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Koskela S, Tammi S, Clancy J, Lucas JAM, Turner TR, Hyvärinen K, Ritari J, Partanen J. MICA and MICB allele assortment in Finland. HLA 2023. [PMID: 36919857 DOI: 10.1111/tan.15023] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/01/2023] [Accepted: 03/04/2023] [Indexed: 03/16/2023]
Abstract
Genetic variation in the MICA and MICB genes located within the major histocompatibility complex region has been reported to be associated with transplantation outcome and susceptibility to autoimmune diseases and infections. Only limited data of polymorphism in these genes in different populations are available. We here report allelic variation at 2-field resolution and the haplotypes of the MICA and MICB genes in Finland (n = 1032 individuals), a north European population with historical bottleneck and founder effects. Altogether 24 MICA and 18 MICB alleles were found, forming 70 estimated MICA-MICB haplotypes. As compared to other populations frequency differences were found, for example, MICA*010:01 was found to be at an allele frequency of 0.133 in Finland which is higher than in other European populations (0.021-0.077), but close to Asian populations (0.151-0.220). Three novel alleles with amino acid change are described. The results demonstrate a relatively high level of polymorphism and population differences in MICA and MICB allele distribution.
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Affiliation(s)
- Satu Koskela
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland.,Finnish Red Cross Blood Service Biobank, Helsinki, Finland
| | - Silja Tammi
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland.,Finnish Red Cross Blood Service Biobank, Helsinki, Finland
| | - Jonna Clancy
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland.,Finnish Red Cross Blood Service Biobank, Helsinki, Finland
| | | | - Thomas R Turner
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | - Kati Hyvärinen
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
| | - Jarmo Ritari
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
| | - Jukka Partanen
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland.,Finnish Red Cross Blood Service Biobank, Helsinki, Finland
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2
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Linn YC, Sundar Raj K, Teo B, Phang CY, Chittezhath M, Koh M. A cost-effective strategy for selection of third-party donors for a virus-specific T-cell bank for an Asian patient population. Cytotherapy 2023; 25:510-520. [PMID: 36882347 DOI: 10.1016/j.jcyt.2023.02.003] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/31/2022] [Accepted: 02/04/2023] [Indexed: 03/08/2023]
Abstract
BACKGROUND AIMS Third party virus-specific T cells (VST) has shown efficacy for opportunistic virus infection which do not have effective treatment or are drug-refractory. We describe our preparatory work in setting up a third-party VST bank for a multi-ethnic Asian population. METHODS Discarded white cells from regular blood bank plateletpheresis donors with known locally prevalent HLA antigens were cultured in small scale to generate VST against Adenovirus, BK virus, Cytomegalovirus, Epstein-Barr virus, and Human Herpes Virus 6. Multi-virus specific T cells (multi-VST) were also generated against all 5 viruses in single cultures. A strategy of allelic typing for donors with good and broad-spectrum cytotoxicity together with consideration on HLA restriction for the virus epitope was used to select combinations of VST lines for a hypothetical third party VST bank. The breadth of coverage based on these selection criteria was validated using our database of 100 post haematopoietic stem cell transplant patients. RESULTS We show that 50%, 42%, 56%, 56% and 42% of single VST cultures demonstrated specific cytotoxicity against AdV, BKV, CMV, EBV and HHV6 respectively. Twenty four of the 36 multi-VST lines showed activity against at least 2 of the 5 viruses studied. A carefully selected combination of just 6 VST lines can offer VST with at least 1 allelic match to 99% of potential recipients, while 92% can find 2 allelic matches and 79% can find 3 allelic matches. CONCLUSIONS This preparatory work confirms that a cost-effective strategy recruiting a small number of pre-characterized donors can generate VST lines with broad coverage for a multi-ethnic Asian patient population, thereby laying the foundation for setting up of a third party VST bank for Asian patients.
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Affiliation(s)
- Yeh-Ching Linn
- Department of Hematology, Singapore General Hospital, Singapore, Republic of Singapore.
| | | | - Bryan Teo
- Department of Clinical and Translational Research, Singapore General Hospital, Singapore, Republic of Singapore
| | - Chew-Yen Phang
- Patient Services, Blood Services Group, Health Sciences Authority, Singapore, Republic of Singapore
| | - Manesh Chittezhath
- Department of Hematology, Singapore General Hospital, Singapore, Republic of Singapore; Cell Therapy Facility, Blood Services Group, Health Sciences Authority, Singapore, Republic of Singapore
| | - Mickey Koh
- Cell Therapy Facility, Blood Services Group, Health Sciences Authority, Singapore, Republic of Singapore; Infection and Immunity Clinical Academic Group, St George's, University of London, London, UK
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3
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Otto M, Zheng Y, Wiehe T. Recombination, selection and the evolution of tandem gene arrays. Genetics 2022; 221:6572811. [PMID: 35460227 PMCID: PMC9252282 DOI: 10.1093/genetics/iyac052] [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] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
Multigene families—immunity genes or sensory receptors, for instance—are often subject to diversifying selection. Allelic diversity may be favored not only through balancing or frequency-dependent selection at individual loci but also by associating different alleles in multicopy gene families. Using a combination of analytical calculations and simulations, we explored a population genetic model of epistatic selection and unequal recombination, where a trade-off exists between the benefit of allelic diversity and the cost of copy abundance. Starting from the neutral case, where we showed that gene copy number is Gamma distributed at equilibrium, we derived also the mean and shape of the limiting distribution under selection. Considering a more general model, which includes variable population size and population substructure, we explored by simulations mean fitness and some summary statistics of the copy number distribution. We determined the relative effects of selection, recombination, and demographic parameters in maintaining allelic diversity and shaping the mean fitness of a population. One way to control the variance of copy number is by lowering the rate of unequal recombination. Indeed, when encoding recombination by a rate modifier locus, we observe exactly this prediction. Finally, we analyzed the empirical copy number distribution of 3 genes in human and estimated recombination and selection parameters of our model.
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Affiliation(s)
- Moritz Otto
- Institut für Genetik, Universität zu Köln, Zülpicher Straße 47a, 50674 Köln, Germany
| | - Yichen Zheng
- Institut für Genetik, Universität zu Köln, Zülpicher Straße 47a, 50674 Köln, Germany
| | - Thomas Wiehe
- Institut für Genetik, Universität zu Köln, Zülpicher Straße 47a, 50674 Köln, Germany
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Kloypan C, Koomdee N, Satapornpong P, Tempark T, Biswas M, Sukasem C. A Comprehensive Review of HLA and Severe Cutaneous Adverse Drug Reactions: Implication for Clinical Pharmacogenomics and Precision Medicine. Pharmaceuticals (Basel) 2021; 14:1077. [PMID: 34832859 PMCID: PMC8622011 DOI: 10.3390/ph14111077] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 12/19/2022] Open
Abstract
Human leukocyte antigen (HLA) encoded by the HLA gene is an important modulator for immune responses and drug hypersensitivity reactions as well. Genetic polymorphisms of HLA vary widely at population level and are responsible for developing severe cutaneous adverse drug reactions (SCARs) such as Stevens-Johnson syndrome (SJS), toxic epidermal necrolysis (TEN), drug reaction with eosinophilia and systemic symptoms (DRESS), maculopapular exanthema (MPE). The associations of different HLA alleles with the risk of drug induced SJS/TEN, DRESS and MPE are strongly supportive for clinical considerations. Prescribing guidelines generated by different national and international working groups for translation of HLA pharmacogenetics into clinical practice are underway and functional in many countries, including Thailand. Cutting edge genomic technologies may accelerate wider adoption of HLA screening in routine clinical settings. There are great opportunities and several challenges as well for effective implementation of HLA genotyping globally in routine clinical practice for the prevention of drug induced SCARs substantially, enforcing precision medicine initiatives.
