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Sumalde AAM, Yang IV, Yarza TKL, Tobias-Grasso CAM, Tantoco MLC, Davidson E, Chan AL, Azamian MS, Cruz TLG, Lalani SR, Reyes-Quintos MRT, Cutiongco-de la Paz EM, Santos-Cortez RLP, Chiong CM. Lack of Methylation Changes in GJB2 and RB1 Non-coding Regions of Cochlear Implant Patients with Sensorineural Hearing Loss. Acta Med Philipp 2023; 57:116-120. [PMID: 37990697 PMCID: PMC10662870 DOI: 10.47895/amp.v57i9.5200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Objective Recent advances in epigenetic studies continue to reveal novel mechanisms of gene regulation and control, however little is known on the role of epigenetics in sensorineural hearing loss (SNHL) in humans. We aimed to investigate the methylation patterns of two regions, one in RB1 and another in GJB2 in Filipino patients with SNHL compared to hearing control individuals. Methods We investigated an RB1 promoter region that was previously identified as differentially methylated in children with SNHL and lead exposure. Additionally, we investigated a sequence in an enhancer-like region within GJB2 that contains four CpGs in close proximity. Bisulfite conversion was performed on salivary DNA samples from 15 children with SNHL and 45 unrelated ethnically-matched individuals. We then performed methylation-specific real-time PCR analysis (qMSP) using TaqMan® probes to determine percentage methylation of the two regions. Results Using qMSP, both our cases and controls had zero methylation at the targeted GJB2 and RB1 regions. Conclusion Our study showed no changes in methylation at the selected CpG regions in RB1 and GJB2 in the two comparison groups with or without SNHL. This may be due to a lack of environmental exposures to these target regions. Other epigenetic marks may be present around these regions as well as those of other HL-associated genes.
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Affiliation(s)
- Angelo Augusto M. Sumalde
- College of Medicine, University of the Philippines Manila, Manila, Philippines
- Department of Otolaryngology – Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), Aurora, Colorado, USA
- Department of Otolaryngology-Head and Neck Surgery, Philippine General Hospital, University of the Philippines Manila, Manila, Philippines
| | - Ivana V. Yang
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), Aurora, Colorado, USA
| | - Talitha Karisse L. Yarza
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | | | - Ma. Leah C. Tantoco
- Department of Otolaryngology-Head and Neck Surgery, Philippine General Hospital, University of the Philippines Manila, Manila, Philippines
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Elizabeth Davidson
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), Aurora, Colorado, USA
| | - Abner L. Chan
- College of Medicine, University of the Philippines Manila, Manila, Philippines
- Department of Otolaryngology-Head and Neck Surgery, Philippine General Hospital, University of the Philippines Manila, Manila, Philippines
| | - Mahshid S. Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Teresa Luisa G. Cruz
- College of Medicine, University of the Philippines Manila, Manila, Philippines
- Department of Otolaryngology-Head and Neck Surgery, Philippine General Hospital, University of the Philippines Manila, Manila, Philippines
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Maria Rina T. Reyes-Quintos
- Department of Otolaryngology-Head and Neck Surgery, Philippine General Hospital, University of the Philippines Manila, Manila, Philippines
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Eva Maria Cutiongco-de la Paz
- National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Philippine Genome Center, UP Diliman Campus, Quezon City, Philippines
| | - Regie Lyn P. Santos-Cortez
- Department of Otolaryngology – Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), Aurora, Colorado, USA
| | - Charlotte M. Chiong
- College of Medicine, University of the Philippines Manila, Manila, Philippines
- Department of Otolaryngology-Head and Neck Surgery, Philippine General Hospital, University of the Philippines Manila, Manila, Philippines
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
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2
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Santos-Cortez RLP, Ong KMC, Carlos-Hiceta A, Tantoco MLC, Yarza TKL, San Agustin ML, Pedro M, Cruz TLG, Cutiongco-de la Paz EM, Abes GT, Llanes EGD, Chan AL, Chiong CM, Reyes-Quintos MRT. Audiologic Measures in an Indigenous Community with A2ML1- and FUT2-Related Otitis Media. Genet Test Mol Biomarkers 2023; 27:12-17. [PMID: 36719978 PMCID: PMC9902046 DOI: 10.1089/gtmb.2022.0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Background: Many indigenous peoples are at elevated risk for otitis media, however there is limited information on hearing loss due to OM in these communities. An Indigenous Filipino community that has previously been described with an elevated prevalence of OM that is due to rare A2ML1 variants and a common FUT2 variant underwent additional phenological testing. In this study, we describe the audiologic profiles in A2ML1- and FUT2-related otitis media and the validity of otoscopy and genotyping for A2ML1 and FUT2 variants in screening for otitis media and hearing loss. Method: We analyzed A2ML1 and FUT2 genotypes together with demographic, otologic and audiologic data from tympanometry and hearing level assessments of 109 indigenous individuals. Results: We confirmed previous findings of a spectrum of nonsyndromic otitis media as associated with A2ML1 variants. A2ML1 and FUT2 variants were associated with high-frequency hearing loss at 4000 Hz. As expected, young age was associated with flat tympanograms, and eardrum perforations due to chronic otitis media were associated with severe-to-profound hearing loss across frequencies. Adding A2ML1 or FUT2 genotypes improved the validity of otoscopy as a screening test to rule out moderate-to-profound hearing loss. Conclusion: Continued multi-disciplinary management and audiologic follow-up using tympanometry and screening audiometry are needed to document and treat otitis media and prevent permanent hearing loss in the indigenous community.
