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Nakwan N, Kunhapan P, Chaiyasung T, Satproedprai N, Singkhamanan K, Mahasirimongkol S, Charalsawadi C. Genome-wide association study identifies WWC2 as a possible locus associated with persistent pulmonary hypertension of the newborn in the Thai population. Transl Pediatr 2023; 12:1-12. [PMID: 36798934 PMCID: PMC9926135 DOI: 10.21037/tp-22-280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 11/22/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND There is known to be significant genetic involvement in persistent pulmonary hypertension of the newborn (PPHN), but to date there is not a clear understanding of this situation, and clarifying that involvement would be of considerable assistance in devising effective treatments for the disease. This case-control study was undertaken to search for genetic variants associated with PPHN in the Thai population using a genome-wide association study (GWAS). METHODS A 659,184 single nucleotide polymorphisms from 387 participants (54 PPHN cases and 333 healthy participants) were genotyped across the human genome using an Illumina Asian Screening Array-24 v1.0 BeadChip Array. After quality control, we obtained 443,063 autosomal SNPs for the GWAS analysis. The FaST-LMM and R packages were used for all statistical analyses. RESULTS For the case-control analysis, the genomic inflation factor (λ) was 1.016, rs149768622 T>C in the first intron of WWC2 gene showed the strongest association with a P value of 3.76E-08 and odds ratio (OR) of 13.24 (95% CI: 3.91-44.78). The variants at the LOC102723906/LOC105377599, CADM4, GPM6A, CIT, RIMBP2, LOC105374510, LOC105375193, PTPRN2, CDK14, and LCORL loci showed suggestive evidence of associations with PPHN (P<1E-05). CONCLUSIONS This GWAS found that rs149768622 T>C in the WWC2 gene was possibly associated with PPHN. However, replication and functional studies are needed to validate this association and further explore the role(s) of the WWC2 gene in PPHN.
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Affiliation(s)
- Narongsak Nakwan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.,Department of Pediatrics, Hat Yai Medical Education Center, Hat Yai Hospital, Songkhla, Thailand
| | - Punna Kunhapan
- Medical Genetics Center, Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Tassamonwan Chaiyasung
- Medical Genetics Center, Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Nusara Satproedprai
- Medical Genetics Center, Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Kamonnut Singkhamanan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Surakameth Mahasirimongkol
- Medical Genetics Center, Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Chariyawan Charalsawadi
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.,Genomic Medicine Center, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
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Nakwan N, Mahasirimongkol S, Satproedprai N, Chaiyasung T, Kunhapan P, Charoenlap C, Singkhamanan K, Charalsawadi C. Possible association between a polymorphism of EPAS1 gene and persistent pulmonary hypertension of the newborn: a case-control study. J Pediatr (Rio J) 2022; 98:383-389. [PMID: 34678164 PMCID: PMC9432230 DOI: 10.1016/j.jped.2021.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE To explore possible genes related to the development of persistent pulmonary hypertension of the newborn (PPHN). METHODS The authors identified 285 single nucleotide polymorphisms (SNPs) of 11 candidate genes (BMPR2, EPAS1, PDE3A, VEGFA, ENG, NOTCH3, SOD3, CPS1, ABCA3, ACVRL1, and SMAD9), using an Illumina Asian Screening Array-24 v1.0 BeadChip Array. The FastLmmC and R package was used for statistical analyses. The chi-square test and Cochrane-Armitage trend test were used to compare the allele and genotype frequencies between the groups and to test the genetic models, respectively. RESULTS A total of 45 PPHN infants and 294 control subjects were analyzed. The most common cause of PPHN was meconium aspiration syndrome. Among the 285 SNPs, 17 SNPs from 6 candidate genes (BMPR2, EPAS1, PDE3A, VEGFA, ENG, and NOTCH3) were significantly associated with PPHN (P < 0.05). After using the Bonferroni correction (P < 0.00018), only the rs17034984 SNP located in intron 1 of the EPAS1 gene remained significantly different between the PPHN and control subjects (P = 0.00014). The frequency of the TC/TT genotype of rs17034984 in the gene with the dominant model was significant in the patients with PPHN (OR = 5.38, 95% CI: 2.15-13.49). The T allele frequency of rs17034984 in the gene showed a significant difference compared with the control subjects (OR = 4.89, 95% CI: 2.03-11.82). CONCLUSIONS The present study suggests that the rs17034984 variant of EPAS1 gene is associated with PPHN.
