Transcriptomic profiling in Malawian patients with acute hypersensitivity reactions to Nevirapine
ABSTRACT: Nevirapine is a non-nucleoside reverse transcriptase inhibitor, a class of antiretroviral drug, used for the treatment of HIV-1 infection. Despite its wide use, nevirapine treatment has been associated with a significant incidence of different kind of hypersensitivity reactions (HSRs). We used microarrays to find significant genes that can relate to Nevirapine-persuaded hypersensitivity reactions in ‘acute’ patients compared to ‘recovered’ and/or ‘tolerant’ patients. Overall design: We have selected 18 patients’ samples, 6 from each group (Acute, Recovered, Tolerant) to investigate Nevirapine induced hypersensitivity reactions using transcriptomic profiling based on microarray technology. Acute:Patient taking nevirapine develops adverse drug reaction (ADR). Recovered: 6 weeks after acute reaction-not longer taking nevirapine. Tolerant: Patient on neviraoine and tolerating treatment.
INSTRUMENT(S): [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
Project description:Hypersensitivity reactions to medications constitute a growing problem in the clinical practice. In order to study the molecular basis underlying the pathogenesis of non-immediate hypersensitivity reactions to drugs, we characterized the gene expression profiles of PBMCs isolated from patients during the acute phase and upon resolution of the clinical symptoms using a cDNA array technology. Eighty five genes were found to be differentially expressed during the acute phase of drug-induced delayed hypersensitivity reactions. Furthermore, ninety two genes with distinct expression patterns during the acute phase of severe and benign diseases were identified. Keywords: Comparison between disease and healty status Expression profiles of 11835 genes were analyzed in peripheral blood mononuclear cells from 13 patients with different clinical entities . Two samples were analyze from each patient. The first blood sample was drawn during the acute phase of the disease. The second blood sample was obtained upon resolutin of the clinical symptoms. The ratio between gene expression levels in both samples was calculated for each patient.
Project description:Hypersensitivity reactions to medications constitute a growing problem in the clinical practice. In order to study the molecular basis underlying the pathogenesis of non-immediate hypersensitivity reactions to drugs, we characterized the gene expression profiles of PBMCs isolated from patients during the acute phase and upon resolution of the clinical symptoms using a cDNA array technology. Eighty five genes were found to be differentially expressed during the acute phase of drug-induced delayed hypersensitivity reactions. Furthermore, ninety two genes with distinct expression patterns during the acute phase of severe and benign diseases were identified. Keywords: Comparison between disease and healty status Overall design: Expression profiles of 11835 genes were analyzed in peripheral blood mononuclear cells from 13 patients with different clinical entities . Two samples were analyze from each patient. The first blood sample was drawn during the acute phase of the disease. The second blood sample was obtained upon resolutin of the clinical symptoms. The ratio between gene expression levels in both samples was calculated for each patient.
Project description:Hypersensitivity reactions are rare, but potentially severe adverse effects of sulfonamide antibiotics. Increased in vitro toxicity of lymphocytes, primarily CD8+ T cells, to sulfonamide drug metabolites as been proposed as a marker for sulfonamide hypersensitivity, but the mechanisms underlying this marker are unknown. Therefore, we used microarrays to compare RNA expression of CD8+ T cell-enriched peripheral blood mononuclear cells of human patients who have had a hypersensitivity (HS) reaction to sulfonamide antibiotics vs. patients who have been tolerant (TOL) to a course of sulfonamide antibiotics. Overall design: 40ml of heparinized blood was obtained from each patient, peripheral blood mononuclear cells were extracted and enriched for CD8+ T cells and RNA was extracted.
