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Rangasamy N, Chinniah R, Ravi PM, Vijayan M, Sivanadham R, K V D, Pandi S, Sevak V, Krishnan P, Karuppiah B. HLA-DRB1* and DQB1* allele and haplotype diversity in eight tribal populations: Global affinities and genetic basis of diseases in South India. INFECTION GENETICS AND EVOLUTION 2020; 89:104685. [PMID: 33359263 DOI: 10.1016/j.meegid.2020.104685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/21/2022]
Abstract
The distribution of HLA class-II DRB1* and DQB1* alleles/ haplotypes were studied in 438 individuals of 8 Dravidian tribal groups inhabiting the Western Ghats, south India. The HLA typing was performed by PCR-SSP method. In order to identify the 5-locus Ancestral Extended Haplotypes (AEH), the alleles of HLA-A, -B and -C loci were typed for DNAs with predominant 2-locus haplotypes. The analyses have revealed allele HLA-DRB1*15 as the most predominant allele (Lowest / Highest range: Urali, 14.81 / Malasar, 48.94), followed by the alleles DRB1*10 (Katunayakan, 1.85 / Paliyan, 48.21), DRB1*14 (Paliyan 4.46 / Katunayakan, 40.74), DRB1*12 (Mannan, 1.64 / Katunayakan, 20.37) and DRB1*03 (Mannan, 1.64 / Urali, 29.63). The most frequent DQB1* alleles were DQB1*02 (Paliyan 3.57 / Urali, 23.15), DQB1*05 (Katunayakan, 27.77 / Paliyan 84.82) and DQB1*06 (Malasar, 8.51 / Kuruman, 33.51). The most predominant two-locus haplotypes observed were DRB1*15-DQB1*05, DRB1*10-DQB1*05, DRB1*15-DQB1*06 and DRB1*04-DQB1*05. The present study of HLA immunogenetics of south Indian tribes have revealed the presence of globally shared two and 5-locus haplotypes. Many of these haplotypes were implicated in a number of diseases in south India. We observed the presence of ancestral extended haplotypes (AEHs), hitherto not reported in Indian populations such as, A*68-B*35-C*02-DRB1*15:01-DQB1*05:01, A*24-B*57-C*06-DRB1*04:01-DQB1*05:01 and A*24-B*35-C*02-DRB1*15:01-DQB1*05:02. The dendrogram based phylogenetic analyses have revealed the Caucasian affinity of Urali, palaeo-Mediterranean and Indo-European affinity of Malasar tribes. The presence of globally shared susceptible and protective haplotypes reiterated the mosaic immunogenetic fabric of south Indian tribes.
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Affiliation(s)
- Nandakumar Rangasamy
- PG & Research Department of Zoology, Periyar EVR College, Tiruchirappalli 620023, Tamil Nadu, India
| | - Rathika Chinniah
- Department of Immunology, Madurai Kamaraj University, Madurai 625021, India
| | - Padma-Malini Ravi
- Department of Immunology, Madurai Kamaraj University, Madurai 625021, India
| | - Murali Vijayan
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, USA
| | | | - Darsa K V
- Department of Environmental Studies, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Sasiharan Pandi
- Department of Immunology, Madurai Kamaraj University, Madurai 625021, India
| | - Vandit Sevak
- Department of Immunology, Madurai Kamaraj University, Madurai 625021, India
| | - Prabhakaran Krishnan
- PG & Research Department of Zoology, Periyar EVR College, Tiruchirappalli 620023, Tamil Nadu, India
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Xu P, Gao QL, Wang YJ, Guo CF, Tang MX, Liu SH, Deng A, Wang YX, Li YB, Zhang HQ. rs6127698 polymorphism in the MC3R gene and susceptibility to multifocal tuberculosis in southern Chinese Han population. INFECTION GENETICS AND EVOLUTION 2020; 82:104292. [PMID: 32240798 DOI: 10.1016/j.meegid.2020.104292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/15/2020] [Accepted: 03/19/2020] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To investigate the relationship between melanocortin-3 receptor (MC3R) gene polymorphism and tuberculosis (TB) susceptibility in Han population in southern China. METHODS A total of 341 patients with TB (173 with pulmonary TB and 168 with multifocal TB) and 359 healthy controls were enrolled. Genotyping was performed by PCR and DNA sequencing, and detection of protein was performed by western blot. RESULTS The distributions of genotype and allele frequencies of rs6127698 differed significantly between the pulmonary and multifocal TB groups, and between the multifocal TB and control groups. The GG genotype was significantly more common among multifocal TB patients than among pulmonary TB patients (P = .009) and those in the control group (P = .001) under the recessive model. GG+GT genotype was more common in multifocal TB than in pulmonary TB (P < .01) and control group (P < .01) under the dominant model. G allele was more common in multifocal TB than in pulmonary TB (P < .0167) and control group (P < .0167). Patients with multifocal TB had an increased expression of MC3R protein than healthy controls (P < .05). CONCLUSIONS In the southern Chinese Han population, the MC3R rs6127698 polymorphism, which accompanying an increased expression of MC3R protein,was associated with susceptibility to multifocal TB. Presence of the G allele increased the risk of developing multifocal TB.