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Affiliation(s)
- Regie Lyn P. Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Center for Children's Surgery, Children's Hospital Colorado, Aurora, Colorado, USA
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Kimberly Mae C. Ong
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine–Philippine General Hospital, Manila, Philippines
| | - Angeli Carlos-Hiceta
- Department of Otorhinolaryngology, University of the Philippines College of Medicine–Philippine General Hospital, Manila, Philippines
| | - Ma. Leah C. Tantoco
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine–Philippine General Hospital, Manila, Philippines
| | - Talitha Karisse L. Yarza
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Ma. Luz San Agustin
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine–Philippine General Hospital, Manila, Philippines
| | - Melquiadesa Pedro
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Teresa Luisa G. Cruz
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine–Philippine General Hospital, Manila, Philippines
| | - Eva Maria Cutiongco-de la Paz
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Philippine Genome Center, University of the Philippines Diliman, Quezon City, Philippines
| | - Generoso T. Abes
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine–Philippine General Hospital, Manila, Philippines
| | - Erasmo Gonzalo d.V. Llanes
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine–Philippine General Hospital, Manila, Philippines
| | - Abner L. Chan
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine–Philippine General Hospital, Manila, Philippines
| | - Charlotte M. Chiong
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine–Philippine General Hospital, Manila, Philippines
| | - Maria Rina T. Reyes-Quintos
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine–Philippine General Hospital, Manila, Philippines
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3
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Frank DN, Giese APJ, Hafren L, Bootpetch TC, Yarza TKL, Steritz MJ, Pedro M, Labra PJ, Daly KA, Tantoco MLC, Szeremeta W, Reyes-Quintos MRT, Ahankoob N, Llanes EGDV, Pine HS, Yousaf S, Ir D, Einarsdottir E, de la Cruz RAR, Lee NR, Nonato RMA, Robertson CE, Ong KMC, Magno JPM, Chiong ANE, Espiritu-Chiong MC, San Agustin ML, Cruz TLG, Abes GT, Bamshad MJ, Cutiongco-de la Paz EM, Kere J, Nickerson DA, Mohlke KL, Riazuddin S, Chan A, Mattila PS, Leal SM, Ryan AF, Ahmed ZM, Chonmaitree T, Sale MM, Chiong CM, Santos-Cortez RLP. Otitis media susceptibility and shifts in the head and neck microbiome due to SPINK5 variants. J Med Genet 2020; 58:442-452. [PMID: 32709676 DOI: 10.1136/jmedgenet-2020-106844] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/06/2020] [Accepted: 05/24/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Otitis media (OM) susceptibility has significant heritability; however, the role of rare variants in OM is mostly unknown. Our goal is to identify novel rare variants that confer OM susceptibility. METHODS We performed exome and Sanger sequencing of >1000 DNA samples from 551 multiethnic families with OM and unrelated individuals, RNA-sequencing and microbiome sequencing and analyses of swabs from the outer ear, middle ear, nasopharynx and oral cavity. We also examined protein localisation and gene expression in infected and healthy middle ear tissues. RESULTS A large, intermarried pedigree that includes 81 OM-affected and 53 unaffected individuals cosegregates two known rare A2ML1 variants, a common FUT2 variant and a rare, novel pathogenic variant c.1682A>G (p.Glu561Gly) within SPINK5 (LOD=4.09). Carriage of the SPINK5 missense variant resulted in increased relative abundance of Microbacteriaceae in the middle ear, along with occurrence of Microbacteriaceae in the outer ear and oral cavity but not the nasopharynx. Eight additional novel SPINK5 variants were identified in 12 families and individuals with OM. A role for SPINK5 in OM susceptibility is further supported by lower RNA counts in variant carriers, strong SPINK5 localisation in outer ear skin, faint localisation to middle ear mucosa and eardrum and increased SPINK5 expression in human cholesteatoma. CONCLUSION SPINK5 variants confer susceptibility to non-syndromic OM. These variants potentially contribute to middle ear pathology through breakdown of mucosal and epithelial barriers, immunodeficiency such as poor vaccination response, alteration of head and neck microbiota and facilitation of entry of opportunistic pathogens into the middle ear.