Project description:House dust mite/HDM atopy patch test/APT elicits positive reactions in the majority of atopic dermatitis/AD and healthy individuals. Experimental systems for new-onset/chronic AD are needed to support rapid therapeutic development, particularly since animal models representing AD pathology in humans are lacking. HDM APT historically simulated AD, but its suitability to model the emerging AD skin phenotype as Th2/Th22 polarized with Th1 and Th17 components is unknown. To assess whether HDM APT tissues reproduce acute or chronic AD, positive HDM APT (n=14) were compared with nonlesional, acute (<72hrs; n=10), and chronic phase AD biopsies (n=8), allergic contact reactions (to nickel [n=10] and fragrance [n=3]) using arrays. Overall design: 14 patients with positive dust mite reactions, were compared to 8 AD patients (acute and chronic lesions). 8 patients out of 14 patients with positive dust mite reactions did not have positive reactions to nickel or fragrance. 5 patients out of 14 patients with positive dust mite reactions had positive reactions to nickel. 1 patient out of 14 patients with positive dust mite reactions had positive reaction to fragrance. 5 other patients with positive nickel reactions and 2 other patients with fragrance reaction but not dustmite reactions were included in the study. The study considered a total of 29 patients (8 Atopic Dermatitis and 21 dust mite/nickel/fragrance positive reactions). Lesional and Non Lesional skin for AD patients were analyzed. Atopic patch skin and non lesional skin for dust mite/nickel/fragrance patients were analyzed. For patients with more than one positive patch reaction a sample from each atopy patch test reaction was obtained. We are submiting here only the samples from dust mite atopic patch skin (14) and the non lesional skin samples related to patients with positive dust mite reaction only (8). The other samples have been submited in: series accession no. GSM815426, GSM815427, GSE36842 and GSE36842.
Project description:Idiosyncratic drug reactions (IDRs) cause significant morbidity and mortality. In an animal model of IDRs, 50-80% of Brown Norway rats exposed to D-penicillamine develop an autoimmune syndrome after several weeks of treatment. The symptoms of the IDR are similar to that observed in humans who take D-penicillamine. The mechanism of this reaction is unknown, and no effective biomarkers have been identified to predict susceptibility. We postulate that cell stress caused by drugs is required to initiate the response. We used a highthroughput approach to identify factors that might represent danger signals by profiling hepatic gene expression 6 h after dosing with D-penicillamine (150 mg/kg). Our results show that the drug-treated animals cluster into two distinct groups. One group exhibits substantial expression changes relative to control animals. The most significantly altered transcripts have a role in stress, energy metabolism, acute phase response, and inflammation. We used quantitative reverse transcriptase polymerase chain reaction to measure transcript levels in liver biopsies of 33 rats and found that resistant animals cluster together. This 'resistant' cluster of animals contains 87.5% (7/8) resistant animals but only 48% (12/25) 'sensitive' animals. This separation is statistically significant at the p 0.01 level. Keywords: Response to Drug Overall design: Single-channel Affy arrays used to profile 4 control Brown Norway rats and 8 D-Penicillamine treated Brown Norway rats.
Project description:An antiepileptic drug carbamazepine is well tolerated by the majority of patients, but can cause severe and potentialy fatal hypersensitivity reactions in a small number of individuals. The aim of this study was to identify genetic predictors of hypersensitivity reactions to carbamazepine. We undertook a genome-wide association study (GWAS) in 22 patients of European ancestry with carbamazepine-induced hypersensitivity syndrome (HSS) and compared our data with genotypes from a healthy population within the WTCCC. We performed imputation of classical HLA alleles according to a recently described method (Science. 2010 Dec 10;330(6010):1551-7. Epub 2010 Nov 4). GWAS statistical analysis was performed using logistic regression with an additive model of inheritance.
