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Chou WH, Chen LC, Wong HSC, Chao CH, Chu HW, Chang WC. Phenomic landscape and pharmacogenomic implications for HLA region in a Taiwan Han Chinese population. Biomark Res 2024; 12:46. [PMID: 38702819 PMCID: PMC11067262 DOI: 10.1186/s40364-024-00591-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/18/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND The human leukocyte antigen (HLA) genes, exhibiting significant genetic diversity, are associated with susceptibility to various clinical diseases and diverse in drug responses. High costs of HLA sequencing and the population-specific architecture of this genetic region necessitate the establishment of a population-specific HLA imputation reference panel. Moreover, there is a lack of understanding about the genetic and phenotypic landscape of HLA variations within the Taiwanese population. METHODS We created models for a Taiwanese-specific HLA imputation reference panel. These models were trained with the array genotype data and HLA sequencing data from 845 Taiwanese subjects. HLA imputation was applied for 59,448 Taiwanese subjects to characterize the HLA allele and haplotype frequencies. Additionally, a phenome-wide association study (PheWAS) was conducted to identify the phenotypes associated with HLA variations. The association of the biallelic HLA variants with the binary and quantitative traits were evaluated with additive logistic and linear regression models, respectively. Furthermore, an omnibus test with likelihood-ratio test was applied for each HLA amino acid position in the multiallelic HLA amino acid polymorphisms to compare the difference between a fitted model and a null model following a χ2 distribution of n-1 degree of freedom at a position with n residues. Finally, we estimated the prevalence of adverse drug reactions (ADR)-related HLA alleles in the Taiwanese population. RESULTS In this study, the reference panel models displayed remarkable accuracy, with averages of 99.3%, 98.9%, and 99.1% for 2-, 4-, 6-digit alleles of the eight classical HLA genes, respectively. For PheWAS, a total of 18,136 significant associations with HLA variants across 26 phenotypes are identified (p < 5×10-8), highlighting the pleiotropy feature of the HLA region. Among the independent signals, 15 are novel, including the association of HLA-B pos 138 variation with ankylosing spondylitis (AS), and rs9266290 and rs9266292 with allergy. Through an analysis spanning the entire HLA region, we identified clusters of phenotype correlations. Finally, the carriers of pharmacogenomic related HLA alleles, including HLA-C*01:02 (35.86%), HLA-B*58:01 (20.9%), and HLA-B*15:02 (8.38%), were characterized in the Taiwanese general population. CONCLUSIONS We successfully delivered the HLA imputation for 59,448 Taiwanese subjects and characterized the genetic and phenotypic landscapes of the HLA variations. In addition, we quantified the estimated prevalence of the ADR-related HLA alleles in the Taiwanese population. The developed HLA imputation reference panel could be used for estimation of population HLA allele frequencies, which can facilitate further studies in the role of HLA variants in a wider range of phenotypes in the population.
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Affiliation(s)
- Wan-Hsuan Chou
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Lu-Chun Chen
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Henry Sung-Ching Wong
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Ching-Hsuan Chao
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.
- Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
- Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
- Department of Pharmacology, National Defense Medical Center, Taipei, Taiwan.
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Del Gaudio A, Covello C, Di Vincenzo F, De Lucia SS, Mezza T, Nicoletti A, Siciliano V, Candelli M, Gasbarrini A, Nista EC. Drug-Induced Acute Pancreatitis in Adults: Focus on Antimicrobial and Antiviral Drugs, a Narrative Review. Antibiotics (Basel) 2023; 12:1495. [PMID: 37887196 PMCID: PMC10604068 DOI: 10.3390/antibiotics12101495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Acute pancreatitis (AP) is an acute inflammation of the pancreas caused by the activation of digestive enzymes in the pancreatic tissue. The main causes of AP are cholelithiasis and alcohol abuse; less commonly, it can be caused by drugs, with a prevalence of up to 5%. Causal associations between drugs and pancreatitis are largely based on case reports or case series with limited evidence. We reviewed the available data on drug-induced AP, focusing on antimicrobial drugs and antivirals, and discussed the current evidence in relation to the classification systems available in the literature. We found 51 suspected associations between antimicrobial and antiviral drugs and AP. The drugs with the most evidence of correlation are didanosine, protease inhibitors, and metronidazole. In addition, other drugs have been described in case reports demonstrating positive rechallenge. However, there are major differences between the various classifications available, where the same drug being assigned to different probability classes. It is likely that the presence in multiple case reports of an association between acute pancreatitis and a drug should serve as a basis for conducting prospective randomized controlled trials to improve the quality of the evidence.
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Affiliation(s)
- Angelo Del Gaudio
- Center for Diagnosis and Treatment of Digestive Diseases, Gastroenterology Department, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy; (A.D.G.); (C.C.); (F.D.V.)
| | - Carlo Covello
- Center for Diagnosis and Treatment of Digestive Diseases, Gastroenterology Department, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy; (A.D.G.); (C.C.); (F.D.V.)
| | - Federica Di Vincenzo
- Center for Diagnosis and Treatment of Digestive Diseases, Gastroenterology Department, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy; (A.D.G.); (C.C.); (F.D.V.)
| | - Sara Sofia De Lucia
- Center for Diagnosis and Treatment of Digestive Diseases, Gastroenterology Department, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy; (A.D.G.); (C.C.); (F.D.V.)
| | - Teresa Mezza
- Pancreas Unit, Centro Malattie Apparato Digerente, Medicina Interna e Gastroenterologia, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy; (T.M.); (A.N.)
| | - Alberto Nicoletti
- Pancreas Unit, Centro Malattie Apparato Digerente, Medicina Interna e Gastroenterologia, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy; (T.M.); (A.N.)
| | - Valentina Siciliano
- Laboratory and Infectious Diseases Sciences, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy;
| | - Marcello Candelli
- Emergency, Anesthesiological and Reanimation Sciences, Fondazione Policlinico Universitario Agostino Gemelli—IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Antonio Gasbarrini
- Center for Diagnosis and Treatment of Digestive Diseases, Gastroenterology Department, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy; (A.D.G.); (C.C.); (F.D.V.)
| | - Enrico Celestino Nista
- Pancreas Unit, Centro Malattie Apparato Digerente, Medicina Interna e Gastroenterologia, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy; (T.M.); (A.N.)
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Anukul N, Jenjaroenpun P, Sirikul C, Wankaew N, Nimsamer P, Roothumnong E, Pithukpakorn M, Leetrakool N, Wongsurawat T. Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing. Front Genet 2023; 14:1213457. [PMID: 37424729 PMCID: PMC10326273 DOI: 10.3389/fgene.2023.1213457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Nanopore sequencing has been examined as a method for rapid and high-resolution human leukocyte antigen (HLA) typing in recent years. We aimed to apply ultrarapid nanopore-based HLA typing for HLA class I alleles associated with drug hypersensitivity, including HLA-A*31:01, HLA-B*15:02, and HLA-C*08:01. Most studies have used the Oxford Nanopore Ligation Sequencing kit for HLA typing, which requires several enzymatic reactions and remains relatively expensive, even when the samples are multiplexed. Here, we used the Oxford Nanopore Rapid Barcoding kit, which is transposase-based, with library preparation taking less than 1 h of hands-on time and requiring minimal reagents. Twenty DNA samples were genotyped for HLA-A, -B, and -C; 11 samples were from individuals of different ethnicity and nine were from Thai individuals. Two primer sets, a commercial set and a published set, were used to amplify the HLA-A, -B, and -C genes. HLA-typing tools that used different algorithms were applied and compared. We found that without using several third-party reagents, the transposase-based method reduced the hands-on time from approximately 9 h to 4 h, making this a viable approach for obtaining same-day results from 2 to 24 samples. However, an imbalance in the PCR amplification of different haplotypes could affect the accuracy of typing results. This work demonstrates the ability of transposase-based sequencing to report 3-field HLA alleles and its potential for race- and population-independent testing at considerably decreased time and cost.
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Affiliation(s)
- Nampeung Anukul
- Division of Transfusion Science, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Research and Innovation Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chonticha Sirikul
- Division of Transfusion Science, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Natnicha Wankaew
- Division of Medical Bioinformatics, Research and Innovation Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pattaraporn Nimsamer
- Division of Medical Bioinformatics, Research and Innovation Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ekkapong Roothumnong
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Manop Pithukpakorn
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nipapan Leetrakool
- Blood Bank Section, Maharaj Nakorn Chiang Mai Hospital, Faculty of Medicines, Chiang Mai University, Chiang Mai, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Research and Innovation Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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Kim M, Yun J, Kang D, Kim TH, Oh M, Lee S, Kang M, Nam Y, Choi J, Yang M, Han SS, Lee H, Cho H, Yang J, Oh K, Kim YS, Jung JW, Lee KH, Kang H. HLA-A*24:02 increase the risk of allopurinol-induced drug reaction with eosinophilia and systemic symptoms in HLA-B*58:01 carriers in a Korean population; a multicenter cross-sectional case-control study. Clin Transl Allergy 2022; 12:e12193. [PMID: 36176736 PMCID: PMC9478421 DOI: 10.1002/clt2.12193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 07/06/2022] [Accepted: 08/22/2022] [Indexed: 11/24/2022] Open
Abstract
Background HLA-B*58:01 is a well-known risk factor for allopurinol-induced severe cutaneous adverse reactions (SCARs). However, only a minority of HLA-B*58:01 carriers suffer SCARs after taking allopurinol. The aim of this study was to investigate subsidiary genetic markers that could identify those at further increased risk of developing allopurinol-induced drug reaction with eosinophilia and systemic symptoms (DRESS) in subjects with HLA-B*58:01. Methods Subjects with B*58:01 were enrolled (21 allopurinol-induced DRESS and 52 allopurinol-tolerant control). HLA-A, -B, -C and -DRB1 alleles were compared. Comparison of risk between HLAs and allopurinol-induced SCAR in separate populations was performed to support the results. Kruskal-Wallis test, Pearson's chi-square test, Fisher's exact test and binary logistic regression were used to analyze the risk of SCAR development. Results Frequencies of A*24:02 (71.4 vs. 17.3%, p < 0.001, odds ratio [OR] = 12.0; 95% confidence interval [CI], 3.6-39.2) were significantly higher in B*58:01 (+) DRESS than B*58:01 (+) tolerant controls. In addition, DRB1*13:02 further increased the risk of DRESS. The phenotype frequency of A*24:02/DRB1*13:02 was significantly higher in the B*58:01 (+) DRESS group than in the B*58:01 (+) tolerant controls (52.4% vs. 5.8%, p < 0.001, OR, 66.0; 95% CI, 6.1-716.2). In 2782 allopurinol user cohort, the overall prevalence of DRESS was 0.22%, which increased to 1.62% and 2.86% in the presence of B*58:01 and B*58:01/A*24:02, respectively. Conclusion The additional secondary screening with A*24:02 and DRB1*13:02 alleles may identify those at further increased risk of allopurinol-induced DRESS in B*58:01 carriers.
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Affiliation(s)
- Mi‐Yeong Kim
- Department of Internal MedicineBusan Paik HospitalInje University College of MedicineBusanKorea
| | - James Yun
- Department of Immunology and RheumatologyNepean HospitalThe University of SydneySydneyAustralia
| | - Dong‐Yoon Kang
- Drug Safety Monitoring CenterSeoul National University HospitalSeoulKorea
| | - Tae Hee Kim
- Department of Internal MedicineBusan Paik HospitalInje University College of MedicineBusanKorea
| | - Min‐Kyung Oh
- Department of PharmacologyInje University College of MedicineBusanKorea
| | - Sunggun Lee
- Department of Internal MedicineHaeundae Paik HospitalInje University College of MedicineBusanKorea
| | - Min‐Gyu Kang
- Department of Internal MedicineChungbuk National University HospitalCheongjuKorea
| | - Young‐Hee Nam
- Department of Internal MedicineDong‐A University College of MedicineBusanKorea
| | - Jeong‐Hee Choi
- Department of Internal MedicineHallym University Dongtan Sacred Heart HospitalHallym University College of MedicineHwaseongKorea
| | - Min‐Suk Yang
- Department of Internal MedicineSMG‐SNU Boramae Medical CenterSeoulKorea
| | - Seung Seok Han
- Department of Internal MedicineSeoul National University College of MedicineSeoulKorea
| | - Hajeong Lee
- Department of Internal MedicineSeoul National University College of MedicineSeoulKorea
| | - Hyun‐Jai Cho
- Department of Internal MedicineSeoul National University College of MedicineSeoulKorea
| | - Jaeseok Yang
- Department of Internal MedicineYonsei University College of MedicineSeverance HospitalSeoulKorea
| | - Kook‐Hwan Oh
- Department of Internal MedicineSeoul National University College of MedicineSeoulKorea
| | - Yon Su Kim
- Department of Internal MedicineSeoul National University College of MedicineSeoulKorea
| | - Jae Woo Jung
- Department of Internal MedicineChung‐Ang University College of MedicineSeoulKorea
| | - Kye Hwa Lee
- Department of Information MedicineAsan Medical CenterSeoulKorea
| | - Hye‐Ryun Kang
- Drug Safety Monitoring CenterSeoul National University HospitalSeoulKorea
- Department of Internal MedicineSeoul National University College of MedicineSeoulKorea
- Institute of Allergy and Clinical ImmunologySeoul National University Medical Research CenterSeoul National University College of MedicineSeoulKorea
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Escobar-Castro K, Hernández-Zaragoza DI, Santizo A, Del Toro-Arreola S, Hernández E, Toledo S M. HLA molecular study of patients in a public kidney transplant program in Guatemala. Hum Immunol 2022; 83:741-748. [PMID: 36028459 DOI: 10.1016/j.humimm.2022.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 11/28/2022]
Abstract
Guatemala is a country located in Central America, and while it is one of the most populated countries in the region, the genetic diversity of the population has been poorly analyzed. Currently, there are no analyses of the distribution of human leukocyte antigen (HLA) system alleles in mixed ancestry (i.e., ladino) populations in Guatemala. The HLA system exhibits the most extensive polymorphism in the human genome and has been extensively analyzed in a large number of studies related to disease association, transplantation, and population genetics (with particular importance in the understanding of diversity in the human population). Here, we present HLA typing data from 127 samples of unrelated individuals from the kidney transplant program of the San Juan de Dios General Hospital (Guatemala City) using a PCR-SSOP-based (PCR-sequence specific oligonucleotide probes) typing method. We found 16 haplotypes that accounted for 39.76 % of the total haplotype diversity, of which thirteen have been reported previously in Native American populations and three have been reported in European populations. The analyses showed no deviations from Hardy-Weinberg equilibrium, and admixture estimates calculated with k = 3 ancestral components showed that Native American was the most represented component, followed by the European component. The African component was less prominent in the Guatemala mixed ancestry sample in comparison to samples from other countries in Central America. The HLA-based admixture results for Central America showed a continuum in the distribution of Native American, European and African ancestries throughout the region, which is consistent with the complex demographic history of the region.
