriasis vulgaris, and multiple sclerosis) associated with MHC class I and class II in the populations of the Arabian Peninsula, specifically Bahrain, Kuwait, Oman, Qatar, Saudi Arabia, the United Arab Emirates, and Yemen. Data available was compared with other three ethnic groups, namely Caucasians, Asians, and Africans. The limited data available in the public domain on the association between MHC gene and autoimmune diseases highlight the challenges in the Middle Eastern region.
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Affiliation(s)
- Halima Al Naqbi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Aurélie Mawart
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Jawaher Alshamsi
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba Al Safar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan K Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- Division of Psychiatry, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia.
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
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Association between FAS gene -670 A/G and -1377 G/A polymorphisms and the risk of autoimmune diseases: a meta-analysis. Biosci Rep 2021; 40:221503. [PMID: 31840751 PMCID: PMC6944657 DOI: 10.1042/bsr20191197] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 12/03/2019] [Accepted: 12/13/2019] [Indexed: 12/16/2022] Open
Abstract
Objectives: FAS plays a critical role in the extrinsic apoptosis pathway in autoimmune diseases. Previous studies investigating the association between FAS gene −670 A/G and −1377 G/A polymorphisms and the risk of autoimmune diseases reported controversial results. We performed the meta-analysis to evaluate the possible association. Methods: Relevant studies were identified by searching the PubMed, Embase, CNKI, and Wanfang databases up to December 2018. Odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were calculated to determine the association. Results: A total of 43 articles including 67 studies (52 studies for FAS −670 A/G and 15 studies for −1377 G/A) were included in the meta-analysis. Our meta-analysis showed that the FAS −670 A/G polymorphism was associated with the risk of autoimmune diseases (GG vs. GA: OR = 1.079, 95% CI = 1.004–1.160, P=0.038), especially in Caucasians (GG vs. GA: OR = 1.12, 95% CI = 1.03–1.23, P=0.012), Asians (G vs. A: OR = 0.89, 95% CI = 0.83–0.96, P=0.002), systemic lupus erythematosus (SLE) (G vs. A: OR = 0.85, 95% CI = 0.77–0.94, P=0.001), multiple sclerosis (MS) (GG+GA vs. AA: OR = 0.83, 95% CI = 0.70–0.99, P=0.043), systemic sclerosis (SSc) (GG vs. GA: OR = 1.20, 95% CI = 1.07–1.36, P=0.003) and Hashimoto’s thyroiditis (HT) (G vs. A: OR = 1.45, 95% CI = 1.10–1.90, P=0.008); the FAS −1377 G/A polymorphism was associated with the risk of autoimmune diseases (A vs. G: OR = 1.11, 95% CI = 1.03–1.20, P=0.008), especially in Asians (A vs. G: OR = 1.15, 95% CI = 1.05–1.25, P=0.002) and high quality studies (A vs. G: OR = 1.14, 95% CI = 1.05–1.24, P=0.002). Conclusion: This meta-analysis demonstrated that the FAS –670A/G and –1377 G/A polymorphisms were associated with the risk of autoimmune diseases.
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Liu J, Ting JP, Al-Azzam S, Ding Y, Afshar S. Therapeutic Advances in Diabetes, Autoimmune, and Neurological Diseases. Int J Mol Sci 2021; 22:ijms22062805. [PMID: 33802091 PMCID: PMC8001105 DOI: 10.3390/ijms22062805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/02/2021] [Accepted: 03/06/2021] [Indexed: 02/08/2023] Open
Abstract
Since 2015, 170 small molecules, 60 antibody-based entities, 12 peptides, and 15 gene- or cell-therapies have been approved by FDA for diverse disease indications. Recent advancement in medicine is facilitated by identification of new targets and mechanisms of actions, advancement in discovery and development platforms, and the emergence of novel technologies. Early disease detection, precision intervention, and personalized treatments have revolutionized patient care in the last decade. In this review, we provide a comprehensive overview of current and emerging therapeutic modalities developed in the recent years. We focus on nine diseases in three major therapeutics areas, diabetes, autoimmune, and neurological disorders. The pathogenesis of each disease at physiological and molecular levels is discussed and recently approved drugs as well as drugs in the clinic are presented.
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Affiliation(s)
- Jinsha Liu
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA; (J.L.); (J.P.T.); (Y.D.)
| | - Joey Paolo Ting
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA; (J.L.); (J.P.T.); (Y.D.)
| | - Shams Al-Azzam
- Professional Scientific Services, Eurofins Lancaster Laboratories, Lancaster, PA 17605, USA;
| | - Yun Ding
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA; (J.L.); (J.P.T.); (Y.D.)
| | - Sepideh Afshar
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA; (J.L.); (J.P.T.); (Y.D.)
- Correspondence:
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Wan WL, Kim ST, Castel B, Charoennit N, Chae E. Genetics of autoimmunity in plants: an evolutionary genetics perspective. THE NEW PHYTOLOGIST 2021; 229:1215-1233. [PMID: 32970825 DOI: 10.1111/nph.16947] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/12/2020] [Indexed: 05/14/2023]
Abstract
Autoimmunity in plants has been found in numerous hybrids as a form of hybrid necrosis and mutant panels. Uncontrolled cell death is a main cellular outcome of autoimmunity, which negatively impacts growth. Its occurrence highlights the vulnerable nature of the plant immune system. Genetic investigation of autoimmunity in hybrid plants revealed that extreme variation in the immune receptor repertoire is a major contributor, reflecting an evolutionary conundrum that plants face in nature. In this review, we discuss natural variation in the plant immune system and its contribution to fitness. The value of autoimmunity genetics lies in its ability to identify combinations of a natural immune receptor and its partner that are predisposed to triggering autoimmunity. The network of immune components for autoimmunity becomes instrumental in revealing mechanistic details of how immune receptors recognize cellular invasion and activate signaling. The list of autoimmunity-risk variants also allows us to infer evolutionary processes contributing to their maintenance in the natural population. Our approach to autoimmunity, which integrates mechanistic understanding and evolutionary genetics, has the potential to serve as a prognosis tool to optimize immunity in crops.
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Affiliation(s)
- Wei-Lin Wan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Sang-Tae Kim
- Department of Life Sciences, The Catholic University of Korea, Bucheon, Gyeonggi-do, 14662, South Korea
| | - Baptiste Castel
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Nuri Charoennit
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Eunyoung Chae
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
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Mukhatayev Z, Ostapchuk YO, Fang D, Le Poole IC. Engineered antigen-specific regulatory T cells for autoimmune skin conditions. Autoimmun Rev 2021; 20:102761. [PMID: 33476816 DOI: 10.1016/j.autrev.2021.102761] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 11/28/2020] [Indexed: 12/15/2022]
Abstract
Regulatory T cells (Tregs) are a subset of T cells responsible for the regulation of immune responses, thereby maintaining immune homeostasis and providing immune tolerance to both self and non-self-antigens. An increasing number of studies revealed Treg numbers and functions in a variety of autoimmune diseases. Treg deficiency can cause the development of several autoimmune skin diseases including vitiligo, alopecia areata, pemphigoid and pemphigus, psoriasis, and systemic sclerosis. Many clinical trials have been performed for autoimmune conditions using polyclonal Tregs, but efficiency can be significantly improved using antigen-specific Tregs engineered using T cell receptor (TCR) or chimeric antigen receptor (CAR) constructs. In this review, we systematically reviewed altered frequencies, impaired functions, and phenotypic features of Tregs in autoimmune skin conditions. We also summarized new advances in TCR and CAR based antigen-specific Tregs tested both in animal models and in clinics. The advantages and limitations of each approach were carefully discussed emphasizing possible clinical relevance to patients with autoimmune skin diseases. Moreover, we have reviewed potential approaches for engineering antigen-specific Tregs, and strategies for overcoming possible hurdles in clinical applications. Thereby, antigen-specific Tregs can be infused using autologous adoptive cell transfer to restore Treg numbers and to provide local immune tolerance for autoimmune skin disorders.
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Affiliation(s)
- Zhussipbek Mukhatayev
- Department of Dermatology, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA; Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan; M.A. Aitkhozhin's Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | | | - Deyu Fang
- Department of Pathology, Northwestern University, Chicago, IL, USA
| | - I Caroline Le Poole
- Department of Dermatology, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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De Haan P, Van Diemen FR, Toscano MG. Viral gene delivery vectors: the next generation medicines for immune-related diseases. Hum Vaccin Immunother 2021; 17:14-21. [PMID: 32412865 PMCID: PMC7872028 DOI: 10.1080/21645515.2020.1757989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/14/2020] [Indexed: 12/12/2022] Open
Abstract
Viruses have evolved to efficiently express their genes in host cells, which makes them ideally suited as gene delivery vectors for gene and immunotherapies. Replication competent (RC) viral vectors encoding foreign or self-proteins induce strong T-cell responses that can be used for the development of effective cancer treatments. Replication-defective (RD) viral vectors encoding self-proteins are non-immunogenic when introduced in a host naïve for the cognate virus. RD viral vectors can be used to develop gene replacement therapies for genetic disorders and tolerization therapies for autoimmune diseases and allergies. Degenerative/inflammatory diseases are associated with chronic inflammation and immune responses that damage the tissues involved. These diseases therefore strongly resemble autoimmune diseases. This review deals with the use of RC and RD viral vectors for unraveling the pathogenesis of immune-related diseases and their application to the development of the next generation prophylactics and therapeutics for todays' major diseases.
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Affiliation(s)
- Peter De Haan
- Department of R&D, Amarna Therapeutics B.V, Leiden, The Netherlands
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Barinotti A, Radin M, Cecchi I, Foddai SG, Rubini E, Roccatello D, Sciascia S, Menegatti E. Genetic Factors in Antiphospholipid Syndrome: Preliminary Experience with Whole Exome Sequencing. Int J Mol Sci 2020; 21:E9551. [PMID: 33333988 PMCID: PMC7765384 DOI: 10.3390/ijms21249551] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 12/18/2022] Open
Abstract
As in many autoimmune diseases, the pathogenesis of the antiphospholipid syndrome (APS) is the result of a complex interplay between predisposing genes and triggering environmental factors, leading to a loss of self-tolerance and immune-mediated tissue damage. While the first genetic studies in APS focused primarily on the human leukocytes antigen system (HLA) region, more recent data highlighted the role of other genes in APS susceptibility, including those involved in the immune response and in the hemostatic process. In order to join this intriguing debate, we analyzed the single-nucleotide polymorphisms (SNPs) derived from the whole exome sequencing (WES) of two siblings affected by APS and compared our findings with the available literature. We identified genes encoding proteins involved in the hemostatic process, the immune response, and the phospholipid metabolism (PLA2G6, HSPG2, BCL3, ZFAT, ATP2B2, CRTC3, and ADCY3) of potential interest when debating the pathogenesis of the syndrome. The study of the selected SNPs in a larger cohort of APS patients and the integration of WES results with the network-based approaches will help decipher the genetic risk factors involved in the diverse clinical features of APS.
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Affiliation(s)
- Alice Barinotti
- Center of Research of Immunopathology and Rare Diseases—Coordinating Center of Piemonte and Aosta Valley Network for Rare Diseases, S. Giovanni Bosco Hospital, Department of Clinical and Biological Sciences, University of Turin, 10154 Turin, Italy; (A.B.); (M.R.); (I.C.); (S.G.F.); (E.R.); (D.R.); (E.M.)
