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Bui A, Orcales F, Kranyak A, Chung BY, Haran K, Smith P, Johnson C, Liao W. The Role of Genetics on Psoriasis Susceptibility, Comorbidities, and Treatment Response. Dermatol Clin 2024; 42:439-469. [PMID: 38796275 DOI: 10.1016/j.det.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2024]
Abstract
This review highlights advances made in psoriasis genetics, including findings from genome-wide association studies, exome-sequencing studies, and copy number variant studies. The impact of genetic variants on various comorbidities and therapeutic responses is discussed.
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Affiliation(s)
- Audrey Bui
- Lake Erie College of Osteopathic Medicine, 5000 Lakewood Ranch Boulevard, Bradenton, FL 34211, USA; Department of Dermatology, University of California San Francisco, 2340 Sutter Street, Box 0808, N431, San Francisco, CA 95115, USA
| | - Faye Orcales
- Department of Dermatology, University of California San Francisco, 2340 Sutter Street, Box 0808, N431, San Francisco, CA 95115, USA
| | - Allison Kranyak
- Department of Dermatology, University of California San Francisco, 2340 Sutter Street, Box 0808, N431, San Francisco, CA 95115, USA
| | - Bo-Young Chung
- Department of Dermatology, Kangnam Sacred Heart Hospital, Hallym University, 22, Gwanpyeong-ro 170beon-gil, Dongan-gu, Anyang-si Gyeonggi-do, 14068, Republic of Korea
| | - Kathryn Haran
- Department of Dermatology, University of California San Francisco, 2340 Sutter Street, Box 0808, N431, San Francisco, CA 95115, USA
| | - Payton Smith
- Department of Dermatology, University of California San Francisco, 2340 Sutter Street, Box 0808, N431, San Francisco, CA 95115, USA
| | - Chandler Johnson
- Department of Dermatology, University of California San Francisco, 2340 Sutter Street, Box 0808, N431, San Francisco, CA 95115, USA
| | - Wilson Liao
- Department of Dermatology, University of California San Francisco, 2340 Sutter Street, Box 0808, N431, San Francisco, CA 95115, USA.
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Pagano C, Ciaglia E, Coppola L, Lopardo V, Raimondo A, Giuseppe M, Lembo S, Laezza C, Bifulco M. Cannabidiol exerts multitarget immunomodulatory effects on PBMCs from individuals with psoriasis vulgaris. Front Immunol 2024; 15:1373435. [PMID: 38601151 PMCID: PMC11004238 DOI: 10.3389/fimmu.2024.1373435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
Introduction The involvement of endocannabinoid system (ECS) in the inflammatory cascade, and the ability of phytocannabinoids, endocannabinoids and their synthetic analogues to modulate it has become an interesting research area for new therapeutic approaches in inflammatory skin diseases. Cannabidiol (CBD) appears to be the most promising among phytocannabinoids, due to the lack of psychotropic effects and low toxicity profile. Its anti-inflammatory action has been highlighted in different preclinical models, ranging from experimental colitis to arthritis and neuroinflammation. Our aim was to evaluate CBD immune-modulatory effects in peripheral blood mononuclear cells (PBMC) of psoriasis individuals with particular attention to both innate and adaptative immune arms. Methods We performed in vitro immune functional experiments to analyze CBD action on various immune cells active in psoriatic lesions. Results The results showed that CBD produced a shift from Th1 to Th2 response, while boosting cytotoxic activity of Natural Killer (NK) cells. Furthermore, it also exerted a potent action on monocyte differentiation as, after CBD treatment, monocytes from psoriatic individuals were unable to migrate in response to inflammatory stimuli and to fully differentiate into mature dendritic cells. Finally, a M2 skewing of monocyte-derived macrophages by CBD also contributed to the fine tuning of the magnitude of immune responses. Conclusions These data uncover new potential immunomodulatory properties of this cannabinoid suggesting a possible therapeutic action in the treatment of multiple inflammatory skin diseases.
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Affiliation(s)
- Cristina Pagano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Elena Ciaglia
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Italy
| | - Laura Coppola
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Valentina Lopardo
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Italy
| | - Annunziata Raimondo
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Italy
| | - Monfrecola Giuseppe
- Section of Dermatology - Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Serena Lembo
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Italy
| | - Chiara Laezza
- Institute of Endocrinology and Experimental Oncology (IEOS), National Research Council (CNR), Naples, Italy
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
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Antonatos C, Grafanaki K, Georgiou S, Evangelou E, Vasilopoulos Y. Disentangling the complexity of psoriasis in the post-genome-wide association era. Genes Immun 2023; 24:236-247. [PMID: 37717118 DOI: 10.1038/s41435-023-00222-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
In recent years, genome-wide association studies (GWAS) have been instrumental in unraveling the genetic architecture of complex diseases, including psoriasis. The application of large-scale GWA studies in psoriasis has illustrated several associated loci that participate in the cutaneous inflammation, however explaining a fraction of the disease heritability. With the advent of high-throughput sequencing technologies and functional genomics approaches, the post-GWAS era aims to unravel the functional mechanisms underlying the inter-individual variability in psoriasis patients. In this review, we present the key advances of psoriasis GWAS in under-represented populations, rare, non-coding and structural variants and epistatic phenomena that orchestrate the interplay between different cell types. We further review the gene-gene and gene-environment interactions contributing to the disease predisposition and development of comorbidities through Mendelian randomization studies and pleiotropic effects of psoriasis-associated loci. We finally examine the holistic approaches conducted in psoriasis through system genetics and state-of-the-art transcriptomic analyses, discussing their potential implication in the expanding field of precision medicine and characterization of comorbidities.
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Affiliation(s)
- Charalabos Antonatos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504, Patras, Greece
| | - Katerina Grafanaki
- Department of Dermatology-Venereology, School of Medicine, University of Patras, 26504, Patras, Greece
| | - Sophia Georgiou
- Department of Dermatology-Venereology, School of Medicine, University of Patras, 26504, Patras, Greece
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, 45110, Greece
- Biomedical Research Institute, Foundation for Research and Technology-Hellas, 45110, Ioannina, Greece
- Department of Epidemiology & Biostatistics, MRC Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
| | - Yiannis Vasilopoulos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504, Patras, Greece.
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Muriuki BM, Forconi CS, Kirwa EK, Maina TK, Ariera BO, Bailey JA, Ghansah A, Moormann AM, Ong’echa JM. Evaluation of KIR3DL1/KIR3DS1 allelic polymorphisms in Kenyan children with endemic Burkitt lymphoma. PLoS One 2023; 18:e0275046. [PMID: 37647275 PMCID: PMC10468049 DOI: 10.1371/journal.pone.0275046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 08/15/2023] [Indexed: 09/01/2023] Open
Abstract
Endemic Burkitt lymphoma (eBL) is a fast-growing germinal center B cell lymphoma, affecting 5-10 per 100,000 children annually, in the equatorial belt of Africa. We hypothesize that co-infections with Plasmodium falciparum (Pf) malaria and Epstein-Barr virus (EBV) impair host natural killer (NK) and T cell responses to tumor cells, and thus increase the risk of eBL pathogenesis. NK cell education is partially controlled by killer immunoglobulin-like receptors and variable expression of KIR3DL1 has been associated with other malignancies. Here, we investigated whether KIR3D-mediated mechanisms contribute to eBL, by testing for an association of KIR3DL1/KIR3DS1 genotypes with the disease in 108 eBL patients and 99 healthy Kenyan children. KIR3DL1 allelic typing and EBV loads were assessed by PCR. We inferred previously observed phenotypes from the genotypes. The frequencies of KIR3DL1/KIR3DL1 and KIR3DL1/KIR3DS1 did not differ significantly between cases and controls. Additionally, none of the study participants was homozygous for KIR3DS1 alleles. EBV loads did not differ by the KIR3DL1 genotypes nor were they different between eBL survivors and non-survivors. Our results suggest that eBL pathogenesis may not simply involve variations in KIR3DL1 and KIR3DS1 genotypes. However, considering the complexity of the KIR3DL1 locus, this study could not exclude a role for copy number variation in eBL pathogenesis.
