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Weeratunga P, Moller DR, Ho LP. Immune mechanisms of granuloma formation in sarcoidosis and tuberculosis. J Clin Invest 2024; 134:e175264. [PMID: 38165044 PMCID: PMC10760966 DOI: 10.1172/jci175264] [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] [Indexed: 01/03/2024] Open
Abstract
Sarcoidosis is a complex immune-mediated disease characterized by clusters of immune cells called granulomas. Despite major steps in understanding the cause of this disease, many questions remain. In this Review, we perform a mechanistic interrogation of the immune activities that contribute to granuloma formation in sarcoidosis and compare these processes with its closest mimic, tuberculosis, highlighting shared and divergent immune activities. We examine how Mycobacterium tuberculosis is sensed by the immune system; how the granuloma is initiated, formed, and perpetuated in tuberculosis compared with sarcoidosis; and the role of major innate and adaptive immune cells in shaping these processes. Finally, we draw these findings together around several recent high-resolution studies of the granuloma in situ that utilized the latest advances in single-cell technology combined with spatial methods to analyze plausible disease mechanisms. We conclude with an overall view of granuloma formation in sarcoidosis.
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Affiliation(s)
- Praveen Weeratunga
- MRC Translational Immunology Discovery Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Ling-Pei Ho
- MRC Translational Immunology Discovery Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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2
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Liao SY, Fingerlin T, Maier L. Genetic predisposition to sarcoidosis. J Autoimmun 2023:103122. [PMID: 37865580 DOI: 10.1016/j.jaut.2023.103122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/04/2023] [Indexed: 10/23/2023]
Abstract
Sarcoidosis is a complex systemic disease with clinical heterogeneity based on varying phenotypes and natural history. The detailed etiology of sarcoidosis remains unknown, but genetic predisposition as well as environmental exposures play a significant role in disease pathogenesis. We performed a comprehensive review of germline genetic (DNA) and transcriptomic (RNA) studies of sarcoidosis, including both previous studies and more recent findings. In this review, we provide an assessment of the following: genetic variants in sarcoidosis susceptibility and phenotypes, ancestry- and sex-specific genetic variants in sarcoidosis, shared genetic architecture between sarcoidosis and other diseases, and gene-environment interactions in sarcoidosis. We also highlight the unmet needs in sarcoidosis genetic studies, including the pressing requirement to include diverse populations and have consistent definitions of phenotypes in the sarcoidosis research community to help advance the application of genetic predisposition to sarcoidosis disease risk and manifestations.
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Affiliation(s)
- Shu-Yi Liao
- National Jewish Health, Department of Medicine, Denver, CO, USA; University of Colorado Anschutz Medical Campus, Department of Medicine, Aurora, CO, USA; Colorado School of Public Health, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA
| | - Tasha Fingerlin
- National Jewish Health, Department of Medicine, Denver, CO, USA; University of Colorado Anschutz Medical Campus, Department of Medicine, Aurora, CO, USA; Colorado School of Public Health, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA; National Jewish Health, Department of Immunology and Genomic Medicine, Denver, CO, USA
| | - Lisa Maier
- National Jewish Health, Department of Medicine, Denver, CO, USA; University of Colorado Anschutz Medical Campus, Department of Medicine, Aurora, CO, USA; Colorado School of Public Health, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA.
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3
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Tan JL, Tan BEX, Cheung JW, Ortman M, Lee JZ. Update on cardiac sarcoidosis. Trends Cardiovasc Med 2023; 33:442-455. [PMID: 35504422 DOI: 10.1016/j.tcm.2022.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 12/17/2022]
Abstract
Cardiac sarcoidosis is an inflammatory myocardial disease of unknown etiology. It is characterized by the deposition of non-caseating granulomas that may involve any part of the heart. Cardiac sarcoidosis is often under-diagnosed or recognized partly due to the heterogeneous clinical presentation of the disease. The three most frequent clinical manifestations of cardiac sarcoidosis are atrioventricular block, ventricular arrhythmias, and heart failure. A definitive diagnosis of cardiac sarcoidosis can be made with histology findings from an endomyocardial biopsy. However, the diagnosis in the majority of cases is based on findings from the clinical presentation and advanced imaging due to the low sensitivity of endomyocardial biopsy. The Heart Rhythm Society (HRS) 2014 expert consensus statement and the Japanese Ministry of Health and Welfare criteria are the two most commonly used diagnostic criteria sets. This review article summarizes the available evidence on cardiac sarcoidosis, focusing on the diagnostic criteria and stepwise approach to its management.
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Affiliation(s)
- Jian Liang Tan
- Division of Cardiovascular Disease, Cooper University Health Care/Cooper Medical School of Rowan University, Camden, New Jersey.
| | - Bryan E-Xin Tan
- Department of Internal Medicine, Rochester General Hospital, Rochester, NY
| | - Jim W Cheung
- Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Matthew Ortman
- Division of Cardiovascular Disease, Cooper University Health Care/Cooper Medical School of Rowan University, Camden, New Jersey
| | - Justin Z Lee
- Department of Cardiology, Mayo Clinic Arizona, Phoenix, Arizona, USA
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4
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Levin AM, She R, Chen Y, Adrianto I, Datta I, Loveless IM, Garman L, Montgomery CG, Li J, Iannuzzi MC, Rybicki BA. Identification of Environmental Exposures Associated with Risk of Sarcoidosis in African Americans. Ann Am Thorac Soc 2023; 20:1274-1282. [PMID: 37209419 PMCID: PMC10502890 DOI: 10.1513/annalsats.202208-722oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/19/2023] [Indexed: 05/22/2023] Open
Abstract
Rationale: Sarcoidosis is a racially disparate granulomatous disease likely caused by environmental exposures, genes, and their interactions. Despite increased risk in African Americans, few environmental risk factor studies in this susceptible population exist. Objectives: To identify environmental exposures associated with the risk of sarcoidosis in African Americans and those that differ in effect by self-identified race and genetic ancestry. Methods: The study sample comprised 2,096 African Americans (1,205 with and 891 without sarcoidosis) compiled from three component studies. Unsupervised clustering and multiple correspondence analyses were used to identify underlying clusters of environmental exposures. Mixed-effects logistic regression was used to evaluate the association of these exposure clusters and the 51 single-component exposures with risk of sarcoidosis. A comparison case-control sample of 762 European Americans (388 with and 374 without sarcoidosis) was used to assess heterogeneity in exposure risk by race. Results: Seven exposure clusters were identified, five of which were associated with risk. The exposure cluster with the strongest risk association was composed of metals (P < 0.001), and within this cluster, exposure to aluminum had the highest risk (odds ratio, 3.30; 95% confidence interval [95% CI], 2.23-4.09; P < 0.001). This effect also differed by race (P < 0.001), with European Americans having no significant association with exposure (odds ratio, 0.86; 95% CI, 0.56-1.33). Within African Americans, the increased risk was dependent on genetic African ancestry (P = 0.047). Conclusions: Our findings support African Americans having sarcoidosis environmental exposure risk profiles that differ from those of European Americans. These differences may underlie racially disparate incidence rates that are partially explained by genetic variation differing by African ancestry.
