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Qian J, Chen Y, Yang X, Wang Q, Zhao J, Deng X, Ding Y, Li S, Liu Y, Tian Z, Shen J, Liao Q, Wang Y, Zuo X, Zhang X, Li M, Cui Y, Yu X, Zeng X. Association Study Identified HLA-DQA1 as a Novel Genetic Risk of Systemic Lupus Erythematosus-Associated Pulmonary Arterial Hypertension. Arthritis Rheumatol 2023; 75:2207-2215. [PMID: 37382296 DOI: 10.1002/art.42641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/19/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
OBJECTIVE Pulmonary arterial hypertension (PAH) is a severe complication of systemic lupus erythematosus (SLE). However, the genetic signatures of SLE-associated PAH have not been well studied. We aimed to identify genetic variants implicated in SLE-associated PAH susceptibility within the major histocompatibility complex (MHC) region and assess the contribution to clinical outcomes. METHODS A total of 172 patients with SLE-associated PAH confirmed by right heart catheterization, 1,303 patients with SLE without PAH, and 9,906 healthy controls were included. Deep sequencing of the MHC region was performed to identify alleles, single-nucleotide polymorphisms, and amino acids. We compared patients with SLE-associated PAH with patients with SLE without PAH and healthy controls. Clinical association study was conducted to explore the contribution to phenotypes. RESULTS A total of 19,881 genetic variants were identified within the MHC region. HLA-DQA1*03:02 was identified as a novel genetic variant associated with SLE-associated PAH in the discovery cohort (P = 5.68 × 10-12 ) and authenticated in an independent replication cohort (P = 1.30 × 10-9 ). The strongest associated amino acid position was mapped to HLA-DQα1 in the region affecting MHC/peptide-CD4+ T cell receptor affinity and antigen binding. Clinical association study demonstrated that patients with SLE-associated PAH with HLA-DQA1*03:02 had significantly lower rates of target role achievement (P = 0.005) and survival (P = 0.04). CONCLUSION This study, based on the largest cohort of SLE-associated PAH, is the first to investigate how MHC region genetic variants contribute to SLE-associated PAH susceptibility. HLA-DQA1*03:02 is a novel genetic risk factor and a prognostic factor in SLE-associated PAH. Patients with SLE with this allele require regular monitoring and careful follow-up for early diagnosis and interventions for potential PAH.
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Affiliation(s)
- Junyan Qian
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | | | - Xinzhuang Yang
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qian Wang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Xiaoyue Deng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Yufang Ding
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Shengjie Li
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongtai Liu
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Zhuang Tian
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | | | | | - Yanhong Wang
- Department of Epidemiology and Bio-Statistics, Institute of Basic Medical Sciences, China Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xianbo Zuo
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Xuejun Zhang
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Xueqing Yu
- Division of Nephrology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xiaofeng Zeng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
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Kim TJ, Lee ST, Moon J, Sunwoo JS, Byun JI, Lim JA, Shin YW, Jun JS, Lee HS, Lee WJ, Yang AR, Choi Y, Park KI, Jung KH, Jung KY, Kim M, Lee SK, Chu K. Anti-LGI1 encephalitis is associated with unique HLA subtypes. Ann Neurol 2017; 81:183-192. [DOI: 10.1002/ana.24860] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Tae-Joon Kim
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
| | - Soon-Tae Lee
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
| | - Jangsup Moon
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
| | - Jun-Sang Sunwoo
- Department of Neurology; Soonchunhyang University Seoul Hospital; Seoul South Korea
| | - Jung-Ick Byun
- Department of Neurology; Kyung Hee University Hospital at Gangdong; Seoul South Korea
| | - Jung-Ah Lim
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
| | - Yong-Won Shin
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
| | - Jin-Sun Jun
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
| | - Han Sang Lee
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
| | - Woo-Jin Lee
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
| | - Ah Reaum Yang
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
| | - Yunhee Choi
- Medical Research Collaborating Center; Seoul National University Hospital; Seoul South Korea