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Affiliation(s)
- Karla Escobar-Castro
- Escuela de Estudios de Postgrado, Facultad de Ciencias Médicas, Universidad de San Carlos de Guatemala (USAC), Guatemala City, Guatemala; Laboratorio de Histocompatibilidad, Departamento de Nefrología y Trasplante, Hospital General San Juan de Dios, Guatemala City, Guatemala
| | - Diana Iraiz Hernández-Zaragoza
- Laboratorio de Genética Molecular, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico; Unidad de Inmunogenética, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico.
| | - Adolfo Santizo
- Laboratorio de Histocompatibilidad, Departamento de Nefrología y Trasplante, Hospital General San Juan de Dios, Guatemala City, Guatemala
| | - Susana Del Toro-Arreola
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Centro Universitario en Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Elisa Hernández
- Laboratorio de Histocompatibilidad, Departamento de Nefrología y Trasplante, Hospital General San Juan de Dios, Guatemala City, Guatemala
| | - Manuel Toledo S
- Departamento de Nefrología y Trasplante, Hospital General San Juan de Dios, Guatemala City, Guatemala
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Lian BSY, Lee HY. Managing the ADR of Stevens-Johnson syndrome/toxic epidermal necrolysis. Expert Opin Drug Saf 2022; 21:1039-1046. [PMID: 35878014 DOI: 10.1080/14740338.2022.2106367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Stevens-Johnson syndrome and toxic epidermal necrolysis are severe, life-threatening adverse drug reactions that are collectively known as epidermal necrolysis. The abrupt detachment of the skin and mucositis results in systemic complications such as fluid and electrolyte disturbances, hypothermia, sepsis, organ failure, and death. Management is multidisciplinary and complex. AREAS COVERED This present article reviews the principles and best practices in the care of patients with epidermal necrolysis. These include having prompt admissions to optimal care facilities, coordinated specialized care during the acute phase, as well as long-term follow-up to manage chronic sequelae. EXPERT OPINION Patients with epidermal necrolysis should be managed in specialized/reference centers that are experienced with the management of the disease. Multi-disciplinary supportive care remains the cornerstone. Current evidence precludes definitive recommendation on any immunomodulatory agent as treatment. Long-term follow-up is required in order to diagnose and treat any chronic sequelae.
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Affiliation(s)
| | - Haur Yueh Lee
- Department of Dermatology, Singapore General Hospital Singapore, Singapore.,Allergy Centre, Singapore General Hospital Singapore, Singapore.,Duke-NUS Medical School, Medicine Academic Clinical Programme, Singapore
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Min F, Fan C, Zeng Y, He N, Zeng T, Qin B, Shi Y. Carbamazepine-modified HLA-A*24:02-bound peptidome: Implication of CORO1A in skin rash. Int Immunopharmacol 2022; 109:108804. [DOI: 10.1016/j.intimp.2022.108804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/01/2022] [Accepted: 04/24/2022] [Indexed: 11/05/2022]
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Elzagallaai AA, Rieder MJ. Genetic markers of drug hypersensitivity in pediatrics: current state and promise. Expert Rev Clin Pharmacol 2022; 15:715-728. [DOI: 10.1080/17512433.2022.2100345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Abdelbaset A Elzagallaai
- Department of Paediatrics Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- Department of Physiology and Pharmacology Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael J Rieder
- Department of Physiology and Pharmacology Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Robarts Research Institute, Western University, London, Ontario, Canada
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Doctor MB, Basu S. Lacrimal Gland Insufficiency in Aqueous Deficiency Dry Eye Disease: Recent Advances in Pathogenesis, Diagnosis, and Treatment. Semin Ophthalmol 2022; 37:801-812. [PMID: 35587465 DOI: 10.1080/08820538.2022.2075706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Aqueous deficiency dry eye disease is a chronic and potentially sight-threatening condition, that occurs due to the dysfunction of the lacrimal glands. The aim of this review was to describe the various recent developments in the understanding, diagnosis and treatment of lacrimal gland insufficiency in aqueous deficiency dry eye disease. METHODS A MEDLINE database search using PubMed was performed using the keywords: "dry eye disease/syndrome", "aqueous deficient/deficiency dry eye disease", "lacrimal gland" and "Sjogren's syndrome". After scanning through 750 relevant abstracts, 73 eligible articles published in the English language from 2016 to 2021 were included in the review. RESULTS Histopathological and ultrastructural studies have revealed new insights into the pathogenesis of cicatrising conjunctivitis-induced aqueous deficiency, where the lacrimal gland acini remain uninvolved and retain their secretory property, while significant ultrastructural changes in the gland have been observed. Recent advances in diagnosis include the techniques of direct clinical assessment of the lacrimal gland morphology and secretion, tear film osmolarity, tear film lysozyme and lactoferrin levels, tear film interferometry and lacrimal gland confocal microscopy. Developments in the treatment of aqueous deficiency dry eye disease, apart from the nanoparticle-based tear substitutes, include secretagogues like diquafosol tetrasodium and rebamipide, anti-inflammatory topical agents like nanomicellar form of cyclosporine and lifitegrast, scleral contact lenses, neurostimulation, and acupuncture for increasing the amount of tear production, minor salivary gland transplantation, faecal microbial transplantation, lacrimal gland regeneration and mesenchymal stem cell therapy. CONCLUSIONS Significant advances in the understanding, diagnosis and management of lacrimal gland insufficiency and its role in aqueous deficiency dry eye disease have taken place within the second half of the last decade. Of which, translational breakthroughs in terms of newer drug formulations and regenerative medicine are most promising.
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Affiliation(s)
- Mariya B Doctor
- Academy of Eye Care Education, L V Prasad Eye Institute, Hyderabad, India.,The Cornea Institute, L V Prasad Eye Institute, Hyderabad, India
| | - Sayan Basu
- The Cornea Institute, L V Prasad Eye Institute, Hyderabad, India.,Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
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Türk D, Fuhr LM, Marok FZ, Rüdesheim S, Kühn A, Selzer D, Schwab M, Lehr T. Novel models for the prediction of drug-gene interactions. Expert Opin Drug Metab Toxicol 2021; 17:1293-1310. [PMID: 34727800 DOI: 10.1080/17425255.2021.1998455] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Adverse drug reactions (ADRs) are among the leading causes of death, and frequently associated with drug-gene interactions (DGIs). In addition to pharmacogenomic programs for implementation of genetic preemptive testing into clinical practice, mathematical modeling can help to understand, quantify and predict the effects of DGIs in vivo. Moreover, modeling can contribute to optimize prospective clinical drug trial activities and to reduce DGI-related ADRs. AREAS COVERED Approaches and challenges of mechanistical DGI implementation and model parameterization are discussed for population pharmacokinetic and physiologically based pharmacokinetic models. The broad spectrum of published DGI models and their applications is presented, focusing on the investigation of DGI effects on pharmacology and model-based dose adaptations. EXPERT OPINION Mathematical modeling provides an opportunity to investigate complex DGI scenarios and can facilitate the development process of safe and efficient personalized dosing regimens. However, reliable DGI model input data from in vivo and in vitro measurements are crucial. For this, collaboration among pharmacometricians, laboratory scientists and clinicians is important to provide homogeneous datasets and unambiguous model parameters. For a broad adaptation of validated DGI models in clinical practice, interdisciplinary cooperation should be promoted and qualification toolchains must be established.
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Affiliation(s)
- Denise Türk
- Clinical Pharmacy, Saarland University, Saarbrücken, Germany
| | | | | | - Simeon Rüdesheim
- Clinical Pharmacy, Saarland University, Saarbrücken, Germany.,Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Anna Kühn
- Clinical Pharmacy, Saarland University, Saarbrücken, Germany
| | - Dominik Selzer
- Clinical Pharmacy, Saarland University, Saarbrücken, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Thorsten Lehr
- Clinical Pharmacy, Saarland University, Saarbrücken, Germany
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White E, Proudlove N, Kallon D. Improving turnaround times for HLA-B*27 and HLA-B*57:01 gene testing: a Barts Health NHS Trust quality improvement project. BMJ Open Qual 2021; 10:bmjoq-2021-001538. [PMID: 34518303 PMCID: PMC8438818 DOI: 10.1136/bmjoq-2021-001538] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/16/2021] [Indexed: 01/11/2023] Open
Abstract
Among other tests, Barts Health NHS Trust clinical transplantation laboratory conducts two important gene-detection tests: human leucocyte antigen (HLA)-B*27 (‘B27’, associated with the diagnosis of ankylosing spondylitis) and HLA-B*57:01 (‘B57’, associated with prediction of abacavir hypersensitivity disorder). The turnaround time (TaT) from sample receipt to return of results is important to clinicians and their patients but was not monitored. Furthermore, we anticipated an imminent increase in demand from a forthcoming pathology service merger, together with long-term increases with the rise of personalised genetic medicine. In this quality improvement project, we identified current TaT performance and sources of delay. Over three plan-do-study-act (PDSA) cycles, we tested three change ideas, two involving using IT to remove manual administrative steps and alert us to samples needing progressing; both were retained. The other change involved separating out the targeted tests; we judged this not worthwhile with current demand levels, although something to be re-examined when volumes increase. During the project, we reduced mean TaT from 3.8 to 3.3 days and increased the proportion within our 5-day target from 78% to 100%. These have been sustained (at 3.4 days and 97%) for the 3 months following our PDSA cycles and illustrate that reducing variation can be as impactful as reducing the mean. We conducted this project during the COVID-19 disruption, which reduced demand substantially. We took advantage of this to allow staff to spend time on these improvement activities. Another interesting feature of the work is that during the project, we compared changes in performance on our targeted B27/B57 tests with that on another comparable test as a control, to consider the impact of the general increased attention (the Hawthorne effect). We found that performance on this control also increased comparably, but then fell away after our project finished, while it did not for B27/B57.
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Affiliation(s)
- Emma White
- Clinical Transplantation Laboratory, Barts Health NHS Trust, London, UK
| | - Nathan Proudlove
- Alliance Manchester Business School, The University of Manchester, Manchester, UK
| | - Delordson Kallon
- Clinical Transplantation Laboratory, Barts Health NHS Trust, London, UK
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12
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Sarri CA, Giannoulis T, Moutou KA, Mamuris Z. HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action. Immunol Lett 2021; 238:75-95. [PMID: 34329645 DOI: 10.1016/j.imlet.2021.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/05/2021] [Accepted: 07/17/2021] [Indexed: 01/24/2023]
Abstract
BACKGROUND HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR). METHODS For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used. RESULTS All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found. CONCLUSIONS Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.
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Affiliation(s)
- Constantina A Sarri
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Themistoklis Giannoulis
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece; Department of Animal Science, University of Thessaly, Trikallon 224, 43100 Karditsa, Greece
| | - Katerina A Moutou
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Zissis Mamuris
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece.
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13
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Ahmed AF, Sukasem C, Sabbah MA, Musa NF, Mohamed Noor DA, Daud NAA. Genetic Determinants in HLA and Cytochrome P450 Genes in the Risk of Aromatic Antiepileptic-Induced Severe Cutaneous Adverse Reactions. J Pers Med 2021; 11:383. [PMID: 34067134 PMCID: PMC8150699 DOI: 10.3390/jpm11050383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 12/19/2022] Open
Abstract
Adverse drug reaction (ADR) is a pressing health problem, and one of the main reasons for treatment failure with antiepileptic drugs. This has become apparent in the event of severe cutaneous adverse reactions (SCARs), which can be life-threatening. In this review, four hypotheses were identified to describe how the immune system is triggered in the development of SCARs, which predominantly involve the human leukocyte antigen (HLA) proteins. Several genetic variations in HLA genes have been shown to be strongly associated with the susceptibility to developing SCARs when prescribed carbamazepine or phenytoin. These genetic variations were also shown to be prevalent in certain populations. Apart from the HLA genes, other genes proposed to affect the risk of SCARs are genes encoding for CYP450 drug-metabolising enzymes, which are involved in the pharmacokinetics of offending drugs. Genetic variants in CYP2C9 and CYPC19 enzymes were also suggested to modulate the risk of SCARs in some populations. This review summarizes the literature on the manifestation and aetiology of antiepileptic-induced SCARs, updates on pharmacogenetic markers associated with this reaction and the implementation of pre-emptive testing as a preventive strategy for SCARs.
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Affiliation(s)
- Ali Fadhel Ahmed
- Discipline of Clinical Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia or (A.F.A.); (D.A.M.N.)
| | - Chonlaphat Sukasem
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok 10400, Thailand
- The Thai Severe Cutaneous Adverse Drug Reaction (THAI-SCAR) Research Group, Chulalongkorn University, Bangkok 10330, Thailand
- Advanced Research and Development Laboratory, Bumrungrad International Hospital, Bangkok 10110, Thailand
| | - Majeed Arsheed Sabbah
- Forensic DNA for Research and Training Centre, Alnahrain University, Baghdad 64074, Iraq;
| | - Nur Fadhlina Musa
- Human Genome Center, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
| | - Dzul Azri Mohamed Noor
- Discipline of Clinical Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia or (A.F.A.); (D.A.M.N.)
| | - Nur Aizati Athirah Daud
- Discipline of Clinical Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia or (A.F.A.); (D.A.M.N.)