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Affiliation(s)
- Albert M. Levin
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Ruicong She
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Yalei Chen
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Indra Adrianto
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Indrani Datta
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Ian M. Loveless
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Lori Garman
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma; and
| | - Courtney G. Montgomery
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma; and
| | - Jia Li
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Michael C. Iannuzzi
- Department of Medical Education, School of Medicine, City University of New York, New York, New York
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5
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Liao SY, Jacobson S, Hamzeh NY, Culver DA, Barkes BQ, Mroz M, Macphail K, Pacheco K, Patel DC, Wasfi YS, Koth LL, Langefeld CD, Leach SM, White E, Montgomery C, Maier LA, Fingerlin TE. Genome-wide association study identifies multiple HLA loci for sarcoidosis susceptibility. Hum Mol Genet 2023; 32:2669-2678. [PMID: 37399103 PMCID: PMC10407706 DOI: 10.1093/hmg/ddad067] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/30/2023] [Accepted: 04/19/2023] [Indexed: 07/05/2023] Open
Abstract
Sarcoidosis is a complex systemic disease. Our study aimed to (1) identify novel alleles associated with sarcoidosis susceptibility; (2) provide an in-depth evaluation of HLA alleles and sarcoidosis susceptibility and (3) integrate genetic and transcription data to identify risk loci that may more directly impact disease pathogenesis. We report a genome-wide association study of 1335 sarcoidosis cases and 1264 controls of European descent (EA) and investigate associated alleles in a study of African Americans (AA: 1487 cases and 1504 controls). The EA and AA cohort was recruited from multiple United States sites. HLA alleles were imputed and tested for association with sarcoidosis susceptibility. Expression quantitative locus and colocalization analysis were performed using a subset of subjects with transcriptome data. Forty-nine SNPs in the HLA region in HLA-DRA, -DRB9, -DRB5, -DQA1 and BRD2 genes were significantly associated with sarcoidosis susceptibility in EA, rs3129888 was also a risk variant for sarcoidosis in AA. Classical HLA alleles DRB1*0101, DQA1*0101 and DQB1*0501, which are highly correlated, were also associated with sarcoidosis. rs3135287 near HLA-DRA was associated with HLA-DRA expression in peripheral blood mononuclear cells and bronchoalveolar lavage from subjects and lung tissue and whole blood from GTEx. We identified six novel SNPs (out of the seven SNPs representing the 49 significant SNPs) and nine HLA alleles associated with sarcoidosis susceptibility in the largest EA population. We also replicated our findings in an AA population. Our study reiterates the potential role of antigen recognition and/or presentation HLA class II genes in sarcoidosis pathogenesis.
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Affiliation(s)
- Shu-Yi Liao
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado School of Public Health, University of Colorado Denver–Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sean Jacobson
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Nabeel Y Hamzeh
- Department of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Daniel A Culver
- Department of Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Briana Q Barkes
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Margarita Mroz
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Kristyn Macphail
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Karin Pacheco
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado School of Public Health, University of Colorado Denver–Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Divya C Patel
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, FL 32610, USA
| | | | - Laura L Koth
- Department of Medicine, University of California-San Fransisco, San Fransisco, CA 94143, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
- Wake Forest University School of Medicine, Center for Precision Medicine, Winston-Salem, NC 27101, USA
| | - Sonia M Leach
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Elizabeth White
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | | | - Lisa A Maier
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado School of Public Health, University of Colorado Denver–Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tasha E Fingerlin
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado School of Public Health, University of Colorado Denver–Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA
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6
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Wang X, Liu Y. Offense and Defense in Granulomatous Inflammation Disease. Front Cell Infect Microbiol 2022; 12:797749. [PMID: 35846773 PMCID: PMC9277142 DOI: 10.3389/fcimb.2022.797749] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Granulomatous inflammation (GI) diseases are a group of chronic inflammation disorders characterized by focal collections of multinucleated giant cells, epithelioid cells and macrophages, with or without necrosis. GI diseases are closely related to microbes, especially virulent intracellular bacterial infections are important factors in the progression of these diseases. They employ a range of strategies to survive the stresses imposed upon them and persist in host cells, becoming the initiator of the fighting. Microbe-host communication is essential to maintain functions of a healthy host, so defense capacity of hosts is another influence factor, which is thought to combine to determine the result of the fighting. With the development of gene research technology, many human genetic loci were identified to be involved in GI diseases susceptibility, providing more insights into and knowledge about GI diseases. The current review aims to provide an update on the most recent progress in the identification and characterization of bacteria in GI diseases in a variety of organ systems and clinical conditions, and examine the invasion and escape mechanisms of pathogens that have been demonstrated in previous studies, we also review the existing data on the predictive factors of the host, mainly on genetic findings. These strategies may improve our understanding of the mechanisms underlying GI diseases, and open new avenues for the study of the associated conditions in the future.
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Affiliation(s)
- Xinwen Wang
- Shaanxi Clinical Research Center for Oral Diseases, National Clinical Research Center for Oral Diseases, State Key Laboratory of Military Stomatology, Department of Oral Medicine, School of Stomatology, The Fourth Military Medical University, Xi’an, China
| | - Yuan Liu
- Shaanxi International Joint Research Center for Oral Diseases, State Key Laboratory of Military Stomatology, Department of Histology and Pathology, School of Stomatology, The Fourth Military Medical University, Xi’an, China
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7
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Abstract
Epigenetic modifications are emerging as important regulatory mechanisms of gene expression in lung disease, given that they are influenced by environmental exposures and genetic variants, and that they regulate immune and fibrotic processes. In this review, we introduce these concepts with a focus on the study of DNA methylation and histone modifications and discuss how they have been applied to lung disease, and how they can be applied to sarcoidosis. This information has implications for other exposure and immunologically mediated lung diseases, such as chronic beryllium disease, hypersensitivity pneumonitis, and asbestosis.