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Affiliation(s)
- Peng Xu
- Department of Spine Surgery, Xiangya Spinal Surgery Center, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Qi-le Gao
- Department of Spine Surgery, Xiangya Spinal Surgery Center, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Yun-Jia Wang
- Department of Spine Surgery, Xiangya Spinal Surgery Center, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China.
| | - Chao-Feng Guo
- Department of Spine Surgery, Xiangya Spinal Surgery Center, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Ming-Xing Tang
- Department of Spine Surgery, Xiangya Spinal Surgery Center, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Shao-Hua Liu
- Department of Spine Surgery, Xiangya Spinal Surgery Center, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Ang Deng
- Department of Spine Surgery, Xiangya Spinal Surgery Center, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Yu-Xiang Wang
- Department of Spine Surgery, Xiangya Spinal Surgery Center, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Yan-Bing Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Hong-Qi Zhang
- Department of Spine Surgery, Xiangya Spinal Surgery Center, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
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Bhattacharyya C, Majumder PP, Pandit B. An exome wide association study of pulmonary tuberculosis patients and their asymptomatic household contacts. INFECTION GENETICS AND EVOLUTION 2019; 71:76-81. [PMID: 30898644 DOI: 10.1016/j.meegid.2019.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 02/27/2019] [Accepted: 03/14/2019] [Indexed: 11/16/2022]
Abstract
Tuberculosis is a leading cause of death in India. To identify genetic variants associated with susceptibility or resistance to Mycobacterium tuberculosis infection, we have performed an exome-wide association study with 0.2 million exonic variants among 119 pairs of tuberculosis patients and their clinically asymptomatic household contacts. The strongest association was identified for rs61104666[A], a synonymous variant (p.E292E) of exon 5 of the gene SIGLEC15 (OR = 2.4, p = 1.49 × 10-5). We also found association of non-coding variants in the 3'UTR region of a gene encoding the class II human leukocyte antigens (HLAs), HLA-DRA. rs13209234[A] (minor allele frequency (MAF) = 13.8%) (OR = 0.35, P = 2.5 × 10-4) and rs3177928[A] (minor allele frequency (MAF) = 13.7%) (OR = 0.35, P = 3.3 × 10-4) were associated with protection from tuberculosis. These two SNPs, rs13209234 and rs3177928, are in complete linkage disequilibrium. These associations remained valid when additional data on freshly recruited individuals were jointly analyzed on 250 patient-control pairs. The identified gene, HLA-DRA, suggest involvement of immune regulation, indicating pathways associated with antigen presentation in tuberculosis infection.
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Affiliation(s)
| | | | - Bhaswati Pandit
- National Institute of Biomedical Genomics, PO: NSS, Kalyani 741251, West Bengal, India.
