1
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Kang JB, Shen AZ, Gurajala S, Nathan A, Rumker L, Aguiar VRC, Valencia C, Lagattuta KA, Zhang F, Jonsson AH, Yazar S, Alquicira-Hernandez J, Khalili H, Ananthakrishnan AN, Jagadeesh K, Dey K, Daly MJ, Xavier RJ, Donlin LT, Anolik JH, Powell JE, Rao DA, Brenner MB, Gutierrez-Arcelus M, Luo Y, Sakaue S, Raychaudhuri S. Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution. Nat Genet 2023; 55:2255-2268. [PMID: 38036787 PMCID: PMC10787945 DOI: 10.1038/s41588-023-01586-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023]
Abstract
The human leukocyte antigen (HLA) locus plays a critical role in complex traits spanning autoimmune and infectious diseases, transplantation and cancer. While coding variation in HLA genes has been extensively documented, regulatory genetic variation modulating HLA expression levels has not been comprehensively investigated. Here we mapped expression quantitative trait loci (eQTLs) for classical HLA genes across 1,073 individuals and 1,131,414 single cells from three tissues. To mitigate technical confounding, we developed scHLApers, a pipeline to accurately quantify single-cell HLA expression using personalized reference genomes. We identified cell-type-specific cis-eQTLs for every classical HLA gene. Modeling eQTLs at single-cell resolution revealed that many eQTL effects are dynamic across cell states even within a cell type. HLA-DQ genes exhibit particularly cell-state-dependent effects within myeloid, B and T cells. For example, a T cell HLA-DQA1 eQTL ( rs3104371 ) is strongest in cytotoxic cells. Dynamic HLA regulation may underlie important interindividual variability in immune responses.
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Affiliation(s)
- Joyce B Kang
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Amber Z Shen
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Saisriram Gurajala
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Laurie Rumker
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Vitor R C Aguiar
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Cristian Valencia
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kaitlyn A Lagattuta
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Fan Zhang
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Seyhan Yazar
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | | | - Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Kushal Dey
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics and Systems Biology Program, Weill Cornell Medicine, New York, NY, USA
| | - Mark J Daly
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ramnik J Xavier
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura T Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Jennifer H Anolik
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Joseph E Powell
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Maria Gutierrez-Arcelus
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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Kang JB, Shen AZ, Sakaue S, Luo Y, Gurajala S, Nathan A, Rumker L, Aguiar VRC, Valencia C, Lagattuta K, Zhang F, Jonsson AH, Yazar S, Alquicira-Hernandez J, Khalili H, Ananthakrishnan AN, Jagadeesh K, Dey K, Daly MJ, Xavier RJ, Donlin LT, Anolik JH, Powell JE, Rao DA, Brenner MB, Gutierrez-Arcelus M, Raychaudhuri S. Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.14.23287257. [PMID: 36993194 PMCID: PMC10055604 DOI: 10.1101/2023.03.14.23287257] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The human leukocyte antigen (HLA) locus plays a critical role in complex traits spanning autoimmune and infectious diseases, transplantation, and cancer. While coding variation in HLA genes has been extensively documented, regulatory genetic variation modulating HLA expression levels has not been comprehensively investigated. Here, we mapped expression quantitative trait loci (eQTLs) for classical HLA genes across 1,073 individuals and 1,131,414 single cells from three tissues, using personalized reference genomes to mitigate technical confounding. We identified cell-type-specific cis-eQTLs for every classical HLA gene. Modeling eQTLs at single-cell resolution revealed that many eQTL effects are dynamic across cell states even within a cell type. HLA-DQ genes exhibit particularly cell-state-dependent effects within myeloid, B, and T cells. Dynamic HLA regulation may underlie important interindividual variability in immune responses.