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Affiliation(s)
- Daniel N Frank
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Arnaud P J Giese
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Maryland, Baltimore, Maryland, USA
| | - Lena Hafren
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tori C Bootpetch
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Talitha Karisse L Yarza
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Newborn Hearing Screening Reference Center, University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Matthew J Steritz
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Melquiadesa Pedro
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Patrick John Labra
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Kathleen A Daly
- Department of Otolaryngology, Head and Neck Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ma Leah C Tantoco
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Newborn Hearing Screening Reference Center, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Wasyl Szeremeta
- Department of Otolaryngology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Maria Rina T Reyes-Quintos
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Newborn Hearing Screening Reference Center, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines.,National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Niaz Ahankoob
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Erasmo Gonzalo D V Llanes
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Newborn Hearing Screening Reference Center, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Harold S Pine
- Department of Otolaryngology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Sairah Yousaf
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Maryland, Baltimore, Maryland, USA
| | - Diana Ir
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | | | - Nanette R Lee
- Department of Anthropology, Sociology and History, University of San Carlos, Cebu City, Philippines
| | | | - Charles E Robertson
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kimberly Mae C Ong
- Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Jose Pedrito M Magno
- Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Alessandra Nadine E Chiong
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | | | - Maria Luz San Agustin
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Teresa Luisa G Cruz
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Generoso T Abes
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Eva Maria Cutiongco-de la Paz
- National Institutes of Health, University of the Philippines Manila, Manila, Philippines.,Philippine Genome Center, University of the Philippines Diliman, Quezon City, Philippines
| | - Juha Kere
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Saima Riazuddin
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Maryland, Baltimore, Maryland, USA
| | - Abner Chan
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Petri S Mattila
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, New York, USA
| | - Allen F Ryan
- Division of Otolaryngology, Department of Surgery, University of California San Diego School of Medicine and Veterans Affairs Medical Center, La Jolla, California, USA
| | - Zubair M Ahmed
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Maryland, Baltimore, Maryland, USA
| | - Tasnee Chonmaitree
- Division of Infectious Diseases, Department of Pediatrics, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Michele M Sale
- Center for Public Health Genomics, School of Medicine, Department of Biochemistry and Molecular Genetics, and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Charlotte M Chiong
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Newborn Hearing Screening Reference Center, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Regie Lyn P Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA .,Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Center for Children's Surgery, Children's Hospital Colorado, Aurora, Colorado, USA
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4
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Larson ED, Magno JPM, Steritz MJ, Llanes EGDV, Cardwell J, Pedro M, Roberts TB, Einarsdottir E, Rosanes RAQ, Greenlee C, Santos RAP, Yousaf A, Streubel SO, Santos ATR, Ruiz AG, Lagrana-Villagracia SM, Ray D, Yarza TKL, Scholes MA, Anderson CB, Acharya A, Gubbels SP, Bamshad MJ, Cass SP, Lee NR, Shaikh RS, Nickerson DA, Mohlke KL, Prager JD, Cruz TLG, Yoon PJ, Abes GT, Schwartz DA, Chan AL, Wine TM, Cutiongco-de la Paz EM, Friedman N, Kechris K, Kere J, Leal SM, Yang IV, Patel JA, Tantoco MLC, Riazuddin S, Chan KH, Mattila PS, Reyes-Quintos MRT, Ahmed ZM, Jenkins HA, Chonmaitree T, Hafrén L, Chiong CM, Santos-Cortez RLP. A2ML1 and otitis media: novel variants, differential expression, and relevant pathways. Hum Mutat 2019; 40:1156-1171. [PMID: 31009165 DOI: 10.1002/humu.23769] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/26/2019] [Accepted: 04/18/2019] [Indexed: 12/16/2022]
Abstract
A genetic basis for otitis media is established, however, the role of rare variants in disease etiology is largely unknown. Previously a duplication variant within A2ML1 was identified as a significant risk factor for otitis media in an indigenous Filipino population and in US children. In this report exome and Sanger sequencing was performed using DNA samples from the indigenous Filipino population, Filipino cochlear implantees, US probands, Finnish, and Pakistani families with otitis media. Sixteen novel, damaging A2ML1 variants identified in otitis media patients were rare or low-frequency in population-matched controls. In the indigenous population, both gingivitis and A2ML1 variants including the known duplication variant and the novel splice variant c.4061 + 1 G>C were independently associated with otitis media. Sequencing of salivary RNA samples from indigenous Filipinos demonstrated lower A2ML1 expression according to the carriage of A2ML1 variants. Sequencing of additional salivary RNA samples from US patients with otitis media revealed differentially expressed genes that are highly correlated with A2ML1 expression levels. In particular, RND3 is upregulated in both A2ML1 variant carriers and high-A2ML1 expressors. These findings support a role for A2ML1 in keratinocyte differentiation within the middle ear as part of otitis media pathology and the potential application of ROCK inhibition in otitis media.