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Affiliation(s)
- Iain R Konigsberg
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lisa A Maier
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Medicine, National Jewish Health, Denver, CO, USA
- Dept of Environmental and Occupational Health, Colorado School of Public Health, Aurora, CO, USA
| | - Ivana V Yang
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
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8
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Jabbari P, Sadeghalvad M, Rezaei N. An inflammatory triangle in Sarcoidosis: PPAR-γ, immune microenvironment, and inflammation. Expert Opin Biol Ther 2021; 21:1451-1459. [PMID: 33798017 DOI: 10.1080/14712598.2021.1913118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Sarcoidosis is an inflammatory disorder characterized by granuloma formation in several organs. Sarcoidosis patients experience higher inflammatory responses resulting in pulmonary fibrosis. Although the precise mechanisms have not been well elucidated, the relationship between the immune system activation and inflammatory status is pivotal in the pathogenesis of sarcoidosis. AREAS COVERED Peroxisome proliferator-activated receptor (PPAR) includes the transcription factors involved in cell metabolism, proliferation, and immune response. In the alveolar macrophages of patients with sarcoidosis, the reduced activity and a decreased level of PPAR-γ have been shown. In this study, we discuss how reducing the level of PPAR-γ could lead to increased inflammation and immune responses in patients with sarcoidosis. EXPERT OPINION Lack of PPAR-γ may contribute to the development of a suitable milieu for the formation of immune-associated pulmonary granuloma. Reduced levels of PPAR-γ in sarcoidosis could result from over-activation of the immune system and elevated inflammatory responses, as well. Due to the anti-inflammatory function of PPAR-γ, identifying the relation between PPAR-γ, sarcoidosis development, and inflammatory state could be essential to identify the appropriate therapeutic targets. The synthesis of PPAR-γ agonists or PPAR-γ ligands may be an effective step toward the treatment of sarcoidosis patients in the future.
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Affiliation(s)
- Parnia Jabbari
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mona Sadeghalvad
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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9
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Meguro A, Ishihara M, Petrek M, Yamamoto K, Takeuchi M, Mrazek F, Kolek V, Benicka A, Yamane T, Shibuya E, Yoshino A, Isomoto A, Ota M, Yatsu K, Shijubo N, Nagai S, Yamaguchi E, Yamaguchi T, Namba K, Kaburaki T, Takase H, Morimoto SI, Hori J, Kono K, Goto H, Suda T, Ikushima S, Ando Y, Takenaka S, Takeuchi M, Yuasa T, Sugisaki K, Ohguro N, Hiraoka M, Kitaichi N, Sugiyama Y, Horita N, Asukata Y, Kawagoe T, Kimura I, Ishido M, Inoko H, Mochizuki M, Ohno S, Bahram S, Remmers EF, Kastner DL, Mizuki N. Genetic control of CCL24, POR, and IL23R contributes to the pathogenesis of sarcoidosis. Commun Biol 2020; 3:465. [PMID: 32826979 PMCID: PMC7442816 DOI: 10.1038/s42003-020-01185-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 07/30/2020] [Indexed: 12/17/2022] Open
Abstract
Sarcoidosis is a genetically complex systemic inflammatory disease that affects multiple organs. We present a GWAS of a Japanese cohort (700 sarcoidosis cases and 886 controls) with replication in independent samples from Japan (931 cases and 1,042 controls) and the Czech Republic (265 cases and 264 controls). We identified three loci outside the HLA complex, CCL24, STYXL1-SRRM3, and C1orf141-IL23R, which showed genome-wide significant associations (P < 5.0 × 10−8) with sarcoidosis; CCL24 and STYXL1-SRRM3 were novel. The disease-risk alleles in CCL24 and IL23R were associated with reduced CCL24 and IL23R expression, respectively. The disease-risk allele in STYXL1-SRRM3 was associated with elevated POR expression. These results suggest that genetic control of CCL24, POR, and IL23R expression contribute to the pathogenesis of sarcoidosis. We speculate that the CCL24 risk allele might be involved in a polarized Th1 response in sarcoidosis, and that POR and IL23R risk alleles may lead to diminished host defense against sarcoidosis pathogens. Akira Meguro et al. report a genome-wide association study for sarcoidosis—a systemic inflammatory disease—in the Japanese population. They identify 3 non-HLA loci with genome-wide significance, 2 of which have not been previously associated with sarcoidosis in any population.
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Affiliation(s)
- Akira Meguro
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Mami Ishihara
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Martin Petrek
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska Str., 77515, Olomouc, Czech Republic
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, 67 Asahimachi, Kurume, Fukuoka, 830-0011, Japan.,Division of Genome Analysis, Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan
| | - Masaki Takeuchi
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.,Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, 10 Center Drive, 10 CRC East/B2-5235, Bethesda, MD, 20892-1849, USA
| | - Frantisek Mrazek
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University, I.P.Pavlova Str. 6, 77520, Olomouc, Czech Republic
| | - Vitezslav Kolek
- Department of Respiratory Medicine, Faculty of Medicine and Dentistry, Palacky University, I. P. Pavlova Str. 6, 77900, Olomouc, Czech Republic
| | - Alzbeta Benicka
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska Str., 77515, Olomouc, Czech Republic
| | - Takahiro Yamane
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Etsuko Shibuya
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Atsushi Yoshino
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Akiko Isomoto
- Division of Genome Analysis, Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan
| | - Masao Ota
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.,Division of Hepatology and Gastroenterology, Department of Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.,INSERM Franco-Japanese "Laboratoire International Associé" (LIA) Nextgen HLA Laboratory, Strasbourg, France.,INSERM Franco-Japanese "Laboratoire International Associé" (LIA) Nextgen HLA Laboratory, Nagano, Japan
| | - Keisuke Yatsu
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Noriharu Shijubo