- Department of Clinical and Biological Sciences, School of Specialization of Clinical Pathology, University of Turin, 10125 Turin, Italy
| | - Massimo Radin
- Center of Research of Immunopathology and Rare Diseases—Coordinating Center of Piemonte and Aosta Valley Network for Rare Diseases, S. Giovanni Bosco Hospital, Department of Clinical and Biological Sciences, University of Turin, 10154 Turin, Italy; (A.B.); (M.R.); (I.C.); (S.G.F.); (E.R.); (D.R.); (E.M.)
| | - Irene Cecchi
- Center of Research of Immunopathology and Rare Diseases—Coordinating Center of Piemonte and Aosta Valley Network for Rare Diseases, S. Giovanni Bosco Hospital, Department of Clinical and Biological Sciences, University of Turin, 10154 Turin, Italy; (A.B.); (M.R.); (I.C.); (S.G.F.); (E.R.); (D.R.); (E.M.)
| | - Silvia Grazietta Foddai
- Center of Research of Immunopathology and Rare Diseases—Coordinating Center of Piemonte and Aosta Valley Network for Rare Diseases, S. Giovanni Bosco Hospital, Department of Clinical and Biological Sciences, University of Turin, 10154 Turin, Italy; (A.B.); (M.R.); (I.C.); (S.G.F.); (E.R.); (D.R.); (E.M.)
- Department of Clinical and Biological Sciences, School of Specialization of Clinical Pathology, University of Turin, 10125 Turin, Italy
| | - Elena Rubini
- Center of Research of Immunopathology and Rare Diseases—Coordinating Center of Piemonte and Aosta Valley Network for Rare Diseases, S. Giovanni Bosco Hospital, Department of Clinical and Biological Sciences, University of Turin, 10154 Turin, Italy; (A.B.); (M.R.); (I.C.); (S.G.F.); (E.R.); (D.R.); (E.M.)
| | - Dario Roccatello
- Center of Research of Immunopathology and Rare Diseases—Coordinating Center of Piemonte and Aosta Valley Network for Rare Diseases, S. Giovanni Bosco Hospital, Department of Clinical and Biological Sciences, University of Turin, 10154 Turin, Italy; (A.B.); (M.R.); (I.C.); (S.G.F.); (E.R.); (D.R.); (E.M.)
- Nephrology and Dialysis, Department of Clinical and Biological Sciences, S. Giovanni Bosco Hospital and University of Turin, 10154 Turin, Italy
| | - Savino Sciascia
- Center of Research of Immunopathology and Rare Diseases—Coordinating Center of Piemonte and Aosta Valley Network for Rare Diseases, S. Giovanni Bosco Hospital, Department of Clinical and Biological Sciences, University of Turin, 10154 Turin, Italy; (A.B.); (M.R.); (I.C.); (S.G.F.); (E.R.); (D.R.); (E.M.)
- Nephrology and Dialysis, Department of Clinical and Biological Sciences, S. Giovanni Bosco Hospital and University of Turin, 10154 Turin, Italy
| | - Elisa Menegatti
- Center of Research of Immunopathology and Rare Diseases—Coordinating Center of Piemonte and Aosta Valley Network for Rare Diseases, S. Giovanni Bosco Hospital, Department of Clinical and Biological Sciences, University of Turin, 10154 Turin, Italy; (A.B.); (M.R.); (I.C.); (S.G.F.); (E.R.); (D.R.); (E.M.)
- Department of Clinical and Biological Sciences, School of Specialization of Clinical Pathology, University of Turin, 10125 Turin, Italy
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Jaiswal KS, Khanna S, Ghosh A, Padhan P, Raghav SK, Gupta B. Differential mitochondrial genome in patients with Rheumatoid Arthritis. Autoimmunity 2020; 54:1-12. [PMID: 33191792 DOI: 10.1080/08916934.2020.1846182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Mitochondria play an important role in cell survival, function and lineage differentiation. Changes in mitochondrial DNA (mtDNA) may control mitochondrial functions and thus may impart an alternative cellular state thereby leading to a disease condition in the body. Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease wherein immune cells become self-reactive causing joint inflammation, swelling and pain in patients. The changes in mtDNA may alter cellular functions thereby directing the immune cells towards an inflammatory phenotype in RA. Therefore, it becomes pertinent to identify changes in mtDNA sequence in immune cells of RA patients to understand the pathogenesis and progression of RA. METHODS mtDNA from peripheral blood mono-nuclear cells (PBMCs) of 23 RA patients and 17 healthy controls (HCs) were sequenced using next-generation sequencing (NGS). Further, single nucleotide polymorphisms (SNPs) and other variable changes in mtDNA hypervariable and coding regions, amino acid changes with a putative impact on disease, levels of heteroplasmy, copy number variations and haplogroup analysis in RA patients and HCs were analysed and compared to identify any association of mtDNA changes and RA disease. RESULTS A total of 382 single nucleotide mtDNA variants were observed, 91 (23.82%) were present in hypervariable region and 291 (76.18%) in coding region of patients and HC. The variant 513 GCA > ACA, with G present in HVR-III, known to control the mitochondrial translation function, was significantly present in RA patients. The CYTB gene had larger number of SNPs in HC samples while RNR2 was more variable in RA patients. A non-synonymous heteroplasmy in ND1 gene was found at a single nucleotide position 3533 in an increased number of RA patients as compared to the controls. A significant increase in mtDNA duplication and a higher frequency of the haplogroup U was also characteristic of RA. Also, the presence of SNPs in mitochondrial tRNA genes at two positions 12308 A > G and 15924 A > G were found to be pathogenic. CONCLUSION We herein observed an altered mtDNA sequence in immune cells of RA patients and thus a possible role of mitochondrial genome in the development of RA. The observed nucleotide changes in mtDNA control region, RNR2 gene, increased heteroplasmy and mtDNA duplication in RA patients may alter sites for transcription factor binding thereby influencing mtDNA gene expression, as well as copy numbers thereby affecting the mitochondrial proteins and their functions. These changes in mtDNA could be one of the probable reasons among many leading to the progression of RA.
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Affiliation(s)
- Kumar Sagar Jaiswal
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Shweta Khanna
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Arup Ghosh
- Laboratory of Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Prasanta Padhan
- Department of Rheumatology, Kalinga Institute of Medical Sciences, Bhubaneswar, India
| | - Sunil Kumar Raghav
- Laboratory of Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Bhawna Gupta
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
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Some Common SNPs of the T-Cell Homeostasis-Related Genes Are Associated with Multiple Sclerosis, but Not with the Clinical Manifestations of the Disease, in the Polish Population. J Immunol Res 2020; 2020:8838014. [PMID: 33224992 PMCID: PMC7673932 DOI: 10.1155/2020/8838014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/30/2022] Open
Abstract
Purpose Multiple sclerosis (MS) is an autoimmune disease, and genetic factors play an important role in its pathogenesis and progression. The aim of our study was to evaluate the frequencies of alleles and genetic variants of the T-cell homeostasis-related genes, in subjects with MS, as well as to investigate the association with MS clinical manifestations and disability. Methods 94 subjects with MS and 160 healthy individuals have been genotyped for seven common single-nucleotide variants in IL-2RA, CTLA4, CD40, and PADI4 genes. The ages of onset, duration of the disease, and clinical condition of the MS subjects were analysed. We used the Chi2 test confirmed with Fisher's exact test for statistical analysis. Results The frequency of allele T and CT/TT genotypes (rs7093069) in the IL2RA gene, as well as the T allele and CT/TT genotypes in rs12722598, were significantly higher in the control group. The significant differences between studied groups we also found for the G allele and GG/GA genotypes of rs3087243 in CTLA4 gene, which were more common among the control group. The heterozygous genotype TC (rs1883832) of CD40 gene was more common in the control subjects, and the frequency of the alleles and genotypes in the rs1748033 of the PADI4 gene did not differ between the studied groups. Between the studied genotypes, we did not observe any significant differences in the age of onset and duration of disease, including sex stratification. Conclusion Our results highlight the protective role of some of the T-cell homeostasis-related genetic variants in MS development, but not in its clinical manifestation.
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62
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Browning SR, Browning BL. Probabilistic Estimation of Identity by Descent Segment Endpoints and Detection of Recent Selection. Am J Hum Genet 2020; 107:895-910. [PMID: 33053335 PMCID: PMC7553009 DOI: 10.1016/j.ajhg.2020.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/25/2020] [Indexed: 12/18/2022] Open
Abstract
Most methods for fast detection of identity by descent (IBD) segments report identity by state segments without any quantification of the uncertainty in the endpoints and lengths of the IBD segments. We present a method for determining the posterior probability distribution of IBD segment endpoints. Our approach accounts for genotype errors, recent mutations, and gene conversions which disrupt DNA sequence identity within IBD segments, and it can be applied to large cohorts with whole-genome sequence or SNP array data. We find that our method's estimates of uncertainty are well calibrated for homogeneous samples. We quantify endpoint uncertainty for 77.7 billion IBD segments from 408,883 individuals of white British ancestry in the UK Biobank, and we use these IBD segments to find regions showing evidence of recent natural selection. We show that many spurious selection signals are eliminated by the use of unbiased estimates of IBD segment endpoints and a pedigree-based genetic map. Eleven of the twelve regions with the greatest evidence for recent selection in our scan have been identified as selected in previous analyses using different approaches. Our computationally efficient method for quantifying IBD segment endpoint uncertainty is implemented in the open source ibd-ends software package.
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Affiliation(s)
- Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
| | - Brian L Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
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63
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Abstract
Although the development of effective vaccines has saved countless lives from infectious diseases, the basic workings of the human immune system are complex and have required the development of animal models, such as inbred mice, to define mechanisms of immunity. More recently, new strategies and technologies have been developed to directly explore the human immune system with unprecedented precision. We discuss how these approaches are advancing our mechanistic understanding of human immunology and are facilitating the development of vaccines and therapeutics for infection, autoimmune diseases, and cancer.
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Affiliation(s)
- Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA.
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Stanford ChEM-H: Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA 94305, USA
- Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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64
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Field MA. Detecting pathogenic variants in autoimmune diseases using high-throughput sequencing. Immunol Cell Biol 2020; 99:146-156. [PMID: 32623783 PMCID: PMC7891608 DOI: 10.1111/imcb.12372] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/22/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022]
Abstract
Sequencing the first human genome in 2003 took 15 years and cost $2.7 billion. Advances in sequencing technologies have since decreased costs to the point where it is now feasible to resequence a whole human genome for $1000 in a single day. These advances have allowed the generation of huge volumes of high‐quality human sequence data used to construct increasingly large catalogs of both population‐level and disease‐causing variation. The existence of such databases, coupled with a high‐quality human reference genome, means we are able to interrogate and annotate all types of genetic variation and identify pathogenic variants for many diseases. Increasingly, sequencing‐based approaches are being used to elucidate the underlying genetic cause of autoimmune diseases, a group of roughly 80 polygenic diseases characterized by abnormal immune responses where healthy tissue is attacked. Although sequence data generation has become routine and affordable, significant challenges remain with no gold‐standard methodology to identify pathogenic variants currently available. This review examines the latest methodologies used to identify pathogenic variants in autoimmune diseases and considers available sequencing options and subsequent bioinformatic methodologies and strategies. The development of reliable and robust sequencing and analytic workflows to detect pathogenic variants is critical to realize the potential of precision medicine programs where patient variant information is used to inform clinical practice.