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Affiliation(s)
- Joyce B. Kang
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Amber Z. Shen
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Yang Luo
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Saisriram Gurajala
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Laurie Rumker
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Vitor R. C. Aguiar
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Cristian Valencia
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Kaitlyn Lagattuta
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Fan Zhang
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Seyhan Yazar
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ashwin N. Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Kushal Dey
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Mark J. Daly
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ramnik J. Xavier
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura T. Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Jennifer H. Anolik
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Deepak A. Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael B. Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Maria Gutierrez-Arcelus
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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Hu L, He D, Zeng H. Association of parental HLA-G polymorphisms with soluble HLA-G expressions and their roles on recurrent implantation failure: A systematic review and meta-analysis. Front Immunol 2022; 13:988370. [PMID: 36532068 PMCID: PMC9751038 DOI: 10.3389/fimmu.2022.988370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/14/2022] [Indexed: 12/04/2022] Open
Abstract
Introduction HLA-G plays a central role in immune tolerance at the maternal-fetal interface. The HLA-G gene is characterized by low allelic polymorphism and restricted tissue expression compared with classical HLA genes. HLA-G polymorphism is associated with HLA-G expression and linked to pregnancy complications. However, the association of parental HLA-G polymorphisms with soluble HLA-G (sHLA-G) expression and their roles in recurrent implantation failure (RIF) is unclear. The study aims to systematically review the association of HLA-G polymorphisms with RIF, the association of sHLA-G expression with RIF, and the association of HLA-G polymorphisms with sHLA-G expressions in patients attending in-vitro fertilization (IVF) treatment. Methods Studies that evaluated the association of HLA-G polymorphisms with RIF, the association between sHLA-G expression with RIF, and the association between HLA-G polymorphisms with sHLA-G expressions in patients attending IVF treatment were included. Meta-analysis was performed by random-effect models. Sensitivity analysis was performed by excluding one study each time. Subgroup analysis was performed based on ethnicity. Results HLA-G 14bp ins variant is associated with a lower expression of sHLA-G in seminal or blood plasma of couples attending IVF treatment. The maternal HLA-G*010101 and paternal HLA-G*010102 alleles are associated with RIF risk compared to other alleles. However, single maternal HLA-G 14bp ins/del polymorphism, HLA-G -725 C>G/T polymorphism, or circulating sHLA-G concentration was not significantly associated with RIF in the general population. HLA-G 14bp ins/ins homozygous genotype or ins variant was associated with a higher risk of RIF in the Caucasian population. Discussion Specific HLA-G alleles or HLA-G polymorphisms are associated with sHLA-G expression in couples attending IVF treatment. Several HLA-G polymorphisms may be related to RIF, considering different ethnic backgrounds. A combined genetic effect should be considered in future studies to confirm the association of HLA-G polymorphisms and sHLA-G expressions in relation to RIF.
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Affiliation(s)
- Lian Hu
- Department of Gynecology and Obstetrics, The Fourth Changsha Hospital, Changsha, China
| | - Dongmei He
- Department of Gynecology and Obstetrics, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Hong Zeng
- Department of Reproductive Medicine Center, Foshan Maternal and Child Health Care Hospital, Southern Medical University, Guangzhou, China,Department of Reproductive Medicine Center, Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Hong Zeng,
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Pollock NR, Harrison GF, Norman PJ. Immunogenomics of Killer Cell Immunoglobulin-Like Receptor (KIR) and HLA Class I: Coevolution and Consequences for Human Health. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2022; 10:1763-1775. [PMID: 35561968 PMCID: PMC10038757 DOI: 10.1016/j.jaip.2022.04.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/12/2022]
Abstract
Interactions of killer cell immunoglobin-like receptors (KIR) with human leukocyte antigens (HLA) class I regulate effector functions of key cytotoxic cells of innate and adaptive immunity. The extreme diversity of this interaction is genetically determined, having evolved in the ever-changing environment of pathogen exposure. Diversity of KIR and HLA genes is further facilitated by their independent segregation on separate chromosomes. That fetal implantation relies on many of the same types of immune cells as infection control places certain constraints on the evolution of KIR interactions with HLA. Consequently, specific inherited combinations of receptors and ligands may predispose to specific immune-mediated diseases, including autoimmunity. Combinatorial diversity of KIR and HLA class I can also differentiate success rates of immunotherapy directed to these diseases. Progress toward both etiopathology and predicting response to therapy is being achieved through detailed characterization of the extent and consequences of the combinatorial diversity of KIR and HLA. Achieving these goals is more tractable with the development of integrated analyses of molecular evolution, function, and pathology that will establish guidelines for understanding and managing risks. Here, we present what is known about the coevolution of KIR with HLA class I and the impact of their complexity on immune function and homeostasis.
