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Jmel H, Boukhalfa W, Gouiza I, Seghaier RO, Dallali H, Kefi R. Pharmacogenetic landscape of pain management variants among Mediterranean populations. Front Pharmacol 2024; 15:1380613. [PMID: 38813106 PMCID: PMC11134176 DOI: 10.3389/fphar.2024.1380613] [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: 02/01/2024] [Accepted: 04/05/2024] [Indexed: 05/31/2024] Open
Abstract
Background Chronic pain is a major socioeconomic burden in the Mediterranean region. However, we noticed an under-representation of these populations in the pharmacogenetics of pain management studies. In this context, we aimed 1) to decipher the pharmacogenetic variant landscape among Mediterranean populations compared to worldwide populations in order to identify therapeutic biomarkers for personalized pain management and 2) to better understand the biological process of pain management through in silico investigation of pharmacogenes pathways. Materials and Methods We collected genes and variants implicated in pain response using the Prisma guidelines from literature and PharmGK database. Next, we extracted these genes from genotyping data of 829 individuals. Then, we determined the variant distribution among the studied populations using multivariate (MDS) and admixture analysis with R and STRUCTURE software. We conducted a Chi2 test to compare the interethnic frequencies of the identified variants. We used SNPinfo web server, miRdSNP database to identify miRNA-binding sites. In addition, we investigated the functions of the identified genes and variants using pathway enrichment analysis and annotation tools. Finally, we performed docking analysis to assess the impact of variations on drug interactions. Results We identified 63 variants implicated in pain management. MDS analysis revealed that Mediterranean populations are genetically similar to Mexican populations and divergent from other populations. STRUCTURE analysis showed that Mediterranean populations are mainly composed of European ancestry. We highlighted differences in the minor allele frequencies of three variants (rs633, rs4680, and rs165728) located in the COMT gene. Moreover, variant annotation revealed ten variants with potential miRNA-binding sites. Finally, protein structure and docking analysis revealed that two missense variants (rs4680 and rs6267) induced a decrease in COMT protein activity and affinity for dopamine. Conclusion Our findings revealed that Mediterranean populations diverge from other ethnic groups. Furthermore, we emphasize the importance of pain-related pathways and miRNAs to better implement these markers as predictors of analgesic responses in the Mediterranean region.
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Affiliation(s)
- Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Genetic Typing Service, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Wided Boukhalfa
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Genetic Typing Service, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Ismail Gouiza
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Genetic Typing Service, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
- MitoLab Team, Unité MitoVasc, Unité Mixte de Recherche Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale U1083, SFR ICAT, University of Angers, Angers, France
| | - Roua Ouled Seghaier
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Genetic Typing Service, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Genetic Typing Service, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
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Jerschow E, Dubin R, Chen CC, iAkushev A, Sehanobish E, Asad M, Chiarella SE, Porcelli SA, Greally J. Aspirin-exacerbated respiratory disease is associated with variants in filaggrin, epithelial integrity, and cellular interactions. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100205. [PMID: 38317805 PMCID: PMC10838899 DOI: 10.1016/j.jacig.2024.100205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 02/07/2024]
Abstract
Background Previous studies have determined that up to 6% of patients with aspirin-exacerbated respiratory disease (AERD) have family history of AERD, indicating a possible link with genetic polymorphisms. However, whole exome sequencing (WES) studies of such associations are currently lacking. Objectives We sought to examine whether WES can identify pathogenic variants associated with AERD. Methods Diagnoses of AERD were confirmed in patients with nasal polyps and asthma. WES was performed using an Illumina sequencing platform. Human Phenotype Ontology terms were used to define the patients' phenotypes. Exomiser was used to annotate, filter, and prioritize possible disease-causing genetic variants. Results Of 39 patients with AERD, 41% reported a family history of asthma and 5% reported a family history of AERD. Pathogenic exome variants in the filaggrin gene (FLG) were found in 2 patients (5%). Other variants not known to be pathogenic were detected in an additional 16 patients (41%) in genes related to epithelial integrity and cellular interactions, including genes encoding desmoglein 3 (DSG3), dynein axonemal heavy chain 9 (DNAH9), collagen type VII alpha 1 chain (COL7A1), collagen type XVII alpha 1 chain (COL17A1), chromodomain helicase DNA binding protein-7 (CHD7), TSC complex subunit 2/tuberous sclerosis-2 protein (TSC2), P-selectin (SELP), and platelet-derived growth factor receptor-alpha (PDGFRA). Conclusion WES identified a monogenic susceptibility to AERD in 5% of patients with FLG pathogenic variants. Other variants not previously identified as pathogenic were found in genes relevant to epithelial integrity and cellular interactions and may further reveal genetic factors that contribute to this condition.