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Affiliation(s)
- Eric D Larson
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado
| | - Jose Pedrito M Magno
- Department of Otorhinolaryngology, University of the Philippines Manila College of Medicine - Philippine General Hospital, Manila, Philippines
| | - Matthew J Steritz
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado
| | - Erasmo Gonzalo D V Llanes
- Department of Otorhinolaryngology, University of the Philippines Manila College of Medicine - Philippine General Hospital, Manila, Philippines.,Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Jonathan Cardwell
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Melquiadesa Pedro
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Tori Bootpetch Roberts
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado
| | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Rose Anne Q Rosanes
- Department of Community Dentistry, College of Dentistry, University of the Philippines Manila, Manila, Philippines
| | - Christopher Greenlee
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado
| | | | - Ayesha Yousaf
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Sven-Olrik Streubel
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado
| | | | - Amanda G Ruiz
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado
| | - Sheryl Mae Lagrana-Villagracia
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Dylan Ray
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado
| | - Talitha Karisse L Yarza
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Newborn Hearing Screening Reference Center, University of the Philippines Manila - National Institutes of Health (NIH), Manila, Philippines
| | - Melissa A Scholes
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado
| | - Catherine B Anderson
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado
| | - Anushree Acharya
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Samuel P Gubbels
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Stephen P Cass
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado
| | - Nanette R Lee
- USC-Office of Population Studies Foundation, Inc. and Department of Anthropology, Sociology and History, University of San Carlos, Cebu, Philippines
| | - Rehan S Shaikh
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Jeremy D Prager
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado
| | - Teresa Luisa G Cruz
- Department of Otorhinolaryngology, University of the Philippines Manila College of Medicine - Philippine General Hospital, Manila, Philippines.,Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Patricia J Yoon
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado
| | - Generoso T Abes
- Department of Otorhinolaryngology, University of the Philippines Manila College of Medicine - Philippine General Hospital, Manila, Philippines.,Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - David A Schwartz
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Abner L Chan
- Department of Otorhinolaryngology, University of the Philippines Manila College of Medicine - Philippine General Hospital, Manila, Philippines.,Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Todd M Wine
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado
| | - Eva Maria Cutiongco-de la Paz
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines.,University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Norman Friedman
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado
| | - Katerina Kechris
- Department of Biostatistics and Bioinformatics, Colorado School of Public Health, Aurora, Colorado
| | - Juha Kere
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ivana V Yang
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Janak A Patel
- Division of Infectious Diseases, Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas
| | - Ma Leah C Tantoco
- Department of Otorhinolaryngology, University of the Philippines Manila College of Medicine - Philippine General Hospital, Manila, Philippines.,Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Saima Riazuddin
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Kenny H Chan
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado
| | - Petri S Mattila
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Maria Rina T Reyes-Quintos