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Affiliation(s)
- Beatrice M. Muriuki
- West African Center for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Catherine S. Forconi
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States of America
| | - Erastus K. Kirwa
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Titus K. Maina
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Bonface O. Ariera
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, United States of America
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Ann M. Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States of America
| | - John M. Ong’echa
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
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5
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Legrand N, Salameh P, Jullien M, Chevallier P, Ferron E, David G, Devilder MC, Willem C, Gendzekhadze K, Parham P, Retière C, Gagne K. Non-Expressed Donor KIR3DL1 Alleles May Represent a Risk Factor for Relapse after T-Replete Haploidentical Hematopoietic Stem Cell Transplantation. Cancers (Basel) 2023; 15:2754. [PMID: 37345091 DOI: 10.3390/cancers15102754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
KIR3DL1 alleles are expressed at different levels on the natural killer (NK) cell surface. In particular, the non-expressed KIR3DL1*004 allele appears to be common in Caucasian populations. However, the overall distribution of non-expressed KIR3DL1 alleles and their clinical relevance after T-replete haploidentical hematopoietic stem cell transplantation (hHSCT) with post-transplant cyclophosphamide remain poorly documented in European populations. In a cohort of French blood donors (N = 278), we compared the distribution of expressed and non-expressed KIR3DL1 alleles using next-generation sequencing (NGS) technology combined with multi-color flow cytometry. We confirmed the predominance of the non-expressed KIR3DL1*004 allele. Using allele-specific constructs, the phenotype and function of the uncommon KIR3DL1*019 allotype were characterized using the Jurkat T cell line and NKL transfectants. Although poorly expressed on the NK cell surface, KIR3DL1*019 is retained within NK cells, where it induces missing self-recognition of the Bw4 epitope. Transposing our in vitro observations to a cohort of hHSCT patients (N = 186) led us to observe that non-expressed KIR3DL1 HSC grafts increased the incidence of relapse in patients with myeloid diseases. Non-expressed KIR3DL1 alleles could, therefore, influence the outcome of hHSCT.
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Affiliation(s)
- Nolwenn Legrand
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Perla Salameh
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Maxime Jullien
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
- Department of Hematology Clinic, Nantes University Hospital, F-44000 Nantes, France
| | - Patrice Chevallier
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
- Department of Hematology Clinic, Nantes University Hospital, F-44000 Nantes, France
| | - Enora Ferron
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Gaelle David
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Marie-Claire Devilder
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Catherine Willem
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Ketevan Gendzekhadze
- Department of Hematology and HCT, HLA Laboratory, City of Hope, Medical Center, Duarte, CA 91010, USA
| | - Peter Parham
- Department of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christelle Retière
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Katia Gagne
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
- LabEx Transplantex, Université de Strasbourg, F-67000 Strasbourg, France
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Sakaue S, Hosomichi K, Hirata J, Nakaoka H, Yamazaki K, Yawata M, Yawata N, Naito T, Umeno J, Kawaguchi T, Matsui T, Motoya S, Suzuki Y, Inoko H, Tajima A, Morisaki T, Matsuda K, Kamatani Y, Yamamoto K, Inoue I, Okada Y. Decoding the diversity of killer immunoglobulin-like receptors by deep sequencing and a high-resolution imputation method. CELL GENOMICS 2022; 2:100101. [PMID: 36777335 PMCID: PMC9903714 DOI: 10.1016/j.xgen.2022.100101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 08/07/2021] [Accepted: 02/02/2022] [Indexed: 12/12/2022]
Abstract
The killer cell immunoglobulin-like receptor (KIR) recognizes human leukocyte antigen (HLA) class I molecules and modulates the function of natural killer cells. Despite its role in immunity, the complex genomic structure has limited a deep understanding of the KIR genomic landscape. Here we conduct deep sequencing of 16 KIR genes in 1,173 individuals. We devise a bioinformatics pipeline incorporating copy number estimation and insertion or deletion (indel) calling for high-resolution KIR genotyping. We define 118 alleles in 13 genes and demonstrate a linkage disequilibrium structure within and across KIR centromeric and telomeric regions. We construct a KIR imputation reference panel (nreference = 689, imputation accuracy = 99.7%), apply it to biobank genotype (ntotal = 169,907), and perform phenome-wide association studies of 85 traits. We observe a dearth of genome-wide significant associations, even in immune traits implicated previously to be associated with KIR (the smallest p = 1.5 × 10-4). Our pipeline presents a broadly applicable framework to evaluate innate immunity in large-scale datasets.
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Affiliation(s)
- Saori Sakaue
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Center for Data Sciences, Harvard Medical School, Boston, MA 02115, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Corresponding author
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Jun Hirata
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirofumi Nakaoka
- Human Genetics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Keiko Yamazaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Public Health, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Makoto Yawata
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, and National University Health System, Singapore 119228, Singapore
- NUSMed Immunology Translational Research Programme, and Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore 117609, Singapore
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
| | - Nobuyo Yawata
- Department of Ocular Pathology and Imaging Science, Kyushu University, 812-8582, Japan
- Singapore Eye Research Institute, Singapore 169856, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Junji Umeno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Takaaki Kawaguchi
- Division of Gastroenterology, Department of Medicine, Tokyo Yamate Medical Center, Tokyo 169-0073, Japan
| | - Toshiyuki Matsui
- Department of Gastroenterology, Fukuoka University Chikushi Hospital, Fukuoka 818-0067, Japan
| | - Satoshi Motoya
- Department of Gastroenterology, Sapporo-Kosei General Hospital, Sapporo 060-0033, Japan
| | - Yasuo Suzuki
- Department of Internal Medicine, Faculty of Medicine, Toho University, Chiba 274-8510, Japan
| | | | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Takayuki Morisaki
- Division of Molecular Pathology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Koichi Matsuda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita 565-0871, Japan
- Corresponding author
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7
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Harrison GF, Leaton LA, Harrison EA, Kichula KM, Viken MK, Shortt J, Gignoux CR, Lie BA, Vukcevic D, Leslie S, Norman PJ. Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1. PLoS Comput Biol 2022; 18:e1009059. [PMID: 35192601 PMCID: PMC8896733 DOI: 10.1371/journal.pcbi.1009059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 03/04/2022] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Highly polymorphic interaction of KIR3DL1 and KIR3DS1 with HLA class I ligands modulates the effector functions of natural killer (NK) cells and some T cells. This genetically determined diversity affects severity of infections, immune-mediated diseases, and some cancers, and impacts the course of immunotherapies, including transplantation. KIR3DL1 is an inhibitory receptor, and KIR3DS1 is an activating receptor encoded by the KIR3DL1/S1 gene that has more than 200 diverse and divergent alleles. Determination of KIR3DL1/S1 genotypes for medical application is hampered by complex sequence and structural variation, requiring targeted approaches to generate and analyze high-resolution allele data. To overcome these obstacles, we developed and optimized a model for imputing KIR3DL1/S1 alleles at high-resolution from whole-genome SNP data. We designed the model to represent a substantial component of human genetic diversity. Our Global imputation model is effective at genotyping KIR3DL1/S1 alleles with an accuracy ranging from 88% in Africans to 97% in East Asians, with mean specificity of 99% and sensitivity of 95% for alleles >1% frequency. We used the established algorithm of the HIBAG program, in a modification named Pulling Out Natural killer cell Genomics (PONG). Because HIBAG was designed to impute HLA alleles also from whole-genome SNP data, PONG allows combinatorial diversity of KIR3DL1/S1 with HLA-A and -B to be analyzed using complementary techniques on a single data source. The use of PONG thus negates the need for targeted sequencing data in very large-scale association studies where such methods might not be tractable.
