1
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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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2
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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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3
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Truong BT, Yarza TKL, Bootpetch Roberts T, Roberts S, Xu J, Steritz MJ, Tobias-Grasso CAM, Azamian M, Lalani SR, Mohlke KL, Lee NR, Cutiongco-de la Paz EM, Reyes-Quintos MRT, Santos-Cortez RLP, Chiong CM. Exome sequencing reveals novel variants and unique allelic spectrum for hearing impairment in Filipino cochlear implantees. Clin Genet 2019; 95:634-636. [PMID: 30828794 DOI: 10.1111/cge.13515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/18/2019] [Accepted: 01/23/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Brittany T Truong
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado
| | - Talitha K L Yarza
- Philippine National Ear Institute, University of the Philippines (UP) Manila-National Institutes of Health (NIH), Manila, Philippines.,Newborn Hearing Screening Reference Center, UP Manila-NIH, Manila, Philippines
| | - Tori Bootpetch Roberts
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado
| | - Susannah Roberts
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado
| | - Jonathan Xu
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado
| | - Matthew J Steritz
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado
| | | | - Mahshid Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Nanette R Lee
- Office of Population Studies Foundation and Department of Anthropology, Sociology and History, University of San Carlos, Cebu, Philippines
| | | | - Maria Rina T Reyes-Quintos
- Philippine National Ear Institute, University of the Philippines (UP) Manila-National Institutes of Health (NIH), Manila, Philippines.,Newborn Hearing Screening Reference Center, UP Manila-NIH, Manila, Philippines.,UP Manila-NIH, Manila 1000, Philippines.,Department of Otorhinolaryngology, UP Manila College of Medicine-Philippine General Hospital, Manila, Philippines
| | - Regie Lyn P Santos-Cortez
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado.,Philippine National Ear Institute, University of the Philippines (UP) Manila-National Institutes of Health (NIH), Manila, Philippines.,Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado
| | - Charlotte M Chiong
- Philippine National Ear Institute, University of the Philippines (UP) Manila-National Institutes of Health (NIH), Manila, Philippines.,Newborn Hearing Screening Reference Center, UP Manila-NIH, Manila, Philippines.,Department of Otorhinolaryngology, UP Manila College of Medicine-Philippine General Hospital, Manila, Philippines
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4
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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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