- Department of Respiratory Medicine, Japan Railway Sapporo Hospital, Higashi-1, Kita-3, Chuo-ku, Sapporo, 060-0033, Japan
| | - Sonoko Nagai
- Kyoto Central Clinic/Clinical Research Center, 56-58 Masuyacho Sanjo-Takakura, Nakagyo-ku, Kyoto, 604-8111, Japan
| | - Etsuro Yamaguchi
- Division of Respiratory Medicine and Allergology, Aichi Medical University, 21 Karimata, Yazako, Nagakute-cho, Aichi-gun, Aichi, 480-1195, Japan
| | - Tetsuo Yamaguchi
- Department of Respiratory Medicine, Japan Railway Tokyo General Hospital, 2-1-3 Yoyogi, Shibuya-ku, Tokyo, 151-0053, Japan
| | - Kenichi Namba
- Department of Ophthalmology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15, W7, Kita-ku, Sapporo, Hokkaido, 060-8638, Japan
| | - Toshikatsu Kaburaki
- Department of Ophthalmology, University of Tokyo School of Medicine, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hiroshi Takase
- Department of Ophthalmology and Visual Science, Tokyo Medical and Dental University Graduate School of Medicine, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Shin-Ichiro Morimoto
- Division of Cardiology, Department of Internal Medicine, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukakecho, Toyoake, Aichi, 470-1192, Japan
| | - Junko Hori
- Department of Ophthalmology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Keiko Kono
- Department of Ophthalmology, Kono Medical Clinic, 3-30-28 Soshigaya, Setagaya-ku, Tokyo, 157-0072, Japan
| | - Hiroshi Goto
- Department of Ophthalmology, Tokyo Medical University, 6-7-1 Nishishinjuku, Shinjuku-ku, Tokyo, 160-0023, Japan
| | - Takafumi Suda
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Soichiro Ikushima
- Department of Respiratory Medicine, Japanese Red Cross Medical Centre, 4-1-22 Hiroo, Shibuya-ku, Tokyo, 150-8953, Japan
| | - Yasutaka Ando
- Department of Ophthalmology, Kitasato Institute Hospital, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8642, Japan.,Department of Ophthalmology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-0016, Japan
| | - Shinobu Takenaka
- Department of Respiratory Diseases, Kumamoto City Hospital, 1-1-60 Kotoh, Kumamoto, Kumamoto, 862-8505, Japan
| | - Masaru Takeuchi
- Department of Ophthalmology, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Takenosuke Yuasa
- Yuasa Eye Clinic, 3-1-1 Nishimoto-cho, Nishi-ku, Osaka, 550-0005, Japan
| | - Katsunori Sugisaki
- Department of Internal Medicine, National Hospital Organization Nishibeppu National Hospital, 4548 Oaza-Tsurumi, Beppu, Oita, 874-0840, Japan
| | - Nobuyuki Ohguro
- Department of Ophthalmology, Japan Community Health care Organization Osaka Hospital, 4-2-78 Fukushima, Fukushima-ku, Osaka, 553-0003, Japan
| | - Miki Hiraoka
- Department of Ophthalmology, School of Medicine, Sapporo Medical University, S1 W16 Chuo-ku, Sapporo, Hokkaido, 060-8543, Japan
| | - Nobuyoshi Kitaichi
- Department of Ophthalmology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15, W7, Kita-ku, Sapporo, Hokkaido, 060-8638, Japan.,Department of Ophthalmology, Health Sciences University of Hokkaido, Ainosato 2-5, Kita-ku, Sapporo, Hokkaido, 002-8072, Japan
| | - Yukihiko Sugiyama
- Division of Pulmonary Medicine, Department of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Nobuyuki Horita
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, 10 Center Drive, 10 CRC East/B2-5235, Bethesda, MD, 20892-1849, USA.,Department of Pulmonology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yuri Asukata
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Tatsukata Kawagoe
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Ikuko Kimura
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Mizuho Ishido
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Hidetoshi Inoko
- INSERM Franco-Japanese "Laboratoire International Associé" (LIA) Nextgen HLA Laboratory, Strasbourg, France.,INSERM Franco-Japanese "Laboratoire International Associé" (LIA) Nextgen HLA Laboratory, Nagano, Japan.,Department of Molecular Life Science, Division of Molecular Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Manabu Mochizuki
- Department of Ophthalmology and Visual Science, Tokyo Medical and Dental University Graduate School of Medicine, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Shigeaki Ohno
- Department of Ophthalmology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15, W7, Kita-ku, Sapporo, Hokkaido, 060-8638, Japan.,Department of Ophthalmology, Health Sciences University of Hokkaido, Ainosato 2-5, Kita-ku, Sapporo, Hokkaido, 002-8072, Japan
| | - Seiamak Bahram
- INSERM Franco-Japanese "Laboratoire International Associé" (LIA) Nextgen HLA Laboratory, Strasbourg, France.,INSERM Franco-Japanese "Laboratoire International Associé" (LIA) Nextgen HLA Laboratory, Nagano, Japan.,Plateforme GENOMAX, Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d'Immunologie et d'Hématologie. Faculté de Médecine, Fédération Hospitalo-Universitaire (FHU) OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Elaine F Remmers
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, 10 Center Drive, 10 CRC East/B2-5235, Bethesda, MD, 20892-1849, USA
| | - Daniel L Kastner
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, 10 Center Drive, 10 CRC East/B2-5235, Bethesda, MD, 20892-1849, USA
| | - Nobuhisa Mizuki
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.
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10
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Calender A, Weichhart T, Valeyre D, Pacheco Y. Current Insights in Genetics of Sarcoidosis: Functional and Clinical Impacts. J Clin Med 2020; 9:E2633. [PMID: 32823753 PMCID: PMC7465171 DOI: 10.3390/jcm9082633] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Sarcoidosis is a complex disease that belongs to the vast group of autoinflammatory disorders, but the etiological mechanisms of which are not known. At the crosstalk of environmental, infectious, and genetic factors, sarcoidosis is a multifactorial disease that requires a multidisciplinary approach for which genetic research, in particular, next generation sequencing (NGS) tools, has made it possible to identify new pathways and propose mechanistic hypotheses. Codified treatments for the disease cannot always respond to the most progressive forms and the identification of new genetic and metabolic tracks is a challenge for the future management of the most severe patients. Here, we review the current knowledge regarding the genes identified by both genome wide association studies (GWAS) and whole exome sequencing (WES), as well the connection of these pathways with the current research on sarcoidosis immune-related disorders.