- Human Genome Center, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
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14
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Satapornpong P, Pratoomwun J, Rerknimitr P, Klaewsongkram J, Nakkam N, Rungrotmongkol T, Konyoung P, Saksit N, Mahakkanukrauh A, Amornpinyo W, Khunarkornsiri U, Tempark T, Wantavornprasert K, Jinda P, Koomdee N, Jantararoungtong T, Rerkpattanapipat T, Wang CW, Naisbitt D, Tassaneeyakul W, Ariyachaipanich M, Roonghiranwat T, Pirmohamed M, Chung WH, Sukasem C. HLA-B*13 :01 Is a Predictive Marker of Dapsone-Induced Severe Cutaneous Adverse Reactions in Thai Patients. Front Immunol 2021; 12:661135. [PMID: 34017337 PMCID: PMC8130671 DOI: 10.3389/fimmu.2021.661135] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/13/2021] [Indexed: 01/25/2023] Open
Abstract
HLA-B*13:01 allele has been identified as the genetic determinant of dapsone hypersensitivity syndrome (DHS) among leprosy and non-leprosy patients in several studies. Dapsone hydroxylamine (DDS-NHOH), an active metabolite of dapsone, has been believed to be responsible for DHS. However, studies have not highlighted the importance of other genetic polymorphisms in dapsone-induced severe cutaneous adverse reactions (SCAR). We investigated the association of HLA alleles and cytochrome P450 (CYP) alleles with dapsone-induced SCAR in Thai non-leprosy patients. A prospective cohort study, 16 Thai patients of dapsone-induced SCARs (5 SJS-TEN and 11 DRESS) and 9 Taiwanese patients of dapsone-induced SCARs (2 SJS-TEN and 7 DRESS), 40 dapsone-tolerant controls, and 470 general Thai population were enrolled. HLA class I and II alleles were genotyped using polymerase chain reaction-sequence specific oligonucleotides (PCR-SSOs). CYP2C9, CYP2C19, and CYP3A4 genotypes were determined by the TaqMan real-time PCR assay. We performed computational analyses of dapsone and DDS-NHOH interacting with HLA-B*13:01 and HLA-B*13:02 alleles by the molecular docking approach. Among all the HLA alleles, only HLA-B*13:01 allele was found to be significantly associated with dapsone-induced SCARs (OR = 39.00, 95% CI = 7.67–198.21, p = 5.3447 × 10−7), SJS-TEN (OR = 36.00, 95% CI = 3.19–405.89, p = 2.1657 × 10−3), and DRESS (OR = 40.50, 95% CI = 6.38–257.03, p = 1.0784 × 10−5) as compared to dapsone-tolerant controls. Also, HLA-B*13:01 allele was strongly associated with dapsone-induced SCARs in Asians (OR = 36.00, 95% CI = 8.67–149.52, p = 2.8068 × 10−7) and Taiwanese (OR = 31.50, 95% CI = 4.80–206.56, p = 2.5519 × 10−3). Furthermore, dapsone and DDS-NHOH fit within the extra-deep sub pocket of the antigen-binding site of the HLA-B*13:01 allele and change the antigen-recognition site. However, there was no significant association between genetic polymorphism of cytochrome P450 (CYP2C9, CYP2C19, and CYP3A4) and dapsone-induced SCARs (SJS-TEN and DRESS). The results of this study support the specific genotyping of the HLA-B*13:01 allele to avoid dapsone-induced SCARs including SJS-TEN and DRESS before initiating dapsone therapy in the Asian population.
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Affiliation(s)
- Patompong Satapornpong
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand.,Division of General Pharmacy Practice, Department of Pharmaceutical Care, College of Pharmacy, Rangsit University, Pathum Thani, Thailand
| | - Jirawat Pratoomwun
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand.,Department of Clinical Chemistry, Faculty of Medical Technology, Huachiew Chalermprakiet University, Samut Prakan, Thailand
| | - Pawinee Rerknimitr
- The Skin and Allergy Research Unit, Chulalongkorn University, Bangkok, Thailand.,Division of Dermatology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jettanong Klaewsongkram
- The Skin and Allergy Research Unit, Chulalongkorn University, Bangkok, Thailand.,Division of Allergy and Clinical Immunology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Nontaya Nakkam
- Department of Pharmacology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Program in Bioinformatics and Computational Biology, Graduated School, Chulalongkorn University, Bangkok, Thailand
| | | | - Niwat Saksit
- Unit of Excellence on Pharmacogenomic Pharmacokinetic and Pharmacotherapeutic Researches (UPPER), School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
| | - Ajanee Mahakkanukrauh
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Warayuwadee Amornpinyo
- Division of Dermatology, Department of Internal Medicine, Khon Kaen Hospital, Khon Kaen, Thailand
| | | | - Therdpong Tempark
- Division of Dermatology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Pimonpan Jinda
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Napatrupron Koomdee
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Thawinee Jantararoungtong
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Ticha Rerkpattanapipat
- Division of Allergy Immunology and Rheumatology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chuang-Wei Wang
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital (CGMH), Taipei, Taiwan.,Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China
| | - Dean Naisbitt
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, United Kingdom
| | | | | | | | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, United Kingdom
| | - Wen-Hung Chung
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital (CGMH), Taipei, Taiwan.,Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China.,Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand.,The Thai Severe Cutaneous Adverse Drug Reaction (THAI-SCAR) Research Group, Bangkok, Thailand
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15
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Elzagallaai AA, Rieder MJ. Model Based Evaluation of Hypersensitivity Adverse Drug Reactions to Antimicrobial Agents in Children. Front Pharmacol 2021; 12:638881. [PMID: 33995043 PMCID: PMC8120305 DOI: 10.3389/fphar.2021.638881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/26/2021] [Indexed: 12/25/2022] Open
Abstract
Drug use in children is-in most cases-supported by extrapolation of data generated from clinical trials in adult populations. This puts children at higher risk of developing adverse drug reactions (ADRs) due to "off-label" use of drugs and dosing issues. Major types of ADRs are drug hypersensitivity reactions, an idiosyncratic type of ADRs that are largely unpredictable and can cause high morbidity and mortality in a hard-to-identify specific population of patients. Lack of a complete understanding of the pathophysiology of DHRs and their unpredictive nature make them problematic in clinical practice and in drug development. In addition, ethical and legal obstacles hinder conducting large clinical trials in children, which in turn make children a "therapeutic orphan" where clear clinical guidelines are lacking, and practice is based largely on the personal experience of the clinician, hence making modeling desirable. This brief review summarizes the current knowledge of model-based evaluation of diagnosis and management of drug hypersensitivity reactions (DHRs) to antimicrobial drugs in the pediatric population. Ethical and legal aspects of drug research in children and the effect of different stages of child development and other factors on the risk of DHRs are discussed. The role of animal models, in vitro models and oral provocation test in management of DHRs are examined in the context of the current understanding of the pathophysiology of DHRs. Finally, recent changes in drug development legislations have been put forward to encourage drug developers to conduct trials in children clearly indicate the urgent need for evidence to support drug safety in children and for modeling to guide these clinical trials.
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Affiliation(s)
- Abdelbaset A Elzagallaai
- Department of Paediatrics, London, ON, Canada.,Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael J Rieder
- Department of Paediatrics, London, ON, Canada.,Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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16
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Zubiaur P, Saiz-Rodríguez M, Villapalos-García G, Navares-Gómez M, Koller D, Abad-Santos F. HCP5 rs2395029 is a rapid and inexpensive alternative to HLA-B*57:01 genotyping to predict abacavir hypersensitivity reaction in Spain. Pharmacogenet Genomics 2021; 31:53-59. [PMID: 33044391 DOI: 10.1097/fpc.0000000000000421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Abacavir (ABC) is an HIV nucleotide-analogue reverse transcriptase inhibitor that can produce a severe hypersensitivity reaction (ABC-HSR) in about 5% of the patients. The HLA-B*57:01 allele is associated with the development of ABC-HSR. Therefore, HLA-B*57:01 genotyping is required prior to the prescription of ABC. The technique routinely used in our laboratory is the sequence-specific oligonucleotide probes (SSOP) reverse hybridization method followed by Sanger sequencing. This technique is time-consuming and expensive. The single-nucleotide polymorphism (SNP) HCP5 rs2395029 was described to be in complete linkage disequilibrium with HLA-B*57:01. In this study, we aimed to assess the linkage disequilibrium between HCP5 rs2395029 and HLA-B*57:01 in patients receiving medical assistance at our hospital. We selected 226 HIV-infected patients from our hospital who had been routinely genotyped since 2009 with the SSOP and Sanger sequencing method: 49 HLA-B*57:01 positives and 177 negatives. We genotyped them for HCP5 rs2395019 by real time PCR (qPCR). We exploratory performed two copy number variation assays flanking HCP5 rs2395019 to explore possible deletions that could break the linkage disequilibrium with HLA-B*57:01. The concordance between HLA-B*57:01 and the HCP5 rs2395029 G allele was absolute, with a specificity and sensitivity of 100% (95% confidence interval: 93.0-100.0% and 98.0-100.0%, respectively) and estimated positive and negative predictive values of 84.4% (48.1-93.9%) and 99.9% (99.4-100.0%), respectively. No deletions were found at HCP5 flanking regions. The duration and cost of the SSOP-based method was considerably higher than the SNP-based method. Therefore, the HCP5 rs2395029 genotyping method may be alternatively used in the clinical practice.
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Affiliation(s)
- Pablo Zubiaur
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM)
| | - Miriam Saiz-Rodríguez
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM)
| | - Gonzalo Villapalos-García
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM)
| | - Marcos Navares-Gómez
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM)
| | - Dora Koller
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM)
| | - Francisco Abad-Santos
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM)
- UICEC Hospital Universitario de la Princesa, Plataforma SCReN (Spanish Clinical Reseach Network), Instituto de Investigación Sanitaria la Princesa (IP)
- Pharmacology Department, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
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17
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Sachdeva M, Maliyar K, Ponzo MG. A Systematic Review of Efficacy and Safety of Monotherapy and Combination Therapy With Biologic for Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis. J Cutan Med Surg 2021; 25:598-615. [PMID: 33631950 DOI: 10.1177/1203475421993779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND Biologic drugs have the potential to halt the progression of Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) by decreasing concentrations of tumor necrosis factor-α, a cytokine implicated in epithelial cell death. The objective of this systematic review is to investigate the efficacy and safety of biologic monotherapy and combination therapy for SJS/TEN. METHODS MEDLINE and EMBASE in OVID were searched on October 28, 2020. Inclusion criteria were original studies containing human participants diagnosed with SJS/TEN and treated with biologics. Studies were excluded if they were literature reviews, systematic reviews, letters to the editor, or conference abstracts. RESULTS The 38 articles reviewed included 27 (71.1%) case reports, 6 (15.8%) case series, 3 (7.9%) retrospective reviews, and 2 (5.3%) RCTs. The age range of the included studies was 2 to 85 years, the mean age was 46.4 years. The mean body surface (BSA) across the 38 included articles was 31.0%. The average actual mortality reported within the 38 included articles was 9.2%. Both biologic monotherapy and combination therapy were associated with improved outcomes in SJS/TEN. Furthermore, anti TNF-alpha therapy, specifically etanercept, showed improved outcomes as monotherapy. CONCLUSIONS Overall, reviewed studies presented a strong case for biologic treatment, both monotherapy and combination use, in SJS/TEN treatment. Based on the number of fatal adverse events observed, biologic monotherapy may be safer compared to combination therapy. Further research with a larger sample size and a randomized control trial design is required.
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Affiliation(s)
- Muskaan Sachdeva
- 7938 University of Toronto, Faculty of Medicine, Toronto, Ontario
| | - Khalad Maliyar
- 7938 University of Toronto, Faculty of Medicine, Toronto, Ontario
| | - Marisa G Ponzo
- 8166 Department of Dermatology and Skin Science, University of British Columbia; Division of Dermatology, St. Paul's Hospital, Vancouver, British Columbia
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18
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Human leukocyte antigen B*0702 is protective against ocular Stevens-Johnson syndrome/toxic epidermal necrolysis in the UK population. Sci Rep 2021; 11:2928. [PMID: 33536518 PMCID: PMC7859395 DOI: 10.1038/s41598-021-82400-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 12/15/2020] [Indexed: 12/16/2022] Open
Abstract
Stevens–Johnson Syndrome and Toxic Epidermal Necrolysis (SJS/TEN) are part of a disease continuum of vesiculobullous mucocutaneous reactions affecting the skin and mucous membranes including the ocular surface. Manifestations of disease range from mild dry eye to progressive conjunctival cicatrisation, limbal epithelial stem cell failure and corneal blindness. In Far Eastern and South East Asian populations where SJS/TEN is prevalent, numerous human leukocyte antigen (HLA) gene variants at the A, B and C loci have been identified as risk factors for developing SJS/TEN with severe ocular complications (SOC). By contrast, the incidence of SJS/TEN with SOC in European countries is relatively low. To date, ocular SJS/TEN risk altering alleles have not been widely investigated in European populations. In this study, we analysed the association of HLA -A, -B and -C alleles with SJS/TEN in 33 patients residing in the UK with age matched controls. The data showed statistically significant novel negative allele association with HLA-B*0702 and a trend with HLA-C*0702 in the patient group, indicating these alleles are protective. Further characterisation of protective and risk alleles in other ethnic groups is required to fully elucidate the putative role of these alleles in the susceptibility of SJS/TEN with or without severe ocular complications in patients in the UK.