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Affiliation(s)
- Genelle F. Harrison
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Laura Ann Leaton
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Erica A. Harrison
- Independent Researcher, Broomfield, Colorado, United States of America
| | - Katherine M. Kichula
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Marte K. Viken
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Jonathan Shortt
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Christopher R. Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Benedicte A. Lie
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Damjan Vukcevic
- School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia
| | - Stephen Leslie
- School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
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8
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Ahn R, Vukcevic D, Motyer A, Nititham J, Squire DM, Hollenbach JA, Norman PJ, Ellinghaus E, Nair RP, Tsoi LC, Oksenberg J, Foerster J, Lieb W, Weidinger S, Franke A, Elder JT, Jorgenson E, Leslie S, Liao W. Large-Scale Imputation of KIR Copy Number and HLA Alleles in North American and European Psoriasis Case-Control Cohorts Reveals Association of Inhibitory KIR2DL2 With Psoriasis. Front Immunol 2021; 12:684326. [PMID: 34177931 PMCID: PMC8231283 DOI: 10.3389/fimmu.2021.684326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/29/2021] [Indexed: 12/14/2022] Open
Abstract
Killer cell immunoglobulin-like receptors (KIR) regulate immune responses in NK and CD8+ T cells via interaction with HLA ligands. KIR genes, including KIR2DS1, KIR3DL1, and KIR3DS1 have previously been implicated in psoriasis susceptibility. However, these previous studies were constrained to small sample sizes, in part due to the time and expense required for direct genotyping of KIR genes. Here, we implemented KIR*IMP to impute KIR copy number from single-nucleotide polymorphisms (SNPs) on chromosome 19 in the discovery cohort (n=11,912) from the PAGE consortium, University of California San Francisco, and the University of Dundee, and in a replication cohort (n=66,357) from Kaiser Permanente Northern California. Stratified multivariate logistic regression that accounted for patient ancestry and high-risk HLA alleles revealed that KIR2DL2 copy number was significantly associated with psoriasis in the discovery cohort (p ≤ 0.05). The KIR2DL2 copy number association was replicated in the Kaiser Permanente replication cohort. This is the first reported association of KIR2DL2 copy number with psoriasis and highlights the importance of KIR genetics in the pathogenesis of psoriasis.
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Affiliation(s)
- Richard Ahn
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Damjan Vukcevic
- Melbourne Integrative Genomics, The University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
- Clinical Epidemiology and Biostatistics Unit, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Allan Motyer
- Melbourne Integrative Genomics, The University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - Joanne Nititham
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
| | - David McG. Squire
- Melbourne Integrative Genomics, The University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - Jill A. Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Paul J. Norman
- Division of Personalized Medicine, Department of Immunology and Microbiology, University of Colorado, San Francisco, CA, United States
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Rajan P. Nair
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, United States
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Jorge Oksenberg
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - John Foerster
- College of Medicine, Dentistry, and Nursing, University of Dundee, Dundee, United Kingdom
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, University Hospital Schleswig Holstein, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - James T. Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
- Ann Arbor Veterans Affairs Hospital, Dermatology, Ann Arbor, MI, United States
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente, Oakland, CA, United States
| | - Stephen Leslie
- Melbourne Integrative Genomics, The University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
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Liu B, Shao Y, Fu R. Current research status of HLA in immune-related diseases. IMMUNITY INFLAMMATION AND DISEASE 2021; 9:340-350. [PMID: 33657268 PMCID: PMC8127548 DOI: 10.1002/iid3.416] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023]
Abstract
Human leukocyte antigen (HLA), also known as human major histocompatibility complex (MHC), is encoded by the HLA gene complex, and is currently known to have the highest gene density and the most polymorphisms among human chromosomal areas. HLA is divided into class I antigens, class II antigens, and class III antigens according to distribution and function. Classical HLA class I antigens include HLA-A, HLA-B, and HLA-C; HLA class II antigens include HLA-DP, HLA-DQ, and HLA-DR; nonclassical HLA class I and II molecules include HLA-F, E, H, X, DN, DO, and DM; and others, such as complement, are class III antigens. HLA is closely related to the body's immune response, regulation, and surveillance and is of great significance in the study of autoimmune diseases, tumor immunity, organ transplantation, and reproductive immunity. HLA is an important research topic that bridges immunology and clinical diseases. With the development of research methods and technologies, there will be more discoveries and broader prospects.
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Affiliation(s)
- Bingnan Liu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Yuanyuan Shao
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Rong Fu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, PR China
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10
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Macías-Barragán J, Montoya-Buelna M, Enciso-Vargas M, Alvarado-Ruíz L, Oceguera-Contreras E, Guerra-Renteria AS, Graciano-Machuca O. Assessment of the Relationship between Clinical Variants of Psoriasis and Killer Immunoglobulin-like Receptor ( KIR) Genes: A Systematic Review with Meta-analysis. Immunol Invest 2020; 51:480-495. [PMID: 33115277 DOI: 10.1080/08820139.2020.1840582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Psoriasis (Ps) is an autoimmune dermatosis. Previous studies have shown an association between KIR genes and susceptibility to some clinical variants of Ps. Therefore, we conducted an exhaustive systematic review with meta-analysis to evaluate the relationship between KIR genes and susceptibility to clinical variants of Ps in the overall population and according to ethnicity. METHODS According to PRISMA guidelines, we performed a systematic review through PubMed and Web of Science to identify relevant available scientific publications about KIR genes and Ps. The quality of the studies was evaluated using the Newcastle-Ottawa scale. Odds ratios (OR) and 95% confidence intervals (95%CI) were estimated using random and fixed effect models for the analyzed genes. Heterogeneity was tested using Cochran's Q-Statistic and I2, and the risk of bias was tested using the Begg test and Egger linear regression. RESULTS A total of 10 case-control studies were included, comprising a variable number of KIR typified genes and psoriasis vulgaris (PsV) as the main clinical variant studied. In the total pooled results, the KIR2DS1 gene (OR = 1.518, p = .010, 95%CI: 1.105 to 2.086) was related to higher susceptibility to PsV, while the KIR2DS4 (OR = 0.563, p = .005, 95%CI: 0.376 to 0.842) and KIR3DL1 (OR = 0.602, p = .040, 95%CI: 0.370 to 0.977) genes were related to protection against PsV. CONCLUSION This meta-analysis demonstrates that subjects that carry the KIR2DS1 gene could have a potential risk factor for the development of PsV. Conversely, KIR2DS4 and 3DL1 genes appear to confer protection against PsV.
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Affiliation(s)
- José Macías-Barragán
- Laboratorio de Sistemas Biológicos, Departamento de Ciencias de la Salud, Centro Universitario de los Valles (Cuvalles), Universidad de Guadalajara (UDG), Ameca, México
| | - Margarita Montoya-Buelna
- Laboratorio de Inmunología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, UDG, Guadalajara, México
| | - Moisés Enciso-Vargas
- Departamento de Ciencias Médicas y de la Vida, Centro Universitario de la Ciénega, UDG, Ocotlán, México
| | - Liliana Alvarado-Ruíz
- Escuela de Ciencias de la Salud, Campus Zapopan, Universidad del Valle de México, Zapopan, México
| | - Edén Oceguera-Contreras
- Laboratorio de Sistemas Biológicos, Departamento de Ciencias de la Salud, Centro Universitario de los Valles (Cuvalles), Universidad de Guadalajara (UDG), Ameca, México
| | - Aracely Suggey Guerra-Renteria
- Laboratorio de Sistemas Biológicos, Departamento de Ciencias de la Salud, Centro Universitario de los Valles (Cuvalles), Universidad de Guadalajara (UDG), Ameca, México.,Escuela de Ciencias de la Salud, Campus Zapopan, Universidad del Valle de México, Zapopan, México
| | - Omar Graciano-Machuca
- Laboratorio de Sistemas Biológicos, Departamento de Ciencias de la Salud, Centro Universitario de los Valles (Cuvalles), Universidad de Guadalajara (UDG), Ameca, México
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11
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Anderson KM, Augusto DG, Dandekar R, Shams H, Zhao C, Yusufali T, Montero-Martín G, Marin WM, Nemat-Gorgani N, Creary LE, Caillier S, Mofrad MRK, Parham P, Fernández-Viña M, Oksenberg JR, Norman PJ, Hollenbach JA. Killer Cell Immunoglobulin-like Receptor Variants Are Associated with Protection from Symptoms Associated with More Severe Course in Parkinson Disease. THE JOURNAL OF IMMUNOLOGY 2020; 205:1323-1330. [PMID: 32709660 DOI: 10.4049/jimmunol.2000144] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/28/2020] [Indexed: 12/12/2022]
Abstract
Immune dysfunction plays a role in the development of Parkinson disease (PD). NK cells regulate immune functions and are modulated by killer cell immunoglobulin-like receptors (KIR). KIR are expressed on the surface of NK cells and interact with HLA class I ligands on the surface of all nucleated cells. We investigated KIR-allelic polymorphism to interrogate the role of NK cells in PD. We sequenced KIR genes from 1314 PD patients and 1978 controls using next-generation methods and identified KIR genotypes using custom bioinformatics. We examined associations of KIR with PD susceptibility and disease features, including age at disease onset and clinical symptoms. We identified two KIR3DL1 alleles encoding highly expressed inhibitory receptors associated with protection from PD clinical features in the presence of their cognate ligand: KIR3DL1*015/HLA-Bw4 from rigidity (p c = 0.02, odds ratio [OR] = 0.39, 95% confidence interval [CI] 0.23-0.69) and KIR3DL1*002/HLA-Bw4i from gait difficulties (p c = 0.05, OR = 0.62, 95% CI 0.44-0.88), as well as composite symptoms associated with more severe disease. We also developed a KIR3DL1/HLA interaction strength metric and found that weak KIR3DL1/HLA interactions were associated with rigidity (pc = 0.05, OR = 9.73, 95% CI 2.13-172.5). Highly expressed KIR3DL1 variants protect against more debilitating symptoms of PD, strongly implying a role of NK cells in PD progression and manifestation.