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Affiliation(s)
- Nicholas R Pollock
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo
| | - Genelle F Harrison
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo.
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5
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Alexandrova M, Manchorova D, Dimova T. Immunity at maternal-fetal interface: KIR/HLA (Allo)recognition. Immunol Rev 2022; 308:55-76. [PMID: 35610960 DOI: 10.1111/imr.13087] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/28/2022] [Accepted: 05/09/2022] [Indexed: 12/15/2022]
Abstract
Both KIR and HLA are the most variable gene families in the human genome. The recognition of the semi-allogeneic embryo-derived trophoblasts by maternal decidual NK (dNK) cells is essential for the establishment of the functional placenta. This recognition is based on the KIR-HLA interactions and trophoblast expresses a specific HLA profile that constitutes classical polymorphic HLA-C and non-classical oligomorphic HLA-E, HLA-F, and HLA-G molecules. This review highlights some features of the KIR/HLA-C (allo)recognition by decidual NK (dNK) cells as a main immune cell population specifically enriched at maternal-fetal interface during human early pregnancy. How KIR/HLA-C axis operates in pregnancy disorders and in the context of transplacental infections is discussed as well. We summarized old and new data on dNK-cell functional plasticity, their selective expression of KIR and fetal maternal/paternal HLA-C haplotypes present. Results showed that KIR-HLA-C combinations and the corresponding axis operate differently in each pregnancy, determined by the variability of both maternal KIR haplotypes and fetus' maternal/paternal HLA-C allotype combinations. Moreover, the maturation of NK cells strongly depends on if or not HLA allotypes for certain KIR are present. We suggest that the unique KIR/HLA combinations reached in each pregnancy (normal and pathological) should be studied according to well-defined guidelines and unified methodologies to have comparable results ease to interpret and use in clinics.
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Affiliation(s)
- Marina Alexandrova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Diana Manchorova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Tanya Dimova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
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6
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Serena C, Clemenza S, Simeone S, Zullino S, Ottanelli S, Rambaldi MP, Vannuccini S, Petraglia F, Mecacci F. Undifferentiated Connective Tissue Disease in Pregnancy: A Topic Yet to be Explored. Front Pharmacol 2022; 13:820760. [PMID: 35126164 PMCID: PMC8811283 DOI: 10.3389/fphar.2022.820760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/07/2022] [Indexed: 01/05/2023] Open
Abstract
Undifferentiated connective tissue disease (UCTD) is characterized by signs and symptoms suggestive of a connective tissue disease (CTD), but not fulfilling criteria for a specific CTD. Although UCTD is probably the most common rheumatic disease diagnosed in pregnant women, data about disease course during pregnancy and perinatal outcomes are very limited. Compared to other CTDs, UCTD seems to have milder clinical manifestations in pregnancy. Its natural history is related to disease activity at conception. In fact, if the disease is in a state of remission or minimal activity at conception, pregnancy outcomes are generally good. On the contrary, patients who become pregnant in a moment of high disease activity and/or who have multiple antibodies positivity show an increased risk of disease flares, evolution to a definite CTD and obstetric complications, such as fetal growth restriction, preeclampsia and preterm birth. Therefore, a preconception assessment is essential in women with UCTD to evaluate maternal and fetal risks, to initiate interventions to optimize disease activity, and to adjust medications to those that are least harmful to the fetus. The aim of the present study was to review the available literature about pregnancy course, maternal and fetal outcomes and therapeutic approaches of pregnant women with UCTD.