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19
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Drug Reaction with Eosinophilia and Systemic Symptoms: A Complex Interplay between Drug, T Cells, and Herpesviridae. Int J Mol Sci 2021; 22:ijms22031127. [PMID: 33498771 PMCID: PMC7865935 DOI: 10.3390/ijms22031127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/14/2022] Open
Abstract
Drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome, also known as drug induced hypersensitivity (DiHS) syndrome is a severe delayed hypersensitivity reaction with potentially fatal consequences. Whilst recognised as T cell-mediated, our understanding of the immunopathogenesis of this syndrome remains incomplete. Here, we discuss models of DRESS, including the role of human leukocyte antigen (HLA) and how observations derived from new molecular techniques adopted in key studies have informed our mechanism-based understanding of the central role of Herpesviridae reactivation and heterologous immunity in these disorders.
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20
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Li YJ, Phillips E, Dellinger A, Nicoletti P, Schutte R, Li D, Ostrov DA, Fontana RJ, Watkins PB, Stolz A, Daly AK, Aithal GP, Barnhart H, Chalasani N. Human Leukocyte Antigen B*14:01 and B*35:01 Are Associated With Trimethoprim-Sulfamethoxazole Induced Liver Injury. Hepatology 2021; 73:268-281. [PMID: 32270503 PMCID: PMC7544638 DOI: 10.1002/hep.31258] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/05/2020] [Accepted: 03/12/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIMS Trimethoprim (TMP)-sulfamethoxazole (SMX) is an important cause of idiosyncratic drug-induced liver injury (DILI), but its genetic risk factors are not well understood. This study investigated the relationship between variants in the human leukocyte antigen (HLA) class 1 and 2 genes and well-characterized cases of TMP-SMX DILI. APPROACH AND RESULTS European American and African American persons with TMP-SMX DILI were compared with respective population controls. HLA sequencing was performed by Illumina MiSeq (Illumina, San Diego, CA) for cases. The HLA genotype imputation with attribute bagging program was used to impute HLA alleles for controls. The allele frequency difference between case patients and controls was tested by Fisher's exact tests for each ethnic group. For European Americans, multivariable logistic regression with Firth penalization was used to test the HLA allelic effect after adjusting for age and the top two principal components. Molecular docking was performed to assess HLA binding with TMP and SMX. The European American subset had 51 case patients and 12,156 controls, whereas the African American subset had 10 case patients and 5,439 controls. Four HLA alleles were significantly associated in the European American subset, with HLA-B*14:01 ranking at the top (odds ratio, 9.20; 95% confidence interval, 3.16, 22.35; P = 0.0003) after covariate adjustment. All carriers of HLA-B*14:01 with TMP-SMX DILI possessed HLA-C*08:02, another significant allele (P = 0.0026). This pattern was supported by HLA-B*14:01-HLA-C*08:02 haplotype association (P = 1.33 × 10-5 ). For the African American patients, HLA-B*35:01 had 2.8-fold higher frequency in case patients than in controls, with 5 of 10 patients carrying this allele. Molecular docking showed cysteine at position 67 in HLA-B*14:01 and phenylalanine at position 67 in HLA-B*35:01 to be the predictive binding sites for SMX metabolites. CONCLUSIONS HLA-B*14:01 is associated with TMP-SMX DILI in European Americans, and HLA-B*35:01 may be a potential genetic risk factor for African Americans.
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Affiliation(s)
- Yi-Ju Li
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC,Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | | | - Andrew Dellinger
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | - Paola Nicoletti
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ryan Schutte
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL
| | - Danmeng Li
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL
| | - David A. Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL
| | | | - Paul B. Watkins
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC
| | - Andrew Stolz
- University of Southern California, Los Angeles, CA
| | - Ann K Daly
- Institute of Translational and Clinical Research, Newcastle University, Newcastle upon Tyne, UK
| | - Guruprasad P Aithal
- Nottingham Digestive Diseases Centre and National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre at the Nottingham University Hospital NHS Trust and University of Nottingham, Nottingham, UK
| | - Huiman Barnhart
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC,Duke Clinical Research Institute, Duke University Medical Center, Durham, NC
| | - Naga Chalasani
- Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, IN
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21
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Krebs K, Bovijn J, Zheng N, Lepamets M, Censin JC, Jürgenson T, Särg D, Abner E, Laisk T, Luo Y, Skotte L, Geller F, Feenstra B, Wang W, Auton A, Raychaudhuri S, Esko T, Metspalu A, Laur S, Roden DM, Wei WQ, Holmes MV, Lindgren CM, Phillips EJ, Mägi R, Milani L, Fadista J. Genome-wide Study Identifies Association between HLA-B ∗55:01 and Self-Reported Penicillin Allergy. Am J Hum Genet 2020; 107:612-621. [PMID: 32888428 PMCID: PMC7536643 DOI: 10.1016/j.ajhg.2020.08.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
Hypersensitivity reactions to drugs are often unpredictable and can be life threatening, underscoring a need for understanding their underlying mechanisms and risk factors. The extent to which germline genetic variation influences the risk of commonly reported drug allergies such as penicillin allergy remains largely unknown. We extracted data from the electronic health records of more than 600,000 participants from the UK, Estonian, and Vanderbilt University Medical Center's BioVU biobanks to study the role of genetic variation in the occurrence of self-reported penicillin hypersensitivity reactions. We used imputed SNP to HLA typing data from these cohorts to further fine map the human leukocyte antigen (HLA) association and replicated our results in 23andMe's research cohort involving a total of 1.12 million individuals. Genome-wide meta-analysis of penicillin allergy revealed two loci, including one located in the HLA region on chromosome 6. This signal was further fine-mapped to the HLA-B∗55:01 allele (OR 1.41 95% CI 1.33-1.49, p value 2.04 × 10-31) and confirmed by independent replication in 23andMe's research cohort (OR 1.30 95% CI 1.25-1.34, p value 1.00 × 10-47). The lead SNP was also associated with lower lymphocyte counts and in silico follow-up suggests a potential effect on T-lymphocytes at HLA-B∗55:01. We also observed a significant hit in PTPN22 and the GWAS results correlated with the genetics of rheumatoid arthritis and psoriasis. We present robust evidence for the role of an allele of the major histocompatibility complex (MHC) I gene HLA-B in the occurrence of penicillin allergy.
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Affiliation(s)
- Kristi Krebs
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Jonas Bovijn
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK
| | - Neil Zheng
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Maarja Lepamets
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Jenny C Censin
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK
| | - Tuuli Jürgenson
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Dage Särg
- Institute of Computer Science, University of Tartu, Tartu 51009, Estonia
| | - Erik Abner
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Triin Laisk
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Yang Luo
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen 2300, Denmark
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen 2300, Denmark
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen 2300, Denmark
| | - Wei Wang
- 23andMe, Inc., Sunnyvale, CA 94086, USA
| | | | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Sven Laur
- Institute of Computer Science, University of Tartu, Tartu 51009, Estonia; STACC, Tartu 51009, Estonia
| | - Dan M Roden
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pharmacology, Vanderbilt University School of Medicine, TN 37232, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Michael V Holmes
- Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK; National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 7LE, UK; Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK; Medical Research Council Population Health Research Unit (MRC PHRU), Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Cecilia M Lindgren
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK; National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 7LE, UK; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Elizabeth J Phillips
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pharmacology, Vanderbilt University School of Medicine, TN 37232, USA; Institute for Immunology & Infectious Diseases, Murdoch University, Murdoch, WA 6150, Australia
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Lili Milani
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.
| | - João Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen 2300, Denmark; Department of Clinical Sciences, Lund University Diabetes Centre, 214 28 Malmö, Sweden; Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland
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22
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Pharmacogenomics of Antibiotics. Int J Mol Sci 2020; 21:ijms21175975. [PMID: 32825180 PMCID: PMC7504675 DOI: 10.3390/ijms21175975] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/12/2020] [Accepted: 08/17/2020] [Indexed: 12/28/2022] Open
Abstract
Although the introduction of antibiotics in medicine has resulted in one of the most successful events and in a major breakthrough to reduce morbidity and mortality caused by infectious disease, response to these agents is not always predictable, leading to differences in their efficacy, and sometimes to the occurrence of adverse effects. Genetic variability, resulting in differences in the pharmacokinetics and pharmacodynamics of antibiotics, is often involved in the variable response, of particular importance are polymorphisms in genes encoding for drug metabolizing enzymes and membrane transporters. In addition, variations in the human leukocyte antigen (HLA) class I and class II genes have been associated with different immune mediated reactions induced by antibiotics. In recent years, the importance of pharmacogenetics in the personalization of therapies has been recognized in various clinical fields, although not clearly in the context of antibiotic therapy. In this review, we make an overview of antibiotic pharmacogenomics and of its potential role in optimizing drug therapy and reducing adverse reactions.
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23
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Barquera R, Hernández-Zaragoza DI, Bravo-Acevedo A, Arrieta-Bolaños E, Clayton S, Acuña-Alonzo V, Martínez-Álvarez JC, López-Gil C, Adalid-Sáinz C, Vega-Martínez MDR, Escobedo-Ruíz A, Juárez-Cortés ED, Immel A, Pacheco-Ubaldo H, González-Medina L, Lona-Sánchez A, Lara-Riegos J, Sánchez-Fernández MGDJ, Díaz-López R, Guizar-López GU, Medina-Escobedo CE, Arrazola-García MA, Montiel-Hernández GD, Hernández-Hernández O, Ramos-de la Cruz FDR, Juárez-Nicolás F, Pantoja-Torres JA, Rodríguez-Munguía TJ, Juárez-Barreto V, Delgado-Aguirre H, Escutia-González AB, Goné-Vázquez I, Benítez-Arvizu G, Arellano-Prado FP, García-Arias VE, Rodríguez-López ME, Méndez-Mani P, García-Álvarez R, González-Martínez MDR, Aquino-Rubio G, Escareño-Montiel N, Vázquez-Castillo TV, Uribe-Duarte MG, Ruíz-Corral MDJ, Ortega-Yáñez A, Bernal-Felipe N, Gómez-Navarro B, Arriaga-Perea AJ, Martínez-Bezies V, Macías-Medrano RM, Aguilar-Campos JA, Solís-Martínez R, Serrano-Osuna R, Sandoval-Sandoval MJ, Jaramillo-Rodríguez Y, Salgado-Adame A, Juárez-de la Cruz F, Novelo-Garza B, Pavón-Vargas MDLÁ, Salgado-Galicia N, Bortolini MC, Gallo C, Bedoya G, Rothhammer F, González-José R, Ruiz-Linares A, Canizales-Quinteros S, Romero-Hidalgo S, Krause J, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. The immunogenetic diversity of the HLA system in Mexico correlates with underlying population genetic structure. Hum Immunol 2020; 81:461-474. [PMID: 32651014 DOI: 10.1016/j.humimm.2020.06.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022]
Abstract
We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) allele groups and alleles by PCR-SSP based typing in a total of 15,318 mixed ancestry Mexicans from all the states of the country divided into 78 sample sets, providing information regarding allelic and haplotypic frequencies and their linkage disequilibrium, as well as admixture estimates and genetic substructure. We identified the presence of 4268 unique HLA extended haplotypes across Mexico and find that the ten most frequent (HF > 1%) HLA haplotypes with significant linkage disequilibrium (Δ'≥0.1) in Mexico (accounting for 20% of the haplotypic diversity of the country) are of primarily Native American ancestry (A*02~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*08~DQB1*04, A*68~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*14~DQB1*03:01, A*24~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*04~DQB1*03:02, A*02~B*40:02~DRB1*04~DQB1*03:02, A*68~B*35~DRB1*04~DQB1*03:02, A*02~B*15:01~DRB1*04~DQB1*03:02). Admixture estimates obtained by a maximum likelihood method using HLA-A/-B/-DRB1 as genetic estimators revealed that the main genetic components in Mexico as a whole are Native American (ranging from 37.8% in the northern part of the country to 81.5% in the southeastern region) and European (ranging from 11.5% in the southeast to 62.6% in northern Mexico). African admixture ranged from 0.0 to 12.7% not following any specific pattern. We were able to detect three major immunogenetic clusters correlating with genetic diversity and differential admixture within Mexico: North, Central and Southeast, which is in accordance with previous reports using genome-wide data. Our findings provide insights into the population immunogenetic substructure of the whole country and add to the knowledge of mixed ancestry Latin American population genetics, important for disease association studies, detection of demographic signatures on population variation and improved allocation of public health resources.