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Affiliation(s)
- Alain Calender
- Department of Molecular and Medical genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France;
- CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory, University Claude Bernard Lyon 1, 69007 Lyon, France
| | - Thomas Weichhart
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, 1090 Vienna, Austria;
| | - Dominique Valeyre
- INSERM UMR 1272, Department of Pulmonology, Avicenne Hospital, University Sorbonne Paris Nord, Saint Joseph Hospital, AP-HP, 75014 Paris, France;
| | - Yves Pacheco
- Department of Molecular and Medical genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France;
- CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory, University Claude Bernard Lyon 1, 69007 Lyon, France
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11
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Terasaki F, Azuma A, Anzai T, Ishizaka N, Ishida Y, Isobe M, Inomata T, Ishibashi-Ueda H, Eishi Y, Kitakaze M, Kusano K, Sakata Y, Shijubo N, Tsuchida A, Tsutsui H, Nakajima T, Nakatani S, Horii T, Yazaki Y, Yamaguchi E, Yamaguchi T, Ide T, Okamura H, Kato Y, Goya M, Sakakibara M, Soejima K, Nagai T, Nakamura H, Noda T, Hasegawa T, Morita H, Ohe T, Kihara Y, Saito Y, Sugiyama Y, Morimoto SI, Yamashina A. JCS 2016 Guideline on Diagnosis and Treatment of Cardiac Sarcoidosis - Digest Version. Circ J 2019; 83:2329-2388. [PMID: 31597819 DOI: 10.1253/circj.cj-19-0508] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fumio Terasaki
- Medical Education Center / Department of Cardiology, Osaka Medical College
| | - Arata Azuma
- Department of Pulmonary Medicine, Nippon Medical School
| | - Toshihisa Anzai
- Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center
| | - Nobukazu Ishizaka
- Department of Internal Medicine (III) / Department of Cardiology, Osaka Medical College
| | - Yoshio Ishida
- Department of Internal Medicine, Kaizuka City Hospital
| | - Mitsuaki Isobe
- Department of Cardiovascular Medicine, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University
| | - Takayuki Inomata
- Department of Cardiology, Kitasato University Kitasato Institute Hospital
| | | | - Yoshinobu Eishi
- Department of Human Pathology, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University
| | - Masafumi Kitakaze
- Department of Clinical Medicine and Development, National Cerebral and Cardiovascular Center
| | - Kengo Kusano
- Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine
| | | | | | - Hiroyuki Tsutsui
- Department of Cardiovascular Medicine, Kyushu University Graduate School of Medical Sciences
| | - Takatomo Nakajima
- Division of Cardiology, Saitama Cardiovascular and Respiratory Center
| | - Satoshi Nakatani
- Division of Functional Diagnostics, Department of Health Sciences, Osaka University Graduate School of Medicine
| | - Taiko Horii
- Department of Cardiovascular Surgery, Kagawa University School of Medicine
| | | | - Etsuro Yamaguchi
- Department of Respiratory Medicine and Allergology, Aichi Medical University School of Medicine
| | | | - Tomomi Ide
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University
| | - Hideo Okamura
- Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center
| | | | - Masahiko Goya
- Department of Cardiology, Tokyo Medical and Dental University
| | - Mamoru Sakakibara
- Department of Cardiovascular Medicine, Hokkaido University Graduate School of Medicine
| | - Kyoko Soejima
- Department of Cardiology, Kyorin University Faculty of Medicine
| | - Toshiyuki Nagai
- Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center
| | | | - Takashi Noda
- Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center
| | - Takuya Hasegawa
- Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center
| | | | - Tohru Ohe
- Department of Cardiology, Sakakibara Heart Institute of Okayama
| | - Yasuki Kihara
- Department of Cardiovascular Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Yoshihiko Saito
- Department of Cardiorenal Medicine and Metabolic Disease, Nara Medical University
| | - Yukihiko Sugiyama
- Division of Pulmonary Medicine, Department of Medicine, Jichi Medical University
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12
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Next-Generation Sequencing Profiles of the Methylome and Transcriptome in Peripheral Blood Mononuclear Cells of Rheumatoid Arthritis. J Clin Med 2019; 8:jcm8091284. [PMID: 31443559 PMCID: PMC6780767 DOI: 10.3390/jcm8091284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 02/06/2023] Open
Abstract
Using next-generation sequencing to decipher methylome and transcriptome and underlying molecular mechanisms contributing to rheumatoid arthritis (RA) for improving future therapies, we performed methyl-seq and RNA-seq on peripheral blood mononuclear cells (PBMCs) from RA subjects and normal donors. Principal component analysis and hierarchical clustering revealed distinct methylation signatures in RA with methylation aberrations noted across chromosomes. Methylation alterations varied with CpG features and genic characteristics. Typically, CpG islands and CpG shores were hypermethylated and displayed the greatest methylation variance. Promoters were hypermethylated and enhancers/gene bodies were hypomethylated, with methylation variance associated with expression variance. RA genetically associated genes preferentially displayed differential methylation and differential expression or interacted with differentially methylated and differentially expressed genes. These differentially methylated and differentially expressed genes were enriched with several signaling pathways and disease categories. 10 genes (CD86, RAB20, XAF1, FOLR3, LTBR, KCNH8, DOK7, PDGFA, PITPNM2, CELSR1) with concomitantly differential methylation in enhancers/promoters/gene bodies and differential expression in B cells were validated. This integrated analysis of methylome and transcriptome identified novel epigenetic signatures associated with RA and highlighted the interaction between genetics and epigenetics in RA. These findings help our understanding of the pathogenesis of RA and advance epigenetic studies in regards to the disease.
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13
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Abstract
Sarcoidosis is a complex, polygenic disease of unknown cause with diverse clinical phenotypes, ranging from self-limited, asymptomatic disease to life-altering symptoms and early disease-related mortality. It is unlikely that a single common environmental exposure (e.g., infection, antigen) entirely explains the disease, and numerous genetic mutations are associated with the disease. As such, it is reasonable to assume, as with other phenotypically diverse diseases, that distinct genetic mechanisms and related biological biomarkers will serve to further define sarcoidosis subphenotypes, mechanisms, and possibly etiology, thus guiding personalized care. The fields of "omics" and systems biology research are widely applied to understand polygenic and phenotypically diverse diseases, such as sarcoidosis. "Omics" refers to technologies that allow comprehensive profiling of sets of molecules in an organism. Systems biology applies advanced computational approaches to make sense of the enormous data sets that are typically generated from "omics" platforms. The primary objectives of this article are to review the available "omics" tools, assess the current status of "omics" and systems biology research in the field of sarcoidosis, and consider how this technology could be applied to advance our understanding of the mechanistic underpinnings of disease and to develop novel treatments.