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Affiliation(s)
- Chiraphat Kloypan
- Unit of Excellence in Integrative Molecular Biomedicine, School of Allied Health Sciences, University of Phayao, Phayao 56000, Thailand;
- Division of Clinical Immunology and Transfusion Science, Department of Medical Technology, School of Allied Health Sciences, University of Phayao, Phayao 56000, Thailand
| | - Napatrupron Koomdee
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.K.); (M.B.)
- Laboratory for Pharmacogenomics, Ramathibodi Hospital, Somdech Phra Debaratana Medical Center SDMC, Bangkok 10400, Thailand
| | - Patompong Satapornpong
- Division of General Pharmacy Practice, Department of Pharmaceutical Care, College of Pharmacy, Rangsit University, Pathum Thani 12000, Thailand;
- Excellence Pharmacogenomics and Precision Medicine Centre, College of Pharmacy, Rangsit University, Pathum Thani 12000, Thailand
| | - Therdpong Tempark
- Division of Dermatology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Mohitosh Biswas
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.K.); (M.B.)
- Laboratory for Pharmacogenomics, Ramathibodi Hospital, Somdech Phra Debaratana Medical Center SDMC, Bangkok 10400, Thailand
- Department of Pharmacy, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.K.); (M.B.)
- Laboratory for Pharmacogenomics, Ramathibodi Hospital, Somdech Phra Debaratana Medical Center SDMC, Bangkok 10400, Thailand
- The Thai Severe Cutaneous Adverse Drug Reaction THAI-SCAR Research-Genomics Thailand, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- The Preventive Genomics & Family Check-Up Services Center, Bumrungrad International Hospital, Pharmacogenomics and Precision Medicine Clinic, Bangkok 10110, Thailand
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3GL, UK
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Liu Z, Xi Q, Zhu L, Yang X, Jin L, Wang J, Zhang T, Zhou X, Zhang D, Peng X, Luo Y, Li Z, Zhang X. TUBB8 Mutations Cause Female Infertility with Large Polar Body Oocyte and Fertilization Failure. Reprod Sci 2021; 28:2942-2950. [PMID: 34160777 DOI: 10.1007/s43032-021-00633-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 12/22/2020] [Accepted: 05/19/2021] [Indexed: 12/18/2022]
Abstract
Tubulin beta 8 class VIII (TUBB8) is a special β-tubulin isotype that mainly expressed in primate oocytes and early embryos and identified as the disease-causing gene of human oocyte maturation arrest. To identify the disease-causing genes in 2 patients with female infertility due to large polar body oocyte or fertilization failure, whole-exome sequencing was performed on the patients and available family members. We identified a novel heterozygous missense mutation c.817C>G (p.L273V) and a recently reported heterozygous missense mutation c.608A>G (p.D203G) in TUBB8 from two patients, respectively. We found oocyte with a large polar body in the patient who carried the p.D203G mutation in TUBB8. Bioinformatics analysis showed that these two mutations are harmful. The results of western blot and RT-PCR experiments showed that the D203G mutation caused a significant decrease in the expression of TUBB8, and immunostaining showed that the TUBB8 mutation caused abnormal microtubule morphology. These findings suggest that TUBB8 mutations resulted in oocyte with a large polar body and fertilization failure in patients.
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Affiliation(s)
- Zhenxing Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qingsong Xi
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lixia Zhu
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xue Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Lei Jin
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiarui Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Tao Zhang
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaopei Zhou
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Dazhi Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Xuejie Peng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yalin Luo
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Zhou Li
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Xianqin Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
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6
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Kulski JK, Suzuki S, Shiina T. Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region. Front Genet 2021; 12:665899. [PMID: 34122517 PMCID: PMC8193847 DOI: 10.3389/fgene.2021.665899] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/12/2021] [Indexed: 12/26/2022] Open
Abstract
The major histocompatibility complex (MHC) on chromosome 6p21 is one of the most single-nucleotide polymorphism (SNP)-dense regions of the human genome and a prime model for the study and understanding of conserved sequence polymorphisms and structural diversity of ancestral haplotypes/conserved extended haplotypes. This study aimed to follow up on a previous analysis of the MHC class I region by using the same set of 95 MHC haplotype sequences downloaded from a publicly available BioProject database at the National Center for Biotechnology Information to identify and characterize the polymorphic human leukocyte antigen (HLA)-class II genes, the MTCO3P1 pseudogene alleles, the indels of transposable elements as haplotypic lineage markers, and SNP-density crossover (XO) loci at haplotype junctions in DNA sequence alignments of different haplotypes across the extended class II region (∼1 Mb) from the telomeric PRRT1 gene in class III to the COL11A2 gene at the centromeric end of class II. We identified 42 haplotypic indels (20 Alu, 7 SVA, 13 LTR or MERs, and 2 indels composed of a mosaic of different transposable elements) linked to particular HLA-class II alleles. Comparative sequence analyses of 136 haplotype pairs revealed 98 unique XO sites between SNP-poor and SNP-rich genomic segments with considerable haplotype shuffling located in the proximity of putative recombination hotspots. The majority of XO sites occurred across various regions including in the vicinity of MTCO3P1 between HLA-DQB1 and HLA-DQB3, between HLA-DQB2 and HLA-DOB, between DOB and TAP2, and between HLA-DOA and HLA-DPA1, where most XOs were within a HERVK22 sequence. We also determined the genomic positions of the PRDM9-recombination suppression sequence motif ATCCATG/CATGGAT and the PRDM9 recombination activation partial binding motif CCTCCCCT/AGGGGAG in the class II region of the human reference genome (NC_ 000006) relative to published meiotic recombination positions. Both the recombination and anti-recombination PRDM9 binding motifs were widely distributed throughout the class II genomic regions with 50% or more found within repeat elements; the anti-recombination motifs were found mostly in L1 fragmented repeats. This study shows substantial haplotype shuffling between different polymorphic blocks and confirms the presence of numerous putative ancestral recombination sites across the class II region between various HLA class II genes.
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Affiliation(s)
- Jerzy K Kulski
- Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia.,Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Shingo Suzuki
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Takashi Shiina
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
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Baxter-Lowe LA. The changing landscape of HLA typing: Understanding how and when HLA typing data can be used with confidence from bench to bedside. Hum Immunol 2021; 82:466-477. [PMID: 34030895 DOI: 10.1016/j.humimm.2021.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022]
Abstract
Human leukocyte antigen (HLA) genes are extraordinary for their extreme diversity and widespread impact on human health and disease. More than 30,000 HLA alleles have been officially named and more alleles continue to be discovered at a rapid pace. HLA typing systems which have been developed to detect HLA diversity have advanced rapidly and are revolutionizing our understanding of HLA's clinical importance. However, continuous improvements in knowledge and technology have created challenges for clinicians and scientists. This review explains how differences in HLA typing systems can impact the HLA types that are assigned. The consequences of differences in laboratory testing methods and reference databases are described. The challenges of using HLA types that are not equivalent are illustrated. A fundamental understanding of the continual expansion of our understanding of HLA diversity and limitations in some of the typing data is essential for using typing data appropriately in clinical and research settings.
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Affiliation(s)
- Lee Ann Baxter-Lowe
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, USA; Department of Pathology, University of Southern California, USA.
