• Alanine aminotransferase (ALT)
• CD8+ T cells
• DILIsym
• drug-induced liver injury (DILI)
• quantitative systems toxicology (QST)

• Animals
• Humans
• Chemical and Drug Induced Liver Injury/immunology
• Chemical and Drug Induced Liver Injury/etiology
• Mice
• CD8-Positive T-Lymphocytes/immunology
• Amodiaquine/administration & dosage
• Amodiaquine/toxicity
• Amodiaquine/adverse effects
• Amodiaquine/immunology
• Ovalbumin/immunology
• Drug Development/methods
• Models, Biological
• Disease Models, Animal

• Humans
• Alleles
• T-Lymphocytes/immunology
• T-Lymphocytes/metabolism
• CD4-Positive T-Lymphocytes/immunology
• CD4-Positive T-Lymphocytes/metabolism

• Janssen Research and Development
• Medical Research Council

• DRESS
• T lymphocytes
• drug hypersensitivity
• glycolysis
• vancomycin

• Humans
• Vancomycin/adverse effects
• Teicoplanin
• CD8-Positive T-Lymphocytes
• Lymphocyte Activation
• Cytokines
• Glycolysis

• MR/X00094X/1 Medical Research Council
• Biotechnology and Biological Sciences Research Council
• Biotechnology and Biological Sciences Research Council
• Medical Research Council

• Ludwig van Beethoven
• ancient DNA
• extra-pair paternity
• genetic genealogy
• genobiography
• geo-genetic triangulation
• hair
• hepatitis B virus
• medical genetics
• the Beethoven genome project

• Child
• HLA-B Antigens/genetics
• HLA-B7 Antigen
• HLA-C Antigens/genetics
• Humans
• Respiratory Insufficiency/chemically induced
• Respiratory Insufficiency/genetics
• Trimethoprim, Sulfamethoxazole Drug Combination/adverse effects

• R01 HG010863 NHGRI NIH HHS
• R01 AI152183 NIAID NIH HHS
• U01 AI154659 NIAID NIH HHS
• R21 AI139021 NIAID NIH HHS
• R01 GM129783 NIGMS NIH HHS
• P50 GM115305 NIGMS NIH HHS

• HLA
• Yersinia pestis
• aDNA
• ancient DNA
• human immunity
• natural selection
• plague

• DNA
• Genomics
• Humans
• Pandemics/history
• Plague/genetics
• Yersinia pestis/genetics

• R01 AI158410 NIAID NIH HHS
• R01 AI158861 NIAID NIH HHS
• R56 AI151549 NIAID NIH HHS
• European Research Council
• US National Institutes of Health

Recent studies have successfully implemented next-generation sequencing (NGS) in HLA typing. We performed HLA NGS in a Korean population to estimate HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies up to an 8-digit resolution, which might be useful for an extended application of HLA results.

A total of 128 samples collected from healthy unrelated Korean adults, previously subjected to Sanger sequencing for 6-digit HLA analysis, were used. NGS was performed for HLA-A, -B, -C, and -DRB1 using the AllType NGS kit (One Lambda, West Hills, CA, USA), Ion Torrent S5 platform (Thermo Fisher Scientific, Waltham, MA, USA), and Type Steam Visual NGS analysis software (One Lambda).

Eight HLA alleles showed frequencies of ≥10% in the Korean population, namely, A*24:02:01:01 (19.5%), A*33:03:01 (15.6%), A*02:01:01:01 (14.5%), A*11:01:01:01 (13.3%), B*15:01:01:01 (10.2%), C*01:02:01 (19.9%), C*03:04:01:02 (11.3%), and DRB1*09:01:02 (10.2%). Nine previous 6-digit HLA alleles were further identified as two or more 8-digit HLA alleles. Of these, eight alleles (A*24:02:01, B*35:01:01, B*40:01:02, B*55:02:01, B*58:01:01, C*03:02:02, C*07:02:01, and DRB1*07:01:01) were identified as two 8-digit HLA alleles, and one allele (B*51:01:01) was identified as three 8-digit HLA alleles. The most frequent four-loci haplotype was HLA-A*33:03:01-B*44:03:01:01-C*14:03-DRB1*13:02:01.