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Affiliation(s)
- Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany; Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.
| | - Diana Iraíz Hernández-Zaragoza
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico; Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Alicia Bravo-Acevedo
- Blood Bank, UMAE Hospital de Gineco Obstetricia No. 4 "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - Stephen Clayton
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany
| | - Víctor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Julio César Martínez-Álvarez
- HLA Laboratory, Central Blood Bank, Hospital de Especialidades, Unidad Médica de Alta Especialidad (UMAE), Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Concepción López-Gil
- Histocompatibility Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 6, Instituto Mexicano del Seguro Social (IMSS), Puebla, Puebla, Mexico
| | - Carmen Adalid-Sáinz
- Laboratory of Histocompatibility, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - María Del Rosario Vega-Martínez
- Molecular Biology and Histocompatibility Laboratory, Hospital Central Sur de Alta Especialidad, Petróleos Mexicanos (PEMEX), Mexico City, Mexico
| | - Araceli Escobedo-Ruíz
- Histocompatibility Laboratory, Hospital de Especialidades, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Eva Dolores Juárez-Cortés
- Histocompatibility Laboratory, Central Blood Bank, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Alexander Immel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany; Institute of Clinical Molecular Biology (IKMB), Kiel University, University Hospital, Schleswig-Holstein, Germany
| | - Hanna Pacheco-Ubaldo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Liliana González-Medina
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Abraham Lona-Sánchez
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Julio Lara-Riegos
- Chemistry Faculty, Universidad Autónoma de Yucatán (UADY), Mérida, Yucatán, Mexico
| | - María Guadalupe de Jesús Sánchez-Fernández
- Department of Nephrology and Transplantation Unit, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Rosario Díaz-López
- Molecular Biology Laboratory, Hospital Central Militar, Secretaría de la Defensa Nacional (SEDENA), Mexico City, Mexico
| | - Gregorio Ulises Guizar-López
- Molecular Biology Laboratory, Hospital Central Militar, Secretaría de la Defensa Nacional (SEDENA), Mexico City, Mexico
| | - Carolina Elizabeth Medina-Escobedo
- Unit of Research and Education in Health, Unidad Médica de Alta Especialidad (UMAE) # 10, Instituto Mexicano del Seguro Social (IMSS), Mérida, Yucatán, Mexico
| | - María Araceli Arrazola-García
- HLA Laboratory, Central Blood Bank, Hospital de Especialidades, Unidad Médica de Alta Especialidad (UMAE), Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | | | - Flor Del Rocío Ramos-de la Cruz
- Histocompatibility Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 6, Instituto Mexicano del Seguro Social (IMSS), Puebla, Puebla, Mexico
| | | | - Jorge Arturo Pantoja-Torres
- Immunology Division, Unidad Médica de Alta Especialidad (UMAE) # 1, Instituto Mexicano del Seguro Social (IMSS), León, Guanajuato, Mexico
| | - Tirzo Jesús Rodríguez-Munguía
- Molecular Biology Laboratory, Hospital General "Norberto Treviño Zapata", Dirección de Servicios de Salud de Tamaulipas, Ciudad Victoria, Tamaulipas, Mexico
| | | | - Héctor Delgado-Aguirre
- Laboratory of Histocompatibility, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | | | - Isis Goné-Vázquez
- Histocompatibility Laboratory, Hospital de Especialidades, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Gamaliel Benítez-Arvizu
- HLA Laboratory, Central Blood Bank, Hospital de Especialidades, Unidad Médica de Alta Especialidad (UMAE), Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Francia Paulina Arellano-Prado
- Pediatrics Hospital, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Víctor Eduardo García-Arias
- Pediatrics Hospital, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Marla Estefanía Rodríguez-López
- Pediatrics Hospital, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Patricia Méndez-Mani
- Histocompatibility Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 6, Instituto Mexicano del Seguro Social (IMSS), Puebla, Puebla, Mexico
| | - Raquel García-Álvarez
- Pharmacology Laboratory, Research Unit, Instituto Nacional de Pediatría (INP), Mexico City, Mexico
| | | | - Guadalupe Aquino-Rubio
- Molecular Biology Laboratory, Hospital General "Norberto Treviño Zapata", Dirección de Servicios de Salud de Tamaulipas, Ciudad Victoria, Tamaulipas, Mexico
| | - Néstor Escareño-Montiel
- Department of Transplantation, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | | | - María Guadalupe Uribe-Duarte
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - María de Jesús Ruíz-Corral
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - Andrea Ortega-Yáñez
- Department of Development Genetics and Molecular Physiology, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | | | - Benjamín Gómez-Navarro
- Central Office of Nephrology, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Agustín Jericó Arriaga-Perea
- Histocompatibility Laboratory, Central Blood Bank, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - Rosa María Macías-Medrano
- Histocompatibility Laboratory, Central Blood Bank, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Jesús Abraham Aguilar-Campos
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - Raúl Solís-Martínez
- Department of Molecular Biology, Laboratorios Diagnóstica, Villahermosa, Tabasco, Mexico
| | - Ricardo Serrano-Osuna
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - Mario J Sandoval-Sandoval
- Central Office of Transplantation, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico; Health Research Division, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - Yolanda Jaramillo-Rodríguez
- Direction of Health Education and Research, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - Antonio Salgado-Adame
- Direction of Health Education and Research, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - Federico Juárez-de la Cruz
- Department of Transplantation, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - Bárbara Novelo-Garza
- Medical Infrastructure Planning Committee, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - María de Los Ángeles Pavón-Vargas
- Histocompatibility Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 6, Instituto Mexicano del Seguro Social (IMSS), Puebla, Puebla, Mexico
| | - Norma Salgado-Galicia
- Molecular Biology and Histocompatibility Laboratory, Hospital Central Sur de Alta Especialidad, Petróleos Mexicanos (PEMEX), Mexico City, Mexico
| | - Maria Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Gabriel Bedoya
- Genética Molecular (GENMOL, Universidad de Antioquia, Medellín, Colombia
| | - Francisco Rothhammer
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile; Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China; Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Sandra Romero-Hidalgo
- Department of Computational Genomics, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany
| | - Joaquín Zúñiga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico; Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Edmond J Yunis
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Carolina Bekker-Méndez
- Immunology and Infectology Research Unit, Infectology Hospital, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Julio Granados
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán" (INCMNSZ), Mexico City, Mexico.
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Moyer AM, Dukek B, Duellman P, Schneider B, Wakefield L, Skierka JM, Avula R, Bhagwate AV, Kalari KR, Kreuter JD, Goetz MP, Boughey JC, Black JL, Gandhi MJ. Concordance between predicted HLA type using next generation sequencing data generated for non-HLA purposes and clinical HLA type. Hum Immunol 2020; 81:423-429. [PMID: 32546429 DOI: 10.1016/j.humimm.2020.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/13/2022]
Abstract
We explored the feasibility of obtaining accurate HLA type using pre-existing NGS data not generated for HLA purposes. 83 exomes and 500 targeted NGS pharmacogenomic panels were analyzed using Omixon HLA Explore, OptiType, and/or HLA-Genotyper software. Results were compared against clinical HLA genotyping. 765 (94.2%) Omixon and 769 (94.7%) HLA-Genotyper of 812 germline allele calls across class I/II loci and 402 (99.5%) of 404 OptiType class I calls were concordant to the second field (i.e. HLA-A*02:01). An additional 19 (2.3%) Omixon, 39 (4.8%) HLA-Genotyper, and 2 (0.5%) OptiType allele calls were first field concordant (i.e. HLA-A*02). Using Omixon, four alleles (0.4%) were discordant and 24 (3.0%) failed to call, while 4 alleles (0.4%) were discordant using HLA-Genotyper. Tumor exomes were also evaluated and were 85.4%, 91.6%, and 100% concordant (Omixon and HLA-Genotyper with 96 alleles tested, and Optitype with 48 class I alleles, respectively). The 15 exomes and 500 pharmacogenomic panels were 100% concordant for each pharmacogenomic allele tested. This work has broad implications spanning future clinical care (pharmacogenomics, tumor response to immunotherapy, autoimmunity, etc.) and research applications.
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Affiliation(s)
- Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Brian Dukek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Patti Duellman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Brittany Schneider
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Laurie Wakefield
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Jennifer M Skierka
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Rajeswari Avula
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Aditya V Bhagwate
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States
| | - Krishna R Kalari
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States
| | - Justin D Kreuter
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Matthew P Goetz
- Department of Medical Oncology, Mayo Clinic, Rochester, MN, United States
| | - Judy C Boughey
- Department of Surgery, Mayo Clinic, Rochester, MN, United States
| | - John L Black
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Manish J Gandhi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.
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Beyond urate lowering: Analgesic and anti-inflammatory properties of allopurinol. Semin Arthritis Rheum 2020; 50:444-450. [DOI: 10.1016/j.semarthrit.2019.11.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/30/2019] [Accepted: 11/08/2019] [Indexed: 01/09/2023]
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26
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Shirayanagi T, Aoki S, Fujimori S, Watanabe K, Aida T, Hirasawa M, Kumagai K, Hoshino T, Ito K. Detection of Abacavir-Induced Structural Alterations in Human Leukocyte Antigen-B*57 : 01 Using Phage Display. Biol Pharm Bull 2020; 43:1007-1015. [DOI: 10.1248/bpb.b20-00102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Tomohiro Shirayanagi
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University
| | - Shigeki Aoki
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University
| | - Sota Fujimori
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University
| | - Kenji Watanabe
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University
| | - Tetsuo Aida
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd
| | - Makoto Hirasawa
- Drug Metabolism & Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd
| | | | - Tyuji Hoshino
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University
| | - Kousei Ito
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University
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Alhilali KA, Al-Attar Z, Gibson A, Tailor A, Meng X, Monshouwer M, Snoeys J, Park BK, Naisbitt DJ. Characterization of Healthy Donor-Derived T-Cell Responses Specific to Telaprevir Diastereomers. Toxicol Sci 2020; 168:597-609. [PMID: 30649540 DOI: 10.1093/toxsci/kfz007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Telaprevir, a protease inhibitor, was used alongside PEGylated interferon-α and ribavirin to treat hepatitis C viral infections. The triple regimen proved successful; however, the appearance of severe skin reactions alongside competition from newer drugs restricted its use. Skin reactions presented with a delayed onset indicative of a T-cell mediated reaction. Thus, the aim of this study was to investigate whether telaprevir and/or its diastereomer, which is generated in humans, activates T-cells. Telaprevir in its S-configured therapeutic form and the R-diastereomer were cultured directly with peripheral blood mononuclear cells from healthy donors prior to the generation of T-cell clones by serial dilution. Drug-specific CD4+ and CD8+ T-cell clones responsive to telaprevir and the R-diastereomer were generated and characterized in terms of phenotype and function. The clones proliferated with telaprevir and diastereomer concentrations of 5-20 µM and secreted IFN-γ, IL-13, and granzyme B. In contrast, the telaprevir M11 metabolite did not stimulate T-cells. The CD8+ T-cell response was MHC I-restricted and dependent on the presence of soluble drug. Flow cytometric analysis showed that clones expressed chemokine receptors CCR4 (skin homing) and CXCR3 (migration to peripheral tissue) and 1 of 3 distinct TCR Vβs; TCR Vβ 2, 5.1, or 22. These data show the propensity of both R- and S-forms of telaprevir to generate skin-homing cytotoxic T-cells that may induce the adverse reactions observed in human patients.
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Affiliation(s)
- Khetam Ali Alhilali
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool L69 3GE, UK.,Department of Pharmacology, Al-Kindy College of Medicine, University of Baghdad, Al-Nahda District, Baghdad, Iraq
| | - Zaid Al-Attar
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool L69 3GE, UK.,Department of Pharmacology, Al-Kindy College of Medicine, University of Baghdad, Al-Nahda District, Baghdad, Iraq
| | - Andrew Gibson
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool L69 3GE, UK
| | - Arun Tailor
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool L69 3GE, UK
| | - Xiaoli Meng
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool L69 3GE, UK
| | | | - Jan Snoeys
- Janssen Research and Development, Beerse 2340, Belgium
| | - B Kevin Park
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool L69 3GE, UK
| | - Dean J Naisbitt
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool L69 3GE, UK
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Ramsbottom KA, Carr DF, Rigden DJ, Jones AR. Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles. PLoS One 2020; 15:e0220754. [PMID: 32027661 PMCID: PMC7004376 DOI: 10.1371/journal.pone.0220754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 01/22/2020] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Adverse drug reactions have been linked with HLA alleles in different studies. These HLA proteins play an essential role in the adaptive immune response for the presentation of self and non-self peptides. Anti-thyroid drugs methimazole and propylthiouracil have been associated with drug induced agranulocytosis (severe lower white blood cell count) in patients with B*27:05, B*38:02 and DRB1*08:03 alleles in different populations: Taiwanese, Vietnamese, Han Chinese and Caucasian. METHODS In this study, informatics methods were used to investigate if any sequence or structural similarities exist between the two associated HLA-B alleles, compared with a set of "control" alleles assumed not be associated, which could help explain the molecular basis of the adverse drug reaction. We demonstrated using MHC Motif Viewer and MHCcluster that the two alleles do not have a propensity to bind similar peptides, and thus at a gross level the structure of the antigen presentation region of the two alleles are not similar. We also performed multiple sequence alignment to identify polymorphisms shared by the risk but not by the control alleles and molecular docking to compare the predicted binding poses of the drug-allele combinations. RESULTS Two residues, Cys67 and Thr80, were identified from the multiple sequence alignments to be unique to these risk alleles alone. The molecular docking showed the poses of the risk alleles to favour the F-pocket of the peptide binding groove, close to the Thr80 residue, with the control alleles generally favouring a different pocket. The data are thus suggestive that Thr80 may be a critical residue in HLA-mediated anti-thyroid drug induced agranulocytosis, and thus can guide future research and risk assessment.
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Affiliation(s)
- Kerry A. Ramsbottom
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Daniel F. Carr
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Andrew R. Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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Abstract
AIM Human leukocyte antigen (HLA-B*58:01) allele screening before allopurinol administration is recommended to prevent gene-mediated severe cutaneous adverse reactions (SCARs). The objective of the analysis was to examine the clinical utility and effects of HLA-B*58:01 genotyping on patient's outcomes in a practice setting. PATIENTS AND METHODS The electronic medical records covering diagnosis, laboratory results, and prescription dispensing for patients who were newly treated with allopurinol or tested for HLA-B*58:01 were obtained from a large medical organization in Taiwan between 2010 and 2014. The uptake of HLA-B*58:01 testing, incidence of allopurinol-associated SCAR, and changes in urate-lowering agent utilization were assessed. RESULTS A total of 17 532 allopurinol new users were identified from 2010 to 2014, and the HLA-B*58:01 test was ordered for 2844 (21.76%) of 13 069 new users when available between 2011 and 2014 in the study. The allopurinol-related SCAR events decreased from 0.21% (22/4460) to 0 (0/2167) after the introduction of HLA-B*58:01 testing, accompanied by a gradual increase from 8% (326/4207) to 31% (674/2167) in genotype testing rate. However, the HLA-B*58:01 testing performed before allopurinol prescription was 60.34%, and ~40% of patients were tested after already taking allopurinol. A shift from allopurinol to other urate-lowering agent regimens appeared among new allopurinol users. CONCLUSION HLA-B*58:01 test was associated with the prevention of allopurinol-induced SCAR. The clinical utility of genotype testing may not be consistent with recommendations for testing, and treatment alternatives are a competitive intervention associated with effective implications in a real-world setting.