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Konte B, Walters JTR, Rujescu D, Legge SE, Pardiñas AF, Cohen D, Pirmohamed M, Tiihonen J, Hartmann AM, Bogers JP, van der Weide J, van der Weide K, Putkonen A, Repo-Tiihonen E, Hallikainen T, Silva E, Ingimarsson O, Sigurdsson E, Kennedy JL, Sullivan PF, Rietschel M, Breen G, Stefansson H, Stefansson K, Collier DA, O'Donovan MC, Giegling I. HLA-DQB1 6672G>C (rs113332494) is associated with clozapine-induced neutropenia and agranulocytosis in individuals of European ancestry. Transl Psychiatry 2021; 11:214. [PMID: 33846298 DOI: 10.1038/s41398-021-01322-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 02/21/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022] Open
Abstract
The atypical antipsychotic clozapine is the only effective medication for treatment-resistant schizophrenia. However, it can also induce serious adverse drug reactions, including agranulocytosis and neutropenia. The mechanism by which it does so is largely unknown, but there is evidence for contributing genetic factors. Several studies identified HLA-DQB1 variants and especially a polymorphism located in HLA-DQB1 (6672G>C, rs113332494) as associated with clozapine-induced agranulocytosis and neutropenia. We analysed the risk allele distribution of SNP rs113332494 in a sample of 1396 controls and 178 neutropenia cases of which 60 developed agranulocytosis. Absolute neutrophil counts of 500/mm3 and 1500/mm3 were used for defining agranulocytosis and neutropenia cases, respectively. We also performed association analyses and analysed local ancestry patterns in individuals of European ancestry, seeking replication and extension of earlier findings. HLA-DQB1 (6672G>C, rs113332494) was associated with neutropenia (OR = 6.20, P = 2.20E-06) and agranulocytosis (OR = 10.49, P = 1.83E-06) in individuals of European ancestry. The association signal strengthened after including local ancestry estimates (neutropenia: OR = 10.38, P = 6.05E-08; agranulocytosis: OR = 16.31, P = 1.39E-06), with effect sizes being considerably larger for agranulocytosis. Using local ancestry estimates for prediction, the sensitivity of rs113332494 increased from 11.28 to 55.64% for neutropenia and from 16.67 to 53.70% for agranulocytosis. Our study further strengthens the evidence implicating HLA-DQB1 in agranulocytosis and neutropenia, suggesting components of the immune system as contributing to this serious adverse drug reaction. Using local ancestry estimates might help in identifying risk variants and improve prediction of haematological adverse effects.
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Kulski JK, Suzuki S, Shiina T. SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction. Front Genet 2021; 11:594318. [PMID: 33537058 PMCID: PMC7848197 DOI: 10.3389/fgene.2020.594318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
The genomic region (~4 Mb) of the human major histocompatibility complex (MHC) on chromosome 6p21 is a prime model for the study and understanding of conserved polymorphic sequences (CPSs) and structural diversity of ancestral haplotypes (AHs)/conserved extended haplotypes (CEHs). The aim of this study was to use a set of 95 MHC genomic sequences downloaded from a publicly available BioProject database at NCBI to identify and characterise polymorphic human leukocyte antigen (HLA) class I genes and pseudogenes, MICA and MICB, and retroelement indels as haplotypic lineage markers, and single-nucleotide polymorphism (SNP) crossover loci in DNA sequence alignments of different haplotypes across the Olfactory Receptor (OR) gene region (~1.2 Mb) and the MHC class I region (~1.8 Mb) from the GPX5 to the MICB gene. Our comparative sequence analyses confirmed the identity of 12 haplotypic retroelement markers and revealed that they partitioned the HLA-A/B/C haplotypes into distinct evolutionary lineages. Crossovers between SNP-poor and SNP-rich regions defined the sequence range of haplotype blocks, and many of these crossover junctions occurred within particular transposable elements, lncRNA, OR12D2, MUC21, MUC22, PSORS1A3, HLA-C, HLA-B, and MICA. In a comparison of more than 250 paired sequence alignments, at least 38 SNP-density crossover sites were mapped across various regions from GPX5 to MICB. In a homology comparison of 16 different haplotypes, seven CEH/AH (7.1, 8.1, 18.2, 51.x, 57.1, 62.x, and 62.1) had no detectable SNP-density crossover junctions and were SNP poor across the entire ~2.8 Mb of sequence alignments. Of the analyses between different recombinant haplotypes, more than half of them had SNP crossovers within 10 kb of LTR16B/ERV3-16A3_I, MLT1, Charlie, and/or THE1 sequences and were in close vicinity to structurally polymorphic Alu and SVA insertion sites. These studies demonstrate that (1) SNP-density crossovers are associated with putative ancestral recombination sites that are widely spread across the MHC class I genomic region from at least the telomeric OR12D2 gene to the centromeric MICB gene and (2) the genomic sequences of MHC homozygous cell lines are useful for analysing haplotype blocks, ancestral haplotypic landscapes and markers, CPSs, and SNP-density crossover junctions.
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Affiliation(s)
- Jerzy K. Kulski
- Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, WA, Australia
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Shingo Suzuki
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Takashi Shiina
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
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Abstract
Runs of homozygosity (ROH) segments, contiguous homozygous regions in a genome were traditionally linked to families and inbred populations. However, a growing literature suggests that ROHs are ubiquitous in outbred populations. Still, most existing genetic studies of ROH in populations are limited to aggregated ROH content across the genome, which does not offer the resolution for mapping causal loci. This limitation is mainly due to a lack of methods for efficient identification of shared ROH diplotypes. Here, we present a new method, ROH-DICE, to find large ROH diplotype clusters, sufficiently long ROHs shared by a sufficient number of individuals, in large cohorts. ROH-DICE identified over 1 million ROH diplotypes that span over 100 SNPs and shared by more than 100 UK Biobank participants. Moreover, we found significant associations of clustered ROH diplotypes across the genome with various self-reported diseases, with the strongest associations found between the extended HLA region and autoimmune disorders. We found an association between a diplotype covering the HFE gene and haemochromatosis, even though the well-known causal SNP was not directly genotyped nor imputed. Using genome-wide scan, we identified a putative association between carriers of an ROH diplotype in chromosome 4 and an increase of mortality among COVID-19 patients. In summary, our ROH-DICE method, by calling out large ROH diplotypes in a large outbred population, enables further population genetics into the demographic history of large populations. More importantly, our method enables a new genome-wide mapping approach for finding disease-causing loci with multi-marker recessive effects at population scale.
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Affiliation(s)
- Ardalan Naseri
- Department of Computer Science, University of Central Florida, Orlando, Florida 32816, USA
| | - Degui Zhi
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, Florida 32816, USA
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11
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Bruijnesteijn J, de Groot NG, Bontrop RE. The Genetic Mechanisms Driving Diversification of the KIR Gene Cluster in Primates. Front Immunol 2020; 11:582804. [PMID: 33013938 PMCID: PMC7516082 DOI: 10.3389/fimmu.2020.582804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/18/2020] [Indexed: 12/26/2022] Open
Abstract
The activity and function of natural killer (NK) cells are modulated through the interactions of multiple receptor families, of which some recognize MHC class I molecules. The high level of MHC class I polymorphism requires their ligands either to interact with conserved epitopes, as is utilized by the NKG2A receptor family, or to co-evolve with the MHC class I allelic variation, which task is taken up by the killer cell immunoglobulin-like receptor (KIR) family. Multiple molecular mechanisms are responsible for the diversification of the KIR gene system, and include abundant chromosomal recombination, high mutation rates, alternative splicing, and variegated expression. The combination of these genetic mechanisms generates a compound array of diversity as is reflected by the contraction and expansion of KIR haplotypes, frequent birth of fusion genes, allelic polymorphism, structurally distinct isoforms, and variegated expression, which is in contrast to the mainly allelic nature of MHC class I polymorphism in humans. A comparison of the thoroughly studied human and macaque KIR gene repertoires demonstrates a similar evolutionarily conserved toolbox, through which selective forces drove and maintained the diversified nature of the KIR gene cluster. This hypothesis is further supported by the comparative genetics of KIR haplotypes and genes in other primate species. The complex nature of the KIR gene system has an impact upon the education, activity, and function of NK cells in coherence with an individual’s MHC class I repertoire and pathogenic encounters. Although selection operates on an individual, the continuous diversification of the KIR gene system in primates might protect populations against evolving pathogens.
