1
|
Liu H, Ling W, Hua X, Moon JY, Williams-Nguyen JS, Zhan X, Plantinga AM, Zhao N, Zhang A, Knight R, Qi Q, Burk RD, Kaplan RC, Wu MC. Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity. MICROBIOME 2023; 11:80. [PMID: 37081571 PMCID: PMC10116795 DOI: 10.1186/s40168-023-01530-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/21/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Understanding human genetic influences on the gut microbiota helps elucidate the mechanisms by which genetics may influence health outcomes. Typical microbiome genome-wide association studies (GWAS) marginally assess the association between individual genetic variants and individual microbial taxa. We propose a novel approach, the covariate-adjusted kernel RV (KRV) framework, to map genetic variants associated with microbiome beta-diversity, which focuses on overall shifts in the microbiota. The KRV framework evaluates the association between genetics and microbes by comparing similarity in genetic profiles, based on groups of variants at the gene level, to similarity in microbiome profiles, based on the overall microbiome composition, across all pairs of individuals. By reducing the multiple-testing burden and capturing intrinsic structure within the genetic and microbiome data, the KRV framework has the potential of improving statistical power in microbiome GWAS. RESULTS We apply the covariate-adjusted KRV to the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) in a two-stage (first gene-level, then variant-level) genome-wide association analysis for gut microbiome beta-diversity. We have identified an immunity-related gene, IL23R, reported in a previous microbiome genetic association study and discovered 3 other novel genes, 2 of which are involved in immune functions or autoimmune disorders. In addition, simulation studies show that the covariate-adjusted KRV has a greater power than other microbiome GWAS methods that rely on univariate microbiome phenotypes across a range of scenarios. CONCLUSIONS Our findings highlight the value of the covariate-adjusted KRV as a powerful microbiome GWAS approach and support an important role of immunity-related genes in shaping the gut microbiome composition. Video Abstract.
Collapse
Affiliation(s)
- Hongjiao Liu
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Wodan Ling
- Division of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Xing Hua
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Jessica S Williams-Nguyen
- Institute for Research and Education to Advance Community Health, Washington State University, Seattle, WA, 98101, USA
| | - Xiang Zhan
- Department of Biostatistics and Beijing International Center for Mathematical Research, Peking University, Beijing, 100191, China
| | - Anna M Plantinga
- Department of Mathematics and Statistics, Williams College, Williamstown, MA, 01267, USA
| | - Ni Zhao
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Angela Zhang
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Rob Knight
- Departments of Pediatrics, Computer Science & Engineering, and Bioengineering; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology & Women's Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Robert C Kaplan
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Michael C Wu
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA.
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
| |
Collapse
|
2
|
Li H, Sun S, Zhang Y, Liu J, Zhao X, Zhao G. Successive onset of Vogt-Koyanagi-Harada syndrome in father and son. BMC Ophthalmol 2023; 23:113. [PMID: 36944975 PMCID: PMC10029775 DOI: 10.1186/s12886-023-02851-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Vogt‒Koyanagi‒Harada (VKH) disease is a multifactorial systemic autoimmune disorder against melanocytes that is characterized by panuveitis. Familial occurrence of VKH disease is rare. Here, we report two cases of a father and his son with characteristic manifestations of VKH disease. CASE PRESENTATION A 53-year-old male with typical clinical symptoms of VKH disease was referred to Tangshan Eye Hospital. Examination showed the presence of ciliochoroidal effusion and exudative retinal detachment in both eyes. The patient was given intravenous methylprednisolone 120 mg for 2 days and intravenous methylprednisolone 80 mg for 1 day followed by 48 mg (1 mg/kg/day) oral methylprednisolone daily, accompanied by oral azathioprine 50 mg daily. Cycloplegic agent (0.5% tropicamide three times daily [TID]) was added. The patient was free of symptoms and recurrence within more than 1-year-follow-up period, the best corrected visual acuity (BVCA) was increased and maintained in both eyes with complete resolution of subretinal fluid. One year and nine months later, case 2 (his son) also presented with the typical clinical symptoms of VKH disease at 29 years of age. The son also recovered from VKH disease after routine and standard treatment. CONCLUSIONS To the best of our knowledge, this is the first VKH disease case report of a father-son relationship. Although genetic factors have been demonstrated to be involved in the pathogenesis of VKH disease, the different inheritance modes of VKH patients need to be further explored and studied.