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Affiliation(s)
- Elina Jerschow
- Mayo Clinic, Rochester, Minn
- Albert Einstein College of Medicine, Bronx, NY
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Lee JU, Kim MK, Park SL, Bae DJ, Chang HS, Park CS, Park JS. Association of ATP8B3 gene polymorphisms with aspirin-exacerbated respiratory disease in asthmatics. Pharmacogenet Genomics 2022; 32:281-287. [PMID: 35997042 DOI: 10.1097/fpc.0000000000000480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Aspirin-exacerbated respiratory disease (AERD), an asthma phenotype, often presents with severe manifestations and it remains widely underdiagnosed because of insufficient awareness of the relationship between the ingestion of nonsteroidal anti-inflammatory drugs, including acetylsalicylic acid (ASA), and asthma exacerbation. Our previous genome-wide association study demonstrated an association between a single nucleotide polymorphism (SNP) of the ATP8B3 gene and the risk of AERD. This study examined AERD-related SNPs of the ATP8B3 gene in a large population. METHODS Twenty-five SNPs of ATP8B3 were genotyped with the GoldenGate assay using VeraCode microbeads in 141 asthmatics with AERD and 995 Aspirin-tolerant asthma (ATA). The genotype distribution was analyzed using logistic regression models. The declines in forced expiratory volume in 1 second (FEV1)following an ASA challenge were compared among the genotypes and haplotypes using a type III generalized linear model. RESULTS The minor allele frequencies (MAFs) of rs10421558 A>G in the 5'UTR and rs10403288 G>A in the intron were significantly lower in the AERD than the ATA [34.0% vs. 43.8%, OR = 0.66 (0.62-0.92), Pcorr = 0.03 and 28.4% vs. 35.4%, OR = 0.62 (0.59-0.89), Pcorr = 0.016, respectively]. BL1ht5 was significantly higher in the AERD [7.6% vs. 1.6%, OR = 12.23 (0.2-0.51), P = 4.7 × 10 -4 , Pcorr = 0.001]. Among them, rs10421558 A>G and BL1ht5 were associated with the percent decline in FEV1 on the oral ASA challenge test. CONCLUSION The minor allele of rs10421558 A>G in the 5'UTR may protect against the development of AERD via the increased production of ATP8B3.