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Affiliation(s)
- Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
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12
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Shen M, Lim SWD, Tan ES, Oon HH, Ren EC. HLA Correlations with Clinical Phenotypes and Risk of Metabolic Comorbidities in Singapore Chinese Psoriasis Patients. Mol Diagn Ther 2020; 23:751-760. [PMID: 31473973 DOI: 10.1007/s40291-019-00423-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Psoriasis is a systemic, chronic inflammatory disease that not only afflicts the skin but is also associated with cardiovascular disease and metabolic syndrome. The strongest susceptibility loci for the disease is within the human leukocyte antigen (HLA) complex, though specific HLA allelic associations vary between populations. OBJECTIVE Our objective was to investigate HLA associations with clinical phenotypes of psoriasis and metabolic syndrome in Chinese psoriasis cases. METHODS We conducted an observational case-control study in Singapore with a cohort of psoriasis cases consecutively recruited from an outpatient specialist dermatological center (n = 120) compared with 130 healthy controls. RESULTS Significant HLA associations with psoriasis were observed with HLA-A*02:07, B*46:01, C*01:02, and C*06:02. The three-locus haplotype of A*02:07-C*01:02-B*46:01 was also significant (odds ratio [OR] 3.07; p = 9.47 × 10-5). We also observed an association between nail psoriasis and HLA-A*02:07 carriers (OR 4.50; p = 0.002), whereas C*06:02 carriers were less prone to have nail involvement (OR 0.16; p = 0.004). HLA-A*02:07 was also identified as a possible risk allele for hypertension (OR 2.90; p < 0.05), and C*01:02 was a possible risk allele for dyslipidemia (OR 3.36; p < 0.05), both known to be common comorbidities in patients with psoriasis. CONCLUSION Our results demonstrate the growing importance of discerning population-specific clinical phenotypes and their association with certain HLA alleles in psoriasis.
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Affiliation(s)
- Meixin Shen
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, #03-06, Immunos Building, Singapore, 138648, Singapore
| | - Soon Wei Daniel Lim
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Eugene S Tan
- National Skin Centre (S) Pte Ltd, 1 Mandalay Rd, Singapore, 308205, Singapore
| | - Hazel H Oon
- National Skin Centre (S) Pte Ltd, 1 Mandalay Rd, Singapore, 308205, Singapore.
| | - Ee Chee Ren
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, #03-06, Immunos Building, Singapore, 138648, Singapore. .,Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, MD4, Level 3, Singapore, 117545, Singapore.
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13
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Simanovsky AL, Madbouly A, Halagan M, Maiers M, Louzoun Y. Single haplotype admixture models using large scale HLA genotype frequencies to reproduce human admixture. Immunogenetics 2019; 71:589-604. [PMID: 31741008 DOI: 10.1007/s00251-019-01144-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/17/2019] [Accepted: 10/19/2019] [Indexed: 12/20/2022]
Abstract
The human leukocyte antigen (HLA) is the most polymorphic region in humans. Anthropologists use HLA to trace populations' migration and evolution. However, recent admixture between populations can mask the ancestral haplotype frequency distribution. We present a statistical method based on high-resolution HLA haplotype frequencies to resolve population admixture using a non-negative matrix factorization formalism and validated using haplotype frequencies from 56 world populations. The result is a minimal set of source components (SCs) decoding roughly 90% of the total variance in the studied admixtures. These SCs agree with the geographical distribution, phylogenies, and recent admixture events of the studied groups. With the growing population of multi-ethnic individuals, or individuals that do not report race/ethnic information, the HLA matching process for stem-cell and solid organ transplants is becoming more challenging. The presented algorithm provides a framework that facilitates the breakdown of highly admixed populations into SCs, which can be used to better match the rapidly growing population of multi-ethnic individuals worldwide.
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Affiliation(s)
| | - Abeer Madbouly
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Michael Halagan
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Martin Maiers
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Yoram Louzoun
- Department of Mathematics and Gonda brain research institute, Bar-Ilan University, 52900, Ramat-Gan, Israel.
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14
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Holmes CM, Violette N, Miller D, Wagner B, Svansson V, Antczak DF. MHC haplotype diversity in Icelandic horses determined by polymorphic microsatellites. Genes Immun 2019; 20:660-70. [PMID: 31068686 DOI: 10.1038/s41435-019-0075-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/07/2019] [Accepted: 03/18/2019] [Indexed: 01/31/2023]
Abstract
The Icelandic horse has been maintained as a closed population in its eponymous homeland for many generations, with no recorded introductions of new horses of any breed since the year 1000 CE. Here we determined the diversity of major histocompatibility complex (MHC) haplotypes in 156 Icelandic horses from two groups, based on a panel of 12 polymorphic intra-MHC microsatellites tested in families of various composition. We identified a total of 79 MHC haplotypes in these two groups, including one documented intra-MHC recombination event from a total of 147 observed meioses. None of these MHC haplotypes have been previously described in any other horse breed. Only one MHC homozygote was found in the entire population studied. These results indicate a very high level of MHC heterozygosity and haplotype diversity in the Icelandic horse. The environment in Iceland is remarkable for its lack of common agents of equine infectious disease, including equine herpesvirus type 1, influenza virus, and streptococcus equi. The driving forces for maintenance of MHC heterozygosity in Icelandic horses must thus be sought outside of these major horse pathogens. Based on our results, we propose that intra-MHC recombination may play a major role in the generation of novel haplotypes.
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15
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Clancy J, Ritari J, Lobier M, Niittyvuopio R, Salmenniemi U, Putkonen M, Itälä-remes M, Partanen J, Koskela S. Increased MHC Matching by C4 Gene Compatibility in Unrelated Donor Hematopoietic Stem Cell Transplantation. Biol Blood Marrow Transplant 2019; 25:891-8. [DOI: 10.1016/j.bbmt.2018.12.759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022]
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16
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Guo J, Chen H, Yang P, Lee YT, Wu M, Przytycka TM, Kwoh CK, Zheng J. LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data. BMC Med Genomics 2018; 11:27. [PMID: 29697370 PMCID: PMC5918432 DOI: 10.1186/s12920-018-0351-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serious human diseases such as birth defects. Although the regulatory mechanism of recombination events is still unclear, DNA sequence polymorphisms have been found to play crucial roles in the regulation of recombination hotspots. Method To facilitate the studies of the underlying mechanism, we developed a database named LDSplitDB which provides an integrative and interactive data mining and visualization platform for the genome-wide association studies of recombination hotspots. It contains the pre-computed association maps of the major histocompatibility complex (MHC) region in the 1000 Genomes Project and the HapMap Phase III datasets, and a genome-scale study of the European population from the HapMap Phase II dataset. Besides the recombination profiles, related data of genes, SNPs and different types of epigenetic modifications, which could be associated with meiotic recombination, are provided for comprehensive analysis. To meet the computational requirement of the rapidly increasing population genomics data, we prepared a lookup table of 400 haplotypes for recombination rate estimation using the well-known LDhat algorithm which includes all possible two-locus haplotype configurations. Conclusion To the best of our knowledge, LDSplitDB is the first large-scale database for the association analysis of human recombination hotspots with DNA sequence polymorphisms. It provides valuable resources for the discovery of the mechanism of meiotic recombination hotspots. The information about MHC in this database could help understand the roles of recombination in human immune system. Database URL http://histone.scse.ntu.edu.sg/LDSplitDB
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Affiliation(s)
- Jing Guo
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore
| | - Hao Chen
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore
| | - Peng Yang
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore.,Institute for Infocomm Research, Agency for Science, Technology & Research, 1 Fusionopolis Way, Singapore, 138632, Singapore
| | - Yew Ti Lee
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore
| | - Min Wu
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore.,Institute for Infocomm Research, Agency for Science, Technology & Research, 1 Fusionopolis Way, Singapore, 138632, Singapore
| | - Teresa M Przytycka
- NCBI, NLM, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland, 20894, USA
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore
| | - Jie Zheng
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore. .,Genome Institute of Singapore, Agency for Science, Technology, and Research, Biopolis, Singapore, 138672, Singapore.