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Affiliation(s)
- Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.,John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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65
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Hildebrand JM, Kauppi M, Majewski IJ, Liu Z, Cox AJ, Miyake S, Petrie EJ, Silk MA, Li Z, Tanzer MC, Brumatti G, Young SN, Hall C, Garnish SE, Corbin J, Stutz MD, Di Rago L, Gangatirkar P, Josefsson EC, Rigbye K, Anderton H, Rickard JA, Tripaydonis A, Sheridan J, Scerri TS, Jackson VE, Czabotar PE, Zhang JG, Varghese L, Allison CC, Pellegrini M, Tannahill GM, Hatchell EC, Willson TA, Stockwell D, de Graaf CA, Collinge J, Hilton A, Silke N, Spall SK, Chau D, Athanasopoulos V, Metcalf D, Laxer RM, Bassuk AG, Darbro BW, Fiatarone Singh MA, Vlahovich N, Hughes D, Kozlovskaia M, Ascher DB, Warnatz K, Venhoff N, Thiel J, Biben C, Blum S, Reveille J, Hildebrand MS, Vinuesa CG, McCombe P, Brown MA, Kile BT, McLean C, Bahlo M, Masters SL, Nakano H, Ferguson PJ, Murphy JM, Alexander WS, Silke J. A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunction. Nat Commun 2020; 11:3150. [PMID: 32561755 PMCID: PMC7305203 DOI: 10.1038/s41467-020-16819-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
MLKL is the essential effector of necroptosis, a form of programmed lytic cell death. We have isolated a mouse strain with a single missense mutation, MlklD139V, that alters the two-helix 'brace' that connects the killer four-helix bundle and regulatory pseudokinase domains. This confers constitutive, RIPK3 independent killing activity to MLKL. Homozygous mutant mice develop lethal postnatal inflammation of the salivary glands and mediastinum. The normal embryonic development of MlklD139V homozygotes until birth, and the absence of any overt phenotype in heterozygotes provides important in vivo precedent for the capacity of cells to clear activated MLKL. These observations offer an important insight into the potential disease-modulating roles of three common human MLKL polymorphisms that encode amino acid substitutions within or adjacent to the brace region. Compound heterozygosity of these variants is found at up to 12-fold the expected frequency in patients that suffer from a pediatric autoinflammatory disease, chronic recurrent multifocal osteomyelitis (CRMO).
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Affiliation(s)
- Joanne M Hildebrand
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
| | - Maria Kauppi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Ian J Majewski
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Zikou Liu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Allison J Cox
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Sanae Miyake
- Department of Biochemistry, Toho University School of Medicine, Ota-ku, Tokyo, 143-8540, Japan
| | - Emma J Petrie
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Michael A Silk
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC, 3052, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Zhixiu Li
- Translational Genomics Group, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT) at Translational Research Institute, Brisbane, Australia
| | - Maria C Tanzer
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Gabriela Brumatti
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Samuel N Young
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Cathrine Hall
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Sarah E Garnish
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Jason Corbin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Michael D Stutz
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.,Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Ladina Di Rago
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Pradnya Gangatirkar
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Emma C Josefsson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Kristin Rigbye
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
| | - Holly Anderton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - James A Rickard
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.,The Royal Melbourne Hospital, Melbourne, VIC, 3050, Australia
| | - Anne Tripaydonis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.,The Royal Melbourne Hospital, Melbourne, VIC, 3050, Australia
| | - Julie Sheridan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Thomas S Scerri
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Victoria E Jackson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Jian-Guo Zhang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Leila Varghese
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.,Ludwig Institute for Cancer Research and de Duve Institute, Brussels, Belgium
| | - Cody C Allison
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Marc Pellegrini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Gillian M Tannahill
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.,GSK Medicines Research Centre, Stevenage, UK
| | - Esme C Hatchell
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Tracy A Willson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Dina Stockwell
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Carolyn A de Graaf
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Janelle Collinge
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Adrienne Hilton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Natasha Silke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Sukhdeep K Spall
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Diep Chau
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.,CSL Limited, Parkville, VIC, 3052, Australia
| | - Vicki Athanasopoulos
- Department of Immunology and Infectious Disease and Centre for Personalised Immunology (NHMRC Centre for Research Excellence), John Curtin School of Medical Research, Australian National University, Canberra, Australia.,Centre for Personalised Immunology (CACPI), Shanghai Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Donald Metcalf
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Ronald M Laxer
- Division of Rheumatology, The Hospital for Sick Children and the University of Toronto, Toronto, ON, Canada
| | - Alexander G Bassuk
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA.,Department of Neurology, University of Iowa Carver College of Medicine and the Iowa Neuroscience Institute, Iowa City, IA, USA
| | - Benjamin W Darbro
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Maria A Fiatarone Singh
- Faculty of Health Sciences and Sydney Medical School, University of Sydney, Sydney, Australia
| | - Nicole Vlahovich
- Department of Sports Medicine, Australian Institute of Sport, Bruce, ACT, Australia
| | - David Hughes
- Department of Sports Medicine, Australian Institute of Sport, Bruce, ACT, Australia
| | - Maria Kozlovskaia
- Department of Sports Medicine, Australian Institute of Sport, Bruce, ACT, Australia.,Faculty of Health, University of Canberra, Canberra, Australia
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC, 3052, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Klaus Warnatz
- Department of Internal Medicine, Clinic for Rheumatology and Clinical Immunology, Medical Center -University of Freiburg, Faculty of Medicine, Freiburg, 79106, Germany.,Center for Chronic Immunodeficiency, Medical Center -University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Nils Venhoff
- Department of Internal Medicine, Clinic for Rheumatology and Clinical Immunology, Medical Center -University of Freiburg, Faculty of Medicine, Freiburg, 79106, Germany
| | - Jens Thiel
- Department of Internal Medicine, Clinic for Rheumatology and Clinical Immunology, Medical Center -University of Freiburg, Faculty of Medicine, Freiburg, 79106, Germany
| | - Christine Biben
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Stefan Blum
- Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - John Reveille
- Memorial Hermann Texas Medical Centre, Houston, TX, USA
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, 3052, Australia
| | - Carola G Vinuesa
- Department of Immunology and Infectious Disease and Centre for Personalised Immunology (NHMRC Centre for Research Excellence), John Curtin School of Medical Research, Australian National University, Canberra, Australia.,Centre for Personalised Immunology (CACPI), Shanghai Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Pamela McCombe
- The University of Queensland, UQ Centre for Clinical Research, Royal Brisbane & Women's Hospital, Brisbane, Australia
| | - Matthew A Brown
- Translational Genomics Group, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT) at Translational Research Institute, Brisbane, Australia.,NIHR Biomedical Research Centre, Kings College, London, UK
| | - Benjamin T Kile
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.,Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Catriona McLean
- Department of Anatomical Pathology, The Alfred Hospital, Prahran, VIC, 3181, Australia
| | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Seth L Masters
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Hiroyasu Nakano
- Department of Biochemistry, Toho University School of Medicine, Ota-ku, Tokyo, 143-8540, Japan
| | - Polly J Ferguson
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Warren S Alexander
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
| | - John Silke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
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66
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Skopelja-Gardner S, Colonna L, Hermanson P, Sun X, Tanaka L, Tai J, Nguyen Y, Snyder JM, Alpers CE, Hudkins KL, Salant DJ, Peng Y, Elkon KB. Complement Deficiencies Result in Surrogate Pathways of Complement Activation in Novel Polygenic Lupus-like Models of Kidney Injury. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:2627-2640. [PMID: 32238460 PMCID: PMC7365257 DOI: 10.4049/jimmunol.1901473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/15/2020] [Indexed: 12/27/2022]
Abstract
Lupus nephritis (LN) is a major contributor to morbidity and mortality in lupus patients, but the mechanisms of kidney damage remain unclear. In this study, we introduce, to our knowledge, novel models of LN designed to resemble the polygenic nature of human lupus by embodying three key genetic alterations: the Sle1 interval leading to anti-chromatin autoantibodies; Mfge8-/- , leading to defective clearance of apoptotic cells; and either C1q-/- or C3-/- , leading to low complement levels. We report that proliferative glomerulonephritis arose only in the presence of all three abnormalities (i.e., in Sle1.Mfge8 -/- C1q -/- and Sle1.Mfge8 -/- C3 -/- triple-mutant [TM] strains [C1q -/-TM and C3-/- TM, respectively]), with structural kidney changes resembling those in LN patients. Unexpectedly, both TM strains had significant increases in autoantibody titers, Ag spread, and IgG deposition in the kidneys. Despite the early complement component deficiencies, we observed assembly of the pathogenic terminal complement membrane attack complex in both TM strains. In C1q-/- TM mice, colocalization of MASP-2 and C3 in both the glomeruli and tubules indicated that the lectin pathway likely contributed to complement activation and tissue injury in this strain. Interestingly, enhanced thrombin activation in C3-/- TM mice and reduction of kidney injury following attenuation of thrombin generation by argatroban in a serum-transfer nephrotoxic model identified thrombin as a surrogate pathway for complement activation in C3-deficient mice. These novel mouse models of human lupus inform the requirements for nephritis and provide targets for intervention.
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Affiliation(s)
| | - Lucrezia Colonna
- Division of Rheumatology, University of Washington, Seattle, WA 98109
| | - Payton Hermanson
- Division of Rheumatology, University of Washington, Seattle, WA 98109
| | - Xizhang Sun
- Division of Rheumatology, University of Washington, Seattle, WA 98109
| | - Lena Tanaka
- Division of Rheumatology, University of Washington, Seattle, WA 98109
| | - Joyce Tai
- Division of Rheumatology, University of Washington, Seattle, WA 98109
| | - Yenly Nguyen
- Division of Rheumatology, University of Washington, Seattle, WA 98109
| | - Jessica M Snyder
- Department of Comparative Medicine, University of Washington, Seattle, WA 98109
| | - Charles E Alpers
- Department of Nephrology, University of Washington, Seattle, WA 98109
| | - Kelly L Hudkins
- Department of Nephrology, University of Washington, Seattle, WA 98109
| | - David J Salant
- Division of Nephrology, Boston University, Boston, MA 02215; and
| | - YuFeng Peng
- Division of Rheumatology, University of Washington, Seattle, WA 98109;
| | - Keith B Elkon
- Division of Rheumatology, University of Washington, Seattle, WA 98109;
- Department of Immunology, University of Washington, Seattle, WA 98109
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67
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Veiga N, Diesendruck Y, Peer D. Targeted lipid nanoparticles for RNA therapeutics and immunomodulation in leukocytes. Adv Drug Deliv Rev 2020; 159:364-376. [PMID: 32298783 DOI: 10.1016/j.addr.2020.04.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/27/2020] [Accepted: 04/10/2020] [Indexed: 12/25/2022]
Abstract
Abnormalities in leukocytes' function are associated with many immune related disorders, such as cancer, autoimmunity and susceptibility to infectious diseases. Recent developments in Genome-wide-association-studies give rise to new opportunities for novel therapeutics. RNA-based modalities, that allow a selective genetic manipulation in vivo, are powerful tools for personalized medicine, enabling downregulation or expression of relevant proteins. Yet, RNA-based therapeutics requires a delivery modality to facilitate the stability, uptake and intracellular release of the RNA molecules. The use of lipid nanoparticles as a drug delivery approach improves the payloads' stability, pharmacokinetics, bio-distribution and therapeutic benefit while reducing side effects. Moreover, a wide variety of targeting moieties allow a precise and modular manipulation of gene expression, together with the ability to identify and selectively affect disease-relevant leukocytes-subsets. Altogether, RNA-based therapeutics, targeting leukocytes subsets, is believed to be one of the most promising therapeutic concepts of the near future, addressing pressing issues in cancer and inflammation heterogeneity.