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Affiliation(s)
- Jong-Uk Lee
- Department of Medical Bioscience, Graduate School, Soonchunhyang University, Asan
| | - Min Kyung Kim
- Department of Medical Bioscience, Graduate School, Soonchunhyang University, Asan
| | - Seung-Lee Park
- Department of Medical Bioscience, Graduate School, Soonchunhyang University, Asan
| | - Da Jeong Bae
- Department of Medical Bioscience, Graduate School, Soonchunhyang University, Asan
| | - Hun Soo Chang
- Department of Anatomy and BK21 FOUR Project, College of Medicine, Soonchunhyang University, Cheonan
| | - Choon-Sik Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital
- PulmoBioPark Co., Ltd. Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Jong Sook Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital
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Landry V, Coburn P, Kost K, Liu X, Li-Jessen NYK. Diagnostic Accuracy of Liquid Biomarkers in Airway Diseases: Toward Point-of-Care Applications. Front Med (Lausanne) 2022; 9:855250. [PMID: 35733871 PMCID: PMC9207186 DOI: 10.3389/fmed.2022.855250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/04/2022] [Indexed: 12/30/2022] Open
Abstract
Background Liquid biomarkers have shown increasing utility in the clinical management of airway diseases. Salivary and blood samples are particularly amenable to point-of-care (POC) testing due to simple specimen collection and processing. However, very few POC tests have successfully progressed to clinical application due to the uncertainty and unpredictability surrounding their diagnostic accuracy. Objective To review liquid biomarkers of airway diseases with well-established diagnostic accuracies and discuss their prospects for future POC applications. Methodology A literature review of publications indexed in Medline or Embase was performed to evaluate the diagnostic accuracy of liquid biomarkers for chronic obstructive pulmonary disease (COPD), asthma, laryngopharyngeal reflux (LPR), and COVID-19. Results Of 3,628 studies, 71 fulfilled the inclusion criteria. Sputum and blood eosinophils were the most frequently investigated biomarkers for the management of asthma and COPD. Salivary pepsin was the only biomarker with a well-documented accuracy for the diagnosis of LPR. Inflammatory blood biomarkers (e.g., CRP, D-dimers, ferritin) were found to be useful to predict the severity, complications, and mortality related to COVID-19 infection. Conclusion Multiple liquid biomarkers have well-established diagnostic accuracies and are thus amenable to POC testing in clinical settings.
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Affiliation(s)
- Vivianne Landry
- Faculty of Medicine, University of Montreal, Montreal, QC, Canada
- School of Communication Sciences & Disorders, McGill University, Montreal, QC, Canada
| | - Patrick Coburn
- School of Communication Sciences & Disorders, McGill University, Montreal, QC, Canada
| | - Karen Kost
- Department of Otolaryngology-Head & Neck Surgery, McGill University, Montreal, QC, Canada
| | - Xinyu Liu
- Department of Mechanical & Industrial Engineering, University of Toronto, Toronto, ON, Canada
| | - Nicole Y. K. Li-Jessen
- School of Communication Sciences & Disorders, McGill University, Montreal, QC, Canada
- Department of Otolaryngology-Head & Neck Surgery, McGill University, Montreal, QC, Canada
- Department of Biomedical Engineering, McGill University, Montreal, QC, Canada
- The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- *Correspondence: Nicole Y. K. Li-Jessen,
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Associations between TMEM196 polymorphisms and NSAID-exacerbated respiratory disease in asthma. Pharmacogenet Genomics 2020; 29:69-75. [PMID: 30694883 DOI: 10.1097/fpc.0000000000000367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND We previously found differences in the minor allele frequency (MAF) of single-nucleotide polymorphisms (SNPs) in transmembrane protein 196 (TMEM196) between 995 patients with aspirin-tolerant asthma (ATA) and 141 asthmatic patients with NSAID-exacerbated respiratory disease (NERD). In this study, we statistically analyzed the distributions of the genotypes and haplotypes of these SNPs to determine the exact association between TMEM196 genetic variants and the risk for NERD. MATERIALS AND METHODS Lewontin's D' and r values were used to measure linkage disequilibrium between the biallelic loci having MAFs more than 0.05, and haplotypes were inferred using the PHASE algorithm (version 2.0). The genotype distribution was analyzed by logistic regression models using age of onset, smoking status (nonsmoker=0, ex-smoker=1, smoker=2), and BMI as covariates. Regression analysis of the association between SNPs and the risk of NERD was analyzed using SPSS version 12.0 and PLINK version 1.9. RESULTS The MAF of rs9886152 C>T was significantly lower in NERD than in ATA [24.8 vs. 34.0%, odds ratio=0.64 (0.48-0.85), P=2.07×10, Pcorr=0.048]. The rate of the rs9886152 C>T minor allele was significantly lower in NERD than in ATA [44.0 vs. 56.4% in the codominant model, P=0.002, Pcorr=0.049, odds ratio=0.64 (0.48-0.85)]. An additional three SNPs (rs9639334 A>G, rs9638765 A>G, and rs2097811 G>A) showed similar associations with the risk of NERD. NERD patients had lower frequencies of the rs9639334 A>G minor allele (51.1 vs. 64.4%, P=0.002, Pcorr=0.043), rs9638765 A>G (49.7 vs. 64.2%, P=0.001, Pcorr=0.017), and rs2097811 G>A (51.1 vs. 64.5%, P=0.002, Pcorr=0.04) compared with ATA patients. Patients homozygous for the minor alleles of the four SNPs showed significantly less of an aspirin-induced decrease in forced expiratory volume in one second compared with those homozygous for the common alleles (P=0.003-0.012). CONCLUSION The minor alleles of the four SNPs in TMEM196 may exert a protective effect against the development of NERD and may be useful genetic markers to predict the risk of NERD.