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17
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Koskela S, Ritari J, Hyvärinen K, Kwan T, Niittyvuopio R, Itälä-Remes M, Pastinen T, Partanen J. Hidden genomic MHC disparity between HLA-matched sibling pairs in hematopoietic stem cell transplantation. Sci Rep 2018; 8:5396. [PMID: 29599509 DOI: 10.1038/s41598-018-23682-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/16/2018] [Indexed: 12/30/2022] Open
Abstract
Matching classical HLA alleles between donor and recipient is an important factor in avoiding adverse immunological effects in HSCT. Siblings with no differences in HLA alleles, either due to identical-by-state or identical-by-descent status, are considered to be optimal donors. We carried out a retrospective genomic sequence and SNP analysis of 336 fully HLA-A, -B, -DRB1 matched and 14 partially HLA-matched sibling HSCT pairs to determine the level of undetected mismatching within the MHC segment as well as to map their recombination sites. The genomic sequence of 34 genes locating in the MHC region revealed allelic mismatching at 1 to 8 additional genes in partially HLA-matched pairs. Also, fully matched pairs were found to have mismatching either at HLA-DPB1 or at non-HLA region within the MHC segment. Altogether, 3.9% of fully HLA-matched HSCT pairs had large genomic mismatching in the MHC segment. Recombination sites mapped to certain restricted locations. The number of mismatched nucleotides correlated with the risk of GvHD supporting the central role of full HLA matching in HSCT. High-density genome analysis revealed that fully HLA-matched siblings may not have identical MHC segments and even single allelic mismatching at any classical HLA gene often implies larger genomic differences along MHC.
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18
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Tan-Koi WC, Sung C, Chong YY, Lateef A, Pang SM, Vasudevan A, Aw D, Lui NL, Lee SX, Ren EC, Koay ES, Tay YK, Lim YL, Lee HY, Dong D, Loke C, Tan L, Limenta M, Lee EJ, Toh D, Chan CL. Tailoring of recommendations to reduce serious cutaneous adverse drug reactions: a pharmacogenomics approach. Pharmacogenomics 2017; 18:881-890. [PMID: 28594314 DOI: 10.2217/pgs-2017-0016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The Health Sciences Authority launched a pharmacogenetics initiative in 2008 to facilitate evaluation of pharmacogenetics associations pertinent for Chinese, Malays and Indians in Singapore. The aim was to reduce the incidence and unpredictability of serious adverse drug reactions, with a focus on serious skin adverse drug reactions. This paper describes the gathering of evidence and weighing of factors that led to different genotyping recommendations for HLA-B*15:02 with carbamazepine and HLA-B*58:01 with allopurinol, despite both having strong genetic associations. Translation of pharmacogenomics at a national level requires careful deliberation of the prevalence of at-risk allele, strength of genetic associations, positive predictive value, cost-effectiveness and availability of alternative therapies. Our experience provides a perspective on translating genomic discoveries in advancing drug safety.
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Affiliation(s)
- Wei Chuen Tan-Koi
- Health Products Regulation Group, Health Sciences Authority, 11 Biopolis Way, 11-03, Helios, Singapore 138667, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Cynthia Sung
- Health Products Regulation Group, Health Sciences Authority, 11 Biopolis Way, 11-03, Helios, Singapore 138667, Singapore.,Health Services & Systems Research Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Yong Yeow Chong
- Department of Rheumatology and Immunology, Singapore General Hospital, Singapore, Singapore.,Internal Medicine Centre, Raffles Hospital, Singapore, Singapore
| | - Aisha Lateef
- Division of Rheumatology, National University Hospital, Singapore, Singapore
| | - Shiu Ming Pang
- Department of Dermatology, Singapore General Hospital, Singapore, Singapore
| | - Archana Vasudevan
- Department of Rheumatology, Changi General Hospital, Singapore, Singapore
| | - Derrick Aw
- Division of Dermatology, National University Hospital, Singapore, Singapore
| | - Nai Lee Lui
- Department of Rheumatology and Immunology, Singapore General Hospital, Singapore, Singapore
| | - Shan Xian Lee
- Department of Dermatology, Changi General Hospital, Singapore, Singapore
| | - Ee Chee Ren
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Evelyn Sc Koay
- Molecular Diagnosis Centre, National University Hospital, Singapore, Singapore.,Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yong Kwang Tay
- Department of Dermatology, Changi General Hospital, Singapore, Singapore
| | | | - Haur Yueh Lee
- Department of Dermatology, Singapore General Hospital, Singapore, Singapore
| | - Di Dong
- Health Services & Systems Research Programme, Duke-NUS Medical School, Singapore, Singapore.,Global Health Research Center, Duke-Kunshan University, Kunshan, China
| | - Celine Loke
- Health Products Regulation Group, Health Sciences Authority, 11 Biopolis Way, 11-03, Helios, Singapore 138667, Singapore
| | - Liesbet Tan
- Health Products Regulation Group, Health Sciences Authority, 11 Biopolis Way, 11-03, Helios, Singapore 138667, Singapore
| | - Michael Limenta
- Health Products Regulation Group, Health Sciences Authority, 11 Biopolis Way, 11-03, Helios, Singapore 138667, Singapore
| | - Edmund Jd Lee
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Dorothy Toh
- Health Products Regulation Group, Health Sciences Authority, 11 Biopolis Way, 11-03, Helios, Singapore 138667, Singapore
| | - Cheng Leng Chan
- Health Products Regulation Group, Health Sciences Authority, 11 Biopolis Way, 11-03, Helios, Singapore 138667, Singapore
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19
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Crispo E, Tunna HR, Hussain N, Rodriguez SS, Pavey SA, Jackson LJ, Rogers SM. The evolution of the major histocompatibility complex in upstream versus downstream river populations of the longnose dace. Ecol Evol 2017; 7:3297-3311. [PMID: 28515867 PMCID: PMC5433983 DOI: 10.1002/ece3.2839] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/28/2017] [Indexed: 11/10/2022] Open
Abstract
Populations in upstream versus downstream river locations can be exposed to vastly different environmental and ecological conditions and can thus harbor different genetic resources due to selection and neutral processes. An interesting question is how upstream–downstream directionality in rivers affects the evolution of immune response genes. We used next‐generation amplicon sequencing to identify eight alleles of the major histocompatibility complex (MHC) class II β exon 2 in the cyprinid longnose dace (Rhinichthys cataractae) from three rivers in Alberta, upstream and downstream of municipal and agricultural areas along contaminant gradients. We used these data to test for directional and balancing selection on the MHC. We also genotyped microsatellite loci to examine neutral population processes in this system. We found evidence for balancing selection on the MHC in the form of increased nonsynonymous variation relative to neutral expectations, and selection occurred at more amino acid residues upstream than downstream in two rivers. We found this pattern despite no population structure or isolation by distance, based on microsatellite data, at these sites. Overall, our results suggest that MHC evolution is driven by upstream–downstream directionality in fish inhabiting this system.
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Affiliation(s)
- Erika Crispo
- Department of Biological Sciences University of Calgary Calgary AB Canada
| | - Haley R Tunna
- Department of Biological Sciences University of Calgary Calgary AB Canada
| | - Noreen Hussain
- Department of Biology Pace University New York NY USA.,Present address: Touro College of Pharmacy New York NY USA
| | - Silvia S Rodriguez
- Department of Biology Pace University New York NY USA.,Present address: Developmental Biology Sloan-Kettering Institute New York NY USA
| | - Scott A Pavey
- University of New Brunswick Saint John & Canadian Rivers Institute Saint John NB Canada
| | - Leland J Jackson
- Department of Biological Sciences University of Calgary Calgary AB Canada
| | - Sean M Rogers
- Department of Biological Sciences University of Calgary Calgary AB Canada
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20
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Zu Y, Tan MH, Ren EC, Ying JY. Facile and phase-defined determination of HLA alleles with morpholino-functionalized nanoparticle probes. Nanomedicine 2016; 13:611-618. [PMID: 27720927 DOI: 10.1016/j.nano.2016.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 08/31/2016] [Accepted: 09/18/2016] [Indexed: 11/15/2022]
Abstract
A number of human leukocyte antigen (HLA) gene alleles have been found to be genetic risk markers for immunologically mediated drug hypersensitivity. Clinical adoption of HLA pharmacogenomics requires facile and accurate allele screening assays. As HLA genes are highly polymorphic, currently available methods are usually labor-intensive and liable to generate false positives. Herein we report a general strategy for screening HLA alleles with nanoparticle probes. Specific HLA alleles can be identified by gauging three to five sequence variants. Single-polymerase chain reaction (PCR) and dual-PCR methods have been proposed to achieve phase-defined determination of the sequence variants. Morpholino-functionalized gold nanoparticle probes allow for colorimetric and highly specific detection. Assays for HLA-B*58:01 and HLA-B*15:02 have been developed and validated with 49 selected human genomic DNA samples. The facile nanoparticle probe-based assays can be implemented easily in molecular diagnostic laboratories for accurate and cost-effective screening of HLA alleles.