Collapse
Affiliation(s)
- Hougang Li
- Tangshan Institute of Ophthalmology, Tangshan Eye Hospital, 063000, Hebei, China
- North China University of Science and Technology Affiliated Eye Hospital, 063000, Hebei, China
| | - Shuo Sun
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute, Tianjin Medical University Eye Hospital, 300384, Tianjin, China
| | - Yanrui Zhang
- Tangshan Institute of Ophthalmology, Tangshan Eye Hospital, 063000, Hebei, China
- North China University of Science and Technology Affiliated Eye Hospital, 063000, Hebei, China
| | - Jinfeng Liu
- Tangshan Institute of Ophthalmology, Tangshan Eye Hospital, 063000, Hebei, China
- North China University of Science and Technology Affiliated Eye Hospital, 063000, Hebei, China
| | - Xuzheng Zhao
- Tangshan Institute of Ophthalmology, Tangshan Eye Hospital, 063000, Hebei, China
- North China University of Science and Technology Affiliated Eye Hospital, 063000, Hebei, China
| | - Guixia Zhao
- Tangshan Institute of Ophthalmology, Tangshan Eye Hospital, 063000, Hebei, China.
- North China University of Science and Technology Affiliated Eye Hospital, 063000, Hebei, China.
| |
Collapse
|
3
|
Huang XF, Brown MA. Progress in the genetics of uveitis. Genes Immun 2022; 23:57-65. [PMID: 35379982 PMCID: PMC9042703 DOI: 10.1038/s41435-022-00168-6] [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: 11/15/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
Abstract
Uveitis is the most common form of intraocular inflammatory disease and is a significant cause of visual impairment worldwide. Aetiologically, uveitis can also be classified into infectious uveitis and non-infectious uveitis. The common non-infectious forms of uveitis include acute anterior uveitis (AAU), Behçet’s disease (BD), Vogt-Koyanagi-Harada (VKH) disease, birdshot chorioretinopathy (BSCR), sarcoid uveitis. In addition, a few monogenic autoinflammatory disorders can also cause uveitis, such as Blau Syndrome and haploinsufficiency of A20 (HA20). Although the exact pathogenesis of non-infectious uveitis is still unclear, it is well-recognised that it involves both genetic and environmental risk factors. A hallmark of uveitis is its strong associations with human leucocyte antigens (HLA). For examples, AAU, BD and BSCR are strongly associated with HLA-B27, HLA-B51, and HLA-A29, respectively. In uveitis studies, multiple GWAS have successfully been conducted and led to identification of novel susceptibility loci, for example, IL23R has been identified in BD, VKH and AAU. In this review, we summarize the latest progress on the genetic associations of both HLA and non-HLA genes with major forms of uveitis, including AAU, BD, VKH, BSCR, sarcoid uveitis, Blau Syndrome and HA20, and potential future research directions.
Collapse
Affiliation(s)
- Xiu-Feng Huang
- The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.,Queensland University of Technology, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Translational Research Institute, Woolloongabba, Qld, Australia
| | - Matthew A Brown
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, England. .,Genomics England, London, UK.
| |
Collapse
|
4
|
Abstract
PURPOSE OF REVIEW Here, we provide an overview of Vogt-Koyanagi-Harada disease (VKH), including recent updates in our understanding of disease pathophysiology, classification and therapeutics. RECENT FINDINGS Advancements in bioinformatics, metabolomics and genomics investigations continue to illuminate VKH pathogenesis, and may provide insight into future therapeutic options. Multimodal imaging is indispensable in the initial evaluation of VKH, and is becoming increasingly important in understanding disease pathogenesis, as well as monitoring therapeutic response. Enhanced VKH classification criteria, released in 2021, provide standardized guidelines and terminology for clinical and research purposes. SUMMARY Modern research and imaging techniques continue to improve our understanding of VKH; more work is needed to further elucidate pathogenic mechanisms and establish optimal therapeutic recommendations.