We identified 8-digit HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies in a healthy Korean population using NGS. These new data can be used as a representative Korean data for further disease-related HLA type analysis.

• 8-digit HLA alleles
• Human leukocyte antigen (HLA)
• Korean population
• Next-generation sequencing
• allele frequency
• haplotype frequency

Drug rash with eosinophilia with systemic symptoms (DRESS) is a serious adverse event associated with use of the glycopeptide antibiotic vancomycin. Vancomycin-induced drug rash with eosinophilia with systemic symptoms is associated with the expression of human leukocyte antigen (HLA)-A*32:01, suggesting that the drug interacts with this HLA to activate CD8+ T cells. The purpose of this study was to utilize peripheral blood mononuclear cell from healthy donors to: (1) investigate whether expression of HLA-A*32:01 is critical for the priming naïve of T cells with vancomycin and (2) generate T-cell clones (TCC) to determine whether vancomycin exclusively activates CD8+ T cells and to define cellular phenotype, pathways of drug presentation and cross-reactivity. Dendritic cells were cultured with naïve T cells and vancomycin for 2 weeks. On day 14, cells were restimulated with vancomycin and T-cell proliferation was assessed by [³H]-thymidine incorporation. Vancomycin-specific TCC were generated by serial dilution and repetitive mitogen stimulation. Naïve T cells from HLA-A*02:01 positive and negative donors were activated with vancomycin; however the strength of the induced response was significantly stronger in donors expressing HLA-A*32:01. Vancomycin-responsive CD4+ and CD8+ TCC from HLA-A*32:01+ donors expressed high levels of CXCR3 and CCR4, and secreted IFN‐γ, IL-13, and cytolytic molecules. Activation of CD8+ TCC was HLA class I-restricted and dependent on a direct vancomycin HLA binding interaction with no requirement for processing. Several TCC displayed cross-reactivity with teicoplanin and daptomycin. To conclude, this study provides evidence that vancomycin primes naïve T cells from healthy donors expressing HLA-A*32:01 through a direct pharmacological binding interaction. Cross-reactivity of CD8+ TCC with teicoplanin provides an explanation for the teicoplanin reactions observed in vancomycin hypersensitive patients.

• HLA
• T-cells
• drug hypersensitivity
• vancomycin

Mitochondrial DNA (mtDNA) is highly polymorphic and encodes 13 proteins which are critical to the production of ATP via oxidative phosphorylation. As mtDNA is maternally inherited and undergoes negligible recombination, acquired mutations have subdivided the human population into several discrete haplogroups. Mitochondrial haplogroup has been found to significantly alter mitochondrial function and impact susceptibility to adverse drug reactions. Despite these findings, there are currently limited models to assess the effect of mtDNA variation upon susceptibility to adverse drug reactions. Platelets offer a potential personalised model of this variation, as their anucleate nature offers a source of mtDNA without interference from the nuclear genome. This study, therefore, aimed to determine the effect of mtDNA variation upon mitochondrial function and drug-induced mitochondrial dysfunction in a platelet model. The mtDNA haplogroup of 383 healthy volunteers was determined using next-generation mtDNA sequencing (Illumina MiSeq). Subsequently, 30 of these volunteers from mitochondrial haplogroups H, J, T and U were recalled to donate fresh, whole blood from which platelets were isolated. Platelet mitochondrial function was tested at basal state and upon treatment with compounds associated with both mitochondrial dysfunction and adverse drug reactions, flutamide, 2-hydroxyflutamide and tolcapone (10–250 μM) using extracellular flux analysis. This study has demonstrated that freshly-isolated platelets are a practical, primary cell model, which is amenable to the study of drug-induced mitochondrial dysfunction. Specifically, platelets from donors of haplogroup J have been found to have increased susceptibility to the inhibition of complex I-driven respiration by 2-hydroxyflutamide. At a time when individual susceptibility to adverse drug reactions is not fully understood, this study provides evidence that inter-individual variation in mitochondrial genotype could be a factor in determining sensitivity to mitochondrial toxicants associated with costly adverse drug reactions.