- Department of Otorhinolaryngology, University of the Philippines Manila College of Medicine - Philippine General Hospital, Manila, Philippines.,Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Newborn Hearing Screening Reference Center, University of the Philippines Manila - National Institutes of Health (NIH), Manila, Philippines.,University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Zubair M Ahmed
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Herman A Jenkins
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado
| | - Tasnee Chonmaitree
- Division of Infectious Diseases, Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas
| | - Lena Hafrén
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Charlotte M Chiong
- Department of Otorhinolaryngology, University of the Philippines Manila College of Medicine - Philippine General Hospital, Manila, Philippines.,Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Newborn Hearing Screening Reference Center, University of the Philippines Manila - National Institutes of Health (NIH), Manila, Philippines
| | - Regie Lyn P Santos-Cortez
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado.,Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Center for Children's Surgery, Children's Hospital Colorado, Aurora, Colorado
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5
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Santos-Cortez RLP, Chiong CM, Frank DN, Ryan AF, Giese APJ, Bootpetch Roberts T, Daly KA, Steritz MJ, Szeremeta W, Pedro M, Pine H, Yarza TKL, Scholes MA, Llanes EGDV, Yousaf S, Friedman N, Tantoco MLC, Wine TM, Labra PJ, Benoit J, Ruiz AG, de la Cruz RAR, Greenlee C, Yousaf A, Cardwell J, Nonato RMA, Ray D, Ong KMC, So E, Robertson CE, Dinwiddie J, Lagrana-Villagracia SM, Gubbels SP, Shaikh RS, Cass SP, Einarsdottir E, Lee NR, Schwartz DA, Gloria-Cruz TLI, Bamshad MJ, Yang IV, Kere J, Abes GT, Prager JD, Riazuddin S, Chan AL, Yoon PJ, Nickerson DA, Cutiongco-de la Paz EM, Streubel SO, Reyes-Quintos MRT, Jenkins HA, Mattila P, Chan KH, Mohlke KL, Leal SM, Hafrén L, Chonmaitree T, Sale MM, Ahmed ZM. FUT2 Variants Confer Susceptibility to Familial Otitis Media. Am J Hum Genet 2018; 103:679-690. [PMID: 30401457 PMCID: PMC6217759 DOI: 10.1016/j.ajhg.2018.09.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/19/2018] [Indexed: 01/30/2023] Open
Abstract
Non-secretor status due to homozygosity for the common FUT2 variant c.461G>A (p.Trp154∗) is associated with either risk for autoimmune diseases or protection against viral diarrhea and HIV. We determined the role of FUT2 in otitis media susceptibility by obtaining DNA samples from 609 multi-ethnic families and simplex case subjects with otitis media. Exome and Sanger sequencing, linkage analysis, and Fisher exact and transmission disequilibrium tests (TDT) were performed. The common FUT2 c.604C>T (p.Arg202∗) variant co-segregates with otitis media in a Filipino pedigree (LOD = 4.0). Additionally, a rare variant, c.412C>T (p.Arg138Cys), is associated with recurrent/chronic otitis media in European-American children (p = 1.2 × 10-5) and US trios (TDT p = 0.01). The c.461G>A (p.Trp154∗) variant was also over-transmitted in US trios (TDT p = 0.01) and was associated with shifts in middle ear microbiota composition (PERMANOVA p < 10-7) and increased biodiversity. When all missense and nonsense variants identified in multi-ethnic US trios with CADD > 20 were combined, FUT2 variants were over-transmitted in trios (TDT p = 0.001). Fut2 is transiently upregulated in mouse middle ear after inoculation with non-typeable Haemophilus influenzae. Four FUT2 variants-namely p.Ala104Val, p.Arg138Cys, p.Trp154∗, and p.Arg202∗-reduced A antigen in mutant-transfected COS-7 cells, while the nonsense variants also reduced FUT2 protein levels. Common and rare FUT2 variants confer susceptibility to otitis media, likely by modifying the middle ear microbiome through regulation of A antigen levels in epithelial cells. Our families demonstrate marked intra-familial genetic heterogeneity, suggesting that multiple combinations of common and rare variants plus environmental factors influence the individual otitis media phenotype as a complex trait.
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Affiliation(s)
- Regie Lyn P Santos-Cortez
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Center for Children's Surgery, Children's Hospital Colorado (CHCO), Aurora, CO 80045, USA; Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines.