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Affiliation(s)
- Kirsten M Anderson
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Danillo G Augusto
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Ravi Dandekar
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Hengameh Shams
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Chao Zhao
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Tasneem Yusufali
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | | | - Wesley M Marin
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Neda Nemat-Gorgani
- Department of Structural Biology and Immunology, Stanford University, Palo Alto, CA 94305
| | - Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA 94304
| | - Stacy Caillier
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Department of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720; and
| | - Peter Parham
- Department of Structural Biology and Immunology, Stanford University, Palo Alto, CA 94305
| | | | - Jorge R Oksenberg
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Jill A Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158;
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12
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Yanovsky RL, Chen H, Leslie S, Carrington M, Liao W. The Interaction of LILRB2 with HLA-B Is Associated with Psoriasis Susceptibility. J Invest Dermatol 2020; 140:1292-1295.e3. [PMID: 31874134 PMCID: PMC7247938 DOI: 10.1016/j.jid.2019.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/26/2019] [Accepted: 12/08/2019] [Indexed: 12/30/2022]
Affiliation(s)
| | - Haoyan Chen
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Stephen Leslie
- Centre for Systems Genomics, Schools of Mathematics and Statistics and BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Wilson Liao
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA.
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13
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Significance of KIR like natural killer cell receptors in autoimmune disorders. Clin Immunol 2020; 216:108449. [PMID: 32376502 DOI: 10.1016/j.clim.2020.108449] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 04/21/2020] [Accepted: 04/27/2020] [Indexed: 12/26/2022]
Abstract
Killer cell immunoglobulin-like receptors (KIRs), act as the regulators for the cytolytic activity of natural killer and certain T cells by interacting with the HLA class I ligands. KIRs have been shown to contribute to the pathogenesis of several autoimmune diseases. However, their specific roles are still not very clear. Autoimmune diseases are multifactorial in nature, highlighting the influence of both genetic and environmental factors. The innate immune response plays an important role in autoimmunity as it alters the self-glycans that mimic molecular patterns found on different intracellular pathogens. Natural killer (NK) cells have an important position in the innate immune response. NK cell receptors are encoded by the leukocyte receptor complex located on the chromosome 19q13.4 and lectin-like receptors on chromosome 12p13. This review focuses on the role of KIRs and their relationship with different autoimmune diseases.
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14
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The Roles of Uterine Natural Killer (NK) Cells and KIR/HLA-C Combination in the Development of Preeclampsia: A Systematic Review. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4808072. [PMID: 32309433 PMCID: PMC7149372 DOI: 10.1155/2020/4808072] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/18/2020] [Accepted: 03/20/2020] [Indexed: 12/21/2022]
Abstract
Preeclampsia (PE) is termed as a systemic disease that involves multiple organs; however, the exact etiology is still quite unclear. It is believed that the poor remodeling of uterine spiral arteries triggers PE, thereby causing failed placentation and producing inflammatory factors. The decline of blood flow results in lowering the nutrients and oxygen received by the fetus and augmenting the placental pressure in PE. Decidual immune cells, especially uterine natural killer (uNK) cells, are involved in the process of placentation. Decidual NK (dNK) cells significantly contribute to the vascular remodeling through the secretion of cytokines and angiogenic mediators in normal placental development. The abnormal activation of NK cells in both the peripheral blood and the decidua was counted among the causes leading to PE. The correlation existing between maternal killer cell immunoglobulin-like receptor (KIR) and HLA-C in trophoblast cells constitutes a robust evidence for the genetic etiology of PE. The combinations of the two kinds of gene systems, together with the KIR genotype in the mother and the HLA-C group in her fetus, are likely to exactly decide the pregnancy outcome. The women, who have the inappropriate match of KIR/HLA-C, are likely to be prone to the augmented risk of PE. However, the combinations of KIR/HLA-C in PE undergo ethnic changes. The extensive prospective research works in Europe, Asia, and Africa are required for providing more findings in PE patients.
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15
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Graciano-Machuca O, Alvarado-Navarro A, Ramírez-Dueñas MG, Villanueva-Quintero DG, Velarde-de la Cruz EE, Machado-Sulbarán AC, Montoya-Buelna M, Sánchez-Hernández PE. Diversity of KIR/HLA Genotypes and Their Association with Psoriasis Vulgaris in the Western Mexican Population. Genes (Basel) 2020; 11:E338. [PMID: 32235781 PMCID: PMC7141133 DOI: 10.3390/genes11030338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 11/17/2022] Open
Abstract
NK and some T cell functions are regulated by the interaction between KIR and HLA molecules. Several studies have shown an association between activating KIR genes and the development of autoimmune diseases, including psoriasis vulgaris (PsV). Our objective was to determine the association between KIR/HLA genes and genotypes with PsV in the Western mestizo Mexican population. One hundred subjects diagnosed with PsV (SP) and 108 healthy subjects (HS) were genotyped for 14 KIR genes, HLA-Bw4, HLA-C1, and HLA-C2 by PCR-single specific primer (SSP). Positive associations of the KIR3DS1 gene (odds ratio (OR) 1.959, p = 0.021), G11 genotype (OR 19.940, p = 0.008), and KIR3DS1/HLA-ABw4 (OR 2.265, p = 0.009) were found with susceptibility to PsV. In contrast, the G1 genotype (OR 0.448, p = 0.031) and KIR3DL1/HLA-Bw4Ile80 (OR 0.522, p = 0.022) were negatively associated with susceptibility to this disease. These results suggest an implication of the KIR3DS1/HLA-ABw4 genotype in PsV pathology.