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68
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Gupta V, Kumar R, Sood U, Singhvi N. Reconciling Hygiene and Cleanliness: A New Perspective from Human Microbiome. Indian J Microbiol 2020; 60:37-44. [PMID: 32089572 PMCID: PMC7000587 DOI: 10.1007/s12088-019-00839-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/03/2019] [Indexed: 12/12/2022] Open
Abstract
The term hygiene is deeply rooted with the concept of maintaining sound health and alertness towards cleanliness, while "hygiene hypothesis" depicts the protective role of microbial community exposure in development of early immunity and initial allergic and aesthetic reactions. The tug-of-war has now been pushed toward the literal term "hygiene" over the "hygiene hypothesis" and has continued with disinfection of all microbial loads from the related environments to avoid infections in humans. With the advancement in the microbiome studies, it became clear that humans possess warm, and significant relationships with diverse microbial community. With this opinion article, we have emphasized on the importance of hygiene hypothesis in immunological responses. We also propose the individual/targeted hygiene instead of application of unanimous hygiene hypothesis. This review also elaborates the common practices that should be employed to maintain hygiene along with the balanced microbiome.
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Affiliation(s)
- Vipin Gupta
- PhiXGen Private Limited, Gurugram, Haryana 122001 India
- Department of Zoology, University of Delhi, Delhi, Delhi 110007 India
| | - Roshan Kumar
- P.G. Department of Zoology, Magadh University, Bodh-Gaya, Bihar 824231 India
| | - Utkarsh Sood
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003 India
| | - Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi, Delhi 110007 India
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Teh SH, You RI, Yang YC, Hsu CY, Pang CY. A cohort study: The Association Between Autoimmune Disorders and Leptospirosis. Sci Rep 2020; 10:3276. [PMID: 32094396 PMCID: PMC7039877 DOI: 10.1038/s41598-020-60267-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 02/10/2020] [Indexed: 11/17/2022] Open
Abstract
There are limited studies on the association between systemic autoimmune rheumatic diseases (SARDs) and leptospirosis. Therefore, this study aims to identify the effects of leptospirosis on the risks of developing SARDs with a nationwide retrospective cohort study. Patients with leptospirosis who did not have a diagnosis of SARDs before the index date were enrolled from the Taiwan National Health Insurance Research Database between 2000 and 2010, as the leptospirosis cohort. For each patient with leptospirosis, one control without a history of leptospirosis and SARDs was randomly selected (non-leptospirosis cohort). Cox proportional hazards regression models were used to analyze the risk of SARDs according to sex, age, and comorbidities. Among the 23 million people in the cohort, 3,393 patients with leptospirosis (68.91% men, mean age 52.65 years) and 33,930 controls were followed for 18,778 and 232,999 person-years, respectively. The incidence of SARDs was higher in the leptospirosis cohort than in the non-leptospirosis cohort (1.38 vs 0.33 per 1000 person-years), with a hazard ratio (HR) of 4.42 (95% confidence interval [CI] = 2.82–6.92). The risk of developing SARDs was highest for leptospirosis patients aged ≥65 years (HR = 2.81% CI = 1.07–7.36) compared with patients aged ≤39 years. Patients with leptospirosis have a 4.42-fold higher risk of SARDs than that in the general population. Further research is warranted to investigate the mechanism underlying this association.
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Affiliation(s)
- Soon-Hian Teh
- Division of Infectious Disease, Department of Internal Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Ren-In You
- Department of Laboratory Medicine and Biotechnology, College of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Yu-Cih Yang
- Management Office for Health Data, China Medical University Hospital, Taichung, Taiwan.,College of Medicine, China Medical University, Taichung, Taiwan
| | - Chung Y Hsu
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan
| | - Cheng-Yoong Pang
- Department of Medical Research, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan. .,Cardiovascular and Metabolomics Research Center, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan. .,Institute of Medical Sciences, College of Medicine, Tzu Chi University, Hualien, Taiwan.
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Anderson W, Thorpe J, Long SA, Rawlings DJ. Efficient CRISPR/Cas9 Disruption of Autoimmune-Associated Genes Reveals Key Signaling Programs in Primary Human T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 203:3166-3178. [PMID: 31722988 PMCID: PMC6904544 DOI: 10.4049/jimmunol.1900848] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/10/2019] [Indexed: 12/18/2022]
Abstract
Risk of autoimmunity is associated with multiple genetic variants. Genome-wide association studies have linked single-nucleotide polymorphisms in the phosphatases PTPN22 (rs2476601) and PTPN2 (rs1893217) to increased risk for multiple autoimmune diseases. Previous mouse studies of loss of function or risk variants in these genes revealed hyperactive T cell responses, whereas studies of human lymphocytes revealed contrasting phenotypes. To better understand this dichotomy, we established a robust gene editing platform to rapidly address the consequences of loss of function of candidate genes in primary human CD4+ T cells. Using CRISPR/Cas9, we obtained efficient gene disruption (>80%) of target genes encoding proteins involved in Ag and cytokine receptor signaling pathways including PTPN22 and PTPN2 Loss-of-function data in all genes studied correlated with previous data from mouse models. Further analyses of PTPN2 gene-disrupted T cells demonstrated dynamic effects, by which hyperactive IL-2R signaling promoted compensatory transcriptional events, eventually resulting in T cells that were hyporesponsive to IL-2. These results imply that altered phosphatase activity promotes evolving phenotypes based on Ag experience and/or other programming signals. This approach enables the discovery of molecular mechanisms modulating risk of autoimmunity that have been difficult to parse in traditional mouse models or cross-sectional human studies.
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Affiliation(s)
- Warren Anderson
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101
- Department of Pathology, University of Washington, Seattle, WA 98195
| | - Jerill Thorpe
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - S Alice Long
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - David J Rawlings
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101;
- Department of Pediatrics, University of Washington, Seattle, WA 98109; and
- Department of Immunology, University of Washington, Seattle, WA 98109
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Domínguez-Andrés J, Netea MG. Impact of Historic Migrations and Evolutionary Processes on Human Immunity. Trends Immunol 2019; 40:1105-1119. [PMID: 31786023 PMCID: PMC7106516 DOI: 10.1016/j.it.2019.10.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 10/04/2019] [Accepted: 10/09/2019] [Indexed: 12/30/2022]
Abstract
The evolution of mankind has constantly been influenced by the pathogens encountered. The various populations of modern humans that ventured out of Africa adapted to different environments and faced a large variety of infectious agents, resulting in local adaptations of the immune system for these populations. The functional variation of immune genes as a result of evolution is relevant in the responses against infection, as well as in the emergence of autoimmune and inflammatory diseases observed in modern populations. Understanding how host-pathogen interactions have influenced the human immune system from an evolutionary perspective might contribute to unveiling the causes behind different immune-mediated disorders and promote the development of new strategies to detect and control such diseases.
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Affiliation(s)
- Jorge Domínguez-Andrés
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Nijmegen Medical Centre, Geert Grooteplein 8, 6500HB Nijmegen, The Netherlands.
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Nijmegen Medical Centre, Geert Grooteplein 8, 6500HB Nijmegen, The Netherlands; Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany; Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania
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72
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Schurman SH, O'Hanlon TP, McGrath JA, Gruzdev A, Bektas A, Xu H, Garantziotis S, Zeldin DC, Miller FW. Transethnic associations among immune-mediated diseases and single-nucleotide polymorphisms of the aryl hydrocarbon response gene ARNT and the PTPN22 immune regulatory gene. J Autoimmun 2019; 107:102363. [PMID: 31759816 DOI: 10.1016/j.jaut.2019.102363] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Because immune responses are sensitive to environmental changes that drive selection of genetic variants, we hypothesized that polymorphisms of some xenobiotic response and immune response genes may be associated with specific types of immune-mediated diseases (IMD), while others may be associated with IMD as a larger category regardless of specific phenotype or ethnicity. OBJECTIVE To examine transethnic gene-IMD associations for single nucleotide polymorphism (SNP) frequencies of prototypic xenobiotic response genes-aryl hydrocarbon receptor (AHR), AHR nuclear translocator (ARNT), AHR repressor (AHRR) - and a prototypic immune response gene, protein tyrosine phosphatase, non-receptor type 22 (PTPN22), in subjects from the Environmental Polymorphisms Registry (EPR). METHODS Subjects (n = 3731) were genotyped for 14 SNPs associated with functional variants of the AHR, ARNT, AHRR, and PTPN22 genes, and their frequencies were compared among African Americans (n = 1562), Caucasians (n = 1838), and Hispanics (n = 331) with previously reported data. Of those genotyped, 2015 EPR subjects completed a Health and Exposure survey. SNPs were assessed via PLINK for associations with IMD, which included those with autoimmune diseases, allergic disorders, asthma, or idiopathic pulmonary fibrosis. Transethnic meta-analyses were performed using METAL and MANTRA approaches. RESULTS ARNT SNP rs11204735 was significantly associated with autoimmune disease by transethnic meta-analyses using METAL (odds ratio, OR [95% confidence interval] = 1.29 [1.08-1.55]) and MANTRA (ORs ranged from 1.29 to 1.30), whereas ARNT SNP rs1889740 showed a significant association with autoimmune disease by METAL (OR = 1.25 [1.06-1.47]). For Caucasian females, PTPN22 SNP rs2476601 was significantly associated with autoimmune disease by allelic association tests (OR = 1.99, [1.30-3.04]). In Caucasians and Caucasian males, PTPN22 SNP rs3811021 was significantly associated with IMD (OR = 1.39 [1.12-1.72] and 1.50 [1.12-2.02], respectively) and allergic disease (OR = 1.39 [1.12-1.71], and 1.62 [1.19-2.20], respectively). In the transethnic meta-analysis, PTPN22 SNP rs3811021 was significantly implicated in IMD by METAL (OR = 1.31 [1.10-1.56]), and both METAL and MANTRA suggested that rs3811021 was associated with IMD and allergic disease in males across all three ethnic groups (IMD METAL OR = 1.50 [1.15-1.95]; IMD MANTRA ORs ranged from 1.47 to 1.50; allergic disease METAL OR = 1.58 [1.20-2.08]; allergic disease MANTRA ORs ranged from 1.55 to 1.59). CONCLUSIONS Some xenobiotic and immune response gene polymorphisms were shown here, for the first time, to have associations across a broad spectrum of IMD and ethnicities. Our findings also suggest a role for ARNT in the development of autoimmune diseases, implicating environmental factors metabolized by this pathway in pathogenesis. Further studies are needed to confirm these data, assess the implications of these findings, define gene-environment interactions, and explore the mechanisms leading to these increasingly prevalent disorders.
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Affiliation(s)
- Shepherd H Schurman
- Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, USA; Research Triangle Park, NC, USA.
| | - Terrance P O'Hanlon
- Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, USA; Bethesda, MD, USA.
| | | | - Artiom Gruzdev
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
| | - Arsun Bektas
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
| | - Hong Xu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, MD, USA.
| | - Stavros Garantziotis
- Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, USA; Research Triangle Park, NC, USA.
| | - Darryl C Zeldin
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
| | - Frederick W Miller
- Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, USA; Research Triangle Park, NC, USA; Bethesda, MD, USA.