| | - Kyung-Il Park
- Department of Neurology; Seoul National University Hospital Healthcare System Gangnam Center; Seoul South Korea
| | - Keun-Hwa Jung
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
| | - Ki-Young Jung
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
| | - Manho Kim
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
- Protein Metabolism Medical Research Center; Seoul National University College of Medicine; Seoul South Korea
| | - Sang Kun Lee
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
| | - Kon Chu
- Department of Neurology; Seoul National University Hospital; Seoul South Korea
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Woo HI, Joo EY, Hong SB, Lee KW, Kang ES. Use of PCR with sequence-specific primers for high-resolution human leukocyte antigen typing of patients with narcolepsy. Ann Lab Med 2011; 32:57-65. [PMID: 22259780 PMCID: PMC3255490 DOI: 10.3343/alm.2012.32.1.57] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 07/22/2011] [Accepted: 10/13/2011] [Indexed: 11/30/2022] Open
Abstract
Background Narcolepsy is a neurologic disorder characterized by excessive daytime sleepiness, symptoms of abnormal rapid eye movement (REM) sleep, and a strong association with HLA-DRB1*1501, -DQA1*0102, and -DQB1*0602. Here, we investigated the clinico-physical characteristics of Korean patients with narcolepsy, their HLA types, and the clinical utility of high-resolution PCR with sequence-specific primers (PCR-SSP) as a simple typing method for identifying DRB1*15/16, DQA1, and DQB1 alleles. Methods The study population consisted of 67 consecutively enrolled patients having unexplained daytime sleepiness and diagnosed narcolepsy based on clinical and neurological findings. Clinical data and the results of the multiple sleep latency test and polysomnography were reviewed, and HLA typing was performed using both high-resolution PCR-SSP and sequence-based typing (SBT). Results The 44 narcolepsy patients with cataplexy displayed significantly higher frequencies of DRB1*1501 (Pc= 0.003), DQA1*0102 (Pc=0.001), and DQB1*0602 (Pc=0.014) than the patients without cataplexy. Among patients carrying DRB1*1501-DQB1*0602 or DQA1*0102, the frequencies of a mean REM sleep latency of less than 20 min in nocturnal polysomnography and clinical findings, including sleep paralysis and hypnagogic hallucination were significantly higher. SBT and PCR-SSP showed 100% concordance for high-resolution typing of DRB1*15/16 alleles and DQA1 and DQB1 loci. Conclusions The clinical characteristics and somnographic findings of narcolepsy patients were associated with specific HLA alleles, including DRB1*1501, DQA1*0102, and DQB1*0602. Application of high-resolution PCR-SSP, a reliable and simple method, for both allele- and locus-specific HLA typing of DRB1*15/16, DQA1, and DQB1 would be useful for characterizing clinical status among subjects with narcolepsy.
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Affiliation(s)
- Hye In Woo
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Yang JH, Sohn YH, Ko SY, Choi SE, Kim MH, Oh HB. Anthropological analysis of Koreans using HLA class II diversity among East Asians. ACTA ACUST UNITED AC 2011; 76:282-8. [PMID: 20522202 DOI: 10.1111/j.1399-0039.2010.01511.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human leukocyte antigens (HLAs) are useful markers for anthropological investigations because the allele and haplotype distributions at these loci vary widely among ethnic groups. HLA frequencies in Koreans, however, have not previously been analyzed on a phylogenetic basis. We determined the allele frequencies of four HLA class II (HLA-DRB1, -DQA1, -DQB1, and -DPB1) loci in 149 unrelated Korean individuals using a sequence-based typing method. A total of 29 HLA-DRB1, 17 HLA-DQA1, 16 HLA-DQB1, and 15 HLA-DPB1 alleles were identified. The most common allele at each locus was DRB1*0901, DQA1*0102, DQB1*0301, and DPB1*0501, respectively. Four-locus allelic association analysis showed the existence of 25 DRB1-DQA1-DQB1-DPB1 haplotypes with a frequency greater than 0.010. A dataset comprising ethnicity-specific information from published literature and the dbMHC database, as well as the allele frequencies determined in this study, was subjected to phylogenetic analysis. The analysis showed that Koreans are most closely related to Japanese and Han Chinese from Shandong province. Correspondence analyses showed that the current Korean population is located in a position intermediate between the northern and southern East Asian groups, supporting the theory of a bi- and/or multidirectional route of migration of early Korean settlers. This report can be used for anthropological studies, and may also be of use in the International Hematopoietic Stem Cell Sharing program.