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Affiliation(s)
- Omar Graciano-Machuca
- Doctorate in Biomedical Sciences, Department of Physiology, University Center of Health Sciences (CUCS), University of Guadalajara (UDG), Guadalajara, Jal. 44340, Mexico
- Laboratory of Biological Systems, Department of Health Sciences, University Center of the Valleys (CUVALLES), UDG, Ameca, Jal. 4660, Mexico
| | - Anabell Alvarado-Navarro
- Research Center in Immunology and Dermatology, Department of Physiology, CUCS, UDG, Guadalajara, Jal. 44340, Mexico
| | | | - Delfina Guadalupe Villanueva-Quintero
- Jalisco Dermatology Institute "Dr. José Barba Rubio", Ministry of Health; Zapopan, Jal. 45190, Mexico
- Inflammatory Diseases Care Center, Guadalajara, Jal. 44630, Mexico
| | - Erandi Enif Velarde-de la Cruz
- Doctorate in Biomedical Sciences, Department of Physiology, University Center of Health Sciences (CUCS), University of Guadalajara (UDG), Guadalajara, Jal. 44340, Mexico
| | - Andrea Carolina Machado-Sulbarán
- Doctorate in Biomedical Sciences, Department of Physiology, University Center of Health Sciences (CUCS), University of Guadalajara (UDG), Guadalajara, Jal. 44340, Mexico
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16
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Reduced Efficacy of Biological Drugs in Psoriatic Patients with HLA-A Bw4-80I KIR Ligands. Mol Diagn Ther 2020; 24:311-314. [PMID: 32189206 DOI: 10.1007/s40291-020-00457-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Biological drugs (biologics) are a highly effective therapy for the moderate to severe form of psoriasis, an immune-mediated dermatosis with a strong immunogenetic component. The interaction between human leukocyte antigen (HLA) class I ligands and killer immunoglobulin-like receptors (KIR) has a functional significance in the education of natural killer (NK) cells, and can thus influence the response to biologics. OBJECTIVE In this study, we investigated the impact of HLA-A and -B KIR ligands in the response to biologics in a cohort of psoriatic patients. METHODS Eighty-five patients with moderate to severe psoriasis treated with biologics (adalimumab, etanercept, infliximab, ustekinumab and secukinumab) were enrolled in the study. Clinical response was evaluated as patients attaining 50%, 75% or 90% reduction in the Psoriasis Area and Severity Index (PASI) (PASI 50, 75 or 90, respectively) over 6 months' follow-up. Poor response was defined as PASI 50, and in this case patients shifted to treatment with a different biologic. Fifty-two patients (61.2%) showed excellent response (PASI 90) to the first biologic, while 33 patients (38.8%), needed two or more biologics before reaching an excellent response (PASI 90) and were considered difficult to treat. RESULTS Only HLA-A Bw4-80I ligands were associated with the response to biologics; in particular, they were linked with reduced response both at univariable analysis (odds ratio [OR] 3.11, 95% confidence interval [CI] 1.19-8.07; p = 0.019) and multivariable analysis (OR 5.02, 95% CI 1.40-17.97; p = 0.013). CONCLUSION We suggest that the HLA-A Bw4-80I epitope could be a marker of reduced responsiveness to biologics. The possible reason for this is an increase of tumour necrosis factor (TNF)-α and the silencing of NK cells through the predominant interaction with the KIR3DL/S pair. HLA-KIR affinities might lead to a more efficient way to prescribe biologics.
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17
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Castaño-Núñez Á, Montes-Cano MA, García-Lozano JR, Ortego-Centeno N, García-Hernández FJ, Espinosa G, Graña-Gil G, Sánchez-Bursón J, Juliá MR, Solans R, Blanco R, Barnosi-Marín AC, Gómez de la Torre R, Fanlo P, Rodríguez-Carballeira M, Rodríguez-Rodríguez L, Camps T, Castañeda S, Alegre-Sancho JJ, Martín J, González-Escribano MF. Association of Functional Polymorphisms of KIR3DL1/DS1 With Behçet's Disease. Front Immunol 2019; 10:2755. [PMID: 31849952 PMCID: PMC6896819 DOI: 10.3389/fimmu.2019.02755] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/11/2019] [Indexed: 11/27/2022] Open
Abstract
Behçet's disease (BD) is an immune-mediated vasculitis related to imbalances between the innate and adaptive immune response. Infectious agents or environmental factors may trigger the disease in genetically predisposed individuals. HLA-B51 is the genetic factor stronger associated with the disease, although the bases of this association remain elusive. NK cells have also been implicated in the etiopathogenesis of BD. A family of NK receptors, Killer-cell Immunoglobulin-like Receptor (KIR), with a very complex organization, is very important in the education and control of the NK cells by the union to their ligands, most of them, HLA class I molecules. This study aimed to investigate the contribution of certain KIR functional polymorphisms to the susceptibility to BD. A total of 466 BD patients and 444 healthy individuals were genotyped in HLA class I (A, B, and C). The set of KIR genes and the functional variants of KIR3DL1/DS1 and KIR2DS4 were also determined. Frequency of KIR3DL1*004 was lower in patients than in controls (0.15 vs. 0.20, P = 0.005, Pc = 0.015; OR = 0.70; 95% CI 0.54–0.90) in both B51 positive and negative individuals. KIR3DL1*004, which encodes a misfolded protein, is included in a common telomeric haplotype with only one functional KIR gene, KIR3DL2. Both, KIR3DL1 and KIR3DL2 sense pathogen-associated molecular patterns but they have different capacities to eliminate them. The education of the NK cells depending on the HLA, the balance of KIR3DL1/KIR3DL2 licensed NK cells and the different capacities of these receptors to eliminate pathogens could be involved in the etiopathogenesis of BD.
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Affiliation(s)
- Ángel Castaño-Núñez
- Department of Immunology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBiS), CSIC, Universidad de Sevilla, Seville, Spain
| | - Marco-Antonio Montes-Cano
- Department of Immunology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBiS), CSIC, Universidad de Sevilla, Seville, Spain
| | - José-Raúl García-Lozano
- Department of Immunology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBiS), CSIC, Universidad de Sevilla, Seville, Spain
| | | | | | - Gerard Espinosa
- Department Autoimmune Diseases, Hospital Universitari Clínic, Barcelona, Spain
| | - Genaro Graña-Gil
- Department of Rheumatology, Complejo Hospitalario Universitario A Coruña, A Coruña, Spain
| | | | - María-Rosa Juliá
- Department of Immunology, Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Roser Solans
- Department of Internal Medicine, Autoimmune Systemic Diseases Unit, Hospital Vall d'Hebron, Universidad Autonoma de Barcelona, Barcelona, Spain
| | - Ricardo Blanco
- Department of Rheumatology, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | | | | | - Patricia Fanlo
- Department of Internal Medicine, Hospital Virgen del Camino, Pamplona, Spain
| | | | | | - Teresa Camps
- Department of Internal Medicine, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Santos Castañeda
- Department of Rheumatology, Hospital de la Princesa, IIS-Princesa, Madrid, Spain
| | | | - Javier Martín
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC, PTS Granada, Granada, Spain
| | - María-Francisca González-Escribano
- Department of Immunology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBiS), CSIC, Universidad de Sevilla, Seville, Spain
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18
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Petrushkin H, Norman PJ, Lougee E, Parham P, Wallace GR, Stanford MR, Fortune F. KIR3DL1/S1 Allotypes Contribute Differentially to the Development of Behçet Disease. THE JOURNAL OF IMMUNOLOGY 2019; 203:1629-1635. [PMID: 31405953 DOI: 10.4049/jimmunol.1801178] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 07/08/2019] [Indexed: 11/19/2022]
Abstract
Behçet disease is a chronic, relapsing-remitting autoinflammatory syndrome with a strong HLA-B*51 association. In this paper, we describe a human cohort of 267 individuals with Behçet disease and 445 matched controls from a tertiary referral center in the U.K. HLA-B*51 was confirmed as a genetic risk factor in this group (p = 0.0006, Bonferroni-Dunn correction for multiple testing [Pc] = 0.0192, odds ratio [OR] 1.92, 95% confidence interval [CI] 1.33-2.76). KIR3DL1/S1 allele-level analysis indicated that low-expressing KIR3DL1/S1 alleles in combination with KIR3DS1 increased the risk of developing Behçet disease (KIR3DL1LOW/KIR3DS1: p = 0.0004, Pc = 0.0040, OR 2.47, 95% CI 1.43-4.25), whereas high-expressing KIR3DL1/S1 alleles in combination with a null-expressing KIR3DL1 reduced the risk of disease (KIR3DL1HIGH/KIR3DL1NULL: p = 0.0035, Pc = 0.0350, OR 0.53, 95% CI 0.33-0.87). Behçet disease can manifest as a purely mucocutaneous disease or can involve other organ systems such as the eyes. In the U.K. cohort studied in this study, KIR3DL1LOW/KIR3DS1 increased the risk of ophthalmic disease (p = 1.2 × 10-5, OR 3.92, 95% CI 2.06-7.47), whereas KIR3DL1HIGH/KIR3DL1NULL reduced the risk of having purely mucocutaneous disease (p = 0.0048, OR 0.45, 95% CI 0.25-0.81). To our knowledge, this is the first analysis of KIR3DL1/S1 allelic variation in Behçet disease and may provide insight into the pathogenic role of HLA-B*51 and its interaction with KIR3DL1/S1.