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IL10 rs1800872 Is Associated with Non-Steroidal Anti-Inflammatory Drugs Exacerbated Respiratory Disease in Mexican-Mestizo Patients. Biomolecules 2020; 10:biom10010104. [PMID: 31936183 PMCID: PMC7023146 DOI: 10.3390/biom10010104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/17/2019] [Accepted: 12/20/2019] [Indexed: 12/23/2022] Open
Abstract
Non-steroidal anti-inflammatory drugs (NSAID) exacerbated respiratory disease (N-ERD) is a disease integrated by asthma, nasal polyps, and hypersensitivity to non-steroidal anti-inflammatory drugs (NSAID). Genetic association studies have explored single nucleotide polymorphisms (SNPs) in genes involved in theoretical pathophysiological mechanisms, but most of these lack replication of findings in second populations. Our objective was to evaluate the association of SNPs in candidate genomic regions described in Asian and European subjects with N-ERD in Mexican-mestizo patients. We designed a replicative study in two stages. We included 381 SNPs selected by fine mapping of associated genes in a microarray, which were tested in three groups: N-ERD (N), asthma (A), and control group (CG); by means of GoldenGate array, positive results by genetic models were validated in the second stage in another population through qPCR with the same methodology. In the allelic model, we identified 11 SNPs in N vs. CG comparison, and five in N vs. A and A vs. CG, respectively. By genetics models, all SNPs in PPARG, rs13239058 in TBXAS1, and rs1554286 and rs1800872 in IL10 were associated in both models. In the second stage, only rs1800872CC showed an association in the dominant model comparing N vs. GC, p = 0.004, OR = 0.44. In conclusion, rs1800872 in IL10 was the only associated with N-ERD in Mexican-mestizo patients.
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The genetic landscape of the human solute carrier (SLC) transporter superfamily. Hum Genet 2019; 138:1359-1377. [PMID: 31679053 PMCID: PMC6874521 DOI: 10.1007/s00439-019-02081-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 10/26/2019] [Indexed: 12/22/2022]
Abstract
The human solute carrier (SLC) superfamily of transporters is comprised of over 400 membrane-bound proteins, and plays essential roles in a multitude of physiological and pharmacological processes. In addition, perturbation of SLC transporter function underlies numerous human diseases, which renders SLC transporters attractive drug targets. Common genetic polymorphisms in SLC genes have been associated with inter-individual differences in drug efficacy and toxicity. However, despite their tremendous clinical relevance, epidemiological data of these variants are mostly derived from heterogeneous cohorts of small sample size and the genetic SLC landscape beyond these common variants has not been comprehensively assessed. In this study, we analyzed Next-Generation Sequencing data from 141,456 individuals from seven major human populations to evaluate genetic variability, its functional consequences, and ethnogeographic patterns across the entire SLC superfamily of transporters. Importantly, of the 204,287 exonic single-nucleotide variants (SNVs) which we identified, 99.8% were present in less than 1% of analyzed alleles. Comprehensive computational analyses using 13 partially orthogonal algorithms that predict the functional impact of genetic variations based on sequence information, evolutionary conservation, structural considerations, and functional genomics data revealed that each individual genome harbors 29.7 variants with putative functional effects, of which rare variants account for 18%. Inter-ethnic variability was found to be extensive, and 83% of deleterious SLC variants were only identified in a single population. Interestingly, population-specific carrier frequencies of loss-of-function variants in SLC genes associated with recessive Mendelian disease recapitulated the ethnogeographic variation of the corresponding disorders, including cystinuria in Jewish individuals, type II citrullinemia in East Asians, and lysinuric protein intolerance in Finns, thus providing a powerful resource for clinical geneticists to inform about population-specific prevalence and allelic composition of Mendelian SLC diseases. In summary, we present the most comprehensive data set of SLC variability published to date, which can provide insights into inter-individual differences in SLC transporter function and guide the optimization of population-specific genotyping strategies in the bourgeoning fields of personalized medicine and precision public health.