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Affiliation(s)
- J H Yang
- Department of Laboratory Medicine, Korea University Medical College, Seoul, Korea
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Lee HW, Hahm KB, Lee JS, Ju YS, Lee KM, Lee KW. Association of the human leukocyte antigen class II alleles with chronic atrophic gastritis and gastric carcinoma in Koreans. J Dig Dis 2009; 10:265-71. [PMID: 19906105 DOI: 10.1111/j.1751-2980.2009.00395.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Gastric carcinogenesis is a multi-step process and is influenced by several etiological agents, including the host's genetic factors. Since whether a patient remains with chronic superficial gastritis (CSG) or progresses to either chronic atrophic gastritis (CAG) or gastric carcinoma (GC) could be a genetic predisposition unique in each population, we hypothesized that host human leukocyte antigen (HLA) alleles could be discriminative in predicting the risk of CSG progression to precancerous CAG and GC in Koreans. METHODS A total of 165 patients with gastric disorders (CSG, 62; CAG, 69 and GC, 34), were selected to investigate the association of HLA class II alleles with the progression of CSG to CAG or GC. HLA genotypes were obtained by the polymerase chain reaction-sequence based typing method. RESULTS The phenotypic frequencies of DRB1*1101 and DQA1*0505 were significantly higher in the CAG group compared to those in the CSG group. In the subjects with Helicobacter pylori (H. pypori) (+), the frequencies of DRB1*1501 and DQB1*0602 were significantly lower in the CAG compared to those in the CSG. Further analysis showed that sex (P < 0.05, OR = 0.41-0.42) and age (P < 0.05, OR = 1.05) also affected the risk of progression from CSG to CAG in H. pylori (+) patients carrying the DRB1*1501 or DQB1*0602 allele. Additionally, the frequency of DRB1*0404 in the GC group was significantly higher than that in the gastritis group. CONCLUSION Our findings strongly imply an association between HLA class II alleles and the risk of CAG development and GC progression in Koreans.
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Affiliation(s)
- Hae-Wan Lee
- Department of Surgery, Hallym University Sacred Heart Hospital, Anyang, Korea
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Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies. Hum Immunol 2008; 69:443-64. [PMID: 18638659 DOI: 10.1016/j.humimm.2008.05.001] [Citation(s) in RCA: 259] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 05/03/2008] [Accepted: 05/07/2008] [Indexed: 12/21/2022]
Abstract
This paper presents a meta-analysis of high-resolution human leukocyte antigen (HLA) allele frequency data describing 497 population samples. Most of the datasets were compiled from studies published in eight journals from 1990 to 2007; additional datasets came from the International Histocompatibility Workshops and from the AlleleFrequencies.net database. In all, these data represent approximately 66,800 individuals from throughout the world, providing an opportunity to observe trends that may not have been evident at the time the data were originally analyzed, especially with regard to the relative importance of balancing selection among the HLA loci. Population genetic measures of allele frequency distributions were summarized across populations by locus and geographic region. A role for balancing selection maintaining much of HLA variation was confirmed. Further, the breadth of this meta-analysis allowed the ranking of the HLA loci, with DQA1 and HLA-C showing the strongest balancing selection and DPB1 being compatible with neutrality. Comparisons of the allelic spectra reported by studies since 1990 indicate that most of the HLA alleles identified since 2000 are very-low-frequency alleles. The literature-based allele-count data, as well as maps summarizing the geographic distributions for each allele, are available online.
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Voorter CEM, Lee KW, Smillie D, Tilanus MGJ, van den Berg-Loonen EM. Sequence-based typing of HLA-DQA1: comprehensive approach showed molecular heterogeneity. ACTA ACUST UNITED AC 2007; 69 Suppl 1:76-81. [PMID: 17445172 DOI: 10.1111/j.1399-0039.2006.761_1.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Within the human leukocyte antigen-DQA1 workshop project the level of molecular heterogeneity of the DQA1 gene was investigated. An improved sequence-based typing protocol was used, enabling analysis of the complete coding sequence, comprising exons 1-4. The participating laboratories implemented the amplification and sequencing primers in their own sequence-based typing approach. The method proved to be sufficiently robust to handle the differences in protocols. All reference samples used for validation were correctly typed for DQA1 by all participating laboratories. Three different populations with a total of 736 individuals were investigated: a population of Korean origin (n= 467), a British Caucasian (n= 114), and a Dutch Caucasian (n= 155) population. Sixteen of the known 28 DQA1 alleles were detected and six new alleles were identified. All novel alleles showed a nucleotide substitution outside exon 2. Comparison of the calculated allele frequencies revealed major differences between the Korean and the Caucasian populations but also between Dutch and British Caucasians. A tight association between DQA1 and DRB1/DQB1 alleles was observed in all three populations.
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Affiliation(s)
- C E M Voorter
- Tissue Typing Laboratory, University Hospital Maastricht, Maastricht, The Netherlands.
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