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Affiliation(s)
- Harry Petrushkin
- Moorfields Eye Hospital National Health Service Foundation Trust, Medical Retina Department, London EC1V 2PD, United Kingdom.,Clinical and Diagnostic Oral Sciences, Queen Mary University of London, Blizard Institute, E1 2AT London, United Kingdom
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, Department of Microbiology and Immunology, University of Colorado, Aurora, CO 80045
| | - Emma Lougee
- Viapath, Clinical Transplantation Laboratory, Guy's Hospital, Guy's and St Thomas' National Health Service Foundation Trust, London SE1 9RT, United Kingdom
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Graham R Wallace
- Centre for Translational Inflammation Research, University of Birmingham Research Laboratories, Queen Elizabeth Hospital, University of Birmingham, Birmingham B15 2TT, United Kingdom; and
| | - Miles R Stanford
- Medical Eye Unit, St Thomas' Hospital, Guy's and St Thomas' National Health Service Foundation Trust, London SE1 7EH, United Kingdom
| | - Farida Fortune
- Clinical and Diagnostic Oral Sciences, Queen Mary University of London, Blizard Institute, E1 2AT London, United Kingdom;
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19
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Wagner I, Schefzyk D, Pruschke J, Schöfl G, Schöne B, Gruber N, Lang K, Hofmann J, Gnahm C, Heyn B, Marin WM, Dandekar R, Hollenbach JA, Schetelig J, Pingel J, Norman PJ, Sauter J, Schmidt AH, Lange V. Allele-Level KIR Genotyping of More Than a Million Samples: Workflow, Algorithm, and Observations. Front Immunol 2018; 9:2843. [PMID: 30564239 PMCID: PMC6288436 DOI: 10.3389/fimmu.2018.02843] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/19/2018] [Indexed: 11/13/2022] Open
Abstract
The killer-cell immunoglobulin-like receptor (KIR) genes regulate natural killer cell activity, influencing predisposition to immune mediated disease, and affecting hematopoietic stem cell transplantation (HSCT) outcome. Owing to the complexity of the KIR locus, with extensive gene copy number variation (CNV) and allelic diversity, high-resolution characterization of KIR has so far been applied only to relatively small cohorts. Here, we present a comprehensive high-throughput KIR genotyping approach based on next generation sequencing. Through PCR amplification of specific exons, our approach delivers both copy numbers of the individual genes and allelic information for every KIR gene. Ten-fold replicate analysis of a set of 190 samples revealed a precision of 99.9%. Genotyping of an independent set of 360 samples resulted in an accuracy of more than 99% taking into account consistent copy number prediction. We applied the workflow to genotype 1.8 million stem cell donor registry samples. We report on the observed KIR allele diversity and relative abundance of alleles based on a subset of more than 300,000 samples. Furthermore, we identified more than 2,000 previously unreported KIR variants repeatedly in independent samples, underscoring the large diversity of the KIR region that awaits discovery. This cost-efficient high-resolution KIR genotyping approach is now applied to samples of volunteers registering as potential donors for HSCT. This will facilitate the utilization of KIR as additional selection criterion to improve unrelated donor stem cell transplantation outcome. In addition, the approach may serve studies requiring high-resolution KIR genotyping, like population genetics and disease association studies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Wesley M. Marin
- San Francisco School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Ravi Dandekar
- San Francisco School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- San Francisco School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Johannes Schetelig
- DKMS, Tübingen, Germany
- Department of Internal Medicine I, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | | | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology, University of Colorado Anschutz Medical, Aurora, CO, United States
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20
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González-Quezada B, Sánchez-Fernández M, Munguía-Saldaña A, Valencia-Macedo M, Flores-Aguilar H, Bonilla-Galán E, Rodríguez-Gómez A, Díaz-Rivera A, Gorodezky C. Allele diversity of the killer cell immunoglobulin-like receptors KIR3DL1/S1 and the combination with their HLA ligands in Mexican Mestizos from Mexico City. Hum Immunol 2018; 79:834-838. [DOI: 10.1016/j.humimm.2018.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/04/2018] [Accepted: 10/17/2018] [Indexed: 01/02/2023]
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21
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Huhn O, Chazara O, Ivarsson MA, Retière C, Venkatesan TC, Norman PJ, Hilton HG, Jayaraman J, Traherne JA, Trowsdale J, Ito M, Kling C, Parham P, Ghadially H, Moffett A, Sharkey AM, Colucci F. High-Resolution Genetic and Phenotypic Analysis of KIR2DL1 Alleles and Their Association with Pre-Eclampsia. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2018; 201:2593-2601. [PMID: 30249807 PMCID: PMC6258046 DOI: 10.4049/jimmunol.1800860] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/22/2018] [Indexed: 12/29/2022]
Abstract
Killer-cell Ig-like receptor (KIR) genes are inherited as haplotypes. They are expressed by NK cells and linked to outcomes of infectious diseases and pregnancy in humans. Understanding how genotype relates to phenotype is difficult because of the extensive diversity of the KIR family. Indeed, high-resolution KIR genotyping and phenotyping in single NK cells in the context of disease association is lacking. In this article, we describe a new method to separate NK cells expressing allotypes of the KIR2DL1 gene carried by the KIR A haplotype (KIR2DL1A) from those expressing KIR2DL1 alleles carried by the KIR B haplotype (KIR2DL1B). We find that in KIR AB heterozygous individuals, different KIR2DL1 allotypes can be detected in both peripheral blood and uterine NK cells. Using this new method, we demonstrate that both blood and uterine NK cells codominantly express KIR2DL1A and KIR2DL1B allotypes but with a predominance of KIR2DL1A variants, which associate with enhanced NK cell function. In a case-control study of pre-eclampsia, we show that KIR2DL1A, not KIR2DL1B, associates with increased disease risk. This method will facilitate our understanding of how individual KIR2DL1 allelic variants affect NK cell function and contribute to disease risk.
