Daniel N. Frank, Arnaud P. J. Giese, Lena Hafren, Tori C. Bootpetch, Talitha Karisse L. Yarza, Matthew J. Steritz, Melquiadesa Pedro, Patrick John Labra, Kathleen A. Daly, Ma. Leah C. Tantoco, Wasyl Szeremeta, Maria Rina T. Reyes-Quintos, Niaz Ahankoob, Erasmo Gonzalo D.V. Llanes, Harold S. Pine, Sairah Yousaf, Diana Ir, Elisabet Einarsdottir, Rhodieleen Anne R. De La Cruz, Nanette R. Lee, Rachelle Marie A. Nonato, Charles E. Robertson, Kimberly Mae C. Ong, Jose Pedrito M. Magno, Alessandra Nadine E. Chiong, Ma. Carmina Espiritu-Chiong, Maria Luz San Agustin, Teresa Luisa G. Cruz, Generoso T. Abes, Michael J. Bamshad, Eva Maria Cutiongco-De La Paz, Juha Kere, Deborah A. Nickerson, Karen L. Mohlke, Saima Riazuddin, Abner Chan, Petri S. Mattila, Suzanne M. Leal, Allen F. Ryan, Zubair M. Ahmed, Tasnee Chonmaitree, Michele M. Sale, Charlotte M. Chiong, Regie Lyn P. Santos-Cortez
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. © 2021 BMJ Publishing Group. All rights reserved.
Department of Medicine, Division of Infectious Diseases, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States; Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland, Baltimore, MD, United States; Department of Otorhinolaryngology Head and Neck Surgery, University of Helsinki, Helsinki University Hospital, Helsinki, Finland; Department of Otolaryngology-Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, United States; 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 Otolaryngology Head and Neck Surgery, University of Minnesota, Minneapolis, MN, United States; Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines; Department of Otolaryngology, University of Texas Medical Branch at Galveston, Galveston, TX, United States; National Institutes of Health, University of the Philippines Manila, Manila, Philippines; Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland; Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland; Department of Anthropology Sociology and History, University of San Carlos, Cebu City, Philippines; Renergy Dermatology and Laser Center, Taguig City, Philippines; Department of Genome Sciences, University of Washington, Seattle, WA, United States; Philippine Genome Center, University of the Philippines Diliman, Quezon City, Philippines; Department of Medical and Molecular Genetics, King's College London, London, United Kingdom; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; 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, NY, United States; Division of Otolaryngology, Department of Surgery, University of California San Diego School of Medicine, Veterans Affairs Medical Center, San Diego, CA, United States; Division of Infectious Diseases, Department of Pediatrics, University of Texas Medical Branch at Galveston, Galveston, TX, United States; Center for Public Health Genomics, School of Medicine, Department of Biochemistry and Molecular Genetics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States; Center for Children's Surgery, Children's Hospital Colorado, Aurora, CO, United States