| | - Charlotte M Chiong
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; National Hearing Screening Reference Center, UP Manila-NIH, Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Daniel N Frank
- Division of Infectious Diseases, Department of Medicine, CUSOM, Aurora, CO 80045, USA
| | - Allen F Ryan
- Division of Otolaryngology, Department of Surgery, University of California San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Arnaud P J Giese
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Tori Bootpetch Roberts
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA
| | - Kathleen A Daly
- Department of Otolaryngology, Head and Neck Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew J Steritz
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA
| | - Wasyl Szeremeta
- Department of Otolaryngology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Melquiadesa Pedro
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines
| | - Harold Pine
- Department of Otolaryngology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Talitha Karisse L Yarza
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; National Hearing Screening Reference Center, UP Manila-NIH, Manila 1000, Philippines
| | - Melissa A Scholes
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Erasmo Gonzalo D V Llanes
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Saira Yousaf
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Norman Friedman
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Ma Leah C Tantoco
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Todd M Wine
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Patrick John Labra
- Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Jeanne Benoit
- Division of Infectious Diseases, Department of Medicine, CUSOM, Aurora, CO 80045, USA
| | - Amanda G Ruiz
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Rhodieleen Anne R de la Cruz
- Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Christopher Greenlee
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Ayesha Yousaf
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | | | - Rachelle Marie A Nonato
- Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Dylan Ray
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA
| | - Kimberly Mae C Ong
- Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Edward So
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Charles E Robertson
- Division of Infectious Diseases, Department of Medicine, CUSOM, Aurora, CO 80045, USA
| | - Jordyn Dinwiddie
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Sheryl Mae Lagrana-Villagracia
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines
| | - Samuel P Gubbels
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA
| | - Rehan S Shaikh
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Stephen P Cass
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA
| | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki 00014, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 141 83, Sweden
| | - Nanette R Lee
- USC-Office of Population Studies Foundation and Department of Anthropology, Sociology and History, University of San Carlos, Cebu City 6000, Philippines
| | | | - Teresa Luisa I Gloria-Cruz
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ivana V Yang
- Department of Medicine, CUSOM, Aurora, CO 80045, USA
| | - Juha Kere
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki 00014, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 141 83, Sweden; Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Generoso T Abes
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Jeremy D Prager
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Saima Riazuddin
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Abner L Chan
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Patricia J Yoon
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Sven-Olrik Streubel
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Maria Rina T Reyes-Quintos
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; National Hearing Screening Reference Center, UP Manila-NIH, Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines; UP Manila - NIH, Manila 1000, Philippines
| | - Herman A Jenkins
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA
| | - Petri Mattila
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, 00029 HUS, Finland
| | - Kenny H Chan
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lena Hafrén
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, 00029 HUS, Finland
| | - Tasnee Chonmaitree
- Department of Pediatrics, Division of Infectious Diseases, UTMB, Galveston, TX 77555, USA
| | - Michele M Sale
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Zubair M Ahmed
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
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6
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Santos-Cortez RLP, Hutchinson DS, Ajami NJ, Reyes-Quintos MRT, Tantoco MLC, Labra PJ, Lagrana SM, Pedro M, Llanes EGDV, Gloria-Cruz TL, Chan AL, Cutiongco-de la Paz EM, Belmont JW, Chonmaitree T, Abes GT, Petrosino JF, Leal SM, Chiong CM. Middle ear microbiome differences in indigenous Filipinos with chronic otitis media due to a duplication in the A2ML1 gene. Infect Dis Poverty 2016; 5:97. [PMID: 27799062 PMCID: PMC5088646 DOI: 10.1186/s40249-016-0189-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/26/2016] [Indexed: 11/10/2022] Open
Abstract
Background Previously rare A2ML1 variants were identified to confer otitis media susceptibility in an indigenous Filipino community and in otitis-prone US children. The goal of this study is to describe differences in the middle ear microbiome between carriers and non-carriers of an A2ML1 duplication variant that increases risk for chronic otitis media among indigenous Filipinos with poor health care access. Methods Ear swabs were obtained from 16 indigenous Filipino individuals with chronic otitis media, of whom 11 carry the A2ML1 duplication variant. Ear swabs were submitted for 16S rRNA gene sequencing. Results Genotype-based differences in microbial richness, structure, and composition were identified, but were not statistically significant. Taxonomic analysis revealed that the relative abundance of the phyla Fusobacteria and Bacteroidetes, and genus Fusobacterium were nominally increased in carriers compared to non-carriers, but were non-significant after correction for multiple testing. We also detected rare bacteria including Oligella that was reported only once in the middle ear. Conclusions These findings suggest that A2ML1-related otitis media susceptibility may be mediated by changes in the middle ear microbiome. Knowledge of middle ear microbial profiles according to genetic background can be potentially useful for therapeutic and prophylactic interventions for otitis media and can guide public health interventions towards decreasing otitis media prevalence within the indigenous Filipino community. Electronic supplementary material The online version of this article (doi:10.1186/s40249-016-0189-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Regie Lyn P Santos-Cortez