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Affiliation(s)
- Yanbing Zu
- Institute of Bioengineering and Nanotechnology, Singapore, Singapore
| | - Min-Han Tan
- Institute of Bioengineering and Nanotechnology, Singapore, Singapore
| | - Ee Chee Ren
- Singapore Immunology Network, 8A Biomedical Grove, Immunos, Singapore, Singapore
| | - Jackie Y Ying
- Institute of Bioengineering and Nanotechnology, Singapore, Singapore.
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21
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Yau AC, Tuncel J, Haag S, Norin U, Houtman M, Padyukov L, Holmdahl R. Conserved 33-kb haplotype in the MHC class III region regulates chronic arthritis. Proc Natl Acad Sci U S A 2016; 113:E3716-24. [PMID: 27303036 DOI: 10.1073/pnas.1600567113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies have revealed many genetic loci associated with complex autoimmune diseases. In rheumatoid arthritis (RA), the MHC gene HLA-DRB1 is the strongest candidate predicting disease development. It has been suggested that other immune-regulating genes in the MHC contribute to the disease risk, but this contribution has been difficult to show because of the strong linkage disequilibrium within the MHC. We isolated genomic regions in the form of congenic fragments in rats to test whether there are additional susceptibility loci in the MHC. By both congenic mapping in inbred strains and SNP typing in wild rats, we identified a conserved, 33-kb large haplotype Ltab-Ncr3 in the MHC-III region, which regulates the onset, severity, and chronicity of arthritis. The Ltab-Ncr3 haplotype consists of five polymorphic immunoregulatory genes: Lta (lymphotoxin-α), Tnf, Ltb (lymphotoxin-β), Lst1 (leukocyte-specific transcript 1), and Ncr3 (natural cytotoxicity-triggering receptor 3). Significant correlation in the expression of the Ltab-Ncr3 genes suggests that interaction of these genes may be important in keeping these genes clustered together as a conserved haplotype. We studied the arthritis association and the spliceo-transcriptome of four different Ltab-Ncr3 haplotypes and showed that higher Ltb and Ncr3 expression, lower Lst1 expression, and the expression of a shorter splice variant of Lst1 correlate with reduced arthritis severity in rats. Interestingly, patients with mild RA also showed higher NCR3 expression and lower LST1 expression than patients with severe RA. These data demonstrate the importance of a conserved haplotype in the regulation of complex diseases such as arthritis.
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22
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Chen Q, Shen M, Heng YK, Theng TSC, Tey HL, Ren EC, Chong WS. Actinic Prurigo in Singaporean Chinese: A Positive Association with HLA-DRB1*03:01. Photochem Photobiol 2016; 92:355-359. [PMID: 26787110 DOI: 10.1111/php.12569] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 12/21/2015] [Indexed: 01/19/2023]
Abstract
Studies have reported the association of human leukocyte antigen (HLA) genes with susceptibility to develop actinic prurigo (AP) in Caucasians, but there were no studies in Asian populations, including the Chinese. Our study was performed to determine if AP is associated with susceptibility or protective HLA alleles or haplotypes in Singaporean Chinese. All Chinese patients diagnosed with AP at National Skin Center, Singapore, from January 2002 to April 2015 were invited to participate in the study. Clinical data and phototesting results were collated, and HLA typing was performed. Among 14 patients included, 11 were male and the mean age was 49.6 (37.9-61.3) years. All patients did not have a family history of AP and none had mucosal involvement, as such these clinical features differed from Caucasian AP patients. The frequency of DRB1*03:01 in AP patients was significantly higher compared to healthy controls (43% vs 16%, P = 0.022, odds ratio (OR) 3.89). Concurrently, the frequency of HLA-B*58:01-DRB1*03:01 haplotype was also significantly increased (25% vs 7%, P = 0.004, OR 4.23). In conclusion, HLA-DRB1*03:01 was associated with AP in Singaporean Chinese patients. This novel allelic association may possibly be utilized as a biological marker to aid in the diagnosis of AP in Chinese patients.
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Affiliation(s)
| | - Meixin Shen
- Singapore Immunology Network, A*STAR, Singapore, Singapore
| | | | | | | | - Ee Chee Ren
- Singapore Immunology Network, A*STAR, Singapore, Singapore
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23
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Zeng QQ, Zhong GH, He K, Sun DD, Wan QH. Molecular characterization of classical and nonclassical MHC class I genes from the golden pheasant (Chrysolophus pictus). Int J Immunogenet 2015; 43:8-17. [PMID: 26700854 DOI: 10.1111/iji.12245] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 11/22/2015] [Indexed: 11/29/2022]
Abstract
Classical major histocompatibility complex (MHC) class I allelic polymorphism is essential for competent antigen presentation. To improve the genotyping efforts in the golden pheasant, it is necessary to differentiate more accurately between classical and nonclassical class I molecules. In our study, all MHC class I genes were isolated from one golden pheasant based on two overlapping PCR amplifications. In total, six full-length class I nucleotide sequences (A-F) were identified, and four were novel. Two (A and C) belonged to the IA1 gene, two (B and D) were alleles derived from the IA2 gene through transgene amplification, and two (E and F) comprised a third novel locus, IA3 that was excluded from the core region of the golden pheasant MHC-B. IA1 and IA2 exhibited the broad expression profiles characteristic of classical loci, while IA3 showed no expression in multiple tissues and was therefore defined as a nonclassical gene. Phylogenetic analysis indicated that the three IA genes in the golden pheasant share a much closer evolutionary relationship than the corresponding sequences in other galliform species. This observation was consistent with high sequence similarity among them, which likely arises from the homogenizing effect of recombination. Our careful distinction between the classical and nonclassical MHC class I genes in the golden pheasant lays the foundation for developing locus-specific genotyping and establishing a good molecular marker system of classical MHC I loci.
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Affiliation(s)
- Q-Q Zeng
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - G-H Zhong
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - K He
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - D-D Sun
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Q-H Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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Lam TH, Tay MZ, Wang B, Xiao Z, Ren EC. Intrahaplotypic Variants Differentiate Complex Linkage Disequilibrium within Human MHC Haplotypes. Sci Rep 2015; 5:16972. [PMID: 26593880 DOI: 10.1038/srep16972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/22/2015] [Indexed: 12/21/2022] Open
Abstract
Distinct regions of long-range genetic fixation in the human MHC region, known as conserved extended haplotypes (CEHs), possess unique genomic characteristics and are strongly associated with numerous diseases. While CEHs appear to be homogeneous by SNP analysis, the nature of fine variations within their genomic structure is unknown. Using multiple, MHC-homozygous cell lines, we demonstrate extensive sequence conservation in two common Asian MHC haplotypes: A33-B58-DR3 and A2-B46-DR9. However, characterization of phase-resolved MHC haplotypes revealed unique intra-CEH patterns of variation and uncovered 127 single nucleotide variants (SNVs) which are missing from public databases. We further show that the strong linkage disequilibrium structure within the human MHC that typically confounds precise identification of genetic features can be resolved using intra-CEH variants, as evidenced by rs3129063 and rs448489, which affect expression of ZFP57, a gene important in methylation and epigenetic regulation. This study demonstrates an improved strategy that can be used towards genetic dissection of diseases.