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Prakash R, Gupta R, Sharma P, Jain S, Chauhan DS, Katoch VM, Tiwari PK. Genotypic diversity of Mycobacterium tuberculosis isolates from North-Central Indian population. Pathog Glob Health 2019; 113:39-48. [PMID: 30821646 DOI: 10.1080/20477724.2019.1583881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND Different strains of Mycobacterium tuberculosis (MTB) are known to have different epidemiological and clinical characteristics. Some of them are widely distributed and associated with drug resistance, whereas others are locally predominated. Molecular epidemiological investigations have always been beneficial in identifying new strains and studying their transmission dynamics. Sahariya a primitive tribe of North Madhya Pradesh, India, has already been reported to have high prevalence of tuberculosis (TB) than their non-tribal neighbours. However, the information about MTB genotypes prevalent in Sahariya tribe and their non-tribal neighbours is not available. METHODS A total of 214 clinical isolates representing Sahariya tribe and non-tribes were analyzed by spoligotyping and MIRU-VNTR typing. RESULTS The EAI3_IND/SIT11 genotype was observed as major genotype in Sahariya tribe followed by CAS1_Delhi/SIT26 genotype. A 3.04 fold higher risk of getting TB with EAI3_IND/SIT11 genotype was observed in Sahariya as compared to the non-tribal population. The EAI_IND/SIT11 genotype also found to have more number of MDR-TB cases in Sahariya as well as true and possible transmission links. In Sahariya tribe, 3 clusters (6 isolates) reflected true transmission links, whereas 8 clusters consisted of 26 isolates revealed possible transmission links within the same geographical location or nearby houses. CONCLUSION The present study highlighted the predominance of EAI3_IND/SIT11 genotype in Sahariya tribe followed by CAS1_Delhi/SIT26 genotype. Combined approach of MIRU-VNTR typing and spoligotyping was observed more favourable in discrimination of MTB genotypes. Further, longitudinal studies using whole genome sequencing can provide more insights into genetic diversity, drug resistance and transmission dynamics of these prevalent genotypes.
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Affiliation(s)
- Ravi Prakash
- a Centre for Genomics, Molecular and Human Genetics , Jiwaji University , Gwalior , India.,b Department of Microbiology and Molecular Biology , National JALMA Institute for Leprosy and other Mycobacterial Diseases , Agra , India.,c Key Laboratory of Medical Molecular Virology , Fudan University , Shanghai , China
| | - Rahul Gupta
- a Centre for Genomics, Molecular and Human Genetics , Jiwaji University , Gwalior , India
| | - Pragya Sharma
- b Department of Microbiology and Molecular Biology , National JALMA Institute for Leprosy and other Mycobacterial Diseases , Agra , India
| | - Sanjay Jain
- d Revised National Tuberculosis Control Programme , District Hospital , Sheopur , India
| | - Devendra Singh Chauhan
- b Department of Microbiology and Molecular Biology , National JALMA Institute for Leprosy and other Mycobacterial Diseases , Agra , India
| | - Vishwa Mohan Katoch
- e Former Secretary, Department of Health Research, Govt. of India and Former Director General , Indian Council of Medical Research , Ansari Nagar , New Delhi , India.,f Rajasthan University of Health Sciences , Jaipur , India
| | - Pramod Kumar Tiwari
- a Centre for Genomics, Molecular and Human Genetics , Jiwaji University , Gwalior , India
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Spoligotyping, phenotypic and genotypic characterization of katG, rpoB gene of M. tuberculosis isolates from Sahariya tribe of Madhya Pradesh India. J Infect Public Health 2019; 12:395-402. [PMID: 30611735 DOI: 10.1016/j.jiph.2018.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Sahariya, a primitive tribal group, residing in Gwalior and Sheopur districts of Madhya Pradesh, India, show high incidence and prevalence of pulmonary tuberculosis (PTB). The study was designed to understand the genetic diversity and phenotype - genotype association of drug resistant M. tuberculosis strains, infecting Sahariya tribe. MATERIALS AND METHODS A total of 103 pulmonary tuberculosis patients from Sahariya tribe were recruited from Gwalior and Sheopur districts. Sputum samples were collected and cultured on LJ slants and drug sensitivity tests were carried out. Genomic DNA was extracted, followed by spoligotyping and genotyping of drug target genes, katG and rpoB, using MAS-PCR, PCR-RFLP and DNA sequencing. RESULT Seventeen different spoligotypes were identified, in which, EAI3_IND/ST11 M. tuberculosis strain appeared predominant, followed by CAS1_Delhi/ST26. Results of our phenotypic drug susceptibility test identified high incidence (12.6%) of isoniazid-resistant tuberculosis, while 4.85% isolates were multi drug resistant (MDR). Further genotyping of drug target genes identified 8.7% of isoniazid-R isolates to have a mutation at katG codon 463, while 3.8% isolates showed mutations at two sites, katG codons 315 and 463. In case of MDR-TB isolates, all from CAS lineage, 3.85% had mutations on katG and rpoB genes, at codon 463 and codon 526, respectively, while 0.97% isolates were harbouring mutations at codons 315, 463 and 531. CONCLUSION Our findings have revealed that EAI3_IND strain is the predominant strain infecting Sahariya. The incidence of isoniazid-R M. tuberculosis strain infection is high, with an increased propensity to evolve into MDR-TB. Therefore, the TB centres should also consider isoniazid-R status of the isolates along with CBNAAT before deciding the drug regimen for the patients.
