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Giese APJ, Ali S, Isaiah A, Aziz I, Riazuddin S, Ahmed ZM. Genomics of Otitis Media (OM): Molecular Genetics Approaches to Characterize Disease Pathophysiology. Front Genet 2020; 11:313. [PMID: 32391049 PMCID: PMC7191070 DOI: 10.3389/fgene.2020.00313] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 03/16/2020] [Indexed: 12/21/2022] Open
Abstract
Otitis media (OM) is an infective and inflammatory disorder known to be a major cause of hearing impairment across all age groups. Both acute and chronic OM result in substantial healthcare utilization related to antibiotic prescription and surgical procedures necessary for its management. Although several studies provided evidence of genetics playing a significant role in the susceptibility to OM, we had limited knowledge about the genes associated with OM until recently. Here we have summarized the known genetic factors that confer susceptibility to various forms of OM in mice and in humans and their genetic load, along with associated cellular signaling pathways. Spotlighted in this review are fucosyltransferase (FUT) enzymes, which have been implicated in the pathogenesis of OM. A comprehensive understanding of the functions of OM-associated genes may provide potential opportunities for its diagnosis and treatment.
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Affiliation(s)
- Arnaud P J Giese
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Saadat Ali
- The Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Amal Isaiah
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Ishrat Aziz
- Department of Biotechnology, Virtual University of Pakistan, Lahore, Pakistan
| | - Saima Riazuddin
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Zubair M Ahmed
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
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Mittal R, Sanchez-Luege SV, Wagner SM, Yan D, Liu XZ. Recent Perspectives on Gene-Microbe Interactions Determining Predisposition to Otitis Media. Front Genet 2019; 10:1230. [PMID: 31850076 PMCID: PMC6901973 DOI: 10.3389/fgene.2019.01230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/06/2019] [Indexed: 01/15/2023] Open
Abstract
A comprehensive understanding about the pathogenesis of otitis media (OM), one of the most common pediatric diseases, has the potential to alleviate a substantial disease burden across the globe. Advancements in genetic and bioinformatic detection methods, as well as a growing interest in the microbiome, has enhanced the capability of researchers to investigate the interplay between host genes, host microbiome, invading bacteria, and resulting OM susceptibility. Early studies deciphering the role of genetics in OM susceptibility assessed the heritability of the phenotype in twin and triplet studies, followed by linkage studies, candidate gene approaches, and genome-wide association studies that have helped in the identification of specific loci. With the advancements in techniques, various chromosomal regions and genes such as FBXO11, TGIF1, FUT2, FNDC1, and others have been implicated in predisposition to OM, yet questions still remain as to whether these implicated genes truly play a causative role in OM and to what extent. Meanwhile, 16S ribosomal RNA (rRNA) sequencing, microbial quantitative trait loci (mbQTL), and microbial genome-wide association studies (mGWAS) have mapped the microbiome of upper airways sites and therefore helped in enabling a more detailed study of interactions between host polymorphisms and host microbiome composition. Variants of specific genes conferring increased OM susceptibility, such as A2ML1, have also been shown to influence the microbial composition of the outer and middle ear in patients with OM, suggesting their role as mediators of disease. These interactions appear to impact the colonization of known otopathogens (Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis), as well as Neisseria, Gemella, Porphyromonas, Alloprevotella, and Fusobacterium populations that have also been implicated in OM pathogenesis. Meanwhile, studies demonstrating an increased abundance of Dolosigranulum and Corynebacterium in healthy patients compared to those with OM suggest a protective role for these bacteria, thereby introducing potential avenues for future probiotic treatment. Incorporating insights from these genetic, microbiome, and host-pathogen studies will allow for a more robust, comprehensive understanding of OM pathogenesis that can ultimately facilitate in the development of exciting new treatment modalities.