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30
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Mutant GNLY is linked to Stevens-Johnson syndrome and toxic epidermal necrolysis. Hum Genet 2019; 138:1267-1274. [PMID: 31642954 DOI: 10.1007/s00439-019-02066-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/25/2019] [Indexed: 12/19/2022]
Abstract
Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are rare severe cutaneous adverse reactions to drugs. Granulysin (GNLY) plays a key role in keratinocyte apoptosis during SJS/TEN pathophysiology. To determine if GNLY-encoding mutations might be related to the protein's functional disturbances, contributing to SJS/TEN pathogenesis, we performed direct sequencing of GNLY's coding region in a group of 19 Colombian SJS/TEN patients. A GNLY genetic screening was implemented in a group of 249 healthy individuals. We identified the c.11G > A heterozygous sequence variant in a TEN case, which creates a premature termination codon (PTC) (p.Trp4Ter). We show that a mutant protein is synthesised, possibly due to a PTC-readthrough mechanism. Functional assays demonstrated that the mutant protein was abnormally located in the nuclear compartment, potentially leading to a toxic effect. Our results argue in favour of GNLY non-synonymous sequence variants contributing to SJS/TEN pathophysiology, thereby constituting a promising, clinically useful molecular biomarker.
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Konvinse KC, Trubiano JA, Pavlos R, James I, Shaffer CM, Bejan CA, Schutte RJ, Ostrov DA, Pilkinton MA, Rosenbach M, Zwerner JP, Williams KB, Bourke J, Martinez P, Rwandamuriye F, Chopra A, Watson M, Redwood AJ, White KD, Mallal SA, Phillips EJ. HLA-A*32:01 is strongly associated with vancomycin-induced drug reaction with eosinophilia and systemic symptoms. J Allergy Clin Immunol 2019; 144:183-192. [PMID: 30776417 PMCID: PMC6612297 DOI: 10.1016/j.jaci.2019.01.045] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/17/2019] [Accepted: 01/23/2019] [Indexed: 01/11/2023]
Abstract
BACKGROUND Vancomycin is a prevalent cause of the severe hypersensitivity syndrome drug reaction with eosinophilia and systemic symptoms (DRESS), which leads to significant morbidity and mortality and commonly occurs in the setting of combination antibiotic therapy, affecting future treatment choices. Variations in HLA class I in particular have been associated with serious T cell-mediated adverse drug reactions, which has led to preventive screening strategies for some drugs. OBJECTIVE We sought to determine whether variation in the HLA region is associated with vancomycin-induced DRESS. METHODS Probable vancomycin-induced DRESS cases were matched 1:2 with tolerant control subjects based on sex, race, and age by using BioVU, Vanderbilt's deidentified electronic health record database. Associations between DRESS and carriage of HLA class I and II alleles were assessed by means of conditional logistic regression. An extended sample set from BioVU was used to conduct a time-to-event analysis of those exposed to vancomycin with and without the identified HLA risk allele. RESULTS Twenty-three subjects met the inclusion criteria for vancomycin-associated DRESS. Nineteen (82.6%) of 23 cases carried HLA-A*32:01 compared with 0 (0%) of 46 of the matched vancomycin-tolerant control subjects (P = 1 × 10-8) and 6.3% of the BioVU population (n = 54,249, P = 2 × 10-16). Time-to-event analysis of DRESS development during vancomycin treatment among the HLA-A*32:01-positive group indicated that 19.2% had DRESS and did so within 4 weeks. CONCLUSIONS HLA-A*32:01 is strongly associated with vancomycin-induced DRESS in a population of predominantly European ancestry. HLA-A*32:01 testing could improve antibiotic safety, help implicate vancomycin as the causal drug, and preserve future treatment options with coadministered antibiotics.
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Affiliation(s)
- Katherine C Konvinse
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA, 37232
| | - Jason A Trubiano
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, AUS, 3084
- The National Centre for Infections in Cancer, Department of Infectious Diseases, Peter MacCallum Cancer Centre, Parkville, Victoria, AUS, 3000
- Department of Medicine, University of Melbourne, Parkville, Victoria, AUS, 3050
| | - Rebecca Pavlos
- Telethon Kids Institute, University of Western Australia, Nedlands, Western Australia, AUS, 6009
| | - Ian James
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, AUS, 6150
| | - Christian M Shaffer
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA, 37232
| | - Cosmin A Bejan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA, 37232
| | - Ryan J Schutte
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA, 32610
| | - David A Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA, 32610
| | - Mark A Pilkinton
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA, 37232
| | - Misha Rosenbach
- Department of Dermatology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA, 19104
| | - Jeffrey P Zwerner
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, Tennessee, USA, 37232
| | - Kristina B Williams
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA, 37232
| | - Jack Bourke
- Department of Clinical Immunology, Fiona Stanley Hospital, Murdoch, Western Australia, AUS, 6150
| | - Patricia Martinez
- Department of Clinical Immunology, Fiona Stanley Hospital, Murdoch, Western Australia, AUS, 6150
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, AUS, 6000
- Division of Pathology and Laboratory Medicine, School of Medicine, Faculty of Medicine, Dentistry and Health Sciences, University of Western Australia, Crawley, Western Australia, AUS, 6009
| | - Francois Rwandamuriye
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, AUS, 6150
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, AUS, 6150
| | - Mark Watson
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, AUS, 6150
| | - Alec J Redwood
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, AUS, 6150
| | - Katie D White
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA, 37232
| | - Simon A Mallal
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA, 37232
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, AUS, 6150
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA, 37232
| | - Elizabeth J Phillips
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA, 37232
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, AUS, 6150
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA, 37232
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA, 37232
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Nguyen DV, Vidal C, Chu HC, van Nunen S. Developing pharmacogenetic screening methods for an emergent country: Vietnam. World Allergy Organ J 2019; 12:100037. [PMID: 31198488 PMCID: PMC6558218 DOI: 10.1016/j.waojou.2019.100037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/24/2019] [Accepted: 05/01/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The finding of strong associations between certain human leukocyte antigen (HLA) genotypes and the development of severe cutaneous adverse drug reactions (SCARs), [for example, HLA-B*57:01 and abacavir (ABC), HLA-B*15:02 and carbamazepine (CBZ) and HLA-B*58:01 and allopurinol], has led to HLA screening being used to prevent SCARs. Screening has been shown to be of great benefit in a number of studies. Clinical translation from bench to bedside, however, depends upon the development of simple, rapid and cost-effective assays to detect these risk alleles. In highly populated developing countries such as Vietnam, where there is a high prevalence of HLA-B*15:02 and HLA-B*58:01 correlating with a high incidence of CBZ- and allopurinol-induced SCARs, the crucial factor in the implementation of comprehensive screening programs to detect these major risk HLA alleles is the availability of suitable assays. BODY We have summarized the role and economic benefits of HLA screening, reviewed published HLA screening methods used currently in pharmacogenetic screening and examined the advantages and disadvantages of assays developed specifically for use in screening for risk alleles in the prevention of HLA-associated SCARs in Vietnam. CONCLUSION The optimal approach we propose may serve as a template for the development of screening programs in other emergent countries.
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Affiliation(s)
- Dinh Van Nguyen
- Respiratory, Allergy and Clinical Immunology, Vinmec International Hospital, Times City and Vin University, Hanoi, Viet Nam
- Northern Clinical School, The University of Sydney, Sydney, Australia
- Department of Allergy and Clinical Immunology, Hanoi Medical University, Hanoi, Viet Nam
| | - Christopher Vidal
- Northern Clinical School, The University of Sydney, Sydney, Australia
| | - Hieu Chi Chu
- Center of Allergology and Clinical Immunology, Bach Mai Hospital, Hanoi, Viet Nam
| | - Sheryl van Nunen
- Northern Clinical School, The University of Sydney, Sydney, Australia
- Department of Clinical Immunology and Allergy, Royal North Shore Hospital, Sydney, Australia
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Liotti L, Caimmi S, Bottau P, Bernardini R, Cardinale F, Saretta F, Mori F, Crisafulli G, Franceschini F, Caffarelli C. Clinical features, outcomes and treatment in children with drug induced Stevens-Johnson syndrome and toxic epidermal necrolysis. ACTA BIO-MEDICA : ATENEI PARMENSIS 2019; 90:52-60. [PMID: 30830062 PMCID: PMC6502171 DOI: 10.23750/abm.v90i3-s.8165] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Indexed: 12/15/2022]
Abstract
Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN), which can be considered a late-onset allergic reaction, can cause serious long-term sequelae. SJS/TEN are considered a spectrum of life-threatening adverse drug reactions. They have the same clinical manifestations and the only difference is in the extent of epidermal detachment. These conditions are associated with high mortality, although incidence of SJS/TEN is rare in children. SJS/TEN is an adverse drug reaction influenced by genes that involve pharmacokinetics, pharmacodynamics and immune response. Infective agents are additional influencing factors. Anticonvulsants and antibiotics, and especially sulphonamides and non-steroidal anti-inflammatory drugs, are among the drugs that were predominantly suspected of triggering SJS/TEN. No evidence-based standardized treatment guidelines for SJS or TEN are currently available. The usual treatment is mainly founded on the withdrawal of the suspected causative agent and supportive therapy. In pediatric patients, the specific therapeutic strategies are controversial and comprise systemic corticosteroids and the use of intravenous immunoglobulin (IVIG). More recently, new therapeutic approaches have been used, such as immunosuppressive therapies, including cyclosporine and TNF-α inhibitors. (www.actabiomedica.it)
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Affiliation(s)
- Lucia Liotti
- Department of Pediatrics, Senigallia Hospital, Senigallia, Italy.
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Sona P, Hong JH, Lee S, Kim BJ, Hong WY, Jung J, Kim HN, Kim HL, Christopher D, Herviou L, Im YH, Lee KY, Kim TS, Jung J. Integrated genome sizing (IGS) approach for the parallelization of whole genome analysis. BMC Bioinformatics 2018; 19:462. [PMID: 30509173 PMCID: PMC6276166 DOI: 10.1186/s12859-018-2499-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 11/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The use of whole genome sequence has increased recently with rapid progression of next-generation sequencing (NGS) technologies. However, storing raw sequence reads to perform large-scale genome analysis pose hardware challenges. Despite advancement in genome analytic platforms, efficient approaches remain relevant especially as applied to the human genome. In this study, an Integrated Genome Sizing (IGS) approach is adopted to speed up multiple whole genome analysis in high-performance computing (HPC) environment. The approach splits a genome (GRCh37) into 630 chunks (fragments) wherein multiple chunks can simultaneously be parallelized for sequence analyses across cohorts. RESULTS IGS was integrated on Maha-Fs (HPC) system, to provide the parallelization required to analyze 2504 whole genomes. Using a single reference pilot genome, NA12878, we compared the NGS process time between Maha-Fs (NFS SATA hard disk drive) and SGI-UV300 (solid state drive memory). It was observed that SGI-UV300 was faster, having 32.5 mins of process time, while that of the Maha-Fs was 55.2 mins. CONCLUSIONS The implementation of IGS can leverage the ability of HPC systems to analyze multiple genomes simultaneously. We believe this approach will accelerate research advancement in personalized genomic medicine. Our method is comparable to the fastest methods for sequence alignment.
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Affiliation(s)
- Peter Sona
- Genome Data Integration Center, Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, Republic of Korea, 34025
| | - Jong Hui Hong
- Genome Data Integration Center, Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, Republic of Korea, 34025
| | - Sunho Lee
- Genome Data Integration Center, Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, Republic of Korea, 34025
| | - Byong Joon Kim
- Genome Data Integration Center, Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, Republic of Korea, 34025
| | - Woon-Young Hong
- Genome Data Integration Center, Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, Republic of Korea, 34025
| | - Jongcheol Jung
- Genome Data Integration Center, Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, Republic of Korea, 34025
| | - Han-Na Kim
- PGM21 (Personalized Genomic Medicine 21), Ewha Womans University Medical Center, 1071, Anyang Cheon-ro, Yangcheon-gu, Seoul, 158-710, Korea
| | - Hyung-Lae Kim
- PGM21 (Personalized Genomic Medicine 21), Ewha Womans University Medical Center, 1071, Anyang Cheon-ro, Yangcheon-gu, Seoul, 158-710, Korea
| | - David Christopher
- Bioinformatics Solutions, 900 N McCarthy Blvd., Milpitas, CA, 95035, USA
| | - Laurent Herviou
- Bioinformatics Solutions, 900 N McCarthy Blvd., Milpitas, CA, 95035, USA
| | - Young Hwan Im
- Bioinformatics Solutions, 900 N McCarthy Blvd., Milpitas, CA, 95035, USA
| | - Kwee-Yum Lee
- Genome Data Integration Center, Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, Republic of Korea, 34025.,Faculty of Medicine, University of Queensland, QLD, Brisbane, 4072, Australia
| | - Tae Soon Kim
- Genome Data Integration Center, Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, Republic of Korea, 34025.,Department of Clinical Medical Sciences, Seoul National University College of Medicine, 71 Ihwajang-gil, Jongno-gu, Seoul, 03087, South Korea
| | - Jongsun Jung
- Genome Data Integration Center, Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, Republic of Korea, 34025.
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Abstract
Pharmacogenomics is a tool for practitioners to provide precision pharmacotherapy using genomics. All providers are likely to encounter genomic data in practice with the expectation that they are able to successfully apply it to patient care. Pharmacogenomics tests for genetic variations in genes that are responsible for drug metabolism, transport, and targets of drug action. Variations can increase the risk for drug toxicity or poor efficacy. Pharmacogenomics can, therefore, be used to help select the best medication or aid in dosing. Nephrologists routinely treat cardiovascular disease and manage patients after kidney transplantation, two situations for which there are several high-evidence clinical recommendations for commonly used anticoagulants, antiplatelets, statins, and transplant medications. Successful use of pharmacogenomics in practice requires that providers are familiar with how to access and use pharmacogenomics resources. Similarly, clinical decision making related to whether to use existing data, whether to order testing, and if data should be used in practice is needed to deliver precision medicine. Pharmacogenomics is applicable to virtually every medical specialty, and nephrologists are well positioned to be implementation leaders.