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Saxena A, Sharma G, Tyagi S, Mourya M, Coshic P, Tiwari PK, Mehra NK, Kanga U. HLA-A*02 repertoires in three defined population groups from North and Central India: Punjabi Khatries, Kashmiri Brahmins and Sahariya Tribe. HLA 2018; 93:16-23. [PMID: 30516033 DOI: 10.1111/tan.13447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 01/30/2023]
Abstract
The allelic family of HLA-A*02 with a repertoire of approximately 1022 alleles represents the predominant and most heterogeneous group at the HLA-A locus. This remarkable diversity signifies its evolutionary relevance. Its population-specific diversity is attributed to environmental factors and pathogen pressure and can be harnessed in biology and medicine, particularly in disease association and for HLA-based vaccination approaches. We therefore investigated the HLA-A*02 repertoire in two North Indian caste populations, viz Punjabi Khatries (PK, N = 250), Kashmiri Brahmins (KB, N = 160) and a Central Indian tribe Sahariya (ST, N = 100) using Luminex-based high-resolution rSSO method. When required, results were confirmed with high-resolution PCR-SSP and/or next-generation sequencing (NGS). In the three populations evaluated, HLA-A*02 was observed with an overall high phenotypic/allelic frequency, however, A*02 repertoire differed among them. A total of six alleles were observed (A*02:01, *02:03, *02:05, *02:06, *02:07 and *02:11) in the caste groups, compared with four (except *02:05 and *02:07) in the tribals. Our striking observation was the high occurrence of A*02:11 at the repertoire level (80.6% in ST, 39% in PK, 31.8% in KB). Globally, this allele is rare, observed with low frequencies in limited ethnic groups. The primordial A*02:01 allele, representative A*02 allele in most ethnicities was observed as the second predominant allele (PK = 27.3%, KB = 31.8% and ST = 11.9%). Extremely high occurrence of A*02:11 in ST may be representation of ancient Austro-Asiatic genetic pool. In caste populations, the observed A*02 repertoire may be a consequence of natural selection and/or admixture from different populations.
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Affiliation(s)
- Abhishweta Saxena
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Gaurav Sharma
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Shweta Tyagi
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Manish Mourya
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Poonam Coshic
- Department of Transfusion Medicine (Blood Bank), All India Institute of Medical Sciences, New Delhi, India
| | - Pramod K Tiwari
- Centre for Genomics Molecular and Human Genetics, School of studies in Zoology, Jiwaji University, Gwalior, India
| | - Narinder K Mehra
- Dr C.G Pandit National Chair and Former Dean (Research), All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
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Harishankar M, Selvaraj P, Bethunaickan R. Influence of Genetic Polymorphism Towards Pulmonary Tuberculosis Susceptibility. Front Med (Lausanne) 2018; 5:213. [PMID: 30167433 PMCID: PMC6106802 DOI: 10.3389/fmed.2018.00213] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/10/2018] [Indexed: 12/11/2022] Open
Abstract
Tuberculosis (TB) is still remains the major threat for human health worldwide. Several case-control, candidate-gene, family studies and genome-wide association studies (GWAS) suggested the association of host genetic factors to TB susceptibility or resistance in various ethnic populations. Moreover, these factors modulate the host immune responses to tuberculosis. Studies have reported genetic markers to predict TB development in human leukocyte antigen (HLA) and non-HLA genes like killer immunoglobulin-like receptor (KIR), toll-like receptors (TLRs), cytokine/chemokines and their receptors, vitamin D receptor (VDR) and SLC11A1 etc. Highly polymorphic HLA loci may influence antigen presentation specificities by modifying peptide binding motifs. The recent meta-analysis studies revealed the association of several HLA alleles in particular class II HLA-DRB1 with TB susceptibility and valuable marker for disease development especially in Asian populations. Case-control studies have found the association of HLA-DR2 in some populations, but not in other populations, this could be due to an ethnic specific association of gene variants. Recently, GWAS conducted in case-control and family based studies in Russia, Chinese Han, Morocco, Uganda and Tanzania revealed the association of genes such as ASAP1, Alkylglycerol monooxygenase (AGMO), Forkhead BoxP1 (FOXP1), C-terminal domain phosphatase 1 (UBLCP1) and intergenic SNP rs932347C/T with TB. Whereas, SNP rs10956514A/G were not associated with TB in western Chinese Han and Tibetan population. In this review, we summarize the recent findings of genetic variants with susceptibility/resistance to TB.