• 2-Hydroxyflutamide
• Adverse drug reaction
• Flutamide
• Haplogroup
• Mitochondria
• Platelets
• Tolcapone
• mtDNA

• Allele frequency
• Haplotype frequency
• Human leukocyte antigen
• Kazak population

Background and Objective: Agranulocytosis is a rare and potentially life-threatening complication of metamizole (dipyrone) intake that is characterized by a loss of circulating neutrophil granulocytes. While the mechanism underlying this adverse drug reaction is not well understood, involvement of the immune system has been suggested. In addition, associations between genetic variants in the Human Leukocyte Antigen (HLA) region and agranulocytosis induced by other drugs have been reported. The aim of the present study was to assess whether genetic variants in classical HLA genes are associated with the susceptibility to metamizole-induced agranulocytosis (MIA) in a European population by targeted resequencing of eight HLA genes.

Design: A case-control cohort of Swiss patients with a history of neutropenia or agranulocytosis associated with metamizole exposure (n = 53), metamizole-tolerant (n = 39) and unexposed controls (n = 161) was recruited for this study. A high-throughput resequencing (HTS) and high-resolution typing method was used to sequence and analyze eight HLA loci in a discovery subset of this cohort (n = 31 cases, n = 38 controls). Identified candidate alleles were investigated in the full Swiss cohort as well as in two independent cohorts from Germany and Spain using HLA imputation from genome-wide SNP array data. In addition, variant calling based on HTS data was performed in the discovery subset for the class I genes HLA-A, -B, and -C using the HLA-specific mapper hla-mapper.

Results: Eight candidate alleles (p < 0.05) were identified in the discovery subset, of which HLA-C^∗04:01 was associated with MIA in the full Swiss cohort (p < 0.01) restricted to agranulocytosis (ANC < 0.5 × 10⁹/L) cases. However, no candidate allele showed a consistent association in the Swiss, German and Spanish cohorts. Analysis of individual sequence variants in class I genes produced consistent results with HLA typing but did not reveal additional small nucleotide variants associated with MIA.

Conclusion: Our results do not support an HLA-restricted T cell-mediated immune mechanism for MIA. However, we established an efficient high-resolution (three-field) eight-locus HTS HLA resequencing method to interrogate the HLA region and demonstrated the feasibility of its application to pharmacogenetic studies.

• HLA
• drug-induced agranulocytosis
• genetic association studies
• high-throughput sequencing
• metamizole (dipyrone)
• next generation sequencing
• pharmacogenetics

• Admixture
• Genetic substructure
• HLA
• Immunogenetics
• Latin American populations
• Mexico
• Population genetics

• Curitiba
• NGS
• human leukocyte antigen
• population genetics

• Adult
• Aged
• Chemical and Drug Induced Liver Injury/diagnosis
• Chemical and Drug Induced Liver Injury/epidemiology
• Chemical and Drug Induced Liver Injury/etiology
• Chemical and Drug Induced Liver Injury/therapy
• Fatty Liver/chemically induced
• Female
• Histocompatibility Testing
• Humans
• Liver Neoplasms/chemically induced
• Male
• Middle Aged
• Mitochondria/drug effects
• Practice Guidelines as Topic
• Risk Factors

• CIOM/RUCAM scale
• DILI
• Idiosyncratic drug-induced liver injury
• biomarkers
• hepatotoxicity
• immunophenotype