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Affiliation(s)
- Caterina Serena
- High Risk Pregnancy Unit, Careggi University Hospital, Florence, Italy
| | - Sara Clemenza
- High Risk Pregnancy Unit, Careggi University Hospital, Florence, Italy
- *Correspondence: Sara Clemenza,
| | - Serena Simeone
- High Risk Pregnancy Unit, Careggi University Hospital, Florence, Italy
| | - Sara Zullino
- High Risk Pregnancy Unit, Careggi University Hospital, Florence, Italy
| | - Serena Ottanelli
- High Risk Pregnancy Unit, Careggi University Hospital, Florence, Italy
| | | | - Silvia Vannuccini
- High Risk Pregnancy Unit, Careggi University Hospital, Florence, Italy
| | - Felice Petraglia
- Department of Biomedical, Experimental and Clinical Sciences, Careggi University Hospital, University of Florence, Florence, Italy
| | - Federico Mecacci
- High Risk Pregnancy Unit, Careggi University Hospital, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences, Careggi University Hospital, University of Florence, Florence, Italy
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7
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Sadovsky Y, Mesiano S, Burton GJ, Lampl M, Murray JC, Freathy RM, Mahadevan-Jansen A, Moffett A, Price ND, Wise PH, Wildman DE, Snyderman R, Paneth N, Capra JA, Nobrega MA, Barak Y, Muglia LJ. Advancing human health in the decade ahead: pregnancy as a key window for discovery: A Burroughs Wellcome Fund Pregnancy Think Tank. Am J Obstet Gynecol 2020; 223:312-321. [PMID: 32565236 PMCID: PMC7303037 DOI: 10.1016/j.ajog.2020.06.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 12/16/2022]
Abstract
Recent revolutionary advances at the intersection of medicine, omics, data sciences, computing, epidemiology, and related technologies inspire us to ponder their impact on health. Their potential impact is particularly germane to the biology of pregnancy and perinatal medicine, where limited improvement in health outcomes for women and children has remained a global challenge. We assembled a group of experts to establish a Pregnancy Think Tank to discuss a broad spectrum of major gestational disorders and adverse pregnancy outcomes that affect maternal-infant lifelong health and should serve as targets for leveraging the many recent advances. This report reflects avenues for future effects that hold great potential in 3 major areas: developmental genomics, including the application of methodologies designed to bridge genotypes, physiology, and diseases, addressing vexing questions in early human development; gestational physiology, from immune tolerance to growth and the timing of parturition; and personalized and population medicine, focusing on amalgamating health record data and deep phenotypes to create broad knowledge that can be integrated into healthcare systems and drive discovery to address pregnancy-related disease and promote general health. We propose a series of questions reflecting development, systems biology, diseases, clinical approaches and tools, and population health, and a call for scientific action. Clearly, transdisciplinary science must advance and accelerate to address adverse pregnancy outcomes. Disciplines not traditionally involved in the reproductive sciences, such as computer science, engineering, mathematics, and pharmacology, should be engaged at the study design phase to optimize the information gathered and to identify and further evaluate potentially actionable therapeutic targets. Information sources should include noninvasive personalized sensors and monitors, alongside instructive "liquid biopsies" for noninvasive pregnancy assessment. Future research should also address the diversity of human cohorts in terms of geography, racial and ethnic distributions, and social and health disparities. Modern technologies, for both data-gathering and data-analyzing, make this possible at a scale that was previously unachievable. Finally, the psychosocial and economic environment in which pregnancy takes place must be considered to promote the health and wellness of communities worldwide.
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Affiliation(s)
- Yoel Sadovsky
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA
| | - Sam Mesiano
- Department of Reproductive Biology, Case Western Reserve University, and Department of Obstetrics and Gynecology, University Hospitals of Cleveland, Cleveland, OH
| | - Graham J Burton
- Centre for Trophoblast Research; University of Cambridge, Cambridge, United Kingdom
| | - Michelle Lampl
- Center for the Study of Human Health, Emory University, Atlanta, GA
| | | | | | - Anita Mahadevan-Jansen
- Vanderbilt Biophotonics Center and Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Ashley Moffett
- Department of Pathology; Centre for Trophoblast Research
| | | | - Paul H Wise
- Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, CA
| | - Derek E Wildman
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL
| | - Ralph Snyderman
- Duke Center for Personalized Health Care, Duke University Medical Center, Durham, NC
| | - Nigel Paneth
- Departments of Epidemiology and Biostatistics and of Pediatrics and Human Development, College of Human Medicine, Michigan State University, East Lansing, MI
| | | | | | - Yaacov Barak
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA
| | - Louis J Muglia
- Office of the President, Burroughs Wellcome Fund, Research Triangle Park, NC.