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Abstract
PURPOSE OF REVIEW NSAIDs are the drugs most frequently involved in hypersensitivity reactions (HSR). These are frequently prescribed at all ages. HSR are of great concern and can affect people at any age. These drugs can induce reactions by stimulating the adaptive immune system (IgE or T cell), known as selective responders or more frequently by abnormalities in biochemical pathways related with prostaglandin metabolism. These are known as cross-intolerant. With some exceptions, skin testing and in-vitro studies are of little value in selective responders. RECENT FINDINGS In the last years, several classifications have been provided based on clinical symptoms, time interval between drug intake and appearance of symptoms, response to other nonchemically related NSAIDs and the underlying disease. Based on this classification, several well differentiated categories within each group of entities cross-intolerant and selective responders are now recognized. The most complex groups for evaluation are cross-intolerant in which three major groups exist: NSAIDs exacerbated respiratory disease, NSAIDs exacerbated cutaneous disease and NSAIDs-induced urticaria/angioedema in the absence of chronic spontaneous urticaria. Within the selective responders, there are two mechanisms involved: drug-specific IgE or T-cell effector responses. New entities have been added to this classification like mixed reactions within the cross-intolerant category, that must manifest as anaphylaxis and multiple immediate selective reactions. SUMMARY The precise evaluation of patients with NSAIDs hypersensitivity following established guidelines will improve not only our understanding but also the management of these entities. As the number of patients affected with NSAIDs is important, further studies are warranted.
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Park JS, Son JH, Park CS, Chang HS. Clinical Implications of Single Nucleotide Polymorphisms in Diagnosis of Asthma and its Subtypes. Yonsei Med J 2019; 60:1-9. [PMID: 30554485 PMCID: PMC6298887 DOI: 10.3349/ymj.2019.60.1.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/11/2018] [Accepted: 09/15/2018] [Indexed: 11/27/2022] Open
Abstract
For the past three decades, a large number of genetic studies have been performed to examine genetic variants associated with asthma and its subtypes in hopes of gaining better understanding of the mechanisms underlying disease pathology and to identify genetic biomarkers predictive of disease outcomes. Various methods have been used to achieve these objectives, including linkage analysis, candidate gene polymorphism analysis, and genome-wide association studies (GWAS); however, the degree to which genetic variants contribute to asthma pathogenesis has proven to be much less significant than originally expected. Subsequent application of GWAS to well-defined phenotypes, such as occupational asthma and non-steroidal anti-inflammatory drugexacerbated respiratory diseases, has overcome some of these limitations, although with only partial success. Recently, a combinatorial analysis of single nucleotide polymorphisms (SNPs) identified by GWAS has been used to develop sets of genetic markers able to more accurately stratify asthma subtypes. In this review, we discuss the implications of the identified SNPs in diagnosis of asthma and its subtypes and the progress being made in combinatorial analysis of genetic variants.