• Bioinformatics
• Biomarkers
• Drug induced liver injury
• Pathway prediction
• Toxicity predictive models

Drug-induced liver injury (DILI) has become a major topic in the field of Hepatology and Gastroenterology. DILI can be clinically divided into three phenotypes: hepatocytic, cholestatic and mixed. Although the clinical manifestations of DILI are variable and the pathogenesis complicated, recent insights using improved preclinical models, have allowed a better understanding of the mechanisms that trigger liver damage. In this review, we will discuss the pathophysiological mechanisms underlying DILI. The toxicity of the drug eventually induces hepatocellular damage through multiple molecular pathways, including direct hepatic toxicity and innate and adaptive immune responses. Drugs or their metabolites, such as the common analgesic, acetaminophen, can cause direct hepatic toxicity through accumulation of reactive oxygen species and mitochondrial dysfunction. The innate and adaptive immune responses play also a very important role in the occurrence of idiosyncratic DILI. Furthermore, we examine common forms of hepatocyte death and their association with the activation of specific signaling pathways.

• Signaling pathways
• Acetaminophen
• Drug-induced liver injury
• Cell death
• Reactive oxygen species

• Acetaminophen/toxicity
• Adaptive Immunity
• Analgesics, Non-Narcotic/toxicity
• Animals
• Apoptosis/drug effects
• Apoptosis/immunology
• Chemical and Drug Induced Liver Injury/etiology
• Chemical and Drug Induced Liver Injury/pathology
• Cholestasis/chemically induced
• Cholestasis/complications
• Cholestasis/immunology
• Cholestasis/pathology
• Hepatocytes/drug effects
• Hepatocytes/pathology
• Humans
• Immunity, Innate
• Liver/cytology
• Liver/drug effects
• Liver/immunology
• Liver/pathology
• Signal Transduction/drug effects

• HLA
• adverse drug reactions
• ethnicity
• immune

The oral thrombin inhibitor ximelagatran was withdrawn in the late clinical trial phase because it adversely affected the liver. In approximately 8% of treated patients, drug-induced liver injury (DILI) was expressed as transient alanine transaminase (ALT) elevations. No evidence of DILI had been revealed in the pre-clinical in vivo studies. A whole genome scan study performed on the clinical study material identified a strong genetic association between the major histocompatibility complex alleles for human leucocyte antigens (HLA) (HLA-DR7 and HLA-DQ2) and elevated ALT levels in treated patients. An immune-mediated pathogenesis was suggested. Here, we evaluated whether HLA transgenic mice models could be used to investigate whether the expression of relevant HLA molecules was enough to reproduce the DILI effects in humans. In silico modelling performed in this study revealed association of both ximelagatran (pro-drug) and melagatran (active drug) to the antigen-presenting groove of the homology modelled HLA-DR7 molecule suggesting “altered repertoire” as a key initiating event driving development of DILI in humans. Transgenic mouse strains (tgms) expressing HLA of serotype HLA-DR7 (HLA-DRB1*0701, -DRA*0102), and HLA-DQ2 (HLA-DQB1*0202,–DQA1*0201) were created. These two lines were crossed with a human (h)CD4 transgenic line, generating the two tgms DR7xhCD4 and DQ2xhCD4. To investigate whether the DILI effects observed in humans could be reproduced in tgms, the mice were treated for 28 days with ximelagatran. Results revealed no signs of DILI when biomarkers for liver toxicity were measured and histopathology was evaluated. In the ximelagatran case, presence of relevant HLA-expression in a pre-clinical model did not fulfil the prerequisite for reproducing DILI observed in patients. Nonetheless, for the first time an HLA-transgenic mouse model has been investigated for use in HLA-associated DILI induced by a low molecular weight compound. This study shows that mimicking of genetic susceptibility, expressed as DILI-associated HLA-types in mice, is not sufficient for reproducing the complex pathogenesis leading to DILI in man.