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Affiliation(s)
| | | | - Philip E. Empey
- Department of Pharmacy and Therapeutics, School of Pharmacy, and
- Institute and of Precision Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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Zhang X, Jin L, Wu Z, Ma W, Chen Y, Chen G, Wang L, Guan M. Clinical evaluation of a substitute of HLA-B*58:01 in different Chinese ethnic groups. Genet Mol Biol 2018; 41:578-584. [PMID: 30080910 PMCID: PMC6136375 DOI: 10.1590/1678-4685-gmb-2017-0258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/23/2018] [Indexed: 11/22/2022] Open
Abstract
The goal of this research was to investigate the linkage disequilibrium between rs9263726 and HLA-B*58:01 in different Chinese ethnic groups (Han, Tibet, and Hui) and to study the feasibility of rs9263726 replacing HLA-B*58:01 as an efficient indicator of potential allopurinol hypersensitivity syndrome. In this study, rs9263726 and HLA-B*58:01 were detected in all samples. For samples of individuals whose rs9263726 genotypes were not consistent with HLA-B*58:01, we did high-resolution typing of HLA-B gene to further confirm the correlation of rs9263726 genotype and special HLA-B alleles. We confirmed that the linkage disequilibrium between rs9263726 and HLA-B*58:01 was more significant in the Han ethnic group (r2=0.886, D'=1.0) than in the Tibet and Hui ethnic groups (for Tibetan, r2=0.606, D'=0.866; for Hui, r2=0.622, D'=0.924). For Han Chinese, samples with the GG genotype of rs9263726 did not carry HLA-B*58:01, while AA genotype samples were homozygous carriers of HLA-B*58:01. However, GA genotype samples of rs9263726 required a more sophisticated HLA-B genotyping assay before it was possible to identify whether they were HLA-B*58:01 carriers or not. For Tibetan and Hui, the linkage disequilibrium between rs9263726 and HLA-B*58:01 was not significant. Therefore, rs9263726 cannot replace HLA-B*58:01 in these two groups.
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Affiliation(s)
- Xinju Zhang
- Department of Central Laboratory, Huashan Hospital, Fudan University, Shanghai, China
| | - Lei Jin
- College of Allied Health Professions, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Zhiyuan Wu
- Department of Laboratory Medicine, North Huashan Hospital, Fudan University, Shanghai, China
| | - Weizhe Ma
- Department of Central Laboratory, Huashan Hospital, Fudan University, Shanghai, China
| | - Yuming Chen
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Gang Chen
- Department of Geriatrics, Huashan Hospital, Fudan University, Shanghai, China
| | - Lixin Wang
- The Medical Laboratory Center of General Hospital of Ningxia Medical University, Yinchuan, China.,The Medical Laboratory of Cardio-Cerebral Vascular Disease Hospital of General Hospital of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Clinical Pathogens, Yinchuan, China
| | - Ming Guan
- Department of Central Laboratory, Huashan Hospital, Fudan University, Shanghai, China.,Department of Laboratory Medicine, North Huashan Hospital, Fudan University, Shanghai, China.,Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, China
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Genetic and nongenetic factors that may predispose individuals to allergic drug reactions. Curr Opin Allergy Clin Immunol 2018; 18:325-332. [DOI: 10.1097/aci.0000000000000459] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Murphy NM, Pouton CW, Irving HR. High Molecular Weight DNA Enrichment with Peptide Nucleic Acid Probes. Methods Mol Biol 2018; 1551:73-85. [PMID: 28138841 DOI: 10.1007/978-1-4939-6750-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Here, we describe how peptide nucleic acid (PNA) probes can be used to enrich genomic DNA fractions to facilitate downstream analysis, such as the haplotype phasing of the isolated genomic pieces. This method enriches for polymorphic regions of fragmented chromosomes by physically separating the desired sequence and flanking regions. The PNA probes used for enrichment are novel synthetic nucleic acids with highly specific targeting and hybridization properties. Using a enrichment technique, we capture high molecular weight genomic DNA using nothing more than a simple modification to standard genomic DNA extraction from blood.
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Affiliation(s)
- Nicholas M Murphy
- Monash Institute of Pharmaceutical Science, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia. .,Preimplantation Genetic Diagnosis, Monash IVF, Melbourne, VIC, Australia.
| | - Colin W Pouton
- Monash Institute of Pharmaceutical Science, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Helen R Irving
- Monash Institute of Pharmaceutical Science, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
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Fricke-Galindo I, LLerena A, Jung-Cook H, López-López M. Carbamazepine adverse drug reactions. Expert Rev Clin Pharmacol 2018; 11:705-718. [PMID: 29898616 DOI: 10.1080/17512433.2018.1486707] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Carbamazepine (CBZ) is used for the treatment of epilepsy and other neurological and psychiatric disorders. The occurrence of adverse reactions (ADRs) to CBZ can negatively impact the quality of life of patients, as well as increase health-care costs. Thus, knowledge of CBZ-induced ADRs is important to achieve safer treatment outcomes. Areas covered: This review describes the clinical features, known mechanisms, and clinical management of the main CBZ-induced ADRs. In addition, pharmacogenetic studies focused on ADRs induced by CBZ are cited. Expert commentary: CBZ-induced ADRs are well known in the literature. The metabolite CBZ-10,11-epoxide plays an important role in the mechanism that underlies the ADRs induced by CBZ. Several factors should be considered for a safer use of CBZ, such as monotherapy prescription when possible, an adequate dose titration, knowledge of previous ADRs in the patient, and routine monitoring of CBZ plasma concentrations in symptomatic patients. Pharmacogenetics is a potential tool for CBZ therapy improvement, and the design of multicenter studies focused on the identification of biomarkers for CBZ-induced ADRs could provide useful information for a safer CBZ therapy.
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Affiliation(s)
- Ingrid Fricke-Galindo
- a Doctorate in Biological and Health Sciences , Metropolitan Autonomous University , Coyoacán, Mexico City , Mexico
| | - Adrián LLerena
- b CICAB Clinical Research Centre , Extremadura University Hospital and Medical School , Badajoz , Spain
| | - Helgi Jung-Cook
- c Department of Pharmacy, Chemistry Faculty , National Autonomous University of Mexico , Mexico City , Mexico.,d Department of Neuropharmacology , National Institute of Neurology and Neurosurgery Manuel Velasco Suárez , Mexico City , Mexico
| | - Marisol López-López
- e Department of Biological Systems , Metropolitan Autonomous University , Coyoacán, Mexico City , Mexico
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Interaction of Nevirapine with the Peptide Binding Groove of HLA-DRB1*01:01 and Its Effect on the Conformation of HLA-Peptide Complex. Int J Mol Sci 2018; 19:ijms19061660. [PMID: 29867033 PMCID: PMC6032195 DOI: 10.3390/ijms19061660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 01/11/2023] Open
Abstract
Human leukocyte antigen (HLA)-DRB1*01:01 has been shown to be involved in nevirapine-induced hepatic hypersensitivity reactions. In the present study, in silico docking simulations and molecular dynamics simulations were performed to predict the interaction mode of nevirapine with the peptide binding groove of HLA-DRB1*01:01 and its possible effect on the position and orientation of the ligand peptide derived from hemagglutinin (HA). In silico analyses suggested that nevirapine interacts with HLA-DRB1*01:01 around the P4 pocket within the peptide binding groove and the HA peptide stably binds on top of nevirapine at the groove. The analyses also showed that binding of nevirapine at the groove will significantly change the inter-helical distances of the groove. An in vitro competitive assay showed that nevirapine (1000 μM) increases the binding of the HA peptide to HLA-DRB1*01:01 in an allele-specific manner. These results indicate that nevirapine might interact directly with the P4 pocket and modifies its structure, which could change the orientation of loaded peptides and the conformation of HLA-DRB1*01:01; these changes could be distinctively recognized by T-cell receptors. Through this molecular mechanism, nevirapine might stimulate the immune system, resulting in hepatic hypersensitivity reactions.
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Roden DM, Van Driest SL, Mosley JD, Wells QS, Robinson JR, Denny JC, Peterson JF. Benefit of Preemptive Pharmacogenetic Information on Clinical Outcome. Clin Pharmacol Ther 2018; 103:787-794. [PMID: 29377064 PMCID: PMC6134843 DOI: 10.1002/cpt.1035] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/08/2018] [Accepted: 01/22/2018] [Indexed: 12/13/2022]
Abstract
The development of new knowledge around the genetic determinants of variable drug action has naturally raised the question of how this new knowledge can be used to improve the outcome of drug therapy. Two broad approaches have been taken: a point-of-care approach in which genotyping for specific variant(s) is undertaken at the time of drug prescription, and a preemptive approach in which multiple genetic variants are typed in an individual patient and the information archived for later use when a drug with a "pharmacogenetic story" is prescribed. This review addresses the current state of implementation, the rationale for these approaches, and barriers that must be overcome. Benefits to pharmacogenetic testing are only now being defined and will be discussed.
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Affiliation(s)
- Dan M. Roden
- Department of Medicine, Vanderbilt University Medical Center Nashville, TN
- Department of Pharmacology, Vanderbilt University Medical Center Nashville, TN
- Department of Biomedical Informatics, Vanderbilt University Medical Center Nashville, TN
| | - Sara L. Van Driest
- Department of Medicine, Vanderbilt University Medical Center Nashville, TN
- Department of Pediatrics, Vanderbilt University Medical Center Nashville, TN
| | - Jonathan D. Mosley
- Department of Medicine, Vanderbilt University Medical Center Nashville, TN
- Department of Biomedical Informatics, Vanderbilt University Medical Center Nashville, TN
| | - Quinn S. Wells
- Department of Medicine, Vanderbilt University Medical Center Nashville, TN
| | - Jamie R. Robinson
- Department of Biomedical Informatics, Vanderbilt University Medical Center Nashville, TN
- Department of Surgery, Vanderbilt University Medical Center Nashville, TN
| | - Joshua C. Denny
- Department of Medicine, Vanderbilt University Medical Center Nashville, TN
- Department of Biomedical Informatics, Vanderbilt University Medical Center Nashville, TN
| | - Josh F. Peterson
- Department of Medicine, Vanderbilt University Medical Center Nashville, TN
- Department of Biomedical Informatics, Vanderbilt University Medical Center Nashville, TN
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Chen SA, Zhang LR, Yang FP, Yang LL, Yang Y, Chen ZH, Jiang ML, Xiong H, Zhu HZ, Qi Z, Xing QH, Luo XQ. HLA-A*02:07 Allele Associates with Clarithromycin-Induced Cutaneous Adverse Drug Reactions in Chinese Patients. Basic Clin Pharmacol Toxicol 2018; 123:308-313. [PMID: 29575644 DOI: 10.1111/bcpt.13011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/05/2018] [Indexed: 01/23/2023]
Abstract
Genetic risk factors could cause cutaneous adverse drug reactions (cADRs) in patients after treatment with clarithromycin. This study explored the association of HLA class I genes with clarithromycin-cADRs in Han Chinese patients. A total of 12 clarithromycin-cADR patients and 34 clarithromycin-tolerant controls were recruited for the high-resolution genotyping of HLA class I genes (HLA-A, HLA-B and HLA-C). The population controls consisted of 283 Han Chinese retrieved from the MHC database for validated comparison. A molecular docking analysis of HLA-A*02:07 protein and clarithromycin was conducted using glide module with Schrödinger Suite. Among all tested HLA alleles, the carrier frequencies of HLA-A*02:07 (58% versus 5.9%, OR = 22.40, 95% CI = 3.58-139.98, p = 8.20 × 10E-5, pc = 1.1 × 10E-3) and HLA-B*46:01 (50% versus 5.9%, OR = 16.00, 95% CI = 2.59-98.99, p = 0.002, pc = 0.03) were significantly higher in clarithromycin-cADRs than in clarithromycin-tolerant controls. However, when compared to population controls, only HLA-A*02:07, and not HLA-B*46:01, reached statistical significance (58% versus 15.5%, OR = 7.61, 95% CI = 2.31-25.04, p = 1.2 × 10E-4, pc = 1.7 × 10E-3). Furthermore, molecular docking data revealed that clarithromycin could bind to and interact with HLA-A*02:07 in two possible binding situations. These data suggest that HLA-A*02:07 might be a genetic risk factor for developing clarithromycin-cADRs in Han Chinese and serve as a useful biomarker for personalized medicine to prevent clarithromycin-cADRs.