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Current affiliation: Department of Otolaryngology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
| | - Diane S Hutchinson
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research (CMMR), Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nadim J Ajami
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research (CMMR), Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ma Rina T Reyes-Quintos
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines
| | - Ma Leah C Tantoco
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines
| | - Patrick John Labra
- Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines
| | - Sheryl Mae Lagrana
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines
| | - Melquiadesa Pedro
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines
| | - Erasmo Gonzalo D V Llanes
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines
| | - Teresa Luisa Gloria-Cruz
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines
| | - Abner L Chan
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines
| | - Eva Maria Cutiongco-de la Paz
- Institute of Human Genetics, UPM-NIH, Manila, 1000, Philippines.,Philippine Genome Center, University of the Philippines, Diliman, Quezon City, 1101, Philippines
| | - John W Belmont
- Departments of Molecular and Human Genetics and Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Current address: Illumina, Inc, San Diego, CA, 92122, USA
| | - Tasnee Chonmaitree
- Division of Pediatric Infectious Disease and Immunology, Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Generoso T Abes
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research (CMMR), Baylor College of Medicine, Houston, TX, 77030, USA
| | - Suzanne M Leal
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Charlotte M Chiong
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines
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7
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Santos-Cortez RLP, Reyes-Quintos MRT, Tantoco MLC, Abbe I, Llanes EGDV, Ajami NJ, Hutchinson DS, Petrosino JF, Padilla CD, Villarta RL, Gloria-Cruz TL, Chan AL, Cutiongco-de la Paz EM, Chiong CM, Leal SM, Abes GT. Genetic and Environmental Determinants of Otitis Media in an Indigenous Filipino Population. Otolaryngol Head Neck Surg 2016; 155:856-862. [PMID: 27484237 DOI: 10.1177/0194599816661703] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/08/2016] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To identify genetic and environmental risk factors for otitis media in an indigenous Filipino population. STUDY DESIGN Cross-sectional study. SETTING Indigenous Filipino community. SUBJECTS AND METHODS Clinical history and information on breastfeeding, tobacco smoke exposure, and swimming were obtained from community members. Heads of households were interviewed for family history and personal beliefs on ear health. Height and weight were measured. Otoscopic findings were described for the presence and character of perforation or discharge. An A2ML1 duplication variant that confers otitis media susceptibility was Sanger sequenced in all DNA samples. Co-occurrence of middle ear bacteria detected by 16S rRNA gene sequencing was determined according to A2ML1 genotype and social cluster. RESULTS The indigenous Filipino population has a ~50% prevalence of otitis media. Young age was associated with otitis media (4 age strata; P = .004); however, age was nonsignificant as a bistratal or continuous variable. There was no association between otitis media and sex, body mass index, breastfeeding, tobacco exposure, or deep swimming. In multivariate analyses, A2ML1 genotype is the strongest predictor of otitis media, with an odds ratio of 3.7 (95% confidence interval: 1.3-10.8; P = .005). When otitis media diagnoses were plotted across ages, otitis media was observed within the first year of life, and chronic otitis media persisted up to adulthood, particularly in A2ML1-variant carriers. CONCLUSION Among indigenous Filipinos, A2ML1 genotype is the primary risk factor for otitis media and main determinant of disease progression, although age, the middle ear microbiome, and social clusters might modulate the effect of the A2ML1 genotype.
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Affiliation(s)
- Regie Lyn P Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ma Rina T Reyes-Quintos
- Philippine National Ear Institute, University of the Philippines Manila-National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine-Philippine General Hospital, Manila, Philippines
| | - Ma Leah C Tantoco
- Philippine National Ear Institute, University of the Philippines Manila-National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine-Philippine General Hospital, Manila, Philippines
| | - Izoduwa Abbe
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Erasmo Gonzalo D V Llanes
- Philippine National Ear Institute, University of the Philippines Manila-National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine-Philippine General Hospital, Manila, Philippines
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research (CMMR), Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Diane S Hutchinson
- Alkek Center for Metagenomics and Microbiome Research (CMMR), Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research (CMMR), Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Carmencita D Padilla
- Institute of Human Genetics, University of the Philippines Manila-National Institutes of Health, Manila, Philippines.,Department of Pediatrics, University of the Philippines College of Medicine-Philippine General Hospital, Manila, Philippines.,Philippine Genome Center, University of the Philippines Diliman, Quezon City, Philippines
| | - Romeo L Villarta
- Philippine National Ear Institute, University of the Philippines Manila-National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine-Philippine General Hospital, Manila, Philippines
| | - Teresa Luisa Gloria-Cruz
- Philippine National Ear Institute, University of the Philippines Manila-National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine-Philippine General Hospital, Manila, Philippines