• Animals
• Azetidines/toxicity
• Benzylamines/toxicity
• Cell Line
• Chemical and Drug Induced Liver Injury/immunology
• Disease Models, Animal
• Female
• HLA-DQ Antigens/genetics
• HLA-DQ Antigens/metabolism
• HLA-DR7 Antigen/genetics
• HLA-DR7 Antigen/metabolism
• Humans
• Lymphocytes/metabolism
• Male
• Mice, Inbred C57BL
• Mice, Transgenic
• Molecular Docking Simulation
• Phenotype

• Clinical type
• Diagnosis
• Differential diagnosis
• Drug-induced liver injury
• Epidemiology
• Pathogenesis
• Pathology
• Prevention
• Recommendations
• Treatment

• Anti-Bacterial Agents/adverse effects
• Anti-Bacterial Agents/toxicity
• Anti-Infective Agents/adverse effects
• Anti-Infective Agents/toxicity
• Chemical and Drug Induced Liver Injury/epidemiology
• Chemical and Drug Induced Liver Injury/pathology
• Chemical and Drug Induced Liver Injury/physiopathology
• Chemical and Drug Induced Liver Injury/prevention & control
• China/epidemiology
• Cholestasis/chemically induced
• Cholestasis/complications
• Cholestasis/pathology
• Diagnosis, Differential
• Dietary Supplements/adverse effects
• Dietary Supplements/toxicity
• Drugs, Chinese Herbal/adverse effects
• Female
• Guidelines as Topic
• Humans
• Incidence
• Liver Diseases/epidemiology
• Liver Diseases/pathology
• Liver Diseases/physiopathology
• Liver Diseases/therapy
• Male
• Prognosis
• Risk Factors
• Severity of Illness Index

• Science and Technology Department of People's Republic of China

• ADR
• HLA variant
• Molecular docking
• Virtual screening

• North Carolina State University

Cutaneous adverse drug reactions (ADRs) are among the most frequent adverse reactions in patients receiving drug therapy. They have a broad spectrum of clinical manifestations, are caused by various drugs, and result from different pathophysiological mechanisms. Hence, their diagnosis and management is challenging.

Severe cutaneous ADRs comprise a group of diseases with major morbidity and mortality, reaching 30 % mortality rate in cases of Toxic Epidermal Necrolysis.

This chapter covers the terminology, epidemiology, pathogenesis and classification of cutaneous ADR, describes the severe cutaneous ADRs and the clinical and laboratory approach to the patient with cutaneous ADR and presents the translation of laboratory-based discoveries on the genetic predisposition and pathogenesis of cutaneous ADRs to clinical management guidelines.

• Adaptive immune system
• Computer modeling
• Idiosyncratic DILI
• Liver injury
• Quantitative systems pharmacology

• DILI
• drug-induced liver injury
• risk factors

• Chemical and Drug Induced Liver Injury/diagnosis
• Chemical and Drug Induced Liver Injury/epidemiology
• Chemical and Drug Induced Liver Injury/etiology
• Female
• Humans
• Male

• Drug-induced liver injury
• T-cell
• biomarker
• hapten
• human leukocyte antigen
• immune response

• MR/L006758/1 Medical Research Council

• Cell Differentiation/drug effects
• Cell Proliferation/drug effects
• Cells, Cultured
• Dermatitis, Allergic Contact/metabolism
• Dermatitis, Allergic Contact/pathology
• Hair Dyes/chemistry
• Hair Dyes/toxicity
• Humans
• Interferon-gamma/metabolism
• Interleukin-13/metabolism
• Interleukins/metabolism
• Leukocytes, Mononuclear/cytology
• Leukocytes, Mononuclear/drug effects
• Leukocytes, Mononuclear/immunology
• Oxidation-Reduction
• Phenylenediamines/chemistry
• Phenylenediamines/toxicity
• T-Lymphocytes/cytology
• T-Lymphocytes/drug effects
• T-Lymphocytes/metabolism
• Interleukin-22