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Affiliation(s)
- Oisín Huhn
- Department of Obstetrics and Gynaecology, University of Cambridge School of Clinical Medicine, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0SW, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- MedImmune Ltd., Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Olympe Chazara
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Martin A Ivarsson
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Christelle Retière
- Etablissement Français du Sang, Université de Nantes, 44011 Nantes, France
- Centre de Recherche en Cancérologie et Immunologie Nantes Angers, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
- Centre de Recherche en Cancérologie et Immunologie Nantes Angers, INSERM U1232, CNRS, Université d'Angers, 49035 Angers, France
| | - Timothy C Venkatesan
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Hugo G Hilton
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Jyothi Jayaraman
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - James A Traherne
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - John Trowsdale
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Mitsutero Ito
- Department of Genetics, University of Cambridge, Cambridge CB2 3DY, United Kingdom; and
| | | | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Ashley Moffett
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Andrew M Sharkey
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom;
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Francesco Colucci
- Department of Obstetrics and Gynaecology, University of Cambridge School of Clinical Medicine, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0SW, United Kingdom;
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
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22
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Calender A, Rollat Farnier PA, Buisson A, Pinson S, Bentaher A, Lebecque S, Corvol H, Abou Taam R, Houdouin V, Bardel C, Roy P, Devouassoux G, Cottin V, Seve P, Bernaudin JF, Lim CX, Weichhart T, Valeyre D, Pacheco Y, Clement A, Nathan N. Whole exome sequencing in three families segregating a pediatric case of sarcoidosis. BMC Med Genomics 2018; 11:23. [PMID: 29510755 PMCID: PMC5839022 DOI: 10.1186/s12920-018-0338-x] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 02/19/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Sarcoidosis (OMIM 181000) is a multi-systemic granulomatous disorder of unknown origin. Despite multiple genome-wide association (GWAS) studies, no major pathogenic pathways have been identified to date. To find out relevant sarcoidosis predisposing genes, we searched for de novo and recessive mutations in 3 young probands with sarcoidosis and their healthy parents using a whole-exome sequencing (WES) methodology. METHODS From the SARCFAM project based on a national network collecting familial cases of sarcoidosis, we selected three families (trios) in which a child, despite healthy parents, develop the disease before age 15 yr. Each trio was genotyped by WES (Illumina HiSEQ 2500) and we selected the gene variants segregating as 1) new mutations only occurring in affected children and 2) as recessive traits transmitted from each parents. The identified coding variants were compared between the three families. Allelic frequencies and in silico functional results were analyzed using ExAC, SIFT and Polyphenv2 databases. The clinical and genetic studies were registered by the ClinicalTrials.gov - Protocol Registration and Results System (PRS) ( https://clinicaltrials.gov ) receipt under the reference NCT02829853 and has been approved by the ethical committee (CPP LYON SUD EST - 2 - REF IRB 00009118 - September 21, 2016). RESULTS We identified 37 genes sharing coding variants occurring either as recessive mutations in at least 2 trios or de novo mutations in one of the three affected children. The genes were classified according to their potential roles in immunity related pathways: 9 to autophagy and intracellular trafficking, 6 to G-proteins regulation, 4 to T-cell activation, 4 to cell cycle and immune synapse, 2 to innate immunity. Ten of the 37 genes were studied in a bibliographic way to evaluate the functional link with sarcoidosis. CONCLUSIONS Whole exome analysis of case-parent trios is useful for the identification of genes predisposing to complex genetic diseases as sarcoidosis. Our data identified 37 genes that could be putatively linked to a pediatric form of sarcoidosis in three trios. Our in-depth focus on 10 of these 37 genes may suggest that the formation of the characteristic lesion in sarcoidosis, granuloma, results from combined deficits in autophagy and intracellular trafficking (ex: Sec16A, AP5B1 and RREB1), G-proteins regulation (ex: OBSCN, CTTND2 and DNAH11), T-cell activation (ex: IDO2, IGSF3), mitosis and/or immune synapse (ex: SPICE1 and KNL1). The significance of these findings needs to be confirmed by functional tests on selected gene variants.
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Affiliation(s)
- Alain Calender
- Genetics Department, Hospices Civils de LYON (HCL), University Hospital, East Pathology Center, LYON, B-A3, 59 Bld Pinel, 69677 BRON Cedex, France
- Inflammation & Immunity of the Respiratory Epithelium - EA7426 (PI3) – South Medical University Hospital – Lyon 1 Claude Bernard University, 165 Chemin du Grand Revoyet, 69310 Pierre-Bénite, France
| | | | - Adrien Buisson
- Genetics Department, Hospices Civils de LYON (HCL), University Hospital, East Pathology Center, LYON, B-A3, 59 Bld Pinel, 69677 BRON Cedex, France
| | - Stéphane Pinson
- Genetics Department, Hospices Civils de LYON (HCL), University Hospital, East Pathology Center, LYON, B-A3, 59 Bld Pinel, 69677 BRON Cedex, France
| | - Abderrazzaq Bentaher
- Inflammation & Immunity of the Respiratory Epithelium - EA7426 (PI3) – South Medical University Hospital – Lyon 1 Claude Bernard University, 165 Chemin du Grand Revoyet, 69310 Pierre-Bénite, France
| | - Serge Lebecque
- Cancer Research Center, INSERM U-1052, CNRS 5286, 69008 Lyon, France
| | - Harriet Corvol
- Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Trousseau, AP-HP, INSERM UMR-S938, Sorbonne University, Paris, France
| | - Rola Abou Taam
- Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Necker, Paris, France
| | - Véronique Houdouin
- Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Robert Debré, INSERM U-1142, University Paris Diderot VII, Paris, France
| | - Claire Bardel
- Department of biostatistics, University Hospital, Hospices Civils de LYON (HCL), Lyon, France
| | - Pascal Roy
- Department of biostatistics, University Hospital, Hospices Civils de LYON (HCL), Lyon, France
| | - Gilles Devouassoux
- Department of Pulmonology, University Hospital, Hôpital Croix Rousse, Lyon, France
| | - Vincent Cottin
- Department of Pulmonology, University Hospital, Hôpital Louis Pradel, Lyon, France
| | - Pascal Seve
- Department of Internal medicine, University Hospital, Hôpital Croix Rousse, Lyon, France
| | | | - Clarice X. Lim
- Medical University of Vienna, Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Währinger Straße 10, 1090 Vienna, Austria
| | - Thomas Weichhart
- Medical University of Vienna, Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Währinger Straße 10, 1090 Vienna, Austria
| | - Dominique Valeyre
- EA2363, University Paris 13, COMUE Sorbonne-Paris-Cité, 74 rue Marcel Cachin, 93009 Bobigny, France
- Assistance Publique Hôpitaux de Paris, Department of Pulmonology, Avicenne University Hospital, 93009 Bobigny, France
| | - Yves Pacheco
- Inflammation & Immunity of the Respiratory Epithelium - EA7426 (PI3) – South Medical University Hospital – Lyon 1 Claude Bernard University, 165 Chemin du Grand Revoyet, 69310 Pierre-Bénite, France
| | - Annick Clement
- AP-HP Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Trousseau, INSERM UMR-S933, Sorbonne University, Paris, France
| | - Nadia Nathan
- AP-HP Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Trousseau, INSERM UMR-S933, Sorbonne University, Paris, France
| | - in the frame of GSF (Groupe Sarcoïdose France)
- Genetics Department, Hospices Civils de LYON (HCL), University Hospital, East Pathology Center, LYON, B-A3, 59 Bld Pinel, 69677 BRON Cedex, France
- Department of biostatistics, University Hospital, Hospices Civils de LYON (HCL), Lyon, France
- Inflammation & Immunity of the Respiratory Epithelium - EA7426 (PI3) – South Medical University Hospital – Lyon 1 Claude Bernard University, 165 Chemin du Grand Revoyet, 69310 Pierre-Bénite, France
- Cancer Research Center, INSERM U-1052, CNRS 5286, 69008 Lyon, France
- Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Trousseau, AP-HP, INSERM UMR-S938, Sorbonne University, Paris, France
- Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Necker, Paris, France
- Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Robert Debré, INSERM U-1142, University Paris Diderot VII, Paris, France
- Department of Pulmonology, University Hospital, Hôpital Croix Rousse, Lyon, France
- Department of Pulmonology, University Hospital, Hôpital Louis Pradel, Lyon, France
- Department of Internal medicine, University Hospital, Hôpital Croix Rousse, Lyon, France
- Histology and Tumor Biology, ER2 UPMC, Hôpital Tenon, Paris, France
- Medical University of Vienna, Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Währinger Straße 10, 1090 Vienna, Austria
- EA2363, University Paris 13, COMUE Sorbonne-Paris-Cité, 74 rue Marcel Cachin, 93009 Bobigny, France
- Assistance Publique Hôpitaux de Paris, Department of Pulmonology, Avicenne University Hospital, 93009 Bobigny, France
- AP-HP Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Trousseau, INSERM UMR-S933, Sorbonne University, Paris, France
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Su N, Wang H, Zhang B, Kang Y, Guo Q, Xiao H, Yang H, Liao S. Maternal natural killer cell immunoglobulin receptor genes and human leukocyte antigen-C ligands influence recurrent spontaneous abortion in the Han Chinese population. Exp Ther Med 2018; 15:327-337. [PMID: 29387191 PMCID: PMC5769230 DOI: 10.3892/etm.2017.5406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 10/30/2017] [Indexed: 02/05/2023] Open
Abstract
The underlying mechanism of recurrent spontaneous abortion (RSA) has remained elusive for many years. Several previous studies have suggested that the killer cell immunoglobulin receptor (KIR) gene family is associated with RSA, however, it is not clear exactly how. The present study detected KIR and human leukocyte antigen-C (HLA-C) genes in 110 Han Chinese women with unexplained RSA and 105 Han Chinese healthy females. The aim of the present study was to determine if certain genotypes were more susceptible to the occurrence of miscarriage. The frequency of KIR genes and different KIR haplotypes in the 2 groups demonstrated no statistical differences. However, in women who had miscarried ≥3 times, the frequency of KIR3DL1 was significantly reduced and the BB haplotype frequency was significantly higher compared with the control group. HLA-C2C2 was significantly increased in the KIR AB and KIR BB groups in the RSA groups compared with the control group. The women in the RSA group who had a homozygous HLA-C2C2 had a significantly higher frequency of the 2DS1 gene compared with the control group. The reduction of inhibitory gene and increased activation combinations may induce the activation of uterine natural killer cells, which may reduce the probability of fetal survival. To the best of our knowledge, the present study is the first report demonstrating the association between maternal KIR and HLA-C genes and RSA in women of a Han Chinese ethnicity. The present study revealed that females who miscarry ≥3 times may be used as selection criteria for RSA and so may exhibit higher research value.