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Gomez-Lopera N, Alfaro JM, Leal SM, Pineda-Trujillo N. Type 1 diabetes loci display a variety of native American and African ancestries in diseased individuals from Northwest Colombia. World J Diabetes 2019; 10:534-545. [PMID: 31798789 PMCID: PMC6885725 DOI: 10.4239/wjd.v10.i11.534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) is a complex disease with a higher incidence in Europeans than other populations. The Colombians Living in Medellin (CLM) is admixed with ancestry contributions from Europeans, Native Americans (NAT) and Africans (AFR).
AIM Our aim was to analyze the genetic admixture component at candidate T1D loci in Colombian individuals with the disease.
METHODS Seventy-four ancestry informative markers (AIMs), which tagged 41 T1D candidate loci/genes, were tested by studying a cohort of 200 Northwest Colombia diseased individuals. T1D status was classified by testing for glutamic acid decarboxylase (GAD-65 kDa) and protein tyrosine-like antigen-2 auto-antibodies in serum samples. Candidate loci/genes included HLA, INS, PTPN22, CTLA4, IL2RA, SUMO4, CLEC16A, IFIH1, EFR3B, IL7R, NRP1 and RNASEH1, amongst others. The 1,000 genome database was used to analyze data from 94 individuals corresponding to the reference CLM. As the data did not comply with a normal distribution, medians were compared between groups using the Mann-Whitney U-test.
RESULTS Both T1D patients and individuals from CLM displayed mainly European ancestry (61.58 vs 62.06) followed by Native American (27.34 vs 27.46) and to a lesser extent the AFR ancestry (10.28 vs 10.65) components. However, compared to CLM, ancestry of T1D patients displayed a decrease of NAT ancestry at gene EFR3B (24.30 vs 37.10) and an increase at genes IFIH1 (32.07 vs 14.99) and IL7R (52.18 vs 39.18). Also, for gene NRP1 (36.67 vs 0.003), we observed a non-AFR contribution (attributed to NAT). Autoimmune patients (positive for any of two auto-antibodies) displayed lower NAT ancestry than idiopathic patients at the MHC region (20.36 vs 31.88). Also, late onset patients presented with greater AFR ancestry than early onset patients at gene IL7R (19.96 vs 6.17). An association analysis showed that, even after adjusting for admixture, an association exists for at least seven such AIMs, with the strongest findings on chromosomes 5 and 10 (gene IL7R, P = 5.56 × 10-6 and gene NRP1, P = 8.70 × 10-19, respectively).
CONCLUSION Although Colombian T1D patients have globally presented with higher European admixture, specific T1D loci have displayed varying levels of Native American and AFR ancestries in diseased individuals.
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Affiliation(s)
- Natalia Gomez-Lopera
- Grupo Mapeo Genetico, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín 050010470, Colombia
| | - Juan M Alfaro
- Grupo Mapeo Genetico, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín 050010470, Colombia
- Sección de Endocrinología Pediátrica, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín 050010470, Colombia
| | - Suzanne M Leal
- Center for Statistical Genetics, Columbia University, New York, NY 10032, United States
| | - Nicolas Pineda-Trujillo
- Grupo Mapeo Genetico, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín 050010470, Colombia
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de Mello CPP, Rumsey J, Slaughter V, Hickman JJ. A human-on-a-chip approach to tackling rare diseases. Drug Discov Today 2019; 24:2139-2151. [PMID: 31412288 PMCID: PMC6856435 DOI: 10.1016/j.drudis.2019.08.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/18/2019] [Accepted: 08/05/2019] [Indexed: 12/20/2022]
Abstract
Drug development for rare diseases, classified as diseases with a prevalence of < 200 000 patients, is limited by the high cost of research and low target population. Owing to a lack of representative disease models, research has been challenging for orphan drugs. Human-on-a-chip (HoaC) technology, which models human tissues in interconnected in vitro microfluidic devices, has the potential to lower the cost of preclinical studies and increase the rate of drug approval by introducing human phenotypic models early in the drug discovery process. Advances in HoaC technology can drive a new approach to rare disease research and orphan drug development.
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Affiliation(s)
| | | | - Victoria Slaughter
- NanoScience Technology Center, University of Central Florida, Orlando, FL 32826, USA
| | - James J Hickman
- NanoScience Technology Center, University of Central Florida, Orlando, FL 32826, USA; Hesperos, Inc., Orlando, FL 32826, USA.
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Ely ZA, Moon JM, Sliwoski GR, Sangha AK, Shen XX, Labella AL, Meiler J, Capra JA, Rokas A. The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins. Genome Biol Evol 2019; 11:2574-2592. [PMID: 31504490 PMCID: PMC6751361 DOI: 10.1093/gbe/evz183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2019] [Indexed: 01/03/2023] Open
Abstract
Immunity genes have repeatedly experienced natural selection during mammalian evolution. Galectins are carbohydrate-binding proteins that regulate diverse immune responses, including maternal-fetal immune tolerance in placental pregnancy. Seven human galectins, four conserved across vertebrates and three specific to primates, are involved in placental development. To comprehensively study the molecular evolution of these galectins, both across mammals and within humans, we conducted a series of between- and within-species evolutionary analyses. By examining patterns of sequence evolution between species, we found that primate-specific galectins showed uniformly high substitution rates, whereas two of the four other galectins experienced accelerated evolution in primates. By examining human population genomic variation, we found that galectin genes and variants, including variants previously linked to immune diseases, showed signatures of recent positive selection in specific human populations. By examining one nonsynonymous variant in Galectin-8 previously associated with autoimmune diseases, we further discovered that it is tightly linked to three other nonsynonymous variants; surprisingly, the global frequency of this four-variant haplotype is ∼50%. To begin understanding the impact of this major haplotype on Galectin-8 protein structure, we modeled its 3D protein structure and found that it differed substantially from the reference protein structure. These results suggest that placentally expressed galectins experienced both ancient and more recent selection in a lineage- and population-specific manner. Furthermore, our discovery that the major Galectin-8 haplotype is structurally distinct from and more commonly found than the reference haplotype illustrates the significance of understanding the evolutionary processes that sculpted variants associated with human genetic disease.
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Affiliation(s)
- Zackery A Ely
- Department of Biological Sciences, Vanderbilt University
| | - Jiyun M Moon
- Department of Biological Sciences, Vanderbilt University
| | | | - Amandeep K Sangha
- Department of Chemistry, Vanderbilt University
- Center for Structural Biology, Vanderbilt University
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University
| | | | - Jens Meiler
- Department of Chemistry, Vanderbilt University
- Center for Structural Biology, Vanderbilt University
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University
- Department of Biomedical Informatics, Vanderbilt University School of Medicine
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University
- Department of Biomedical Informatics, Vanderbilt University School of Medicine
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Wang MH, Friton JJ, Raffals LE, Leighton JA, Pasha SF, Picco MF, Cushing KC, Monroe K, Nix BD, Newberry RD, Faubion WA. Novel Genetic Risk Variants Can Predict Anti-TNF Agent Response in Patients With Inflammatory Bowel Disease. J Crohns Colitis 2019; 13:1036-1043. [PMID: 30689765 PMCID: PMC7185197 DOI: 10.1093/ecco-jcc/jjz017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 12/16/2018] [Accepted: 01/20/2019] [Indexed: 02/08/2023]
Abstract
BACKGROUND It is important to identify patients with inflammatory bowel disease [IBD] refractory to anti-tumour necrosis factor [TNF] therapy, to avoid potential adverse effects and to adopt different treatment strategies. We aimed to identify and validate clinical and genetic factors to predict anti-TNF response in patients with IBD. MATERIALS AND METHODS Mayo Clinic and Washington University IBD genetic association study cohorts were used as discovery and replicate datasets, respectively. Clinical factors included sex, age at diagnosis, disease duration and phenotype, disease location, bowel resection, tobacco use, family history of IBD, extraintestinal manifestations, and response to anti-TNF therapy. RESULTS Of 474 patients with IBD treated with anti-TNF therapy, 41 [8.7%] were refractory to therapy and 433 [91.3%] had response. Multivariate analysis showed history of immunomodulator use (odds ratio 10.2, p = 8.73E-4) and bowel resection (odds ratio 3.24, p = 4.38E-4) were associated with refractory response to anti-TNF agents. Among genetic loci, two [rs116724455 in TNFSF4/18, rs2228416 in PLIN2] were successfully replicated and another four [rs762787, rs9572250, rs144256942, rs523781] with suggestive evidence were found. An exploratory risk model predictability [area under the curve] increased from 0.72 [clinical predictors] to 0.89 after adding genetic predictors. Through identified clinical and genetic predictors, we constructed a preliminary anti-TNF refractory score to differentiate anti-TNF non-responders (mean [standard deviation] score, 5.49 [0.99]) from responders (2.65 [0.39]; p = 4.33E-23). CONCLUSIONS Novel and validated genetic loci, including variants in TNFSF, were found associated with anti-TNF response in patients with IBD. Future validation of the exploratory risk model in a large prospective cohort is warranted.
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Affiliation(s)
- Ming-Hsi Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA,Corresponding author: Ming-Hsi Wang, MD, PhD, Division of Gastroenterology and Hepatology, Mayo Clinic, 4500 San Pablo Rd, Jacksonville, FL 32224, USA. Tel.: 904-953-6970; fax: 904-953-6225;
| | - Jessica J Friton
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Laura E Raffals
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Jonathan A Leighton
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, AZ, USA
| | - Shabana F Pasha
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, AZ, USA
| | - Michael F Picco
- Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Kelly C Cushing
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Division of Gastroenterology, Washington University School of Medicine, St. Louis, MI, USA
| | - Kelly Monroe
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, MI, USA
| | - Billy D Nix
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, MI, USA
| | - Rodney D Newberry
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, MI, USA
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
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Kostev K, Madelung M. Prescription-based prevalence of biological therapy in patients with psoriasis, rheumatoid arthritis, and inflammatory bowel diseases. Biologicals 2019; 61:52-54. [PMID: 31327630 DOI: 10.1016/j.biologicals.2019.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/08/2019] [Accepted: 07/12/2019] [Indexed: 12/28/2022] Open
Abstract
The aim of this study was to determine the proportion of biological prescriptions over time. This study is based on data from IMS® Diagnosis Monitor and included patients who had received a biological drug in dermatology practices due to psoriasis (PSO), gastroenterology practices due to Crohn's disease (CD) or ulcerative colitis (UC), or rheumatology practices due to rheumatoid arthritis (RA) between April 2015 and December 2018. We analyzed 1,748,948 CD/UC-related prescriptions, 3,968,879 RA-related prescriptions, and 7,321,496 PSO-related prescriptions. Of these, 343,263 (19.6%) prescriptions for IBD, 92,343 (16.2%) prescriptions for RA, and 169,573 (6.9%) prescriptions for PSO were for biologicals. The proportion of biologicals has increased continuously over 4 years, namely from 16.3% to 21.3% (p < 0.01) for CD/UC treatment prescribed by gastroenterologists, from 12.4% to 16.0% (p < 0.01) for RA treatment prescribed by rheumatologists, and from 3.2% to 7.7% (p < 0.01) for PSO treatment prescribed by dermatologists. The proportions of biological therapies and their increase over time were age- and sex-dependent. In summary, we were able to show a significant increase in the proportion of biologicals used to treat CD/UC, RA, and PSO over the last four years.