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Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Sebastian V Sanchez-Luege
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Shannon M Wagner
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States.,Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States.,Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States
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Homøe P, Kværner K, Casey JR, Damoiseaux RAMJ, van Dongen TMA, Gunasekera H, Jensen RG, Kvestad E, Morris PS, Weinreich HM. Panel 1: Epidemiology and Diagnosis. Otolaryngol Head Neck Surg 2017; 156:S1-S21. [DOI: 10.1177/0194599816643510] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Objective To create a literature review between 2011 and June 1, 2015, on advances in otitis media (OM) epidemiology and diagnosis (including relevant audiology studies). Data Sources Electronic search engines (PubMed, EMBASE, and Cochrane Library) with a predefined search strategy. Review Methods Articles with appropriate epidemiologic methodology for OM, including acute mastoiditis and eustachian tube dysfunction. Items included OM worldwide and in high-risk populations, OM-related hearing loss, news in OM diagnostics, prenatal risk factors and comorbidities, postnatal risk factors, genetics, microbiological epidemiology, guidelines, and quality of life. Conclusions Diagnostic evidence and genetic studies are increasing; guidelines are introduced worldwide; and there is evidence of benefit of pneumococcal conjugate vaccines. New risk factors and comordities are identified in the study period, and quality of life is affected in children and their families. Implications for Practice Chronic suppurative OM occurs worldwide and contributes to lifelong hearing loss. Uniform definitions are still lacking and should be provided. An association between HIV and chronic suppurative OM has been found. Tympanometry is recommended for diagnosis, with or without pneumatic otoscopy. Video otoscopy, algorithms, and validated questionnaires may assist clinicians. Childhood obesity is associated with OM. Heritability accounts for 20% to 50% of OM diagnoses. OM-prone children seem to produce weaker immunologic responses to pneumococcal conjugate vaccines. Clinicians tend to individualize treatment without adhering to guidelines.
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Affiliation(s)
- Preben Homøe
- Department of Otorhinolaryngology and Maxillofacial Surgery, Zealand University Hospital, University of Copenhagen, Køge, Denmark
| | - Kari Kværner
- Centre for Connected Care, Oslo University Hospital, Oslo, Norway
- BI Norwegian Business School, Oslo, Norway
| | | | - Roger A. M. J. Damoiseaux
- Julius Centre for Health Sciences and Primary Care, University Medical Centre, Utrecht, The Netherlands
| | - Thijs M. A. van Dongen
- Julius Centre for Health Sciences and Primary Care, University Medical Centre, Utrecht, The Netherlands
| | - Hasantha Gunasekera
- Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Ramon G. Jensen
- Department of Otorhinolaryngology and Maxillofacial Surgery, Zealand University Hospital, University of Copenhagen, Køge, Denmark
| | - Ellen Kvestad
- ENT Department, Oslo University Hospital and Division of Mental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Peter S. Morris
- Department of Paediatrics, Royal Darwin Hospital and Menzies School of Health Research, Darwin, Australia
| | - Heather M. Weinreich
- Department of Otolaryngology–Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, USA
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Lin J, Hafrén H, Kerschner J, Jian-Dong L, Brown S, Zheng QY, Preciado D, Nakamura Y, Huang Q, Zhang Y. Panel 3: Genetics and Precision Medicine of Otitis Media. Otolaryngol Head Neck Surg 2017; 156:S41-S50. [PMID: 28372532 PMCID: PMC6211190 DOI: 10.1177/0194599816685559] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 12/01/2016] [Indexed: 12/31/2022]
Abstract
Objective The objective is to perform a comprehensive review of the literature up to 2015 on the genetics and precision medicine relevant to otitis media. Data Sources PubMed database of the National Library of Medicine. Review Methods Two subpanels were formed comprising experts in the genetics and precision medicine of otitis media. Each of the panels reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The entire panel met at the 18th International Symposium on Recent Advances in Otitis Media in June 2015 and discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members. Conclusion Many genes relevant to otitis media have been identified in the last 4 years in advancing our knowledge regarding the predisposition of the middle ear mucosa to commensals and pathogens. Advances include mutant animal models and clinical studies. Many signaling pathways are involved in the predisposition of otitis media. Implications for Practice New knowledge on the genetic background relevant to otitis media forms a basis of novel potential interventions, including potential new ways to treat otitis media.