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Affiliation(s)
- Sheng-An Chen
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Li-Rong Zhang
- Department of Pharmacology, School of Medicine, Zhengzhou University, Zhengzhou, China
| | - Fan-Ping Yang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Lin-Lin Yang
- Department of Pharmacology, School of Medicine, Zhengzhou University, Zhengzhou, China.,Drug Discovery and Design Center, The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai, China
| | - Ying Yang
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zi-Hua Chen
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Meng-Lin Jiang
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hao Xiong
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Hui-Zhong Zhu
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zheng Qi
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qing-He Xing
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiao-Qun Luo
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
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Dapsone-induced severe cutaneous adverse drug reactions are strongly linked with HLA-B*13: 01 allele in the Thai population. Pharmacogenet Genomics 2018; 27:429-437. [PMID: 28885988 DOI: 10.1097/fpc.0000000000000306] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVES A previous publication in Chinese leprosy patients showed that the HLA-B*13:01 allele is a strong genetic marker for dapsone-induced drug hypersensitivity reactions, however there are no data describing whether HLA-B*13:01 is a valid marker for prediction of dapsone-induced drug hypersensitivity reactions in other ethnicities or nonleprosy patients. The aim of this study is to investigate whether there is an association between HLA genotypes and dapsone-induced severe cutaneous adverse reactions (SCARs) in Thai nonleprosy patients. PATIENTS AND METHODS HLA-B genotypes of 15 patients with dapsone-induced SCARs (11 drug reaction with eosinophilia and systemic symptoms, 4 Stevens-Johnson syndrome/toxic epidermal necrolysis), 29 control patients, and 986 subjects from the general Thai population were determined by the reverse PCR sequence-specific oligonucleotides probe. RESULTS The HLA-B*13:01 allele was significantly associated with dapsone-induced SCARs compared with dapsone-tolerant controls (odds ratio: 54.00, 95% confidence interval: 7.96-366.16, P=0.0001) and the general population (odds ratio: 26.11, 95% confidence interval: 7.27-93.75, P=0.0001). In addition, HLA-B*13:01 associated with dapsone-induced SJS-TEN (OR: 40.50, 95% confidence interval: 2.78-591.01, P=0.0070) and DRESS (OR: 60.75, 95% confidence interval: 7.44-496.18, P=0.0001). CONCLUSION This study demonstrated an association between HLA-B*13:01 and dapsone-induced SCARs including Stevens-Johnson syndrome/toxic epidermal necrolysis and drug reaction with eosinophilia and systemic symptoms in nonleprosy patients. Moreover, these results suggest that the HLA-B*13:01 allele may be a useful genetic marker for prediction of dapsone-induced SCARs in Thai and Han-Chinese populations.
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Kilb BKJ, Kurmis AP, Parry M, Sherwood K, Keown P, Masri BA, Duncan CP, Garbuz DS. Frank Stinchfield Award: Identification of the At-risk Genotype for Development of Pseudotumors Around Metal-on-metal THAs. Clin Orthop Relat Res 2018; 476. [PMID: 29529651 PMCID: PMC6259707 DOI: 10.1007/s11999.0000000000000028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Once touted as the future of hip arthroplasty, metal-on-metal (MoM) bearing surfaces have fallen sharply from favor with the emergence of a strong body of evidence demonstrating unacceptably high premature implant failure rates. The previously unpredictable development of adverse local tissue reactions (ALTRs) has been a substantive contributor to this. Although the underlying pathophysiology of these so-called "pseudotumors" is now well understood, the fundamental predisposing patient risk factors have remained elusive. QUESTIONS/PURPOSES The aim of this research, as a clinical-genotype correlation analysis, was to identify specific alleles (genes) associated with the development of ALTRs in patients with in situ MoM THAs. METHODS A case-control study of patients who received a large-head, primary MoM THA between 2005 and 2008 was performed with a minimum followup of 5 years. Twenty-six patients who had undergone revision of a primary MoM THA secondary to symptomatic ALTRs were recruited. The mean timeframe from primary MoM THA to symptomatic revision was 5.5 years (range, 1-10 years). Twenty-eight control subjects were randomly selected asymptomatic patients with no evidence of ALTRs on protocol-specific screening. Baseline demographics and high-resolution genotype (human leukocyte antigen [HLA] Class II) were collected for all patients. Cohorts were similar with respect to age at the time of primary MoM THA (mean, 54.8 versus 54.9 years, p = 0.95) and serum cobalt (mean, 5.5 versus 8.5 μg/L, p = 0.09) and chromium concentrations (mean, 2.9 versus 4.2 μg/L, p = 0.27). The association between genotype and revision surgery secondary to ALTRs was determined with gender as a covariate. RESULTS The prevalence of the risk genotype was 30% (16 of 54) among the entire cohort. Adjusting for sex, the odds of revision were 6.1 times greater among patients with the risk genotype present than among patients without (95% confidence interval [CI], 1.5-25.4; p = 0.01). Among females, the specificity of the risk genotype was 1.0 (95% CIexact, 0.5-1.0; pexact = 0.03), and for males, it was 0.8 (95% CIexact, 0.6-0.9; pexact < 0.01). CONCLUSIONS The findings of this study suggest that, among patients with a primary MoM THA, allelic variation within the HLA Class II loci may be a strong, independent risk factor associated with the need for subsequent revision surgery secondary to pseudotumor formation. CLINICAL RELEVANCE Given the hypothesis-generating nature of this novel undertaking, confirmatory prospective clinical studies are required to further elucidate this correlation and to explore the clinical utility of targeted genetic screening in this specific population. This research may, however, represent a key missing piece in the puzzle that is metal ion-induced pseudotumor formation.
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Affiliation(s)
- Brett K J Kilb
- B. K. J. Kilb, A. P. Kurmis, M. Parry, B. A. Masri, C. P. Duncan, D. S., Garbuz Department of Orthopaedics, University of British Columbia, Vancouver, British Columbia, Canada K. Sherwood, P. Keown Department of Pathology (&) Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada P. Keown, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada A. P. Kurmis, Discipline of Medical Specialties, University of Adelaide, Adelaide, SA, Australia
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Jiao Y, Li R, Wu C, Ding Y, Liu Y, Jia D, Wang L, Xu X, Zhu J, Zheng M, Jia J. High-sensitivity HLA typing by Saturated Tiling Capture Sequencing (STC-Seq). BMC Genomics 2018; 19:50. [PMID: 29334893 PMCID: PMC5769328 DOI: 10.1186/s12864-018-4431-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/03/2018] [Indexed: 12/04/2022] Open
Abstract
Background Highly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious diseases. Additionally, it is routinely performed for identifying matched donors in transplantation medicine. Although many HLA typing approaches have been developed, the complexity, low-efficiency and high-cost of current HLA-typing assays limit their application in population-based high-throughput HLA typing for donors, which is required for creating large-scale databases for transplantation and precision medicine. Results Here, we present a cost-efficient Saturated Tiling Capture Sequencing (STC-Seq) approach to capturing 14 HLA class I and II genes. The highly efficient capture (an approximately 23,000-fold enrichment) of these genes allows for simplified allele calling. Tests on five genes (HLA-A/B/C/DRB1/DQB1) from 31 human samples and 351 datasets using STC-Seq showed results that were 98% consistent with the known two sets of digitals (field1 and field2) genotypes. Additionally, STC can capture genomic DNA fragments longer than 3 kb from HLA loci, making the library compatible with the third-generation sequencing. Conclusions STC-Seq is a highly accurate and cost-efficient method for HLA typing which can be used to facilitate the establishment of population-based HLA databases for the precision and transplantation medicine. Electronic supplementary material The online version of this article (10.1186/s12864-018-4431-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Jiao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Ran Li
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Chao Wu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Yibin Ding
- School of Mathematical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Yanning Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China
| | - Danmei Jia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Lifeng Wang
- Beijing Ming-tian Genetics Ltd, Beijing, 100070, People's Republic of China
| | - Xiang Xu
- School of Mathematical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Jing Zhu
- Beijing Ming-tian Genetics Ltd, Beijing, 100070, People's Republic of China.
| | - Min Zheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China. .,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China.
| | - Junling Jia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China. .,Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China.
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Designing Predictive Models for Beta-Lactam Allergy Using the Drug Allergy and Hypersensitivity Database. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2018; 6:139-148.e2. [DOI: 10.1016/j.jaip.2017.04.045] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/26/2017] [Accepted: 04/17/2017] [Indexed: 02/07/2023]
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Park HW, Kim SH, Chang YS, Kim SH, Jee YK, Lee AY, Jang IJ, Park HS, Min KU. The Fas Signaling Pathway Is a Common Genetic Risk Factor for Severe Cutaneous Drug Adverse Reactions Across Diverse Drugs. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2018; 10:555-561. [PMID: 30088374 PMCID: PMC6082816 DOI: 10.4168/aair.2018.10.5.555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/25/2018] [Accepted: 06/01/2018] [Indexed: 11/20/2022]
Abstract
PURPOSE Human leukocyte antigen (HLA) has been recognized as the most important genetic risk factor for severe cutaneous adverse drug reactions (SCARs) caused by certain drugs. However, cumulated observations suggest the presence of genetic risk factors for SCARs other than drug-specific HLA. We aimed to identify a common genetic risk factor of SCARs across multiple drugs. METHODS We performed 2 independent genome-wide association studies (GWASs). A total of 68 and 38 subjects with a diagnosis of SCAR were enrolled in each GWAS. Their allele frequencies were compared to those of healthy subjects in Korea. RESULTS No single nucleotide polymorphism (SNP) with genome-wide significance was found in either GWAS. We next selected and annotated the 200 top-ranked SNPs from each GWAS. These 2 sets of annotated genes were then entered into the web interface of ConsensusPathDB for a pathway-level analysis. The Fas signaling pathway was significantly over-represented in each gene set from the 2 GWASs. CONCLUSIONS Our observations suggest that the Fas signaling pathway may be a common genetic risk factor for SCARs across multiple drugs.
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Affiliation(s)
- Heung Woo Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.,Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul, Korea.
| | - Sang Heon Kim
- Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Yoon Seok Chang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sang Hoon Kim
- Department of Internal Medicine, Eulji University School of Medicine, Daejeon, Korea
| | - Young Koo Jee
- Department of Internal Medicine, Dankook University College of Medicine, Cheonan, Korea
| | - Ai Young Lee
- Department of Dermatology, Dongguk University Ilsan Hospital, Goyang, Korea
| | - In Jin Jang
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine, Seoul, Korea
| | - Hae Sim Park
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, Korea
| | - Kyung Up Min
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.,Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul, Korea
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Association of Human Leukocyte Antigen Class 1 genes with Stevens Johnson Syndrome with severe ocular complications in an Indian population. Sci Rep 2017; 7:15960. [PMID: 29162886 PMCID: PMC5698496 DOI: 10.1038/s41598-017-15965-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/03/2017] [Indexed: 12/17/2022] Open
Abstract
Stevens Johnson syndrome (SJS) is part of a spectrum of adverse drug reactions resulting in the destruction of skin, mucous membranes, and the ocular surface. A similar, more severe form of the disorder included in this spectrum is toxic epidermal necrolysis (TEN). Approximately 35% of patients suffer chronic sequelae such as vascularization, corneal scarring, conjunctival inversion to the cornea, keratinization, symblepharon, scarring of the palpebral conjunctiva, trichiasis, and severe dry eye. We focused on 80 Indian patients with SJS/TEN with severe ocular complications (SOC) and investigated the association of alleles at HLA -A, HLA-B and HLA-C loci; the controls were 50 healthy Indian volunteers. Genotyping at HLA-A, HLA-B, and HLA-C loci showed a significant positive association with HLA-A*33:03, HLA-B*44:03, and HLA-C*07:01 alleles, and a significant negative association with HLA-B*57:01 and HLA-C*06:02. This indicates that HLA-A*33:03, HLA-B*44:03 and HLA-C*07:01 are risk alleles, and HLA-B*57:01 and HLA-C*06:02 are protective alleles in this population. We also found that the haplotypes consisting of HLA-B*44:03 and HLA-C*07:01 were strongly associated with SJS/TEN with SOC in our Indian population (p = 1.1 × 10−7, odds ratio = 11.0). Describing the association of the haplotype could facilitate the understanding of increased risk factors for developing SJS/TEN with SOC.
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Brandt O, Bircher AJ. Spättypreaktionen auf oral und parenteral verabreichte Arzneimittel. J Dtsch Dermatol Ges 2017. [DOI: 10.1111/ddg.13362_g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Oliver Brandt
- Allergologische Poliklinik; Dermatologische Klinik; Universitätsspital Basel; Schweiz
| | - Andreas J. Bircher
- Allergologische Poliklinik; Dermatologische Klinik; Universitätsspital Basel; Schweiz
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Trubiano JA, Stone CA, Grayson ML, Urbancic K, Slavin MA, Thursky KA, Phillips EJ. The 3 Cs of Antibiotic Allergy-Classification, Cross-Reactivity, and Collaboration. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2017; 5:1532-1542. [PMID: 28843343 PMCID: PMC5681410 DOI: 10.1016/j.jaip.2017.06.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/08/2017] [Accepted: 06/16/2017] [Indexed: 12/22/2022]
Abstract
Antibiotic allergy labeling is highly prevalent and negatively impacts patient outcomes and antibiotic appropriateness. Reducing the prevalence and burden of antibiotic allergies requires the engagement of key stakeholders such as allergists, immunologists, pharmacists, and infectious diseases physicians. To help address this burden of antibiotic allergy overlabeling, we review 3 key antibiotic allergy domains: (1) antibiotic allergy classification, (2) antibiotic cross-reactivity, and (3) multidisciplinary collaboration. We review the available evidence and research gaps of currently used adverse drug reaction classification systems, antibiotic allergy cross-reactivity, and current and future models of antibiotic allergy care.
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Affiliation(s)
- Jason A Trubiano
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia; Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Centre for Improving Cancer Outcomes through Enhanced Infection Services, National Health and Medical Research Council Centre of Research Excellence, The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
| | - Cosby A Stone
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - M Lindsay Grayson
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia; Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
| | - Karen Urbancic
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia; Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Pharmacy, Austin Health, Melbourne, Victoria, Australia
| | - Monica A Slavin
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Centre for Improving Cancer Outcomes through Enhanced Infection Services, National Health and Medical Research Council Centre of Research Excellence, The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Karin A Thursky
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Centre for Improving Cancer Outcomes through Enhanced Infection Services, National Health and Medical Research Council Centre of Research Excellence, The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia; National Centre for Antimicrobial Stewardship, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Elizabeth J Phillips
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn; Institute for Immunology & Infectious Diseases, Murdoch University, Murdoch, WA, Australia; Department of Medicine, Pathology, Microbiology, Immunology, Vanderbilt University Medical Center, Nashville, Tenn; Department of Pharmacology, Vanderbilt University Medical School, Nashville, Tenn
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