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Natri H, Garcia AR, Buetow KH, Trumble BC, Wilson MA. The Pregnancy Pickle: Evolved Immune Compensation Due to Pregnancy Underlies Sex Differences in Human Diseases. Trends Genet 2019; 35:478-488. [PMID: 31200807 PMCID: PMC6611699 DOI: 10.1016/j.tig.2019.04.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 01/16/2023]
Abstract
We hypothesize that, ancestrally, sex-specific immune modulation evolved to facilitate survival of the pregnant person in the presence of an invasive placenta and an immunologically challenging pregnancy - an idea we term the 'pregnancy compensation hypothesis' (PCH). Further, we propose that sex differences in immune function are mediated, at least in part, by the evolution of gene content and dosage on the sex chromosomes, and are regulated by reproductive hormones. Finally, we propose that changes in reproductive ecology in industrialized environments exacerbate these evolved sex differences, resulting in the increasing risk of autoimmune disease observed in females, and a counteracting reduction in diseases such as cancer that can be combated by heightened immune surveillance. The PCH generates a series of expectations that can be tested empirically and that may help to identify the mechanisms underlying sex differences in modern human diseases.
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Affiliation(s)
- Heini Natri
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
| | - Angela R Garcia
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
| | - Kenneth H Buetow
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
| | - Benjamin C Trumble
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA; School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA.
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Urnikyte A, Flores-Bello A, Mondal M, Molyte A, Comas D, Calafell F, Bosch E, Kučinskas V. Patterns of genetic structure and adaptive positive selection in the Lithuanian population from high-density SNP data. Sci Rep 2019; 9:9163. [PMID: 31235771 PMCID: PMC6591479 DOI: 10.1038/s41598-019-45746-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/14/2019] [Indexed: 12/16/2022] Open
Abstract
The analysis of geographically specific regions and the characterization of fine-scale patterns of genetic diversity may facilitate a much better understanding of the microevolutionary processes affecting local human populations. Here we generated genome-wide high-density SNP genotype data in 425 individuals from six geographical regions in Lithuania and combined our dataset with available ancient and modern data to explore genetic population structure, ancestry components and signatures of natural positive selection in the Lithuanian population. Our results show that Lithuanians are a homogenous population, genetically differentiated from neighbouring populations but within the general expected European context. Moreover, we not only confirm that Lithuanians preserve one of the highest proportions of western, Scandinavian and eastern hunter-gather ancestry components found in European populations but also that of an steppe Early to Middle Bronze Age pastoralists, which together configure the genetic distinctiveness of the Lithuanian population. Finally, among the top signatures of positive selection detected in Lithuanians, we identified several candidate genes related with diet (PNLIP, PPARD), pigmentation (SLC24A5, TYRP1 and PPARD) and the immune response (BRD2, HLA-DOA, IL26 and IL22).
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Affiliation(s)
- A Urnikyte
- Department of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661, Vilnius, Lithuania
| | - A Flores-Bello
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - M Mondal
- Institute of Genomics, University of Tartu, Riia 23b, Tartu, 51010 Tartu, Estonia
| | - A Molyte
- Department of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661, Vilnius, Lithuania
| | - D Comas
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - F Calafell
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - E Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain.
| | - V Kučinskas
- Department of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661, Vilnius, Lithuania.
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Kaur T, Thakur K, Singh J, Arora S, Kaur M. Genotypic-Phenotypic Screening of Galectin-3 in Relation to Risk Towards Rheumatoid Arthritis. Arch Med Res 2019; 50:214-224. [DOI: 10.1016/j.arcmed.2019.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/06/2019] [Accepted: 07/25/2019] [Indexed: 12/12/2022]
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82
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Frias MA, Virzi J, Batuca J, Pagano S, Satta N, Delgado Alves J, Vuilleumier N. ELISA methods comparison for the detection of auto-antibodies against apolipoprotein A1. J Immunol Methods 2019; 469:33-41. [PMID: 30926534 DOI: 10.1016/j.jim.2019.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/25/2019] [Accepted: 03/25/2019] [Indexed: 01/20/2023]
Abstract
BACKGROUND Autoantibodies against apolipoprotein A1 (anti-apoA1 IgG) have emerged as an independent biomarker for cardiovascular disease and mortality. Across studies, different ELISA methods have been used to measure the level of circulating anti-apoA1 IgG which could lead to substantial result differences between assays. OBJECTIVES To make a comparative study of available anti-apoA1 IgG detection methods and to determine whether the choice of matrix sample (serum vs plasma) could influence the results. METHODS Blood samples were obtained from 160 healthy blood donors and collected on 4 different matrixes (serum, plasma-EDTA, -citrate, -lithium-heparinate). Anti-apoA1 IgG was measured using two homemade (Geneva's and Lisbon's) and one commercial ELISA kits. Passing-Bablok and Bland-Altman were used to compare the results. Anti-apoA1 IgG seropositivity cut-offs were defined according to the user's/manufacturer's criterion. RESULTS The current results showed substantial differences between those 3 assays. The dynamic ranges were significantly different, the commercial kit displaying the narrowest one. Passing-Bablok analysis demonstrated important proportional and constant biases between assays. The anti-apoA1 IgG seropositivity rate in Geneva, Lisbon and commercial assays varied between 24.5% and 1.9%. Matrix comparisons demonstrated that the matrix choice (plasma versus serum) influenced anti-apoA1 IgG results as well as the seropositivity rate in an assay-dependent manner. The coating antigen source was identified as important factor underlying results heterogeneity across assays. CONCLUSIONS These results highlight the impact of the method and the cut-off used on anti-apoA1 IgG results and emphasize the need of standardizing existing assays. Given the important matrix influence, we suggest to use serum as matrix of choice.
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Affiliation(s)
- Miguel A Frias
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland; Department of Medical Specialties, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, 1205 Geneva, Switzerland.
| | - Julien Virzi
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland; Department of Medical Specialties, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, 1205 Geneva, Switzerland
| | - Joana Batuca
- CEDOC, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Sabrina Pagano
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland; Department of Medical Specialties, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, 1205 Geneva, Switzerland
| | - Natahlie Satta
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland; Department of Medical Specialties, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, 1205 Geneva, Switzerland
| | - Jose Delgado Alves
- CEDOC, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal; Department of Medicine IV/Immune-mediated Systemic Diseases Unit, Fernando Fonseca Hospital, Amadora, Portugal
| | - Nicolas Vuilleumier
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland; Department of Medical Specialties, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, 1205 Geneva, Switzerland
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83
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Putlyaeva LV, Demin DE, Korneev KV, Kasyanov AS, Tatosyan KA, Kulakovskiy IV, Kuprash DV, Schwartz AM. Potential Markers of Autoimmune Diseases, Alleles rs115662534(T) and rs548231435(C), Disrupt the Binding of Transcription Factors STAT1 and EBF1 to the Regulatory Elements of Human CD40 Gene. BIOCHEMISTRY (MOSCOW) 2019; 83:1534-1542. [PMID: 30878028 DOI: 10.1134/s0006297918120118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
CD40 receptor is expressed on B lymphocytes and other professional antigen-presenting cells. The binding of CD40 to its ligand CD154 on the surface of T helper cells plays an important role in the activation of B lymphocytes required for production of antibodies, in particular, against autoantigens. Association of several single nucleotide polymorphisms (SNPs) located in the non-coding areas of human CD40 locus with the elevated risk of autoimmune diseases has been demonstrated. The most studied of these SNPs is rs4810485 located in the first intron of the CD40 gene. Expression of the CD40 gene in B lymphocytes of donors homozygous for the common allelic variant of this polymorphism (G) is higher than in B cells from donors carrying the minor (T) variant. We investigated the enhancer activity of this fragment of the CD40 locus in human B cell lines and showed that it is independent on the rs4810485 alleles. However, the minor allelic variants of the rs4810485-linked SNPs rs548231435 and rs115662534 were associated with a significant decrease in the activity of the CD40 promoter due to the impairments in the binding of EBF1 and STAT1 transcription factors, respectively.
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Affiliation(s)
- L V Putlyaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - D E Demin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,Moscow Institute of Physics and Technology, Department of Molecular and Biological Physics, Dolgoprudny, Moscow Region, 141701, Russia
| | - K V Korneev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - A S Kasyanov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - K A Tatosyan
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - I V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia.,Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - D V Kuprash
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia. .,Moscow Institute of Physics and Technology, Department of Molecular and Biological Physics, Dolgoprudny, Moscow Region, 141701, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - A M Schwartz
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia. .,Moscow Institute of Physics and Technology, Department of Molecular and Biological Physics, Dolgoprudny, Moscow Region, 141701, Russia
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84
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Di Marco M, Ramassone A, Pagotto S, Anastasiadou E, Veronese A, Visone R. MicroRNAs in Autoimmunity and Hematological Malignancies. Int J Mol Sci 2018; 19:ijms19103139. [PMID: 30322050 PMCID: PMC6213554 DOI: 10.3390/ijms19103139] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/02/2018] [Indexed: 12/13/2022] Open
Abstract
Autoimmunity and hematological malignancies are often concomitant in patients. A causal bidirectional relationship exists between them. Loss of immunological tolerance with inappropriate activation of the immune system, likely due to environmental and genetic factors, can represent a breeding ground for the appearance of cancer cells and, on the other hand, blood cancers are characterized by imbalanced immune cell subsets that could support the development of the autoimmune clone. Considerable effort has been made for understanding the proteins that have a relevant role in both processes; however, literature advances demonstrate that microRNAs (miRNAs) surface as the epigenetic regulators of those proteins and control networks linked to both autoimmunity and hematological malignancies. Here we review the most up-to-date findings regarding the miRNA-based molecular mechanisms that underpin autoimmunity and hematological malignancies.
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Affiliation(s)
- Mirco Di Marco
- Ageing Research Center and Translational medicine-CeSI-MeT, 66100 Chieti, Italy.
- Department of Medical, Oral and Biotechnological Sciences (DSMOB), "G. d'Annunzio" University Chieti-Pescara, 66100 Chieti, Italy.
| | - Alice Ramassone
- Ageing Research Center and Translational medicine-CeSI-MeT, 66100 Chieti, Italy.
- Department of Medical, Oral and Biotechnological Sciences (DSMOB), "G. d'Annunzio" University Chieti-Pescara, 66100 Chieti, Italy.
| | - Sara Pagotto
- Ageing Research Center and Translational medicine-CeSI-MeT, 66100 Chieti, Italy.
- Department of Medical, Oral and Biotechnological Sciences (DSMOB), "G. d'Annunzio" University Chieti-Pescara, 66100 Chieti, Italy.
| | - Eleni Anastasiadou
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
| | - Angelo Veronese
- Ageing Research Center and Translational medicine-CeSI-MeT, 66100 Chieti, Italy.
- Department of Medicine and Aging Science (DMSI), "G. d'Annunzio" University Chieti-Pescara, 66100 Chieti, Italy.
| | - Rosa Visone
- Ageing Research Center and Translational medicine-CeSI-MeT, 66100 Chieti, Italy.
- Department of Medical, Oral and Biotechnological Sciences (DSMOB), "G. d'Annunzio" University Chieti-Pescara, 66100 Chieti, Italy.