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Affiliation(s)
- Jong Sook Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Ji Hye Son
- Department of Interdisciplinary Program in Biomedical Science, Graduate School, Soonchunhyang University, Bucheon, Korea
| | - Choon Sik Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Hun Soo Chang
- Department of Interdisciplinary Program in Biomedical Science, Graduate School, Soonchunhyang University, Bucheon, Korea.
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Dahlin A, Weiss ST. Genetic and Epigenetic Components of Aspirin-Exacerbated Respiratory Disease. Immunol Allergy Clin North Am 2017; 36:765-789. [PMID: 27712769 DOI: 10.1016/j.iac.2016.06.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aspirin-exacerbated respiratory disease (AERD) severity and its clinical phenotypes are characterized by genetic variation within pathways for arachidonic acid metabolism, inflammation, and immune responses. Epigenetic effects, including DNA methylation and histone protein modification, contribute to regulation of many genes that contribute to inflammatory states in AERD. The development of noninvasive, predictive clinical tests using data from genetic, epigenetic, pharmacogenetic, and biomarker studies will improve precision medicine efforts for AERD and asthma treatment.
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Affiliation(s)
- Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA.
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Wang S, Jeong HH, Kim D, Wee K, Park HS, Kim SH, Sohn KA. Integrative information theoretic network analysis for genome-wide association study of aspirin exacerbated respiratory disease in Korean population. BMC Med Genomics 2017; 10:31. [PMID: 28589859 PMCID: PMC5461529 DOI: 10.1186/s12920-017-0266-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Aspirin Exacerbated Respiratory Disease (AERD) is a chronic medical condition that encompasses asthma, nasal polyposis, and hypersensitivity to aspirin and other non-steroidal anti-inflammatory drugs. Several previous studies have shown that part of the genetic effects of the disease may be induced by the interaction of multiple genetic variants. However, heavy computational cost as well as the complexity of the underlying biological mechanism has prevented a thorough investigation of epistatic interactions and thus most previous studies have typically considered only a small number of genetic variants at a time. METHODS In this study, we propose a gene network based analysis framework to identify genetic risk factors from a genome-wide association study dataset. We first derive multiple single nucleotide polymorphisms (SNP)-based epistasis networks that consider marginal and epistatic effects by using different information theoretic measures. Each SNP epistasis network is converted into a gene-gene interaction network, and the resulting gene networks are combined as one for downstream analysis. The integrated network is validated on existing knowledgebase of DisGeNET for known gene-disease associations and GeneMANIA for biological function prediction. RESULTS We demonstrated our proposed method on a Korean GWAS dataset, which has genotype information of 440,094 SNPs for 188 cases and 247 controls. The topological properties of the generated networks are examined for scale-freeness, and we further performed various statistical analyses in the Allergy and Asthma Portal (AAP) using the selected genes from our integrated network. CONCLUSIONS Our result reveals that there are several gene modules in the network that are of biological significance and have evidence for controlling susceptibility and being related to the treatment of AERD.
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Affiliation(s)
- Sehee Wang
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea
| | - Hyun-Hwan Jeong
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, 77030, USA.,Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Dokyoon Kim
- Department of Biomedical & Translational Informatics, Geisinger Health System, Danville, PA, 17822, USA.,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Kyubum Wee
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea
| | - Hae-Sim Park
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea
| | - Seung-Hyun Kim
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea. .,Translational Research Laboratory for Inflammatory Disease, Clinical Trial Center, Ajou University Medical Center, Suwon, South Korea.
| | - Kyung-Ah Sohn
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea.