• G0700654 Medical Research Council
• MR/L006758/1 Medical Research Council
• Biotechnology and Biological Sciences Research Council

In 1965, Sir Austin Bradford Hill published nine “viewpoints” to help determine if observed epidemiologic associations are causal. Since then, the “Bradford Hill Criteria” have become the most frequently cited framework for causal inference in epidemiologic studies. However, when Hill published his causal guidelines—just 12 years after the double-helix model for DNA was first suggested and 25 years before the Human Genome Project began—disease causation was understood on a more elementary level than it is today. Advancements in genetics, molecular biology, toxicology, exposure science, and statistics have increased our analytical capabilities for exploring potential cause-and-effect relationships, and have resulted in a greater understanding of the complexity behind human disease onset and progression. These additional tools for causal inference necessitate a re-evaluation of how each Bradford Hill criterion should be interpreted when considering a variety of data types beyond classic epidemiology studies. Herein, we explore the implications of data integration on the interpretation and application of the criteria. Using examples of recently discovered exposure–response associations in human disease, we discuss novel ways by which researchers can apply and interpret the Bradford Hill criteria when considering data gathered using modern molecular techniques, such as epigenetics, biomarkers, mechanistic toxicology, and genotoxicology.

• Bradford Hill
• Causal inference
• Causation
• Data integration
• Molecular epidemiology

Drug-induced liver injury (DILI) is a major concern for public health, as well as for drug development in the pharmaceutical industry, since it can cause liver failure and lead to drug withdrawal from the market and black box warnings. Thus, it is important to identify biomarkers for early prediction to increase our understanding of mechanisms underlying DILI that will ultimately aid in the exploration of novel therapeutic strategies to prevent or manage DILI. DILI can be subdivided into 'intrinsic' and 'idiosyncratic' categories, although the validity of this classification remains controversial. Idiosyncratic DILI occurs in a minority of susceptible individuals with a prolonged latency, while intrinsic DILI results from drug-induced direct hepatotoxicity over the course of a few days. The rare occurrence of idiosyncratic DILI requires multicenter collaborative investigations and phenotype standardization. Recent progress in research on idiosyncratic DILI is based on key developments in 3 areas: (1) newly developed high-throughput genotyping across the whole genome allowing for the identification of genetic susceptibility markers, (2) new mechanistic concepts on the pathogenesis of DILI revealing a key role of drug-responsive T lymphocytes in the immunological response, and (3) broad multidisciplinary approaches using different platform "-omics" technologies that have identified novel biomarkers for the prediction of DILI. An association of a specific human leukocyte antigen (HLA) allele with DILI has been reported for several drugs. HLA-restricted T-cell immune responses have also been investigated using lymphocytes and T-cell clones isolated from patients. A microRNA, miR-122, has been discovered as a promising biomarker for the early prediction of DILI. In this review, we summarize recent advances in research on idiosyncratic DILI with an understanding of the key role of adaptive immune systems.

• Drug-induced liver injury
• T-cell
• biomarker
• hapten
• human leukocyte antigen
• immune response

• drug-induced liver injury
• genome-wide association study
• hepatotoxicity
• human leucocyte antigen
• pharmacogenetics

• HLA
• antituberculosis drug-induced liver injuries
• antituberculosis treatment
• case-control study
• pharmacogenetics

• Adult
• Aged
• Antitubercular Agents/adverse effects
• Antitubercular Agents/therapeutic use
• Case-Control Studies
• Chemical and Drug Induced Liver Injury/genetics
• Cohort Studies
• Female
• Follow-Up Studies
• Genetic Predisposition to Disease/genetics
• HLA-DQ beta-Chains/genetics
• Humans
• Male
• Middle Aged
• Odds Ratio
• Polymorphism, Genetic/genetics
• Prospective Studies
• Tuberculosis/drug therapy