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14
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Duan Q, Xu Z, Raffield L, Chang S, Wu D, Lange EM, Reiner AP, Li Y. A robust and powerful two-step testing procedure for local ancestry adjusted allelic association analysis in admixed populations. Genet Epidemiol 2018; 42:288-302. [PMID: 29226381 PMCID: PMC5851818 DOI: 10.1002/gepi.22104] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 09/07/2017] [Accepted: 10/20/2017] [Indexed: 12/23/2022]
Abstract
Genetic association studies in admixed populations allow us to gain deeper understanding of the genetic architecture of human diseases and traits. However, population stratification, complicated linkage disequilibrium (LD) patterns, and the complex interplay of allelic and ancestry effects on phenotypic traits pose challenges in such analyses. These issues may lead to detecting spurious associations and/or result in reduced statistical power. Fortunately, if handled appropriately, these same challenges provide unique opportunities for gene mapping. To address these challenges and to take these opportunities, we propose a robust and powerful two-step testing procedure Local Ancestry Adjusted Allelic (LAAA) association. In the first step, LAAA robustly captures associations due to allelic effect, ancestry effect, and interaction effect, allowing detection of effect heterogeneity across ancestral populations. In the second step, LAAA identifies the source of association, namely allelic, ancestry, or the combination. By jointly modeling allele, local ancestry, and ancestry-specific allelic effects, LAAA is highly powerful in capturing the presence of interaction between ancestry and allele effect. We evaluated the validity and statistical power of LAAA through simulations over a broad spectrum of scenarios. We further illustrated its usefulness by application to the Candidate Gene Association Resource (CARe) African American participants for association with hemoglobin levels. We were able to replicate independent groups' previously identified loci that would have been missed in CARe without joint testing. Moreover, the loci, for which LAAA detected potential effect heterogeneity, were replicated among African Americans from the Women's Health Initiative study. LAAA is freely available at https://yunliweb.its.unc.edu/LAAA.
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Affiliation(s)
- Qing Duan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Statistics, University of North Carolina, Chapel Hill, NC, USA
| | - Zheng Xu
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE
- Initiative of Quantitative Life Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Suhua Chang
- Institute of Psychology, Chinese Academy of Science, Beijing, China
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Periodontology, University of North Carolina, Chapel Hill, NC, USA
| | - Ethan M. Lange
- Department of Medicine, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO, USA
- Department of Biostatistics and Informatics, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Alex P. Reiner
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
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15
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Th17-lineage cells in pulmonary sarcoidosis and Löfgren's syndrome: Friend or foe? J Autoimmun 2018; 87:82-96. [DOI: 10.1016/j.jaut.2017.12.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 12/12/2017] [Indexed: 01/17/2023]
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16
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The Pathogenesis of Pulmonary Sarcoidosis and Implications for Treatment. Chest 2017; 153:1432-1442. [PMID: 29224832 DOI: 10.1016/j.chest.2017.11.030] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/20/2017] [Accepted: 11/26/2017] [Indexed: 12/31/2022] Open
Abstract
Thoracic sarcoidosis is the most common form of sarcoidosis, encompassing a heterogeneous group of patients with a wide range of clinical features and associated outcomes. The distinction between isolated thoracic lymphadenopathy and pulmonary involvement matters. Morbidity is often higher, and long-term outcomes are worse for the latter. Although inflammatory infiltrates in pulmonary sarcoidosis may resolve, persistent disease activity is common and can result in lung fibrosis. Given the distinct clinical features and natural history of pulmonary sarcoidosis, its pathogenesis may differ in important ways from other sarcoidosis manifestations. This review highlights recent advances in the pathogenesis of pulmonary sarcoidosis, including the nature of the sarcoidosis antigen, the role of serum amyloid A and other host factors that contribute to alterations in innate immunity, factors that shape adaptive T-cell profiles in the lung, and how these mechanisms influence the maintenance of granulomatous inflammation in sarcoidosis. We discuss questions raised by recent findings, including the role of innate immunity in the pathogenesis, the meaning of immune cell exhaustion, and mechanisms that may contribute to lung fibrosis in sarcoidosis. We conclude with a reflection on when and how immunosuppressive therapies may be helpful for pulmonary sarcoidosis, a consideration of nonpharmacologic management strategies, and a survey of potential novel therapeutic targets for this vexing disease.
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17
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Moller DR, Rybicki BA, Hamzeh NY, Montgomery CG, Chen ES, Drake W, Fontenot AP. Genetic, Immunologic, and Environmental Basis of Sarcoidosis. Ann Am Thorac Soc 2017; 14:S429-S436. [PMID: 29073364 PMCID: PMC5822412 DOI: 10.1513/annalsats.201707-565ot] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/24/2017] [Indexed: 12/24/2022] Open
Abstract
Sarcoidosis is a multisystem disease with tremendous heterogeneity in disease manifestations, severity, and clinical course that varies among different ethnic and racial groups. To better understand this disease and to improve the outcomes of patients, a National Heart, Lung, and Blood Institute workshop was convened to assess the current state of knowledge, gaps, and research needs across the clinical, genetic, environmental, and immunologic arenas. We also explored to what extent the interplay of the genetic, environmental, and immunologic factors could explain the different phenotypes and outcomes of patients with sarcoidosis, including the chronic phenotypes that have the greatest healthcare burden. The potential use of current genetic, epigenetic, and immunologic tools along with study approaches that integrate environmental exposures and precise clinical phenotyping were also explored. Finally, we made expert panel-based consensus recommendations for research approaches and priorities to improve our understanding of the effect of these factors on the health outcomes in sarcoidosis.
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Affiliation(s)
- David R. Moller
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore Maryland
| | - Ben A. Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, Michigan
| | | | - Courtney G. Montgomery
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Edward S. Chen
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore Maryland
| | - Wonder Drake
- Vanderbilt University School of Medicine, Nashville, Tennessee; and
| | - Andrew P. Fontenot
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
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18
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Polygenic risk assessment reveals pleiotropy between sarcoidosis and inflammatory disorders in the context of genetic ancestry. Genes Immun 2017; 18:88-94. [PMID: 28275240 PMCID: PMC5407914 DOI: 10.1038/gene.2017.3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/07/2016] [Accepted: 11/21/2016] [Indexed: 12/26/2022]
Abstract
Sarcoidosis is a complex disease of unknown etiology characterized by the presence of granulomatous inflammation. Though various immune system pathways have been implicated in disease, the relationship between the genetic determinants of sarcoidosis and other inflammatory disorders has not been characterized. Herein, we examined the degree of genetic pleiotropy common to sarcoidosis and other inflammatory disorders to identify shared pathways and disease systems pertinent to sarcoidosis onset. To achieve this, we quantify the association of common variant polygenic risk scores from nine complex inflammatory disorders with sarcoidosis risk. Enrichment analyses of genes implicated in pleiotropic associations were further used to elucidate candidate pathways. In European-Americans, we identify significant pleiotropy between risk of sarcoidosis and risk of asthma (R2=2.03%; p=8.89×10−9), celiac disease (R2=2.03%; p=8.21×10−9), primary biliary cirrhosis (R2=2.43%; p=2.01×10−10), and rheumatoid arthritis (R2=4.32%; p=2.50×10−17). These associations validate in African Americans only after accounting for the proportion of genome-wide European ancestry, where we demonstrate similar effects of polygenic risk for African-Americans with the highest levels of European ancestry. Variants and genes implicated in European-American pleiotropic associations were enriched for pathways involving interleukin-12, interleukin-27, and cell adhesion molecules, corroborating the hypothesized immunopathogenesis of disease.