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Affiliation(s)
- Murugesan Harishankar
- Department of Immunology, National Institute of Research in Tuberculosis, Chennai, India
| | - Paramasivam Selvaraj
- Department of Immunology, National Institute of Research in Tuberculosis, Chennai, India
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Mishra G, Poojary SS, Jain S, Tiwari PK. Genotype-phenotype relationship of CCL5 in pulmonary tuberculosis infection in Sahariya tribe: A pilot study. Indian J Med Res 2018; 146:768-773. [PMID: 29664036 PMCID: PMC5926349 DOI: 10.4103/ijmr.ijmr_1582_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background & objectives: Sahariya, a primitive tribe of Central India, has shown significantly increased incidence of pulmonary tuberculosis (PTB). Our previous study on Sahariya showed a significant association of −403G>A single nucleotide polymorphism (SNP) of CCL5 with susceptibility to PTB. Hence, this study was aimed to analyze a genotype-phenotype relationship of this disease-associated SNP to develop a potential diagnostic marker for TB in this tribe. Methods: The present study was carried out on 70 plasma samples from Sahariya tribe, wherein the plasma CCL5 level was determined using a commercially available ELISA kit. Results: The level of CCL5 decreased significantly in patients who were on therapy/completed their therapy [inactive TB patient/inactive PTB (IPTB)], particularly with AA genotype of −403G>A (P=0.046). The level, with AA genotype, was also found to gradually decrease in sputum 3+ and 1+/2+ than in sputum-negative samples. Similarly, the CCL5 level was found to be higher in sputum-positive/active TB patients than in IPTB group and healthy controls. Interpretation & conclusions: Our results suggested that the CCL5 level was influenced collectively not only by the genotypes of −403G>A SNP and bacillary load but also by the treatment. Thus, CCL5 may be considered for the development of a diagnostic marker and also as an indicator of recovery.
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Affiliation(s)
- Gunja Mishra
- Department of Molecular & Human Genetics, Centre for Genomics, Jiwaji University, Gwalior, India
| | - Satish S Poojary
- Department of Molecular & Human Genetics, Centre for Genomics, Jiwaji University, Gwalior, India
| | - Sanjay Jain
- Revised National Tuberculosis Control Programme Unit, District Hospital, Sheopur, India
| | - Pramod Kumar Tiwari
- Department of Molecular & Human Genetics, Centre for Genomics, Jiwaji University, Gwalior, India
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Stein CM, Sausville L, Wejse C, Sobota RS, Zetola NM, Hill PC, Boom WH, Scott WK, Sirugo G, Williams SM. Genomics of human pulmonary tuberculosis: from genes to pathways. CURRENT GENETIC MEDICINE REPORTS 2017; 5:149-166. [PMID: 29805915 DOI: 10.1007/s40142-017-0130-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Purpose of review Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), remains a major public health threat globally. Several lines of evidence support a role for host genetic factors in resistance/susceptibility to TB disease and MTB infection. However, results across candidate gene and genome-wide association studies (GWAS) are largely inconsistent, so a cohesive genetic model underlying TB risk has not emerged. Recent Findings Despite the difficulties in identifying consistent genetic associations, genetic studies of TB and MTB infection have revealed a few well-documented loci. These well validated genes are presented in this review, but there remains a large gap in how these genes translate into better understanding of TB. To address this, we present a pathway based extension of standard association analyses, seeding the results with the best validated genes from candidate gene and GWAS studies. Summary Several pathways were significantly enriched using pathway analyses that may help to explain population patterns of TB risk. In conclusion, we advocate for novel approaches to the study of host genetic analysis of TB that extend traditional association approaches.