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85
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Fu Y, Tessneer KL, Li C, Gaffney PM. From association to mechanism in complex disease genetics: the role of the 3D genome. Arthritis Res Ther 2018; 20:216. [PMID: 30268153 PMCID: PMC6162955 DOI: 10.1186/s13075-018-1721-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Genome-wide association studies (GWAS) and fine mapping studies in autoimmune diseases have identified thousands of genetic variants, the majority of which are located in non-protein-coding enhancer regions. Enhancers function within the context of the three-dimensional (3D) genome to form long-range DNA looping events with target gene promoters that spatially and temporally regulate gene expression. Investigating the functional significance of GWAS variants in the context of the 3D genome is essential for mechanistic understanding of these variants and how they influence disease pathology by altering DNA looping between enhancers and the target gene promoters they regulate. In this review, we discuss the functional complexity of the 3D genome and the technological approaches used to characterize DNA looping events. We then highlight examples from the literature that illustrate how functional mapping of the 3D genome can assist in defining mechanisms that influence pathogenic gene expression. We conclude by highlighting future advances necessary to fully integrate 3D genome analyses into the functional workup of GWAS variants in the continuing effort to improve the health of patients with autoimmune diseases.
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Affiliation(s)
- Yao Fu
- Division of Genomics and Data Sciences, Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK 73104 USA
| | - Kandice L Tessneer
- Division of Genomics and Data Sciences, Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK 73104 USA
| | - Chuang Li
- School of Electrical and Computer Engineering, University of Oklahoma, Devan Energy Hall 150, 110 West Boyd Street, Norman, OK 73019 USA
| | - Patrick M Gaffney
- Division of Genomics and Data Sciences, Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK 73104 USA
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86
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Abstract
Animal models have been tremendously useful to translational research, but there is a need to maximize their predictive value to human disease. This Comment proposes novel strategies that consider evolutionary history and the presence, absence or modification of molecular networks in one species that are being studied in the other.
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Affiliation(s)
- Peter B Ernst
- Center for Veterinary Sciences and Comparative Medicine, Department of Pathology, University of California San Diego, La Jolla, CA, USA.
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA.
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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87
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Abstract
Human genetic diversity is the result of population genetic forces. This genetic variation influences disease risk and contributes to health disparities. Natural selection is an important influence on human genetic variation. Because immune and inflammatory function genes are enriched for signals of positive selection, the prevalence of rheumatic disease-risk alleles seen in different populations is partially the result of differing selective pressures (eg, due to pathogens). This review summarizes the genetic regions associated with susceptibility to different rheumatic diseases and concomitant evidence for natural selection, including known agents of selection exerting selective pressure in these regions.
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Affiliation(s)
- Paula S Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, 96 Jonathan Lucas Street, Suite 816, Charleston, SC 29425, USA; Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA.
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88
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Nesic MJ, Maric NP. Population-based differences in immune system response contribute to an increased risk of schizophrenia in African migrants? Rev Neurosci 2018; 29:347-353. [PMID: 29150991 DOI: 10.1515/revneuro-2017-0037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/05/2017] [Indexed: 11/15/2022]
Abstract
Among the highest incidences of schizophrenia is the one documented in second-generation migrants of African descent in the Western countries. Interestingly, people of African and European ancestry demonstrate significant genetic-based differences in immune system regulation and response. As a result, the pro-inflammatory phenotype is more pronounced in people of African descent than it is in Europeans. At the same time, the role of the immune system in the etiology of schizophrenia is gaining increased recognition. Here, we propose that the population-specific genetic variation within the immune system interacts with unfavourable environments to contribute to a higher risk of schizophrenia in people of African ancestry. Our hypothesis is supported by recent findings from two separate fields of research-population genetics and psychoneuroimmunology. Moreover, we highlight the need to include African populations in genetic studies of schizophrenia.
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Affiliation(s)
- Milica J Nesic
- Clinic for Psychiatry, Clinical Centre of Serbia, Pasterova 2, 11000 Belgrade, Serbia
| | - Nadja P Maric
- Clinic for Psychiatry, Clinical Centre of Serbia, Pasterova 2, 11000 Belgrade, Serbia
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89
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Autoimmune-Disease-Prone NOD Mice Help To Reveal a New Genetic Locus for Reducing Pulmonary Disease Caused by Mycoplasma pulmonis. Infect Immun 2018; 86:IAI.00812-17. [PMID: 29263105 DOI: 10.1128/iai.00812-17] [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: 11/10/2017] [Accepted: 12/07/2017] [Indexed: 11/20/2022] Open
Abstract
Mycoplasmas are bacterial pathogens of a range of animals, including humans, and are a common cause of respiratory disease. However, the host genetic factors that affect resistance to infection or regulate the resulting pulmonary inflammation are not well defined. We and others have previously demonstrated that nonobese diabetic (NOD) mice can be used to investigate disease loci that affect bacterial infection and autoimmune diabetes. Here we show that NOD mice are more susceptible than C57BL/6 (B6) mice to infection with Mycoplasma pulmonis, a natural model of pulmonary mycoplasmosis. The lungs of infected NOD mice had higher loads of M. pulmonis and more severe inflammatory lesions. Moreover, congenic NOD mice that harbored different B6-derived chromosomal intervals enabled identification and localization of a new mycoplasmosis locus, termed Mpr2, on chromosome 13. These congenic NOD mice demonstrated that the B6 allele for Mpr2 reduced the severity of pulmonary inflammation caused by infection with M. pulmonis and that this was associated with altered cytokine and chemokine concentrations in the infected lungs. Mpr2 also colocalizes to the same genomic interval as Listr2 and Idd14, genetic loci linked to listeriosis resistance and autoimmune diabetes susceptibility, respectively, suggesting that allelic variation within these loci may affect the development of both infectious and autoimmune disease.
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90
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Abstract
Genetic investigations of fibrotic diseases, including those of late onset, often yield unanticipated insights into disease pathogenesis. This Review focuses on pathways underlying lung fibrosis that are generalizable to other organs. Herein, we discuss genetic variants subdivided into those that shorten telomeres, activate the DNA damage response, change resident protein expression or function, or affect organelle activity. Genetic studies provide a window into the downstream cascade of maladaptive responses and pathways that lead to tissue fibrosis. In addition, these studies reveal interactions between genetic variants, environmental factors, and age that influence the phenotypic spectrum of disease. The discovery of forces counterbalancing inherited risk alleles identifies potential therapeutic targets, thus providing hope for future prevention or reversal of fibrosis.
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91
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Vertebrate food products as a potential source of prion-like α-synuclein. NPJ PARKINSONS DISEASE 2017; 3:33. [PMID: 29184902 PMCID: PMC5701169 DOI: 10.1038/s41531-017-0035-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/27/2017] [Accepted: 11/02/2017] [Indexed: 02/08/2023]
Abstract
The aberrant aggregation of the protein α-synuclein is thought to be involved in Parkinson’s disease (PD). However, the factors that lead to initiation and propagation of α-synuclein aggregation are not clearly understood. Recently, the hypothesis that α-synuclein aggregation spreads via a prion-like mechanism originating in the gut has gained much scientific attention. If α-synuclein spreads via a prion-like mechanism, then an important question becomes, what are the origins of this prion-like species? Here we review the possibility that α-synuclein aggregation could be seeded via the ingestion of a prion-like α-synuclein species contained within food products originating from vertebrates. To do this, we highlight current evidence for the gut-to-brain hypothesis of PD, and put this in context of available routes of α-synuclein prion infectivity via the gastrointestinal (GI) tract. We then discuss meat as a ready exogenous source of α-synuclein and how certain risk factors, including inflammation, may allow for dietary α-synuclein to pass from the GI lumen into the host to induce pathology. Lastly, we review epidemiological evidence that dietary factors may be involved in PD. Overall, research to date has yet to directly test the contribution of dietary α-synuclein to the mechanism of initiation and progression of the disease. However, numerous experimental findings, including the potent seeding and spreading behavior of α-synuclein fibrils, seem to support, at least in part, the feasibility of an infection with a prion α-synuclein particle via the GI tract. Further studies are required to determine whether dietary α-synuclein contributes to seeding pathology in the gut.
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92
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Arakelyan A, Nersisyan L, Poghosyan D, Khondkaryan L, Hakobyan A, Löffler-Wirth H, Melanitou E, Binder H. Autoimmunity and autoinflammation: A systems view on signaling pathway dysregulation profiles. PLoS One 2017; 12:e0187572. [PMID: 29099860 PMCID: PMC5669448 DOI: 10.1371/journal.pone.0187572] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/23/2017] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION Autoinflammatory and autoimmune disorders are characterized by aberrant changes in innate and adaptive immunity that may lead from an initial inflammatory state to an organ specific damage. These disorders possess heterogeneity in terms of affected organs and clinical phenotypes. However, despite the differences in etiology and phenotypic variations, they share genetic associations, treatment responses and clinical manifestations. The mechanisms involved in their initiation and development remain poorly understood, however the existence of some clear similarities between autoimmune and autoinflammatory disorders indicates variable degrees of interaction between immune-related mechanisms. METHODS Our study aims at contributing to a holistic, pathway-centered view on the inflammatory condition of autoimmune and autoinflammatory diseases. We have evaluated similarities and specificities of pathway activity changes in twelve autoimmune and autoinflammatory disorders by performing meta-analysis of publicly available gene expression datasets generated from peripheral blood mononuclear cells, using a bioinformatics pipeline that integrates Self Organizing Maps and Pathway Signal Flow algorithms along with KEGG pathway topologies. RESULTS AND CONCLUSIONS The results reveal that clinically divergent disease groups share common pathway perturbation profiles. We identified pathways, similarly perturbed in all the studied diseases, such as PI3K-Akt, Toll-like receptor, and NF-kappa B signaling, that serve as integrators of signals guiding immune cell polarization, migration, growth, survival and differentiation. Further, two clusters of diseases were identified based on specifically dysregulated pathways: one gathering mostly autoimmune and the other mainly autoinflammatory diseases. Cluster separation was driven not only by apparent involvement of pathways implicated in adaptive immunity in one case, and inflammation in the other, but also by processes not explicitly related to immune response, but rather representing various events related to the formation of specific pathophysiological environment. Thus, our data suggest that while all of the studied diseases are affected by activation of common inflammatory processes, disease-specific variations in their relative balance are also identified.
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Affiliation(s)
- Arsen Arakelyan
- Bioinformatics Group, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, Armenia
- Department of Bioinformatics and Bioengineering, Russian-Armenian University, Yerevan, Armenia
| | - Lilit Nersisyan
- Bioinformatics Group, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, Armenia
- Zaven and Sonia Akian College of Science and Engineering, American University of Armenia, Yerevan, Armenia
| | - David Poghosyan
- Group of Immune Response Regulation, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, Armenia
| | - Lusine Khondkaryan
- Group of Immune Response Regulation, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, Armenia
| | - Anna Hakobyan
- Bioinformatics Group, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, Armenia
| | - Henry Löffler-Wirth
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Evie Melanitou
- Department of Parasitology and Insect Vectors, Institut Pasteur, Paris, France
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany
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93
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Tavakolpour S. Towards personalized medicine for patients with autoimmune diseases: Opportunities and challenges. Immunol Lett 2017; 190:130-138. [DOI: 10.1016/j.imlet.2017.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 08/03/2017] [Indexed: 02/06/2023]
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94
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Genome-Wide Analysis of Genetic Risk Factors for Rheumatic Heart Disease in Aboriginal Australians Provides Support for Pathogenic Molecular Mimicry. J Infect Dis 2017; 216:1460-1470. [DOI: 10.1093/infdis/jix497] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/20/2017] [Indexed: 12/20/2022] Open
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95
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Gallo A, Vukic D, Michalík D, O’Connell MA, Keegan LP. ADAR RNA editing in human disease; more to it than meets the I. Hum Genet 2017; 136:1265-1278. [DOI: 10.1007/s00439-017-1837-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/22/2017] [Indexed: 01/08/2023]
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96
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Ugalde-Morales E, Li J, Humphreys K, Ludvigsson JF, Yang H, Hall P, Czene K. Common shared genetic variation behind decreased risk of breast cancer in celiac disease. Sci Rep 2017; 7:5942. [PMID: 28725034 PMCID: PMC5517429 DOI: 10.1038/s41598-017-06287-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 06/09/2017] [Indexed: 02/06/2023] Open
Abstract
There is epidemiologic evidence showing that women with celiac disease have reduced risk of later developing breast cancer, however, the etiology of this association is unclear. Here, we assess the extent of genetic overlap between the two diseases. Through analyses of summary statistics on densely genotyped immunogenic regions, we show a significant genetic correlation (r = −0.17, s.e. 0.05, P < 0.001) and overlap (Ppermuted < 0.001) between celiac disease and breast cancer. Using individual-level genotype data from a Swedish cohort, we find higher genetic susceptibility to celiac disease summarized by polygenic risk scores to be associated with lower breast cancer risk (ORper-SD, 0.94, 95% CI 0.91 to 0.98). Common single nucleotide polymorphisms between the two diseases, with low P-values (PCD < 1.00E-05, PBC ≤ 0.05), mapped onto genes enriched for immunoregulatory and apoptotic processes. Our results suggest that the link between breast cancer and celiac disease is due to a shared polygenic variation of immune related regions, uncovering pathways which might be important for their development.