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8
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Barth C, de Lange AMG. Towards an understanding of women's brain aging: the immunology of pregnancy and menopause. Front Neuroendocrinol 2020; 58:100850. [PMID: 32504632 DOI: 10.1016/j.yfrne.2020.100850] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/23/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023]
Abstract
Women are at significantly greater risk of developing Alzheimer's disease and show higher prevalence of autoimmune conditions relative to men. Women's brain health is historically understudied, and little is therefore known about the mechanisms underlying epidemiological sex differences in neurodegenerative diseases, and how female-specific factors may influence women's brain health across the lifespan. In this review, we summarize recent studies on the immunology of pregnancy and menopause, emphasizing that these major immunoendocrine transition phases may play a critical part in women's brain aging trajectories.
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Affiliation(s)
- Claudia Barth
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Ann-Marie G de Lange
- Department of Psychology, University of Oslo, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK.
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9
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Sacks G, Finkelstein E. Natural killer cells and reproductive success. Am J Reprod Immunol 2020; 85:e13291. [DOI: 10.1111/aji.13291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/15/2020] [Indexed: 12/30/2022] Open
Affiliation(s)
- Gavin Sacks
- IVFAustralia Sydney Australia
- University of New South Wales Sydney Australia
- St George hospital and Royal Hospital for Women Sydney Australia
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Barbitoff YA, Tsarev AA, Vashukova ES, Maksiutenko EM, Kovalenko LV, Belotserkovtseva LD, Glotov AS. A Data-Driven Review of the Genetic Factors of Pregnancy Complications. Int J Mol Sci 2020; 21:ijms21093384. [PMID: 32403311 PMCID: PMC7246997 DOI: 10.3390/ijms21093384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 01/01/2023] Open
Abstract
Over the recent years, many advances have been made in the research of the genetic factors of pregnancy complications. In this work, we use publicly available data repositories, such as the National Human Genome Research Institute GWAS Catalog, HuGE Navigator, and the UK Biobank genetic and phenotypic dataset to gain insights into molecular pathways and individual genes behind a set of pregnancy-related traits, including the most studied ones—preeclampsia, gestational diabetes, preterm birth, and placental abruption. Using both HuGE and GWAS Catalog data, we confirm that immune system and, in particular, T-cell related pathways are one of the most important drivers of pregnancy-related traits. Pathway analysis of the data reveals that cell adhesion and matrisome-related genes are also commonly involved in pregnancy pathologies. We also find a large role of metabolic factors that affect not only gestational diabetes, but also the other traits. These shared metabolic genes include IGF2, PPARG, and NOS3. We further discover that the published genetic associations are poorly replicated in the independent UK Biobank cohort. Nevertheless, we find novel genome-wide associations with pregnancy-related traits for the FBLN7, STK32B, and ACTR3B genes, and replicate the effects of the KAZN and TLE1 genes, with the latter being the only gene identified across all data resources. Overall, our analysis highlights central molecular pathways for pregnancy-related traits, and suggests a need to use more accurate and sophisticated association analysis strategies to robustly identify genetic risk factors for pregnancy complications.
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Affiliation(s)
- Yury A. Barbitoff
- Bioinformatics Institute, 197342 St. Petersburg, Russia; (Y.A.B.); (A.A.T.)
- Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 St. Petersburg, Russia;
- Department of Genomic Medicine, D.O.Ott Research Institute for Obstetrics, Gynaecology and Reproductology, 199034 St. Petersburg, Russia;
| | - Alexander A. Tsarev
- Bioinformatics Institute, 197342 St. Petersburg, Russia; (Y.A.B.); (A.A.T.)
- Department of Biochemistry, Saint-Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena S. Vashukova
- Department of Genomic Medicine, D.O.Ott Research Institute for Obstetrics, Gynaecology and Reproductology, 199034 St. Petersburg, Russia;
| | - Evgeniia M. Maksiutenko
- Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 St. Petersburg, Russia;
- St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Liudmila V. Kovalenko
- Department of Pathology, Medical Institute, Surgut State University, 628416 Surgut, Russia;
| | - Larisa D. Belotserkovtseva
- Department of Obstetrics, Gynecology and Perinatology, Medical Institute, Surgut State University, 628416 Surgut, Russia;
| | - Andrey S. Glotov
- Department of Genomic Medicine, D.O.Ott Research Institute for Obstetrics, Gynaecology and Reproductology, 199034 St. Petersburg, Russia;
- Laboratory of Biobanking and Genomic Medicine, Saint-Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence:
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