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Affiliation(s)
- Catherine M Stein
- Department of Population and Quantitative Health Sciences, Cleveland, OH.,Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH
| | - Lindsay Sausville
- Department of Population and Quantitative Health Sciences, Cleveland, OH
| | - Christian Wejse
- Dept of Infectious Diseases/Center for Global Health, Aarhus University, Aarhus, Denmark
| | - Rafal S Sobota
- The Ken and Ruth Davee Department of Neurology, Northwestern University, Chicago, IL
| | - Nicola M Zetola
- Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA 19104, USA.,Botswana-UPenn Partnership, Gaborone, Botswana.,Department of Medicine, University of Botswana, Gaborone, Botswana
| | - Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - W Henry Boom
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH
| | - William K Scott
- Department of Human Genetics and Genomics, University of Miami School of Medicine, Miami, FL
| | - Giorgio Sirugo
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Cleveland, OH
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Pharmacogenomic implications of the evolutionary history of infectious diseases in Africa. THE PHARMACOGENOMICS JOURNAL 2016; 17:112-120. [PMID: 27779243 PMCID: PMC5380847 DOI: 10.1038/tpj.2016.78] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/06/2016] [Accepted: 07/19/2016] [Indexed: 12/20/2022]
Abstract
As the common birthplace of all human populations, modern humans have lived longer on the African continent than in any other geographical region of the world. This long history, along with the evolutionary need to adapt to environmental challenges such as exposure to infectious agents, has led to greater genetic variation in Africans. The vast genetic variation in Africans also extends to genes involved in the absorption, distribution, metabolism and excretion of pharmaceuticals. Ongoing cataloging of these clinically relevant variants reveals huge allele-frequency differences within and between African populations. Here, we examine Africa's large burden of infectious disease, discuss key examples of known genetic variation modulating disease risk, and provide examples of clinically relevant variants critical for establishing dosing guidelines. We propose that a more systematic characterization of the genetic diversity of African ancestry populations is required if the current benefits of precision medicine are to be extended to these populations.
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Buteme HK, Axelsson-Robertson R, Benson L, Joloba ML, Boom WH, Kallenius G, Maeurer M. Human leukocyte antigen class 1 genotype distribution and analysis in persons with active tuberculosis and household contacts from Central Uganda. BMC Infect Dis 2016; 16:504. [PMID: 27659198 PMCID: PMC5034515 DOI: 10.1186/s12879-016-1833-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 09/14/2016] [Indexed: 11/10/2022] Open
Abstract
Background To determine the distribution of Human leukocyte antigen (HLA) class I genotypes in a Ugandan population of persons with tuberculosis (TB) and establish the relationship between class I HLA types and Mycobacterium tuberculosis (MTB) disease. Methods Blood samples were drawn from HIV negative individuals with active TB and HIV negative household controls. DNA was extracted from blood samples and HLA typed by the polymerase chain reaction-sequence specific primer method. The allelic frequencies were determined by direct count. Results HLA-A*02, B*15, C*07, C*03, B*58, C*04, A*01, A*74, C*02 and A*30 were the dominant genotypes in this Ugandan cohort. There were differences in the distribution of HLA types between the individuals with active TB and the household controls with only HLA-A*03 allele showing a statistically significant difference (p = 0.017 crude; OR = 6.29 and p = 0.016; OR = 11.67 after adjustment for age). However, after applying the Benjamini and Hochberg adjustment for multiple comparisons the difference was no longer statistically significant (p = 0.374 and p = 0.176 respectively). Conclusions We identified a number of HLA class I alleles in a population from Central Uganda which will enable us to carry out a functional characterization of CD8+ T-cell mediated immune responses to MTB. Our results do not show a positive association between the HLA class I alleles and TB in this Ugandan population however the study sample was too small to draw any firm conclusions about the role of HLA class I alleles and TB development in Uganda. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1833-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Helen K Buteme
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O Box 7072, Kampala, Uganda. .,Department of Clinical Science and Education, Karolinska Institute, Södersjukhuset, SE-118 83, Stockholm, Sweden.