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Affiliation(s)
- Narongsak Nakwan
- Prince of Songkla University, Faculty of Medicine, Department of Biomedical Sciences, Hat Yai, Thailand; Hat Yai Hospital, Hat Yai Medical Education Center, Department of Pediatrics, Hat Yai, Thailand
| | - Surakameth Mahasirimongkol
- Ministry of Public Heath, Department of Medical Sciences, Division of Genomic Medicine and Innovation Support, Medical Genetics Center, Nonthaburi, Thailand
| | - Nusara Satproedprai
- Ministry of Public Heath, Department of Medical Sciences, Division of Genomic Medicine and Innovation Support, Medical Genetics Center, Nonthaburi, Thailand
| | - Tassamonwan Chaiyasung
- Ministry of Public Heath, Department of Medical Sciences, Division of Genomic Medicine and Innovation Support, Medical Genetics Center, Nonthaburi, Thailand
| | - Punna Kunhapan
- Ministry of Public Heath, Department of Medical Sciences, Division of Genomic Medicine and Innovation Support, Medical Genetics Center, Nonthaburi, Thailand
| | - Cheep Charoenlap
- Hat Yai Hospital, Hat Yai Medical Education Center, Department of Anatomical Pathology, Hat Yai, Thailand
| | - Kamonnut Singkhamanan
- Prince of Songkla University, Faculty of Medicine, Department of Biomedical Sciences, Hat Yai, Thailand
| | - Chariyawan Charalsawadi
- Prince of Songkla University, Faculty of Medicine, Department of Pathology, Hat Yai, Thailand.
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3
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Wang YF, Wei W, Tangtanatakul P, Zheng L, Lei Y, Lin Z, Qian C, Qin X, Hou F, Zhang X, Shao L, Satproedprai N, Mahasirimongkol S, Pisitkun P, Song Q, Lau YL, Zhang Y, Hirankarn N, Yang W. Multi-ancestral GWAS identifies shared and Asian-specific loci for SLE and links type III interferon signaling and lysosomal function to the disease. Arthritis Rheumatol 2021; 74:840-848. [PMID: 34783190 DOI: 10.1002/art.42021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/21/2021] [Accepted: 11/09/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is a prototype autoimmune disease with differences in prevalence and severity among ancestral groups. This study aims to identify novel genetic components either shared or distinct between Asian and European populations. METHODS Both trans-ancestral and ancestry-specific meta-analyses of genome-wide association studies (GWAS) for SLE were performed, involving 30,604 participants of European, Chinese or Thai origin. Using public epigenomic data and expression quantitative trait loci, fine-mapping analyses were conducted to identify putative causal variants and genes for the newly identified loci. Performance of polygenic risk scores (PRS) for the Thai cohort was evaluated comparing different training data. RESULTS We identified ten novel SLE susceptibility loci, four of which were found by Asian-specific meta-analyses. A 1bp deletion upstream of IFNLR1 was found associated with SLE, with the risk allele correlated with increased expression of IFNLR1. This gene encodes interferon lambda receptor 1, pointing to the role of type III interferon signaling in SLE. An intronic variant in SLC29A3 was found associated with SLE only in Asians. The putative risk variant may modulate SLC29A3 expression in a monocyte-specific manner. SLC29A3 encodes a lysosomal nucleoside transporter, and subsequent analyses suggest reduced lysosomal function and phagocytosis might be the mechanism underlying this association. In addition, trans-ancestral meta-analysis was proved to be valuable in risk prediction for individuals without ancestry-matched data. CONCLUSION Multi-ancestral GWAS identified both shared and Asian-specific loci for SLE, and functional annotation pointed to the involvement of increased type III interferon signaling and reduced lysosomal function in SLE.