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Affiliation(s)
- Ning Su
- Department of Obstetrics and Gynecology, People's Hospital of Zhengzhou University, Zhengzhou, Henan 450003, P.R. China
- Henan Medical Genetics Institute, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Hongdan Wang
- Henan Medical Genetics Institute, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Bowei Zhang
- International Office for Research and Development, Henan Red Cross Blood Center, Zhengzhou, Henan 450000, P.R. China
| | - Yiqing Kang
- International Office for Research and Development, Henan Red Cross Blood Center, Zhengzhou, Henan 450000, P.R. China
| | - Qiannan Guo
- Henan Medical Genetics Institute, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Hai Xiao
- Henan Medical Genetics Institute, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Hecai Yang
- International Office for Research and Development, Henan Red Cross Blood Center, Zhengzhou, Henan 450000, P.R. China
| | - Shixiu Liao
- Henan Medical Genetics Institute, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
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24
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Berinstein J, Pollock R, Pellett F, Thavaneswaran A, Chandran V, Gladman DD. Association of variably expressed KIR3dl1 alleles with psoriatic disease. Clin Rheumatol 2017; 36:2261-2266. [DOI: 10.1007/s10067-017-3784-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/26/2017] [Accepted: 07/31/2017] [Indexed: 10/19/2022]
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25
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Béziat V, Hilton HG, Norman PJ, Traherne JA. Deciphering the killer-cell immunoglobulin-like receptor system at super-resolution for natural killer and T-cell biology. Immunology 2016; 150:248-264. [PMID: 27779741 PMCID: PMC5290243 DOI: 10.1111/imm.12684] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/12/2016] [Accepted: 10/17/2016] [Indexed: 12/13/2022] Open
Abstract
Killer-cell immunoglobulin-like receptors (KIRs) are components of two fundamental biological systems essential for human health and survival. First, they contribute to host immune responses, both innate and adaptive, through their expression by natural killer cells and T cells. Second, KIR play a key role in regulating placentation, and hence reproductive success. Analogous to the diversity of their human leucocyte antigen class I ligands, KIR are extremely polymorphic. In this review, we describe recent developments, fuelled by methodological advances, that are helping to decipher the KIR system in terms of haplotypes, polymorphisms, expression patterns and their ligand interactions. These developments are delivering deeper insight into the relevance of KIR in immune system function, evolution and disease.
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Affiliation(s)
- Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France
| | - Hugo G Hilton
- Departments of Structural Biology and Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - Paul J Norman
- Departments of Structural Biology and Microbiology & Immunology, Stanford University, Stanford, CA, USA
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26
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Norman P, Hollenbach J, Nemat-Gorgani N, Marin W, Norberg S, Ashouri E, Jayaraman J, Wroblewski E, Trowsdale J, Rajalingam R, Oksenberg J, Chiaroni J, Guethlein L, Traherne J, Ronaghi M, Parham P. Defining KIR and HLA Class I Genotypes at Highest Resolution via High-Throughput Sequencing. Am J Hum Genet 2016; 99:375-91. [PMID: 27486779 DOI: 10.1016/j.ajhg.2016.06.023] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 06/23/2016] [Indexed: 12/12/2022] Open
Abstract
The physiological functions of natural killer (NK) cells in human immunity and reproduction depend upon diverse interactions between killer cell immunoglobulin-like receptors (KIRs) and their HLA class I ligands: HLA-A, HLA-B, and HLA-C. The genomic regions containing the KIR and HLA class I genes are unlinked, structurally complex, and highly polymorphic. They are also strongly associated with a wide spectrum of diseases, including infections, autoimmune disorders, cancers, and pregnancy disorders, as well as the efficacy of transplantation and other immunotherapies. To facilitate study of these extraordinary genes, we developed a method that captures, sequences, and analyzes the 13 KIR genes and HLA-A, HLA-B, and HLA-C from genomic DNA. We also devised a bioinformatics pipeline that attributes sequencing reads to specific KIR genes, determines copy number by read depth, and calls high-resolution genotypes for each KIR gene. We validated this method by using DNA from well-characterized cell lines, comparing it to established methods of HLA and KIR genotyping, and determining KIR genotypes from 1000 Genomes sequence data. This identified 116 previously uncharacterized KIR alleles, which were all demonstrated to be authentic by sequencing from source DNA via standard methods. Analysis of just two KIR genes showed that 22% of the 1000 Genomes individuals have a previously uncharacterized allele or a structural variant. The method we describe is suited to the large-scale analyses that are needed for characterizing human populations and defining the precise HLA and KIR factors associated with disease. The methods are applicable to other highly polymorphic genes.
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Huth TK, Brenu EW, Staines DR, Marshall-Gradisnik SM. Killer Cell Immunoglobulin-like Receptor Genotype and Haplotype Investigation of Natural Killer Cells from an Australian Population of Chronic Fatigue Syndrome/Myalgic Encephalomyelitis Patients. GENE REGULATION AND SYSTEMS BIOLOGY 2016; 10:43-9. [PMID: 27346947 PMCID: PMC4913894 DOI: 10.4137/grsb.s39861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/04/2016] [Accepted: 05/05/2016] [Indexed: 11/20/2022]
Abstract
Killer cell immunoglobulin-like receptor (KIR) genes encode for activating and inhibitory surface receptors, which are correlated with the regulation of Natural Killer (NK) cell cytotoxic activity. Reduced NK cell cytotoxic activity has been consistently reported in Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (CFS/ME) patients, and KIR haplotypes and allelic polymorphism remain to be investigated. The aim of this article was to conduct a pilot study to examine KIR genotypes, haplotypes, and allelic polymorphism in CFS/ME patients and nonfatigued controls (NFCs). Comparison of KIR and allelic polymorphism frequencies revealed no significant differences between 20 CFS/ME patients and 20 NFCs. A lower frequency of the telomeric A/B motif (P < 0.05) was observed in CFS/ME patients compared with NFCs. This pilot study is the first to report the differences in the frequency of KIR on the telomeric A/B motif in CFS/ME patients. Further studies with a larger CFS/ME cohort are required to validate these results.
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Affiliation(s)
- T K Huth
- National Centre for Neuroimmunology and Emerging Diseases, Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia.; School of Medical Science, Griffith University, Southport, QLD, Australia
| | - E W Brenu
- National Centre for Neuroimmunology and Emerging Diseases, Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia.; School of Medical Science, Griffith University, Southport, QLD, Australia
| | - D R Staines
- National Centre for Neuroimmunology and Emerging Diseases, Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia.; School of Medical Science, Griffith University, Southport, QLD, Australia
| | - S M Marshall-Gradisnik
- National Centre for Neuroimmunology and Emerging Diseases, Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia.; School of Medical Science, Griffith University, Southport, QLD, Australia
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