| | - Rebecca Axelsson-Robertson
- Department of Microbiology, Tumor and Cell Biology (MTC), Nobels vag 16, KI Solna Campus Karolinska Institute, Box 280, SE-171 77, Stockholm, Sweden
| | - Lina Benson
- Department of Clinical Science and Education, Karolinska Institute, Södersjukhuset, SE-118 83, Stockholm, Sweden
| | - Moses L Joloba
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O Box 7072, Kampala, Uganda
| | - W Henry Boom
- Tuberculosis Research Unit, Case Western Reserve University and University Hospitals' Case Medical Center, 10900 Euclid Avenue, BRB 1031, Cleveland, OH, 44106-4984, USA
| | - Gunilla Kallenius
- Department of Clinical Science and Education, Karolinska Institute, Södersjukhuset, SE-118 83, Stockholm, Sweden
| | - Markus Maeurer
- Department of Microbiology, Tumor and Cell Biology (MTC), Nobels vag 16, KI Solna Campus Karolinska Institute, Box 280, SE-171 77, Stockholm, Sweden
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Kashyap M, Farooq U, Jaiswal V. Homology modelling of frequent HLA class-II alleles: A perspective to improve prediction of HLA binding peptide and understand the HLA associated disease susceptibility. INFECTION GENETICS AND EVOLUTION 2016; 44:234-244. [PMID: 27421208 DOI: 10.1016/j.meegid.2016.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/24/2016] [Accepted: 07/05/2016] [Indexed: 11/30/2022]
Abstract
Human leukocyte antigen (HLA) plays significant role via the regulation of immune system and contribute in the progression and protection of many diseases. HLA molecules bind and present peptides to T- cell receptors which generate the immune response. HLA peptide interaction and molecular function of HLA molecule is the key to predict peptide binding and understanding its role in different diseases. The availability of accurate three dimensional (3D) structures is the initial step towards this direction. In the present work, homology modelling of important and frequent HLA-DRB1 alleles (07:01, 11:01 and 09:01) was done and acceptable models were generated. These modelled alleles were further refined and cross validated by using several methods including Ramachandran plot, Z-score, ERRAT analysis and root mean square deviation (RMSD) calculations. It is known that numbers of allelic variants are related to the susceptibility or protection of various infectious diseases. Difference in amino acid sequences and structures of alleles were also studied to understand the association of HLA with disease susceptibility and protection. Susceptible alleles showed more amino acid variations than protective alleles in three selected diseases caused by different pathogens. Amino acid variations at binding site were found to be more than other part of alleles. RMSD values were also higher at variable positions within binding site. Higher RMSD values indicate that mutations occurring at peptide binding site alter protein structure more than rest of the protein. Hence, these findings and modelled structures can be used to design HLA-DRB1 binding peptides to overcome low prediction accuracy of HLA class II binding peptides. Furthermore, it may help to understand the allele specific molecular mechanisms involved in susceptibility/resistance against pathogenic diseases.
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Affiliation(s)
- Manju Kashyap
- Faculty of Applied sciences and Biotechnology, Shoolini University, Solan, Himachal, Pradesh, India
| | - Umar Farooq
- Faculty of Applied sciences and Biotechnology, Shoolini University, Solan, Himachal, Pradesh, India
| | - Varun Jaiswal
- School of Electrical and Computer Science Engineering, Shoolini University, Solan, Himachal Pradesh, India.