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Affiliation(s)
- Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China.,Shenzhen Futian hospital for rheumatic diseases, Shenzhen, China
| | - Wei Wei
- Medical Research Center, Affiliated Hospital of Jining Medical University, Shandong, China.,Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Shandong, China
| | - Pattarin Tangtanatakul
- Department of Transfusion Sciences and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Lichuan Zheng
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yao Lei
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Zhiming Lin
- Department of Rheumatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Chengmin Qian
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Xiao Qin
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Shandong, China
| | - Fei Hou
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Shandong, China
| | - Xinyu Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China.,Department of Rheumatology and Lupus Research Institute, The Affiliated Hospital of Jining Medical University, Shandong, China
| | - Li Shao
- Department of Rheumatology and Lupus Research Institute, The Affiliated Hospital of Jining Medical University, Shandong, China
| | - Nusara Satproedprai
- Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | | | - Prapaporn Pisitkun
- Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Qin Song
- Department of Rheumatology and Lupus Research Institute, The Affiliated Hospital of Jining Medical University, Shandong, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yan Zhang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Nattiya Hirankarn
- Centre of Excellent in Immunology and Immune-Mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
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Shotelersuk V, Wichadakul D, Ngamphiw C, Srichomthong C, Phokaew C, Wilantho A, Pakchuen S, Nakhonsri V, Shaw PJ, Wasitthankasem R, Piriyapongsa J, Wangkumhang P, Assawapitaksakul A, Chetruengchai W, Lapphra K, Khuninthong A, Makarawate P, Suphapeetiporn K, Mahasirimongkol S, Satproedprai N, Porntaveetus T, Pisitkun P, Praphanphoj V, Kantaputra P, Tassaneeyakul W, Tongsima S. The Thai reference exome (T-REx) variant database. Clin Genet 2021; 100:703-712. [PMID: 34496037 DOI: 10.1111/cge.14060] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 01/19/2023]
Abstract
To maximize the potential of genomics in medicine, it is essential to establish databases of genomic variants for ethno-geographic groups that can be used for filtering and prioritizing candidate pathogenic variants. Populations with non-European ancestry are poorly represented among current genomic variant databases. Here, we report the first high-density survey of genomic variants for the Thai population, the Thai Reference Exome (T-REx) variant database. T-REx comprises exome sequencing data of 1092 unrelated Thai individuals. The targeted exome regions common among four capture platforms cover 30.04 Mbp on autosomes and chromosome X. 345 681 short variants (18.27% of which are novel) and 34 907 copy number variations were found. Principal component analysis on 38 469 single nucleotide variants present worldwide showed that the Thai population is most genetically similar to East and Southeast Asian populations. Moreover, unsupervised clustering revealed six Thai subpopulations consistent with the evidence of gene flow from neighboring populations. The prevalence of common pathogenic variants in T-REx was investigated in detail, which revealed subpopulation-specific patterns, in particular variants associated with erythrocyte disorders such as the HbE variant in HBB and the Viangchan variant in G6PD. T-REx serves as a pivotal addition to the current databases for genomic medicine.