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Lee JU, Chang HS, Lee HJ, Bae DJ, Son JH, Park JS, Choi JS, Hwang HG, Park CS. Association of interleukin-25 levels with development of aspirin induced respiratory diseases. Respir Med 2016; 123:71-78. [PMID: 28137499 DOI: 10.1016/j.rmed.2016.11.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 01/04/2023]
Abstract
BACKGROUND Aspirin-exacerbated respiratory diseases (AERD) are caused by ingestion of non-steroidal anti-inflammatory drugs and are characterized by acute bronchospasms and marked infiltration of eosinophils, the latter being attributable to altered synthesis of cysteinyl leukotrienes (LT) and prostaglandins (PG). Recently, the innate Th2 response is revealed to induce eosinophil infiltration in allergic inflammation, however the role of the innate Th2 response has not been studies in AERD. Thus, we evaluated the relationship between the innate Th2 cytokines including IL-25, thymic stromal lymphopoietin (TSLP) and IL-33 and the development of AERD. METHODS AND MATERIALS Plasma IL-25, IL-33, and TSLP levels were measured before and after aspirin challenge in subjects with AERD (n = 25) and aspirin-tolerant asthma (ATA, n = 25) by enzyme-linked immunosorbent assay (ELISA). Pre and post-aspirin challenge levels of LTC4 and PGD2 were measured using ELISA. RESULTS Basal plasma IL-25 levels were significantly higher in AERD group than in normal controls and in ATA group (p = 0.025 and 0.031, respectively). IL-33 and TSLP levels were comparable in the AERD and ATA groups. After the aspirin challenge, the IL-25 levels were markedly decreased in the ATA group (p = 0.024), while not changed in the AERD group. The post-challenge IL-25 levels of all asthmatic subjects were significantly correlated with aspirin challenge - induced declines in FEV1 (r = 0.357, p = 0.011), but not with basal and post challenge LTC4 and PGD2 levels. CONCLUSIONS IL-25 is associated with bronchospasm after aspirin challenge, possibly via mechanisms other than altered LTC4 and PGD2 production.
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Affiliation(s)
- Jong-Uk Lee
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Republic of Korea
| | - Hun Soo Chang
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Republic of Korea; Genome Research Center, Division of Allergy and Respiratory Medicine, Soonchunhyang University, Bucheon Hospital, Republic of Korea
| | - Hyeon Ju Lee
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Republic of Korea
| | - Da-Jeong Bae
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Republic of Korea
| | - Ji-Hye Son
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Republic of Korea
| | - Jong-Sook Park
- Genome Research Center, Division of Allergy and Respiratory Medicine, Soonchunhyang University, Bucheon Hospital, Republic of Korea
| | - Jae Sung Choi
- Division of Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University, Cheonan Hospital, Republic of Korea
| | - Hun Gyu Hwang
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University, Gumi Hospital, Republic of Korea
| | - Choon-Sik Park
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Republic of Korea; Genome Research Center, Division of Allergy and Respiratory Medicine, Soonchunhyang University, Bucheon Hospital, Republic of Korea.
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13
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Pham DL, Kim JH, Trinh THK, Park HS. What we know about nonsteroidal anti-inflammatory drug hypersensitivity. Korean J Intern Med 2016; 31:417-32. [PMID: 27030979 PMCID: PMC4855107 DOI: 10.3904/kjim.2016.085] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 03/05/2016] [Indexed: 02/07/2023] Open
Abstract
Nonsteroidal anti-inf lammatory drugs (NSAIDs) are widely prescribed for the treatment of inflammatory diseases, but their use is frequently related to hypersensitivity reactions. This review outlines our current knowledge of NSAID hypersensitivity (NHS) with regard to its pathogenic, molecular, and genetic mechanisms, as well as diagnosis and treatment. The presentation of NHS varies from a local (skin and/or airways) reaction to systemic reactions, including anaphylaxis. At the molecular level, NHS reactions can be classified as cross-reactive (mediated by cyclooxygenase inhibition) or selective (specific activation of immunoglobulin E antibodies or T cells). Genetic polymorphisms and epigenetic factors have been shown to be closely associated with NHS, and may be useful as predictive markers. To diagnose NHS, inhalation or oral challenge tests are applied, with the exclusion of any cross-reactive NSAIDs. For patients diagnosed with NHS, absolute avoidance of NSAIDs/aspirin is essential, and pharmacological treatment, including biologics, is often used to control their respiratory and cutaneous symptoms. Finally, desensitization is recommended only for selected patients with NHS. However, further research is required to develop new diagnostic methods and more effective treatments against NHS.