Collapse
Affiliation(s)
- Ashlin Joye
- Casey Eye Institute, Oregon Health and Science University
| | - Eric Suhler
- Department of Ophthalmology - Casey Eye Institute, Oregon Health and Science University, VA Portland Healthcare System, Portland, Oregon, USA
| |
Collapse
|
5
|
Wu PB, Zhang Y, Nie G, Huang X, Yu YJ, Yin AN, Zhou R, He CP, Wang P. Association between genetic variants in ZNF365 and inflammatory bowel disease risk in Caucasians: a meta-analysis and trial sequential analysis. Expert Rev Clin Immunol 2021; 17:915-921. [PMID: 34092165 DOI: 10.1080/1744666x.2021.1939012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
OBJECTIVE The published studies regarding the relationships between zinc finger 365 (ZNF365) polymorphisms and inflammatory bowel disease (IBD) risk in Caucasians have yielded conflicting results. Therefore, we performed a meta-analysis to clarify this issue. METHODS The Electronic databases of PubMed, Web of Science, Wiley Online Library, and EMBASE were searched for eligible studies up to 31 November 2020. The quality of eligible studies was evaluated using the Newcastle-Ottawa Scale. The pooled odds ratios (ORs) with 95% confidence intervals (CIs) under different genetic models were calculated to assess the strength of associations. RESULTS A total of 22 relevant case-control studies with 9542 ulcerative colitis (UC) patients and 13,886 controls, as well as 13,651 Crohn's disease (CD) patients and 15,256 controls, were involved in our meta-analysis. rs10761659 polymorphism significantly decreased CD and UC risk (except for the heterozygous model and the dominant model in UC), and rs10995271 polymorphism was significantly associated with UC (except for the heterozygous model and dominant model) rather than CD. CONCLUSIONS The meta-analysis demonstrated that the rs10761659 polymorphism might be a protective factor for both UC and CD in Caucasians, while the rs10995271 polymorphism might be a risk factor for UC rather than CD in Caucasians.
Collapse
Affiliation(s)
- Peng-Bo Wu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Yu Zhang
- Infrastructure Management Department, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Gang Nie
- Department of Dermatovenereology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong China
| | - Xu Huang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Yuan-Jie Yu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - An-Ning Yin
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Rui Zhou
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Chun-Ping He
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Peng Wang
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan Hubei Province, China
| |
Collapse
|
6
|
Takeuchi M, Mizuki N, Ohno S. Pathogenesis of Non-Infectious Uveitis Elucidated by Recent Genetic Findings. Front Immunol 2021; 12:640473. [PMID: 33912164 PMCID: PMC8072111 DOI: 10.3389/fimmu.2021.640473] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/22/2021] [Indexed: 01/01/2023] Open
Abstract
Uveitis is a generic term for inflammation of the uvea, which includes the iris, ciliary body, and choroid. Prevalence of underlying non-infectious uveitis varies by race and region and is a major cause of legal blindness in developed countries. Although the etiology remains unclear, the involvement of both genetic and environmental factors is considered important for the onset of many forms of non-infectious uveitis. Major histocompatibility complex (MHC) genes, which play a major role in human immune response, have been reported to be strongly associated as genetic risk factors in several forms of non-infectious uveitis. Behçet’s disease, acute anterior uveitis (AAU), and chorioretinopathy are strongly correlated with MHC class I-specific alleles. Moreover, sarcoidosis and Vogt-Koyanagi-Harada (VKH) disease are associated with MHC class II-specific alleles. These correlations can help immunogenetically classify the immune pathway involved in each form of non-infectious uveitis. Genetic studies, including recent genome-wide association studies, have identified several susceptibility genes apart from those in the MHC region. These genetic findings help define the common or specific pathogenesis of ocular inflammatory diseases by comparing the susceptibility genes of each form of non-infectious uveitis. Interestingly, genome-wide association of the interleukin (IL)23R region has been identified in many of the major forms of non-infectious uveitis, such as Behçet’s disease, ocular sarcoidosis, VKH disease, and AAU. The interleukin-23 (IL-23) receptor, encoded by IL23R, is expressed on the cell surface of Th17 cells. IL-23 is involved in the homeostasis of Th17 cells and the production of IL-17, which is an inflammatory cytokine, indicating that a Th17 immune response is a common key in the pathogenesis of non-infectious uveitis. Based on the findings from the immunogenetics of non-infectious uveitis, a personalized treatment approach based on the patient’s genetic make-up is expected.
Collapse
Affiliation(s)
- Masaki Takeuchi
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuhisa Mizuki
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Shigeaki Ohno
- Department of Ophthalmology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| |
Collapse
|