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Chen M, Tang W, Hou L, Liu R, Dong Z, Han X, Zhang X, Wan D, Yu S. Tumor Necrosis Factor (TNF) -308G>A, Nitric Oxide Synthase 3 (NOS3) +894G>T Polymorphisms and Migraine Risk: A Meta-Analysis. PLoS One 2015; 10:e0129372. [PMID: 26098763 PMCID: PMC4476787 DOI: 10.1371/journal.pone.0129372] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 05/07/2015] [Indexed: 01/15/2023] Open
Abstract
Background and Objective Conflicting data have been reported on the association between tumor necrosis factor (TNF) –308G>A and nitric oxide synthase 3 (NOS3) +894G>T polymorphisms and migraine. We performed a meta-analysis of case-control studies to evaluate whether the TNF –308G>A and NOS3 +894G>T polymorphisms confer genetic susceptibility to migraine. Method We performed an updated meta-analysis for TNF –308G>A and a meta-analysis for NOS3 +894G>T based on studies published up to July 2014. We calculated study specific odds ratios (OR) and 95% confidence intervals (95% CI) assuming allele contrast, dominant model, recessive model, and co-dominant model as pooled effect estimates. Results Eleven studies in 6682 migraineurs and 22591 controls for TNF –308G>A and six studies in 1055 migraineurs and 877 controls for NOS3 +894G>T were included in the analysis. Neither indicated overall associations between gene polymorphisms and migraine risk. Subgroup analyses suggested that the “A” allele of the TNF –308G>A variant increases the risk of migraine among non-Caucasians (dominant model: pooled OR = 1.82; 95% CI 1.15 – 2.87). The risk of migraine with aura (MA) was increased among both Caucasians and non-Caucasians. Subgroup analyses suggested that the “T” allele of the NOS3 +894G>T variant increases the risk of migraine among non-Caucasians (co-dominant model: pooled OR = 2.10; 95% CI 1.14 – 3.88). Conclusions Our findings appear to support the hypothesis that the TNF –308G>A polymorphism may act as a genetic susceptibility factor for migraine among non-Caucasians and that the NOS3 +894G>T polymorphism may modulate the risk of migraine among non-Caucasians.
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Affiliation(s)
- Min Chen
- Department of Neurology, Chinese PLA General Hospital, Beijing, China
- Department of Neurology, the First People’s Hospital of Nanyang, Nanyang, Henan Province, China
| | - Wenjing Tang
- Department of Neurology, Chinese PLA General Hospital, Beijing, China
| | - Lei Hou
- Department of Neurology, Chinese PLA General Hospital, Beijing, China
| | - Ruozhuo Liu
- Department of Neurology, Chinese PLA General Hospital, Beijing, China
| | - Zhao Dong
- Department of Neurology, Chinese PLA General Hospital, Beijing, China
| | - Xun Han
- Department of Neurology, Chinese PLA General Hospital, Beijing, China
| | - Xiaofei Zhang
- Department of Neurology, Chinese PLA General Hospital, Beijing, China
| | - Dongjun Wan
- Department of Neurology, Chinese PLA General Hospital, Beijing, China
| | - Shengyuan Yu
- Department of Neurology, Chinese PLA General Hospital, Beijing, China
- * E-mail:
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Zhang GL, Keskin DB, Lin HN, Lin HH, DeLuca DS, Leppanen S, Milford EL, Reinherz EL, Brusic V. Human leukocyte antigen typing using a knowledge base coupled with a high-throughput oligonucleotide probe array analysis. Front Immunol 2014; 5:597. [PMID: 25505899 PMCID: PMC4245923 DOI: 10.3389/fimmu.2014.00597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 11/06/2014] [Indexed: 01/11/2023] Open
Abstract
Human leukocyte antigens (HLA) are important biomarkers because multiple diseases, drug toxicity, and vaccine responses reveal strong HLA associations. Current clinical HLA typing is an elimination process requiring serial testing. We present an alternative in situ synthesized DNA-based microarray method that contains hundreds of thousands of probes representing a complete overlapping set covering 1,610 clinically relevant HLA class I alleles accompanied by computational tools for assigning HLA type to 4-digit resolution. Our proof-of-concept experiment included 21 blood samples, 18 cell lines, and multiple controls. The method is accurate, robust, and amenable to automation. Typing errors were restricted to homozygous samples or those with very closely related alleles from the same locus, but readily resolved by targeted DNA sequencing validation of flagged samples. High-throughput HLA typing technologies that are effective, yet inexpensive, can be used to analyze the world's populations, benefiting both global public health and personalized health care.
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Affiliation(s)
- Guang Lan Zhang
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Computer Science, Metropolitan College, Boston University , Boston, MA , USA
| | - Derin B Keskin
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA ; Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute , Boston, MA , USA
| | - Hsin-Nan Lin
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Institute of Information Science, Academia Sinica , Taipei , Taiwan
| | - Hong Huang Lin
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Medicine, Boston University School of Medicine , Boston, MA , USA
| | - David S DeLuca
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA
| | | | - Edgar L Milford
- Department of Medicine, Harvard Medical School , Boston, MA , USA ; Histocompatibility and Tissue Typing Laboratory, Brigham and Women's Hospital , Boston, MA , USA
| | - Ellis L Reinherz
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA ; Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute , Boston, MA , USA
| | - Vladimir Brusic
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Computer Science, Metropolitan College, Boston University , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA
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Choo JA, Liu J, Toh X, Grotenbreg GM, Ren EC. The immunodominant influenza A virus M158-66 cytotoxic T lymphocyte epitope exhibits degenerate class I major histocompatibility complex restriction in humans. J Virol 2014; 88:10613-23. [PMID: 24990997 DOI: 10.1128/JVI.00855-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED Cytotoxic T lymphocytes recognizing conserved peptide epitopes are crucial for protection against influenza A virus (IAV) infection. The CD8 T cell response against the M158-66 (GILGFVFTL) matrix protein epitope is immunodominant when restricted by HLA-A*02, a major histocompatibility complex (MHC) molecule expressed by approximately half of the human population. Here we report that the GILGFVFTL peptide is restricted by multiple HLA-C*08 alleles as well. We observed that M158-66 was able to elicit cytotoxic T lymphocyte (CTL) responses in both HLA-A*02- and HLA-C*08-positive individuals and that GILGFVFTL-specific CTLs in individuals expressing both restriction elements were distinct and not cross-reactive. The crystal structure of GILGFVFTL-HLA-C*08:01 was solved at 1.84 Å, and comparison with the known GILGFVFTL-HLA-A*02:01 structure revealed that the antigen bound both complexes in near-identical conformations, accommodated by binding pockets shaped from shared as well as unique residues. This discovery of degenerate peptide presentation by both HLA-A and HLA-C allelic variants eliciting unique CTL responses to IAV infection contributes fundamental knowledge with important implications for vaccine development strategies. IMPORTANCE The presentation of influenza A virus peptides to elicit immunity is thought to be narrowly restricted, with a single peptide presented by a specific HLA molecule. In this study, we show that the same influenza A virus peptide can be more broadly presented by both HLA-A and HLA-C molecules. This discovery may help to explain the differences in immunity to influenza A virus between individuals and populations and may also aid in the design of vaccines.