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19
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Bioinformatics analysis of gene expression profile data to screen key genes involved in pulmonary sarcoidosis. Gene 2016; 596:98-104. [PMID: 27682024 DOI: 10.1016/j.gene.2016.09.037] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 08/29/2016] [Accepted: 09/24/2016] [Indexed: 01/18/2023]
Abstract
BACKGROUND Sarcoidosis is a multisystemic inflammatory and granulomatous disease that occurs in almost all populations and affects multiple organs. Meanwhile, its most common manifestation is pulmonary sarcoidosis. This study aimed to identify effective biomarkers for the diagnosis and therapy of pulmonary sarcoidosis. METHODS GSE16538 was downloaded from Gene Expression Omnibus, including 6 pulmonary sarcoidosis samples and 6 normal lung samples. Then, differentially expressed genes (DEGs) were identified by limma package in R. After the expression values of the DEGs were extracted, hierarchical clustering analysis was performed for the DEGs using the pheatmap package in R. Subsequently, protein-protein interaction (PPI) pairs among the DEGs were searched by STRING or REACTOME databases, and then PPI networks were visualized by Cytoscape software. Using DAVID and KOBAS, functional and pathway enrichment analyses separately were performed for the DEGs involved in the PPI network. RESULTS Total 208 DEGs were identified in pulmonary sarcoidosis samples, including 179 up-regulated genes and 29 down-regulated genes. Hierarchical clustering showed that the DEGs could clearly distinguish the pulmonary sarcoidosis samples from the normal lung samples. In the PPI network constructed by STRING database, CXCL9, STAT1, CCL5, CXCL11 and GBP1 had higher degrees and betweenness values, and could interact with each other. Functional enrichment showed that CXCL9, CXCL11 and CCL5 were enriched in immune response. Moreover, STAT1 was enriched in pathways of chemokine signaling pathway and JAK-STAT signaling pathway. CONCLUSION CXCL9, CXCL11, STAT1, CCL5 and GBP1 might be implicated in pulmonary sarcoidosis through interacting with each other.
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20
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Abstract
PURPOSE OF REVIEW Nonnecrotizing granulomas in the affected organ are the hallmark of sarcoidosis. This review summarizes most recent genetic findings in sarcoidosis with a focus on genes that might influence granuloma formation or resolution. Specific results in multiple ethnic groups and certain clinical subphenotypes, such as extra-pulmonary organ involvement, are discussed. RECENT FINDINGS Associations of genetic variants in antigen-presenting molecules (HLA-DRB1) were shown to confer risk to sarcoidosis and certain disease phenotypes in populations of different ethnic origins. Specific DRB1 alleles, such as *0301 and *0302, appear to confer protection against chronic disease, but in an ethnic-specific manner illustrating the extensive genetic heterogeneity and complexity at this locus. Mechanistic studies of putative sarcoid antigens lend further credence to a role of HLA-DRB1 in disease pathogenesis. With relevance to granuloma formation, genes involved in apoptotic processes and immune cell activation were further confirmed (ANXA11 and BTNL2) in multiple ethnicities; others were newly identified (XAF1). Linking mechanism to clinical application, a TNF variant was shown to correlate with anti-TNF response in sarcoidosis patients. SUMMARY The investigation of known and novel risk variants for sarcoidosis and specific clinical phenotypes in various ethnicities highlights the genetic complexity of the disease. Detailed subanalysis of disease phenotypes revealed the potential for prediction of extra-pulmonary organ involvement and therapy response based on the patient's genotype.
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21
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Levin AM, Adrianto I, Datta I, Iannuzzi MC, Trudeau S, Li J, Drake WP, Montgomery CG, Rybicki BA. Association of HLA-DRB1 with Sarcoidosis Susceptibility and Progression in African Americans. Am J Respir Cell Mol Biol 2015; 53:206-16. [PMID: 25506722 DOI: 10.1165/rcmb.2014-0227oc] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
HLA-DRB1 is a sarcoidosis risk gene, and the *03:01 allele is strongly associated with disease resolution in European sarcoidosis cases. Whereas the HLA-DRB1 variation is associated with sarcoidosis susceptibility in African Americans, DRB1 risk alleles are not as well defined, and associations with disease resolution have not been studied. Associations between genotyped and imputed HLA-DRB1 alleles and disease susceptibility/resolution were evaluated in a sample of 1,277 African-American patients with sarcoidosis and 1,467 control subjects. In silico binding assays were performed to assess the functional significance of the associated alleles. Increased disease susceptibility was associated with the HLA-DRB1 alleles *12:01 (odds ratio [OR], 2.11; 95% confidence interval [CI], 1.65-2.69; P = 3.2 × 10(-9)) and *11:01 (OR, 1.69; 95% CI, 1.42-2.01; P = 3.0 × 10(-9)). The strongest protective association was found with *03:01 (OR, 0.56; 95% CI, 0.44-0.73; P = 1.0 × 10(-5)). The African-derived allele *03:02 was associated with decreased risk of persistent radiographic disease (OR, 0.52; 95% CI, 0.37-0.72; P = 1.3 × 10(-4)), a finding consistent across the three component studies comprising the analytic sample. The DRB1*03:01 association with disease persistence was dependent upon local ancestry, with carriers of at least one European allele at DRB1 at a decreased risk of persistent disease (OR, 0.36; 95% CI, 0.14-0.94; P = 0.037). Results of in silico binding analyses showed that DRB1*03:01 consistently demonstrated the highest binding affinities for six bacterial peptides previously found in sarcoidosis granulomas, whereas *12:01 displayed the lowest binding affinities. This study has identified DRB1*03:01 and *03:02 as novel alleles associated with disease susceptibility and course in African Americans. Further investigation of DRB1*03 alleles may uncover immunologic factors that favor sarcoidosis protection and resolution among African Americans.