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Affiliation(s)
- Emilio Ugalde-Morales
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - Jingmei Li
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Human Genetics, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jonas F Ludvigsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatrics, Örebro University Hospital, Örebro, Sweden
| | - Haomin Yang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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97
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Danila MI, Laufer VA, Reynolds RJ, Yan Q, Liu N, Gregersen PK, Lee A, Kern M, Langefeld CD, Arnett DK, Bridges SL. Dense Genotyping of Immune-Related Regions Identifies Loci for Rheumatoid Arthritis Risk and Damage in African Americans. Mol Med 2017; 23:177-187. [PMID: 28681901 DOI: 10.2119/molmed.2017.00081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 06/19/2017] [Indexed: 12/29/2022] Open
Abstract
Over 100 risk loci for rheumatoid arthritis (RA) have been identified in individuals of European and Asian descent, but the genetic basis for RA in African Americans is less well understood. We genotyped 610 African Americans with autoantibody positive RA and 933 African American controls on the ImmunoChip (iChip) array. Using multivariable regression we evaluated the association between iChip markers and the risk of RA and radiographic severity. The single nucleotide polymorphism (SNP) rs1964995 (OR = 1.97, p = 1.28 × 10-15) near HLA-DRB1 was the most strongly associated risk SNP for RA susceptibility; SNPs in AFF3, TNFSF11, and TNFSF18 loci were suggestively associated (10-4 < p < 3.1 × 10-6). Trans-ethnic fine mapping of AFF3 identified a 90% credible set containing previously studied variants including rs9653442, rs7608424, and rs6712515 as well as the novel candidate variant rs11681966; several of these likely influence AFF3 gene expression level. Variants in TNFRSF9, CTLA4, IL2RA, C5/TRAF1, and ETS1 - but no variants within the major histocompatibility complex - were associated with RA radiographic severity. Conditional regression and pairwise linkage disequilibrium (LD) analyses suggest that additional pathogenic variants may be found in ETS1 and IL2RA beyond those found in other ethnicities. In summary, we use the dense genotyping of the iChip array and unique LD structure of African Americans to validate known risk loci for RA susceptibility and radiographic severity, and to better characterize the associations of AFF3, ETS1, and IL2RA.
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Affiliation(s)
- Maria I Danila
- University of Alabama at Birmingham, Division of Clinical Immunology and Rheumatology
| | - Vincent Albert Laufer
- University of Alabama at Birmingham, Division of Clinical Immunology and Rheumatology
| | - Richard J Reynolds
- University of Alabama at Birmingham, Division of Clinical Immunology and Rheumatology
| | - Qi Yan
- University of Pittsburgh, Division of Pulmonary Medicine, Allergy and Immunology; Department of Pediatrics
| | - Nianjun Liu
- Indiana University School of Public Health - Bloomington, Department of Epidemiology and Biostatistics
| | | | | | | | | | | | - S Louis Bridges
- University of Alabama at Birmingham, Division of Clinical Immunology and Rheumatology
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98
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Comorbidity in Chronic Fatigue Syndrome/Myalgic Encephalomyelitis: A Nationwide Population-Based Cohort Study. PSYCHOSOMATICS 2017; 58:533-543. [PMID: 28596045 DOI: 10.1016/j.psym.2017.04.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 01/25/2023]
Abstract
BACKGROUND Previous studies have shown evidence of comorbid conditions in chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME). OBJECTIVE To estimate the prevalence of comorbidities and assess their associations using a nationwide population-based database of a Spanish CFS/ME cohort. METHOD A nationally representative, retrospective, cross-sectional cohort study (2008-2015) assessed 1757 Spanish subjects who met both the 1994 Centers for Disease Control and Prevention/Fukuda definition and 2003 Canadian Criteria for CFS/ME. Sociodemographic and clinical data, comorbidities, and patient-reported outcome measures at baseline were recorded. A cluster analysis based on baseline clinical variables was performed to classify patients with CFS/ME into 5 categories according to comorbidities. A multivariate logistic regression analysis was conducted adjusting for potential confounding effects such as age and sex; response and categorical predictor variables were also assessed. RESULTS A total of 1757 CFS/ME patients completed surveys were collected. We identified 5 CFS/ME clusters: group 1-fibromyalgia, myofascial pain, multiple chemical hypersensitivity, sicca syndrome, epicondylitis, and thyroiditis; group 2-alterations of ligaments and subcutaneous tissue, hypovitaminosis D, psychopathology, ligamentous hyperlaxity, and endometriosis. These 2 subgroups comprised mainly older women, with low educational level, unemployment, high levels of fatigue, and poor quality of life; group 3-with hardly any comorbidities, comprising mainly younger women, university students or those already employed, with lower levels of fatigue, and better quality of life; group 4-poorly defined comorbidities; and group 5-hypercholesterolemia. CONCLUSION Over 80% of a large population-based cohort of Spanish patients with CFS/ME presented comorbidities. Among the 5 subgroups created, the most interesting were groups 1-3. Future research should consider multidisciplinary approaches for the management and treatment of CFS/ME with comorbid conditions.
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99
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Antiochos P, Marques-Vidal P, Virzi J, Pagano S, Satta N, Hartley O, Montecucco F, Mach F, Kutalik Z, Waeber G, Vollenweider P, Vuilleumier N. Anti-Apolipoprotein A-1 IgG Predict All-Cause Mortality and Are Associated with Fc Receptor-Like 3 Polymorphisms. Front Immunol 2017; 8:437. [PMID: 28458671 PMCID: PMC5394854 DOI: 10.3389/fimmu.2017.00437] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 03/28/2017] [Indexed: 01/18/2023] Open
Abstract
Background Autoantibodies against apolipoprotein A-1 (anti-apoA-1 IgG) have emerged as an independent biomarker for cardiovascular disease and mortality. However, their association with all-cause mortality in the community, as well as their genetic determinants, have not been studied. Objective To determine whether anti-apoA-1 IgG: (a) predict all-cause mortality in the general population and (b) are associated with single-nucleotide polymorphisms (SNPs) in a genome-wide association study (GWAS). Methods Clinical, biological, and genetic data were obtained from the population-based, prospective CoLaus study, including 5,220 participants (mean age 52.6 years, 47.3% men) followed over a median duration of 5.6 years. The primary study outcome was all-cause mortality. Results After multivariate adjustment, anti-apoA-1 IgG positivity independently predicted all-cause mortality: hazard ratio (HR) = 1.54, 95% confidence interval (95% CI): 1.11–2.13, P = 0.01. A dose–effect relationship was also observed, each SD of logarithmically transformed anti-apoA-1 IgG being associated with a 15% increase in mortality risk: HR = 1.15, 95% CI: 1.02–1.28, P = 0.028. The GWAS yielded nine SNPs belonging to the Fc receptor-like 3 (FCRL3) gene, which were significantly associated with anti-apoA-1 IgG levels, with the lead SNP (rs6427397, P = 1.54 × 10−9) explaining 0.67% of anti-apoA-1 IgG level variation. Conclusion Anti-apoA-1 IgG levels (a) independently predict all-cause mortality in the general population and (b) are linked to FCRL3, a susceptibility gene for numerous autoimmune diseases. Our findings indicate that preclinical autoimmunity to anti-apoA-1 IgG may represent a novel mortality risk factor.
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Affiliation(s)
- Panagiotis Antiochos
- Department of Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Pedro Marques-Vidal
- Department of Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Julien Virzi
- Division of Laboratory Medicine, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.,Faculty of Medicine, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
| | - Sabrina Pagano
- Division of Laboratory Medicine, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.,Faculty of Medicine, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
| | - Nathalie Satta
- Division of Laboratory Medicine, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.,Faculty of Medicine, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
| | - Oliver Hartley
- Faculty of Medicine, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Fabrizio Montecucco
- Division of Laboratory Medicine, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.,Division of Cardiology, Foundation for Medical Researches, Department of Medical Specialties, University of Geneva, Geneva, Switzerland.,First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - François Mach
- Division of Cardiology, Foundation for Medical Researches, Department of Medical Specialties, University of Geneva, Geneva, Switzerland
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gerard Waeber
- Department of Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Peter Vollenweider
- Department of Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Nicolas Vuilleumier
- Division of Laboratory Medicine, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.,Faculty of Medicine, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
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100
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Rawlings DJ, Metzler G, Wray-Dutra M, Jackson SW. Altered B cell signalling in autoimmunity. Nat Rev Immunol 2017; 17:421-436. [PMID: 28393923 DOI: 10.1038/nri.2017.24] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recent work has provided new insights into how altered B cell-intrinsic signals - through the B cell receptor (BCR) and key co-receptors - function together to promote the pathogenesis of autoimmunity. These combined signals affect B cells at two distinct stages: first, in the selection of the naive repertoire; and second, during extrafollicular or germinal centre activation responses. Thus, dysregulated signalling can lead to both an altered naive BCR repertoire and the generation of autoantibody-producing B cells. Strikingly, high-affinity autoantibodies predate and predict disease in several autoimmune disorders, including type 1 diabetes and systemic lupus erythematosus. This Review summarizes how, rather than being a downstream consequence of autoreactive T cell activation, dysregulated B cell signalling can function as a primary driver of many human autoimmune diseases.
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Affiliation(s)
- David J Rawlings
- Seattle Children's Research Institute, 1900 9th Avenue, Seattle, Washington 98101, USA.,Department of Immunology, University of Washington School of Medicine.,Department of Pediatrics, University of Washington School of Medicine, 750 Republican Street, Seattle, Washington 98109, USA
| | - Genita Metzler
- Seattle Children's Research Institute, 1900 9th Avenue, Seattle, Washington 98101, USA.,Department of Immunology, University of Washington School of Medicine
| | - Michelle Wray-Dutra
- Seattle Children's Research Institute, 1900 9th Avenue, Seattle, Washington 98101, USA.,Department of Immunology, University of Washington School of Medicine
| | - Shaun W Jackson
- Seattle Children's Research Institute, 1900 9th Avenue, Seattle, Washington 98101, USA.,Department of Pediatrics, University of Washington School of Medicine, 750 Republican Street, Seattle, Washington 98109, USA
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