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Affiliation(s)
- Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Duangdao Wichadakul
- Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Chumpol Ngamphiw
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Chureerat Phokaew
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Alisa Wilantho
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sujiraporn Pakchuen
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Vorthunju Nakhonsri
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand.,Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Philip James Shaw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Rujipat Wasitthankasem
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Jittima Piriyapongsa
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Pongsakorn Wangkumhang
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Adjima Assawapitaksakul
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Keswadee Lapphra
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Athiphat Khuninthong
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | | | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Surakameth Mahasirimongkol
- Genomic Medicine Center, Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Nusara Satproedprai
- Genomic Medicine Center, Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Thantrira Porntaveetus
- Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Prapaporn Pisitkun
- Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Verayuth Praphanphoj
- Center for Medical Genetics Research, Rajanukul Institute, Department of Mental Health, Ministry of Public Health Bangkok, Bangkok, Thailand
| | - Piranit Kantaputra
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai, Thailand
| | | | - Sissades Tongsima
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
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Soe PT, Hanthamrongwit J, Saelee C, Kyaw SP, Khaenam P, Warit S, Satproedprai N, Mahasirimongkol S, Yanai H, Chootong P, Leepiyasakulchai C. Circulating IgA/IgG memory B cells against Mycobacterium tuberculosis dormancy-associated antigens Rv2659c and Rv3128c in active and latent tuberculosis. Int J Infect Dis 2021; 110:75-82. [PMID: 34284090 DOI: 10.1016/j.ijid.2021.07.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE To elucidate the antigenic potential of dormancy-associated antigens Rv2659c and Rv3128c of Mycobacterium tuberculosis by examining the persistence of specific IgG and IgA memory B cells (MBCs) among patients with active tuberculosis (TB), household contacts with latent tuberculosis (LTBI), and an endemic healthy control group. METHODS Fresh peripheral blood mononuclear cells from the three study groups were used to enumerate the numbers of IgG and IgA MBCs specific to recombinant protein Rv2659c and Rv3128c by ELISpot assay. The composition of MBC subsets IgA+ and IgG + was analyzed by flow cytometry. RESULTS The number of IgA MBCs specific to antigen Rv2659c was significantly higher in the LTBI group than the TB group. In contrast, no significant difference was found in IgA or IgG MBCs against antigen Rv3128c. The number of IgA+ MBCs was significantly higher than that of IgG+ MBCs in the classical MBC subset of the LTBI group. CONCLUSION The results indicated that the dormancy-associated antigen Rv2659c induced an IgA MBCs response in individuals with latent TB, and IgA+ classical MBCs formed a major portion of the MBCs subset. This new knowledge will be beneficial for the development of novel TB vaccines and their control of latent TB.
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Affiliation(s)
- Phyu Thwe Soe
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand; Department of Medical Laboratory Technology, University of Medical Technology, Mandalay, Myanmar
| | - Jariya Hanthamrongwit
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Chutiphon Saelee
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Soe Paing Kyaw
- Clinical Pathology Laboratory, (1000) Bedded General Hospital, Nay Pyi Taw, Myanmar
| | - Prasong Khaenam
- Center of Standardization and Product Validation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Saradee Warit
- Industrial Tuberculosis Team, IMMBRG, National Center for Genetic Engineering and Biotechnology (BIOTEC), NSTDA, Pathum Thani, Thailand
| | - Nusara Satproedprai
- Genomic Medicine and Innovation Support Division, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Surakameth Mahasirimongkol
- Genomic Medicine and Innovation Support Division, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Hideki Yanai
- Department of Clinical Laboratory, Fukujuji Hospital, Japan Anti-Tuberculosis Association (JATA), Tokyo, Japan
| | - Patchanee Chootong
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Chaniya Leepiyasakulchai
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.