Project description:Background: Reactions in Leprosy are immune exacerbations that cause debilitating consequences like nerve damage and permanent deformities. Prediction of these reactional states using appropriate biomarkers would enable early treatment interventions to prevent nerve function impairment. The current study investigated whole transcriptomic expression profiles of Mycobacterium leprae (M. leprae) that differentiate leprosy cases in type 2 (Erythema Nodosum Leprosum) reactions with those without reactions in host skin tissue derived RNA. Methods: Post clinical examination, excisional skin biopsy specimens were collected from skin lesions of subjects with and without type 2 reaction. Total RNA was extracted following the Trizol protocol and bacterial RNA was enriched in the samples. A 2 x 400K gene expression array (whole genome tiling array) was designed with the probes having 60-mer oligonucleotides tiling every 10bp of the genome sequence of M. leprae (NC_011896.1). The array comprised 420288 features which include probes and Agilent controls. The quality of RNA was estimated using BioAnalyzer (Agilent Technologies) followed by labelling, reverse transcription, amplification and hybridization to the arrays. The hybridized slides were scanned on a G2600D scanner (Agilent Technologies). The data thus acquired is analysed using GeneSpring GX Version 12.1 software. Data was normalized and fold difference in expression was noted from 359,922 probes which include sense and antisense orientations of 179,961 probes. The differentially expressing M. leprae genomic regions between type 2 reactions and non reactional cases were noted. Results: Considering a statistical cut-off value of 0.6 for fold difference in expression between the test and the control samples, a set of 107 genes indicated statistically significant up-regulation with volcano plot p-values less than 0.05. Functional characterization revealed higher-expression of genes encoding transmembrane proteins (12), regulatory proteins (9), fatty acid biosynthesis (6), amino acid metabolism (13), nucleic acid metabolism (7), DNA replication and repair (7), Secretory proteins (2) Krebs Cycle (1), Glycolysis (1), Drug Efflux Protein (1),Stress Response Protein (1), Energy Metabolism (2), Pantothenate biosynthesis (1), Metalloproteins (3), Hydrolases (1) and Hypothetical Proteins (40). Additionally there are 157 genes that are down regulated in cases with reaction. Conclusion: Differential expression of genes in the human skin biopsy specimens among leprosy cases with type 2 reaction in contrast to those without reaction suggests the role of pathogen associated gene expression triggers with the aetiology of these reactions. As most of the transmembrane and cell wall proteins possess epitope and surface exposed domains, higher expression levels of genes encoding these proteins may have a possible role in enhancing host immune responses characteristic of type 2 reactions in leprosy. Overall design: Post clinical examination, excisional skin biopsy specimens were collected from skin lesions of subjects with and without type 2 reaction. Total RNA was extracted following the Trizol protocol and bacterial RNA was enriched in the samples. A 2 x 400K gene expression array (whole genome tiling array) was designed with the probes having 60-mer oligonucleotides tiling every 10bp of the genome sequence of M. leprae (NC_011896.1).
Project description:Hypersensitivity (HS) reactions to sulfonamide antibiotics occur uncommonly, but with potentially severe clinical manifestations. A familial predisposition to sulfonamide HS is suspected, but robust predictive genetic risk factors have yet to be identified. Strongly linked genetic polymorphisms have been used clinically as screening tests for other HS reactions prior to administration of high-risk drugs. The purpose of this study was to evaluate for genetic risk of sulfonamide HS in the immunocompetent population using genome-wide association. Ninety-one patients with symptoms after trimethoprim-sulfamethoxazole (TMP-SMX) attributable to "probable" drug HS based on medical record review and the Naranjo Adverse Drug Reaction Probability Scale, and 184 age- and sex-matched patients who tolerated a therapeutic course of TMP-SMX, were included in a genome-wide association study using both common and rare variant techniques. Additionally, two subgroups of HS... (for more see dbGaP study page.)
Project description:To investigate the plasticity of Lipolysaccharide (LPS) tolerance, we employed microarray profiling to analyse the gene expression profile in macrophage. Four macrophage populations were induced; Untreated macrophages (Control group), Acute response to LPS (LPS activation group), LPS tolerance (T – Tolerant group) and recovered (R = recovered macrophage group) Using transcriptional analysis we demonstrate that recovery from LPS tolerance (R – Recovery), as defined by cytokine gene expression, is associated with a global change in the transcriptional profile of macrophage. This data confirms that LPS tolerance is a transient state which results in induction of novel hybrid macrophage activation state with a unique transcriptional signature. Bone marrow derived macrophages were polarised into three activation states; Acute response to LPS (A), LPS tolerant (T) and recovered (R). Gene expression was measured at 4 hours post stimulation with LPS. Three independent experiments were performed to measure gene expression changes between each macrophage group.