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Affiliation(s)
- Albert M Levin
- 1 Department of Public Health Sciences and.,2 Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Indra Adrianto
- 3 Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Indrani Datta
- 1 Department of Public Health Sciences and.,2 Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Michael C Iannuzzi
- 4 Department of Medicine, Upstate Medical University, Syracuse, New York; and
| | | | - Jia Li
- 1 Department of Public Health Sciences and.,2 Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Wonder P Drake
- 5 Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Courtney G Montgomery
- 3 Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
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22
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Abstract
Sarcoidosis is a disease with highly variable presentation and progression; although it is hypothesized that disease phenotype is related to genetic variation, how much of this variability is driven by genetic factors is not known. The HLA region is the most strongly and consistently associated genetic risk factor for sarcoidosis, supporting the notion that sarcoidosis is an exposure-mediated immunologic disease. Most of the genetic etiology of sarcoidosis remains unknown in terms of the specific variants that increase risk in various populations, their biologic functions, and how they interact with environmental exposures.
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Affiliation(s)
| | - Nabeel Hamzeh
- Division of Environmental Occupational Health and Sciences, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA; Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Lisa A Maier
- Division of Environmental Occupational Health and Sciences, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA; Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
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Abstract
Sarcoidosis is a multisystem inflammatory disease, the aetiology of which has still to be resolved. The proposed mechanism is that a susceptible genotype is exposed to one or more potential antigens. A sustained inflammatory response follows, which ultimately results in pathognomonic granuloma formation. Various clinical phenotypes exist with specific genetic associations influencing disease susceptibility, protection, and clinical progression. Occupational and environmental factors, including microbial elements, may then effect the development of this disease. Sarcoidosis is a heterogeneous disease, showing geographic and racial variation in clinical presentation. It demonstrates a familial tendency and clear genotype associations. Additionally, it appears to cluster within closely associated populations (eg, work colleagues) and appears to be related to selected occupations and environmental exposures. Frequently occult, but occasionally fatal, this disease has a very variable prognosis. It is also unusual in having no specific biomarker. The epidemiology and multiple factors that appear to influence the aetiology of sarcoidosis illustrate why this disease state is frequently described as a clinical enigma.
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Affiliation(s)
- Simon Dubrey
- Department of Cardiology, Hillingdon Hospital, Uxbridge, Middlesex, UK
| | - Shreena Shah
- The Medical Admissions Unit, Queens Hospital, Romford, Essex, UK
| | - Timothy Hardman
- Niche Science & Technology Ltd., Unit 26, Richmond-Upon-Thames, London, UK
| | - Rakesh Sharma
- Department of Cardiology, The Royal Brompton Hospital, London, UK
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24
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Lareau CA, Adrianto I, Levin AM, Iannuzzi MC, Rybicki BA, Montgomery CG. Fine mapping of chromosome 15q25 implicates ZNF592 in neurosarcoidosis patients. Ann Clin Transl Neurol 2015; 2:972-7. [PMID: 26478897 PMCID: PMC4603380 DOI: 10.1002/acn3.229] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/24/2015] [Accepted: 07/04/2015] [Indexed: 12/31/2022] Open
Abstract
Neurosarcoidosis is a clinical subtype of sarcoidosis characterized by the presence of granulomas in the nervous system. Here, we report a highly significant association with a variant (rs75652600, P = 3.12 × 10−8, odds ratios = 4.34) within a zinc finger gene, ZNF592, from an imputation-based fine-mapping study of the chromosomal region 15q25 in African-Americans with neurosarcoidosis. We validate the association with ZNF592, a gene previously shown to cause cerebellar ataxia, in a cohort of European-Americans with neurosarcoidosis by uncovering low-frequency variants with a similar risk effect size (chr15:85309284, P = 0.0021, odds ratios = 5.36).
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Affiliation(s)
- Caleb A Lareau
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation Oklahoma City, Oklahoma ; Departments of Biostatistics, Harvard University Cambridge, Massachusetts
| | - Indra Adrianto
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation Oklahoma City, Oklahoma
| | - Albert M Levin
- Department of Public Health Services, Henry Ford Health System Detroit, Michigan ; Center for Bioinformatics, Henry Ford Health System Detroit, Michigan
| | | | - Benjamin A Rybicki
- Department of Public Health Services, Henry Ford Health System Detroit, Michigan
| | - Courtney G Montgomery
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation Oklahoma City, Oklahoma
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25
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Levin AM, Adrianto I, Datta I, Iannuzzi MC, Trudeau S, McKeigue P, Montgomery CG, Rybicki BA. Performance of HLA allele prediction methods in African Americans for class II genes HLA-DRB1, -DQB1, and -DPB1. BMC Genet 2014; 15:72. [PMID: 24935557 PMCID: PMC4074844 DOI: 10.1186/1471-2156-15-72] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 06/11/2014] [Indexed: 12/23/2022] Open
Abstract
Background The expense of human leukocyte antigen (HLA) allele genotyping has motivated the development of imputation methods that use dense single nucleotide polymorphism (SNP) genotype data and the region’s haplotype structure, but the performance of these methods in admixed populations (such as African Americans) has not been adequately evaluated. We compared genotype-based—derived from both genome-wide genotyping and targeted sequencing—imputation results to existing allele data for HLA–DRB1, −DQB1, and –DPB1. Results In European Americans, the newly-developed HLA Genotype Imputation with Attribute Bagging (HIBAG) method outperformed HLA*IMP:02. In African Americans, HLA*IMP:02 performed marginally better than HIBAG pre-built models, but HIBAG models constructed using a portion of our African American sample with both SNP genotyping and four-digit HLA class II allele typing had consistently higher accuracy than HLA*IMP:02. However, HIBAG was significantly less accurate in individuals heterozygous for local ancestry (p ≤0.04). Accuracy improved in models with equal numbers of African and European chromosomes. Variants added by targeted sequencing and SNP imputation further improved both imputation accuracy and the proportion of high quality calls. Conclusion Combining the HIBAG approach with local ancestry and dense variant data can produce highly-accurate HLA class II allele imputation in African Americans.
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Affiliation(s)
- Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, 1 Ford Place, 3E, 48202 Detroit, MI, USA.
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