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Tangtanatakul P, Thumarat C, Satproedprai N, Kunhapan P, Chaiyasung T, Klinchanhom S, Wang YF, Wei W, Wongshinsri J, Chiewchengchol D, Rodsaward P, Ngamjanyaporn P, Suangtamai T, Mahasirimongkol S, Pisitkun P, Hirankarn N. Meta-analysis of genome-wide association study identifies FBN2 as a novel locus associated with systemic lupus erythematosus in Thai population. Arthritis Res Ther 2020; 22:185. [PMID: 32771030 PMCID: PMC7414652 DOI: 10.1186/s13075-020-02276-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/26/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Differences in the expression of variants across ethnic groups in the systemic lupus erythematosus (SLE) patients have been well documented. However, the genetic architecture in the Thai population has not been thoroughly examined. In this study, we carried out genome-wide association study (GWAS) in the Thai population. METHODS Two GWAS cohorts were independently collected and genotyped: discovery dataset (487 SLE cases and 1606 healthy controls) and replication dataset (405 SLE cases and 1590 unrelated disease controls). Data were imputed to the density of the 1000 Genomes Project Phase 3. Association studies were performed based on different genetic models, and pathway enrichment analysis was further examined. In addition, the performance of disease risk estimation for individuals in Thai GWAS was assessed based on the polygenic risk score (PRS) model trained by other Asian populations. RESULTS Previous findings on SLE susceptible alleles were well replicated in the two GWAS. The SNPs on HLA class II (rs9270970, A>G, OR = 1.82, p value = 3.61E-26), STAT4 (rs7582694, C>G, OR = 1.57, p value = 8.21E-16), GTF2I (rs73366469, A>G, OR = 1.73, p value = 2.42E-11), and FAM167A-BLK allele (rs13277113, A>G, OR = 0.68, p value = 1.58E-09) were significantly associated with SLE in Thai population. Meta-analysis of the two GWAS identified a novel locus at the FBN2 that was specifically associated with SLE in the Thai population (rs74989671, A>G, OR = 1.54, p value = 1.61E-08). Functional analysis showed that rs74989671 resided in a peak of H3K36me3 derived from CD14+ monocytes and H3K4me1 from T lymphocytes. In addition, we showed that the PRS model trained from the Chinese population could be applied in individuals of Thai ancestry, with the area under the receiver-operator curve (AUC) achieving 0.76 for this predictor. CONCLUSIONS We demonstrated the genetic architecture of SLE in the Thai population and identified a novel locus associated with SLE. Also, our study suggested a potential use of the PRS model from the Chinese population to estimate the disease risk for individuals of Thai ancestry.
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Affiliation(s)
- Pattarin Tangtanatakul
- Department of Transfusion Sciences and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Chisanu Thumarat
- Section of Translational Medicine, Faculty of Medicine, Mahidol University, Ramathibodi Hospital, Bangkok, Thailand
| | - Nusara Satproedprai
- Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Punna Kunhapan
- Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | | | - Siriwan Klinchanhom
- Centre of Excellent in Immunology and Immune-Mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, 1873 Ratchadamri Road, Pathum wan, Bangkok, 10330, Thailand
| | - Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Sandy Bay, Hong Kong
- Shenzhen Futian Hospital for Rheumatic Disease, Shenzhen, People's Republic of China
| | - Wei Wei
- Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, China
- Collaborative Innovation Centre for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | | | - Direkrit Chiewchengchol
- Centre of Excellent in Immunology and Immune-Mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, 1873 Ratchadamri Road, Pathum wan, Bangkok, 10330, Thailand
| | - Pongsawat Rodsaward
- Centre of Excellent in Immunology and Immune-Mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, 1873 Ratchadamri Road, Pathum wan, Bangkok, 10330, Thailand
| | - Pintip Ngamjanyaporn
- Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Thanitta Suangtamai
- Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | - Prapaporn Pisitkun
- Section of Translational Medicine, Faculty of Medicine, Mahidol University, Ramathibodi Hospital, Bangkok, Thailand
| | - Nattiya Hirankarn
- Centre of Excellent in Immunology and Immune-Mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, 1873 Ratchadamri Road, Pathum wan, Bangkok, 10330, Thailand.