| | - Abner L Chan
- Philippine National Ear Institute, University of the Philippines Manila-National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine-Philippine General Hospital, Manila, Philippines
| | - Eva Maria Cutiongco-de la Paz
- Institute of Human Genetics, University of the Philippines Manila-National Institutes of Health, Manila, Philippines.,Department of Pediatrics, University of the Philippines College of Medicine-Philippine General Hospital, Manila, Philippines.,Philippine Genome Center, University of the Philippines Diliman, Quezon City, Philippines
| | - Charlotte M Chiong
- Philippine National Ear Institute, University of the Philippines Manila-National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine-Philippine General Hospital, Manila, Philippines
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Generoso T Abes
- Philippine National Ear Institute, University of the Philippines Manila-National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, University of the Philippines College of Medicine-Philippine General Hospital, Manila, Philippines
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8
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Santos-Cortez RLP, Chiong CM, Reyes-Quintos MRT, Tantoco MLC, Wang X, Acharya A, Abbe I, Giese AP, Smith JD, Allen EK, Li B, Cutiongco-de la Paz EM, Garcia MC, Llanes EGD, Labra PJ, Gloria-Cruz TLI, Chan AL, Wang GT, Daly KA, Shendure J, Bamshad MJ, Nickerson DA, Patel JA, Riazuddin S, Sale MM, Chonmaitree T, Ahmed ZM, Abes GT, Leal SM. Rare A2ML1 variants confer susceptibility to otitis media. Nat Genet 2015; 47:917-20. [PMID: 26121085 PMCID: PMC4528370 DOI: 10.1038/ng.3347] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 06/03/2015] [Indexed: 11/15/2022]
Abstract
A duplication variant within the middle ear-specific gene A2ML1 cosegregates with otitis media in an indigenous Filipino pedigree (LOD score = 7.5 at reduced penetrance) and lies within a founder haplotype that is also shared by 3 otitis-prone European-American and Hispanic-American children but is absent in non-otitis-prone children and >62,000 next-generation sequences. We identified seven additional A2ML1 variants in six otitis-prone children. Collectively, our studies support a role for A2ML1 in the pathophysiology of otitis media.
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Affiliation(s)
- Regie Lyn P. Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Charlotte M. Chiong
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Ma. Rina T. Reyes-Quintos
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Ma. Leah C. Tantoco
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
| | - Xin Wang
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Izoduwa Abbe
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Arnaud P. Giese
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - E. Kaitlynn Allen
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - Biao Li
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Eva Maria Cutiongco-de la Paz
- Institute of Human Genetics, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Pediatrics, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Marieflor Cristy Garcia
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Erasmo Gonzalo D.V. Llanes
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Patrick John Labra
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Teresa Luisa I. Gloria-Cruz
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Abner L. Chan
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Gao T. Wang
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Kathleen A. Daly
- Department of Otolaryngology, Head and Neck Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Michael J. Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Janak A. Patel
- Division of Pediatric Infectious Disease and Immunology, Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Michele M. Sale
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | | | - Tasnee Chonmaitree
- Division of Pediatric Infectious Disease and Immunology, Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Generoso T. Abes
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Suzanne M. Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Reyes-Quintos MRT, Santos RLP, Tantoco MLC, Roldan RA, Fellizar KR, Dalizay-Cruz MAM, Abes GT, Chiong CM. Otoscopic and Audiologic Findings in an Ati Community in Boracay. Philipp J Otolaryngol Head Neck Surg 2007. [DOI: 10.32412/pjohns.v22i1-2.791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Background: Certain indigenous populations have been noted by the World Health Organization (WHO) to have the highest prevalence rates for chronic suppurative otitis media (CSOM), including the Australian Aborigines (28-43%), Greenlanders (2-10%) and Alaskan Eskimos (2-10%).
Objectives: To determine the prevalence of common ear problems, particularly CSOM, among the indigenous Ati or Aeta community in Bolabog, Boracay, and to determine their hearing sensitivity using screening audiometry.
Methods:
Study Design: Descriptive cross-sectional study.
Setting: A small Ati community in Bolabog, Boracay.
Population: A total of 63 adults and children underwent medical interview and otoscopy. Additionally 24 had their hearing screened by audiometry.
Results: About a quarter of the population participated in the study, including 41 children (40% of all children) and 22 adults (18% of all adults). Forty-six percent of children and 23% of adults who were examined had previous history of ear discharge, while 22% of children and 45% of adults who were examined had history of hearing loss. Seventeen percent of children had history of hearing loss in the family. CSOM was found in 18 (43.90%) children and 8 (36.36%) adults. Impacted cerumen was found in 17.1% of children. Eleven female children underwent screening audiometry. Of these, eight had normal hearing and three had abnormal findings. Thirteen adults were also tested, five of whom were male and had normal hearing bilaterally. Four of eight female adults had abnormal hearing, of which three were unilateral.
Conclusions: The Ati population in Bolabog, Boracay belongs to a group with the highest prevalence rates for CSOM (27.0%). A bigger sample for screening audiometry is required for proper estimation of hearing loss prevalence. Both environmental and genetic factors may have increased the prevalence of CSOM in the Ati population of Boracay.
Keywords: Hearing loss, chronic suppurative otitis media, Boracay, indigenous community, Ati, Aeta
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