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de Groot N, Doxiadis GGM, Otting N, de Vos-Rouweler AJM, Bontrop RE. Differential recombination dynamics within the MHC of macaque species. Immunogenetics 2014; 66:535-44. [PMID: 24934118 PMCID: PMC4156779 DOI: 10.1007/s00251-014-0783-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [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: 04/04/2014] [Accepted: 05/21/2014] [Indexed: 10/27/2022]
Abstract
A panel of 15 carefully selected microsatellites (short tandem repeats, STRs) has allowed us to study segregation and haplotype stability in various macaque species. The STRs span the major histocompatibility complex (MHC) region and map in more detail from the centromeric part of the Mhc-A to the DR region. Two large panels of Indian rhesus and Indonesian/Indochinese cynomolgus macaques have been subjected to pedigree analysis, allowing the definition of 161 and 36 different haplotypes and the physical mapping of 10 and 5 recombination sites, respectively. Although most recombination sites within the studied section of the Indian rhesus monkey MHC are situated between the Mhc-A and Mhc-B regions, the resulting recombination rate for this genomic segment is low and similar to that in humans. In contrast, in Indonesian/Indochinese macaques, two recombination sites, which appear to be absent in rhesus macaques, map between the class III and II regions. As a result, the mean recombination frequency of the core MHC, Mhc-A to class II, is higher in Indonesian/Indochinese cynomolgus than in Indian rhesus macaques, but as such is comparable to that in humans. The present communication demonstrates that the dynamics of recombination 'hot/cold spots' in the MHC, as well as their frequencies, may differ substantially between highly related macaque species.
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Affiliation(s)
- Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
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Gonzalez G, Koyanagi KO, Aoki K, Kitaichi N, Ohno S, Kaneko H, Ishida S, Watanabe H. Intertypic modular exchanges of genomic segments by homologous recombination at universally conserved segments in human adenovirus species D. Gene 2014; 547:10-7. [PMID: 24726548 DOI: 10.1016/j.gene.2014.04.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 03/28/2014] [Accepted: 04/08/2014] [Indexed: 11/20/2022]
Abstract
Human adenovirus species D (HAdV-D), which is composed of clinically and epidemiologically important pathogens worldwide, contains more taxonomic "types" than any other species of the genus Mastadenovirus, although the mechanisms accounting for the high level of diversity remain to be disclosed. Recent studies of known and new types of HAdV-D have indicated that intertypic recombination between distant types contributes to the increasing diversity of the species. However, such findings raise the question as to how homologous recombination events occur between diversified types since homologous recombination is suppressed as nucleotide sequences diverge. In order to address this question, we investigated the distribution of the recombination boundaries in comparison with the landscape of intergenomic sequence conservation assessed according to the synonymous substitution rate (dS). The results revealed that specific genomic segments are conserved between even the most distantly related genomes; we call these segments "universally conserved segments" (UCSs). These findings suggest that UCSs facilitate homologous recombination, resulting in intergenomic segmental exchanges of UCS-flanking genomic regions as recombination modules. With the aid of such a mechanism, the haploid genomes of HAdV-Ds may have been reshuffled, resulting in chimeric genomes out of diversified repertoires in the HAdV-D population analogous to the MHC region reshuffled via crossing over in vertebrates. In addition, some HAdVs with chimeric genomes may have had the opportunity to avoid host immune responses thereby causing epidemics.
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Affiliation(s)
- Gabriel Gonzalez
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Kanako O Koyanagi
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Koki Aoki
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Nobuyoshi Kitaichi
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan; Department of Ophthalmology, Health Sciences University of Hokkaido, Sapporo 002-8072, Japan
| | - Shigeaki Ohno
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Hisatoshi Kaneko
- Department of Ophthalmology, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan; Hobara Eye clinic, Date 960-0612, Japan
| | - Susumu Ishida
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Hidemi Watanabe
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan.
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Toh DS, Tan LL, Aw DC, Pang SM, Lim SH, Thirumoorthy T, Lee HY, Tay YK, Tan SK, Vasudevan A, Lateef A, Chong YY, Chan YC, Loke C, Chan CL, Koay ES, Ren EC, Lee EJ, Sung C. Building pharmacogenetics into a pharmacovigilance program in Singapore: using serious skin rash as a pilot study. Pharmacogenomics J 2014; 14:316-21. [PMID: 24394201 DOI: 10.1038/tpj.2013.46] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/24/2013] [Accepted: 11/26/2013] [Indexed: 11/09/2022]
Abstract
To study the possible genetic associations with adverse drug reactions (ADR), the Singapore Health Sciences Authority (HSA) has piloted a program to collect DNA and phenotype data of ADR cases as part of its pharmacovigilance program. Between 2009 and 2012, HSA screened 158 cases of Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). To assess the association between HLA-B*1502 and carbamazepine (CBZ)-induced SJS/TEN, 13 cases and 26 drug-tolerant controls were analyzed. All 13 CBZ-SJS/TEN cases and 3/26 controls were HLA-B*1502 positive (odds ratio 181, 95% confidence interval: 8.7-3785, P=6.9 × 10(-8)). Discussions of the finding with the Ministry of Health and an expert panel led to the decision to make HLA-B*1502 testing the standard of care prior to first use of CBZ in Asians and to subsidize the genotyping test at public hospitals. This program illustrates the role of a regulatory authority in advancing the use of pharmacogenetics for drug safety.
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Wennerström A, Vlachopoulou E, Lahtela LE, Paakkanen R, Eronen KT, Seppänen M, Lokki ML. Diversity of extended HLA-DRB1 haplotypes in the Finnish population. PLoS One 2013; 8:e79690. [PMID: 24278156 PMCID: PMC3836878 DOI: 10.1371/journal.pone.0079690] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/23/2013] [Indexed: 11/18/2022] Open
Abstract
The Major Histocompatibility Complex (MHC, 6p21) codes for traditional HLA and other host response related genes. The polymorphic HLA-DRB1 gene in MHC Class II has been associated with several complex diseases. In this study we focus on MHC haplotype structures in the Finnish population. We explore the variability of extended HLA-DRB1 haplotypes in relation to the other traditional HLA genes and a selected group of MHC class III genes. A total of 150 healthy Finnish individuals were included in the study. Subjects were genotyped for HLA alleles (HLA-A, -B, -DRB1, -DQB1, and -DPB1). The polymorphism of TNF, LTA, C4, BTNL2 and HLA-DRA genes was studied with 74 SNPs (single nucleotide polymorphism). The C4A and C4B gene copy numbers and a 2-bp silencing insertion at exon 29 in C4A gene were analysed with quantitative genomic realtime-PCR. The allele frequencies for each locus were calculated and haplotypes were constructed using both the traditional HLA alleles and SNP blocks. The most frequent Finnish A∼B∼DR -haplotype, uncommon in elsewhere in Europe, was A*03∼B*35∼DRB1*01∶01. The second most common haplotype was a common European ancestral haplotype AH 8.1 (A*01∼B*08∼DRB1*03∶01). Extended haplotypes containing HLA-B, TNF block, C4 and HLA-DPB1 strongly increased the number of HLA-DRB1 haplotypes showing variability in the extended HLA-DRB1 haplotype structures. On the contrary, BTNL2 block and HLA-DQB1 were more conserved showing linkage with the HLA-DRB1 alleles. We show that the use of HLA-DRB1 haplotypes rather than single HLA-DRB1 alleles is advantageous when studying the polymorphisms and LD patters of the MHC region. For disease association studies the HLA-DRB1 haplotypes with various MHC markers allows us to cluster haplotypes with functionally important gene variants such as C4 deficiency and cytokines TNF and LTA, and provides hypotheses for further assessment. Our study corroborates the importance of studying population-specific MHC haplotypes.
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Affiliation(s)
- Annika Wennerström
- Transplantation Laboratory, Haartman Institute, Helsinki, Finland
- * E-mail:
| | | | - L. Elisa Lahtela
- Transplantation Laboratory, Haartman Institute, Helsinki, Finland
| | - Riitta Paakkanen
- Transplantation Laboratory, Haartman Institute, Helsinki, Finland
| | - Katja T. Eronen
- Transplantation Laboratory, Haartman Institute, Helsinki, Finland
| | - Mikko Seppänen
- Division of Infectious Diseases, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
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