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Souza de Lima D, Morishi Ogusku M, Porto dos Santos M, de Melo Silva CM, Alves de Almeida V, Assumpção Antunes I, Boechat AL, Ramasawmy R, Sadahiro A. Alleles of HLA-DRB1*04 Associated with Pulmonary Tuberculosis in Amazon Brazilian Population. PLoS One 2016; 11:e0147543. [PMID: 26901036 PMCID: PMC4764689 DOI: 10.1371/journal.pone.0147543] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/04/2016] [Indexed: 12/16/2022] Open
Abstract
Immunogenetic host factors are associated with susceptibility or protection to tuberculosis (TB). Strong associations of HLA class II genes with TB are reported. We analyzed the HLA-DRB1*04 alleles to identify subtypes associated with pulmonary TB and their interaction with risk factors such as alcohol, smoking, and gender in 316 pulmonary TB patients and 306 healthy individuals from the Brazilian Amazon. The HLA-DRB1*04 was prevalent in patients with pulmonary TB (p<0.0001; OR = 2.94; 95% CI = 2.12 to 4.08). Direct nucleotide sequencing of DRB1 exon 2 identified nine subtypes of HLA-DRB1*04. The subtype HLA-DRB1*04:11:01 (p = 0.0019; OR = 2.23; 95% CI = 1.34 to 3.70) was associated with susceptibility to pulmonary TB while DRB1*04:07:01 (p<0.0001; OR = 0.02; 95% CI = 0.001 to 0.33) to protection. Notably, the interaction between alcohol and HLA-DRB1*04:11:01 increased the risk for developing pulmonary TB (p = 0.0001; OR = 51.3; 95% CI = 6.81 to 386). Multibacillary pulmonary TB, the clinical presentation of disease transmission, was strongly associated with interaction to alcohol (p = 0.0026; OR = 11.1; 95% CI = 3.99 to 30.9), HLA-DRB1*04:11:01 (p = 0.0442; OR = 2.01; 95% CI = 1.03 to 3.93) and DRB1*04:92 (p = 0.0112; OR = 8.62; 95% CI = 1.63 to 45.5). These results show that HLA-DRB1*04 are associated with pulmonary TB. Interestingly, three subtypes, DRB1*04:07:01, DRB1*04:11:01 and DRB1*04:92 of the HLA-DRB1*04 could be potential immunogenetic markers that may help to explain mechanisms involved in disease development.
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Affiliation(s)
- Dhêmerson Souza de Lima
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
- * E-mail:
| | - Mauricio Morishi Ogusku
- Laboratório de Micobacteriologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brasil
| | - Maisa Porto dos Santos
- Laboratório de Micobacteriologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brasil
| | - Cláudia Maria de Melo Silva
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas (FCF), Manaus, Amazonas, Brasil
| | - Vanessa Alves de Almeida
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
| | | | - Antonio Luiz Boechat
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
| | - Rajendranath Ramasawmy
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT/HVD), Manaus, Amazonas, Brasil
- Universidade Nilton Lins, Manaus, Amazonas, Brasil
| | - Aya Sadahiro
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
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14
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Wamala D, Buteme HK, Kirimunda S, Kallenius G, Joloba M. Association between human leukocyte antigen class II and pulmonary tuberculosis due to mycobacterium tuberculosis in Uganda. BMC Infect Dis 2016; 16:23. [PMID: 26803588 PMCID: PMC4724396 DOI: 10.1186/s12879-016-1346-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 01/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis (Mtb) is reported to infect about a third of the world's population but only 10% are thought to develop active tuberculosis (TB) disease. Host immunity regulated by human leukocyte antigens (HLA) is an important determinant of the outcome of the disease. Here we investigate HLA class II gene polymorphisms in susceptibility to TB, and whether particular HLA class II alleles were associated with TB in Uganda. METHODS HIV negative patients with pulmonary TB (n = 43) and genetically related healthy household controls (n = 42) were typed for their HLA II class alleles using polymerase chain reaction sequence specific primer amplification. RESULTS The HLA-DQB1*03:03 allele was significantly less frequent in patients compared to healthy controls (10% in controls versus 0% in patients, p = 0.003). After correction for multiple comparisons the difference remained significant (p = 0.018). CONCLUSIONS Our results suggest that the HLA-DQB1*03:03 allele may be associated with resistance to TB.
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Affiliation(s)
- Dan Wamala
- Department of Pathology, Mulago Hospital and Makerere University, Kampala, Uganda. .,Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.
| | - Helen Koyokoyo Buteme
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Samuel Kirimunda
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gunilla Kallenius
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Moses Joloba
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
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