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Affiliation(s)
- Jizhen Lin
- Department of Otolaryngology–Head and Neck Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hena Hafrén
- Departments of Otorhinolaryngology–Head and Neck Surgery, Helsinki University Hospital, Helsinki, Finland
| | - Joseph Kerschner
- Department of Otorhinolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Li Jian-Dong
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | - Steve Brown
- Medical Research Council Harwell Institute, Oxfordshire, UK
| | - Qing Y. Zheng
- Department of Otolaryngology–Head and Neck Surgery, Case Western University, Cleveland, Ohio, USA
| | - Diego Preciado
- Shiekh Zayed Institute for Pediatric Surgical Innovation, Pediatric Otolaryngology, Children’s National Health System, Washington, DC, USA
| | | | - Qiuhong Huang
- Department of Otolaryngology, Sun Yat-sen University, Guangzhou, China
| | - Yan Zhang
- Department of Otolaryngology, Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
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Engelken J, Espadas G, Mancuso FM, Bonet N, Scherr AL, Jímenez-Álvarez V, Codina-Solà M, Medina-Stacey D, Spataro N, Stoneking M, Calafell F, Sabidó E, Bosch E. Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver. Mol Biol Evol 2016; 33:738-54. [PMID: 26582562 PMCID: PMC4760079 DOI: 10.1093/molbev/msv267] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Essential trace elements possess vital functions at molecular, cellular, and physiological levels in health and disease, and they are tightly regulated in the human body. In order to assess variability and potential adaptive evolution of trace element homeostasis, we quantified 18 trace elements in 150 liver samples, together with the expression levels of 90 genes and abundances of 40 proteins involved in their homeostasis. Additionally, we genotyped 169 single nucleotide polymorphism (SNPs) in the same sample set. We detected significant associations for 8 protein quantitative trait loci (pQTL), 10 expression quantitative trait loci (eQTLs), and 15 micronutrient quantitative trait loci (nutriQTL). Six of these exceeded the false discovery rate cutoff and were related to essential trace elements: 1) one pQTL for GPX2 (rs10133290); 2) two previously described eQTLs for HFE (rs12346) and SELO (rs4838862) expression; and 3) three nutriQTLs: The pathogenic C282Y mutation at HFE affecting iron (rs1800562), and two SNPs within several clustered metallothionein genes determining selenium concentration (rs1811322 and rs904773). Within the complete set of significant QTLs (which involved 30 SNPs and 20 gene regions), we identified 12 SNPs with extreme patterns of population differentiation (FST values in the top 5% percentile in at least one HapMap population pair) and significant evidence for selective sweeps involving QTLs at GPX1, SELENBP1, GPX3, SLC30A9, and SLC39A8. Overall, this detailed study of various molecular phenotypes illustrates the role of regulatory variants in explaining differences in trace element homeostasis among populations and in the human adaptive response to environmental pressures related to micronutrients.
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Affiliation(s)
- Johannes Engelken
- †These authors contributed equally to this work. ‡Deceased October 23, 2015. Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Guadalupe Espadas
- †These authors contributed equally to this work. Proteomics Unit, Center of Genomics Regulation, Barcelona, Spain Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesco M Mancuso
- Proteomics Unit, Center of Genomics Regulation, Barcelona, Spain Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuria Bonet
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Spain
| | - Anna-Lena Scherr
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Victoria Jímenez-Álvarez
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Marta Codina-Solà
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniel Medina-Stacey
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nino Spataro
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Francesc Calafell
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Center of Genomics Regulation, Barcelona, Spain Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Bosch
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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Esposito S, Marchisio P, Orenti A, Spena S, Bianchini S, Nazzari E, Rosazza C, Zampiero A, Biganzoli E, Principi N. Genetic Polymorphisms of Functional Candidate Genes and Recurrent Acute Otitis Media With or Without Tympanic Membrane Perforation. Medicine (Baltimore) 2015; 94:e1860. [PMID: 26496338 PMCID: PMC4620788 DOI: 10.1097/md.0000000000001860] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Evaluation of the genetic contribution to the development of recurrent acute otitis media (rAOM) remains challenging. This study aimed to evaluate the potential association between single nucleotide polymorphisms (SNPs) in selected genes and rAOM and to analyze whether genetic variations might predispose to the development of complicated recurrent cases, such as those with tympanic membrane perforation (TMP).A total of 33 candidate genes and 47 SNPs were genotyped in 200 children with rAOM (116 with a history of TMP) and in 200 healthy controls.INFγ rs 12369470CT was significantly less common in the children with rAOM than in healthy controls (odds ratio [OR] 0.5, 95% confidence interval [CI] 0.25-1, P = 0.04). Although not significant, interleukin (IL)-1β rs 1143627G and toll-like receptor (TLR)-4 rs2737191AG were less frequently detected in the children with rAOM than in controls. The opposite was true for IL-8 rs2227306CT, which was found more frequently in the children with rAOM than in healthy controls. The IL-10 rs1800896TC SNP and the IL-1α rs6746923A and AG SNPs were significantly more and less common, respectively, among children without a history of TMP than among those who suffered from this complication (OR 2.17, 95% CI 1.09-4.41, P = 0.02, and OR 0.42, 95% CI 0.21-0.84, P = 0.01).This study is the first report suggesting an association between variants in genes encoding for factors of innate or adaptive immunity and the occurrence of rAOM with or without TMP, which confirms the role of genetics in conditioning susceptibility to AOM.
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Affiliation(s)
- Susanna Esposito
- From the Pediatric High Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy (SE, PM, SS, SB, EN, CR, AZ, NP); and Unit of Medical Statistics, Biometry and Bioinformatics "G.A. Maccacaro", Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy (AO, EB)
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