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Affiliation(s)
- Duy Le Pham
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, Korea
| | - Ji-Hye Kim
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, Korea
| | - Tu Hoang Kim Trinh
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, Korea
| | - Hae-Sim Park
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, Korea
- Correspondence to Hae-Sim Park, M.D. Department of Allergy and Clinical Immunology, Ajou University Hospital, 164 World cup-ro, Yeongtong-gu, Suwon 16499, Korea Tel: +82-31-219-5150 Fax: +82-31-219-5154 E-mail:
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14
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Genetic basis of hypersensitivity reactions to nonsteroidal anti-inflammatory drugs. Curr Opin Allergy Clin Immunol 2016; 15:285-93. [PMID: 26110677 DOI: 10.1097/aci.0000000000000178] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW NSAIDs are the main triggers of hypersensitivity reactions to drugs. However, the full genetic and molecular basis of these reactions has yet to be uncovered. In this article, we have summarized research from recent years into the effects of genetic variants on the different clinical entities induced by NSAID hypersensitivity, focusing on prostaglandin and leukotriene-related genes as well as others beyond the arachidonic acid pathway. RECENT FINDINGS We introduce recent contributions of high-throughput approaches including genome-wide association studies as well as available information from epigenetics and next-generation sequencing. Finally, we give our thoughts on future directions in this field, including the scope for bioinformatics and systems biology and the need for clear patient phenotyping. SUMMARY The full genetic and molecular basis of clinical entities induced by NSAIDs hypersensitivity has yet to be uncovered, and despite commendable efforts over recent years, no clinically proven genetic markers currently exist for these disorders. It is clear that we will continue to find more about these reactions in the coming years, concurrently with improvements in technology and experimental techniques, and a precise definition of different phenotypes.
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Sommer DD, Rotenberg BW, Sowerby LJ, Lee JM, Janjua A, Witterick IJ, Monteiro E, Gupta MK, Au M, Nayan S. A novel treatment adjunct for aspirin exacerbated respiratory disease: the low-salicylate diet: a multicenter randomized control crossover trial. Int Forum Allergy Rhinol 2016; 6:385-91. [DOI: 10.1002/alr.21678] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 09/25/2015] [Accepted: 10/09/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Doron D. Sommer
- Division of Otolaryngology-Head and Neck Surgery; Department of Surgery McMaster University; Hamilton Canada
| | - Brian W. Rotenberg
- Department of Otolaryngology-Head and Neck Surgery; Western University; London Canada
| | - Leigh J. Sowerby
- Department of Otolaryngology-Head and Neck Surgery; Western University; London Canada
| | - John M. Lee
- Department of Otolaryngology-Head and Neck Surgery; University of Toronto; Toronto Canada
| | - Arif Janjua
- Division of Otolaryngology-Head and Neck Surgery; University of British Columbia; Vancouver Canada
| | - Ian J. Witterick
- Department of Otolaryngology-Head and Neck Surgery; University of Toronto; Toronto Canada
| | - Eric Monteiro
- Department of Otolaryngology-Head and Neck Surgery; University of Toronto; Toronto Canada
| | - Michael K. Gupta
- Division of Otolaryngology-Head and Neck Surgery; Department of Surgery McMaster University; Hamilton Canada
| | - Michael Au
- Department of Otolaryngology-Head and Neck Surgery; University of Toronto; Toronto Canada
| | - Smriti Nayan
- Division of Otolaryngology-Head and Neck Surgery; Department of Surgery McMaster University; Hamilton Canada
- Department of Otolaryngology-Head and Neck Surgery; Cambridge Memorial Hospital; Cambridge Canada
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