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7
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Luekitinun N, Mahasirimongkol S, Satproedprai N, Miyahara R, Kawkitinarong K. The Pleural and blood gene expression level of GBP5 and STAT1 were associated with pleural tuberculosis: TB pleura diagnostic biomarkers. Tuberculosis (Edinb) 2019. [DOI: 10.1183/13993003.congress-2019.pa550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Omae Y, Toyo-Oka L, Yanai H, Nedsuwan S, Wattanapokayakit S, Satproedprai N, Smittipat N, Palittapongarnpim P, Sawanpanyalert P, Inunchot W, Pasomsub E, Wichukchinda N, Mushiroda T, Kubo M, Tokunaga K, Mahasirimongkol S. Pathogen lineage-based genome-wide association study identified CD53 as susceptible locus in tuberculosis. J Hum Genet 2017; 62:1015-1022. [PMID: 28878339 PMCID: PMC5709719 DOI: 10.1038/jhg.2017.82] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 07/11/2017] [Accepted: 07/14/2017] [Indexed: 01/12/2023]
Abstract
Tuberculosis (TB) is known to be affected by host genetic factors. We reported a specific genetic risk factor through a genome-wide association study (GWAS) that focused on young age onset TB. In this study, we further focused on the heterogeneity of Mycobacterium tuberculosis (M. tb) lineages and assessed its possible interaction with age at onset on host genetic factors. We identified the pathogen lineage in 686 Thai TB cases and GWAS stratified by both infected pathogen lineage information and age at onset revealed a genome-wide significant association of one single-nucleotide polymorphism (SNP) on chromosome 1p13, which was specifically associated with non-Beijing lineage-infected old age onset cases (P=2.54E-08, OR=1.74 (95% CI=1.43–2.12)), when we compared them to the population-matched healthy controls. This SNP locates near the CD53 gene, which encodes a leukocyte surface glycoprotein. Interestingly, the expression of CD53 was also correlated with the patients’ active TB status. This is the first report of a pathogen lineage-based genome-wide association study. The results suggested that host genetic risk in TB is depended upon the pathogen genetic background and demonstrate the importance of analyzing the interaction between host and pathogen genomes in TB.
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Affiliation(s)
- Yosuke Omae
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Licht Toyo-Oka
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideki Yanai
- Fukujuji Hospital and Research Institute of Tuberculosis (RIT), Japan Anti-Tuberculosis Association (JATA), Kiyose, Japan
| | - Supalert Nedsuwan
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiang Rai, Thailand
| | - Sukanya Wattanapokayakit
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Nusara Satproedprai
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Nat Smittipat
- Tuberculosis Research Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | | | | | - Wimala Inunchot
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Ekawat Pasomsub
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Nuanjun Wichukchinda
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Surakameth Mahasirimongkol
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
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Rienthong S, Boonin C, Chaiyasirinrote B, Satproedprai N, Mahasirimongkol S, Yoshida H, Kondo Y, Namwat C, Rienthong D. Evaluation of a novel line-probe assay for genotyping-based diagnosis of Mycobacterium tuberculosis in Thailand. Int J Tuberc Lung Dis 2015; 19:817-22. [DOI: 10.5588/ijtld.14.0311] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Bordignon J, Probst CM, Mosimann ALP, Pavoni DP, Stella V, Buck GA, Satproedprai N, Fawcett P, Zanata SM, de Noronha L, Krieger MA, Duarte Dos Santos CN. Expression profile of interferon stimulated genes in central nervous system of mice infected with dengue virus Type-1. Virology 2008; 377:319-29. [PMID: 18570970 DOI: 10.1016/j.virol.2008.04.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 03/03/2008] [Accepted: 04/24/2008] [Indexed: 11/27/2022]
Abstract
Dengue virus (DENV) infection can cause a self-limiting disease (dengue fever) or a more severe clinical presentation known as dengue hemorrhagic fever (DHF)/dengue shock syndrome (DSS). Furthermore, data from recent dengue epidemics in Brazil indicate that the neurological manifestations are becoming more prevalent. However, the neuropathogenesis of dengue are not well understood. The balance between viral replication efficiency and innate immunity--in opposition during the early stages of infection--determines the clinical outcome of DENV infection. In this study, we investigated the effects of DENV infection on the transcription profile of the central nervous system (CNS) of mice. We observed in infected mice the up-regulation of 151 genes possibly involved in neuropathogenesis of dengue. Conversely, they may have a protective effect. Ingenuity Systems software analysis demonstrated, that the main pathways modulated by DENV infection in the mouse CNS are involved in interferon signaling and antigen presentation.
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Affiliation(s)
- Juliano Bordignon
- Instituto de Biologia Molecular do Paraná, Rua Prof Algacyr Munhoz Máder 3775, 81350-010, Curitiba, Paraná, Brazil
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