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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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Sciascia S, Roccatello D, Salvatore M, Carta C, Cellai LL, Ferrari G, Lumaka A, Groft S, Alanay Y, Azam M, Baynam G, Cederroth H, Cutiongco-de la Paz EM, Dissanayake VHW, Giugliani R, Gonzaga-Jauregui C, Hettiarachchi D, Kvlividze O, Landoure G, Makay P, Melegh B, Ozbek U, Puri RD, Romero VI, Scaria V, Jamuar SS, Shotelersuk V, Gahl WA, Wiafe SA, Bodamer O, Posada M, Taruscio D. Unmet needs in countries participating in the undiagnosed diseases network international: an international survey considering national health care and economic indicators. Front Public Health 2023; 11:1248260. [PMID: 37822540 PMCID: PMC10562568 DOI: 10.3389/fpubh.2023.1248260] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/08/2023] [Indexed: 10/13/2023] Open
Abstract
Background Patients, families, the healthcare system, and society as a whole are all significantly impacted by rare diseases (RDs). According to various classifications, there are currently up to 9,000 different rare diseases that have been recognized, and new diseases are discovered every month. Although very few people are affected by each uncommon disease individually, millions of people are thought to be impacted globally when all these conditions are considered. Therefore, RDs represent an important public health concern. Although crucial for clinical care, early and correct diagnosis is still difficult to achieve in many nations, especially those with low and middle incomes. Consequently, a sizeable amount of the overall burden of RD is attributable to undiagnosed RD (URD). Existing barriers and policy aspects impacting the care of patients with RD and URD remain to be investigated. Methods To identify unmet needs and opportunities for patients with URD, the Developing Nations Working Group of the Undiagnosed Diseases Network International (DNWG-UDNI) conducted a survey among its members, who were from 20 different nations. The survey used a mix of multiple choice and dedicated open questions covering a variety of topics. To explore reported needs and analyze them in relation to national healthcare economical aspects, publicly available data on (a) World Bank ranking; (b) Current health expenditure per capita; (c) GDP per capita; (d) Domestic general government health expenditure (% of GDP); and (e) Life expectancy at birth, total (years) were incorporated in our study. Results This study provides an in-depth evaluation of the unmet needs for 20 countries: low-income (3), middle-income (10), and high-income (7). When analyzing reported unmet needs, almost all countries (N = 19) indicated that major barriers still exist when attempting to improve the care of patients with UR and/or URD; most countries report unmet needs related to the availability of specialized care and dedicated facilities. However, while the countries ranked as low income by the World Bank showed the highest prevalence of referred unmet needs across the different domains, no specific trend appeared when comparing the high, upper, and low-middle income nations. No overt trend was observed when separating countries by current health expenditure per capita, GDP per capita, domestic general government health expenditure (% of GDP) and life expectancy at birth, total (years). Conversely, both the GDP and domestic general government health expenditure for each country impacted the presence of ongoing research. Conclusion We found that policy characteristics varied greatly with the type of health system and country. No overall pattern in terms of referral for unmet needs when separating countries by main economic or health indicators were observed. Our findings highlight the importance of identifying actionable points (e.g., implemented orphan drug acts or registries where not available) in order to improve the care and diagnosis of RDs and URDs on a global scale.
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Affiliation(s)
- Savino Sciascia
- Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) With Nephrology and Dialysis Unit, San Giovanni Bosco Hub Hospital, ASL Città di Torino and University of Turin, Turin, Italy
| | - Dario Roccatello
- Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) With Nephrology and Dialysis Unit, San Giovanni Bosco Hub Hospital, ASL Città di Torino and University of Turin, Turin, Italy
| | - Marco Salvatore
- National Center for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Claudio Carta
- National Center for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Laura L. Cellai
- National Center for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Gianluca Ferrari
- National Center for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Aimè Lumaka
- Reference Center for Rare and Undiagnosed Diseases, University of Kinshasa, Kinshasa, Democratic Republic of Congo
- Service de Génétique Humaine, University Hospitals of Liège, Liège, Belgium
| | - Stephen Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Yasemin Alanay
- ACURARE-Rare and Undiagnosed Diseases Center, Acibadem University, Istanbul, Türkiye
| | - Maleeha Azam
- COMSATS University Islamabad, Islamabad, Pakistan
| | - Gareth Baynam
- Rare Care, Clinical Center of Expertise for Rare and Undiagnosed Diseases, Perth Children's Hospital, Perth, WA, Australia
| | | | - Eva Maria Cutiongco-de la Paz
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | | | - Roberto Giugliani
- House of Rares, Medical Genetics Service, HCPA, Department Genetics UFRGS and DASA, Porto Alegre, Brazil
| | - Claudia Gonzaga-Jauregui
- International Laboratory for Human Genome Research, Universidad Nacional Autonoma de Mexico, Juriquilla, Queretaro, Mexico
| | - Dineshani Hettiarachchi
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Oleg Kvlividze
- Georgian Foundation for Genetic and Rare Diseases (GeRaD), School of Medicine, New Vision University, Tbilisi, Georgia
| | - Guida Landoure
- Faculté de Médecine et d'Odontostomatologie, l'Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Prince Makay
- Reference Center for Rare and Undiagnosed Diseases, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Béla Melegh
- Department of Medical Genetics, School of Medicine, University of Pécs, Pécs, Hungary
| | - Ugur Ozbek
- ACURARE-Rare and Undiagnosed Diseases Center, Acibadem University, Istanbul, Türkiye
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Vanessa I. Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Saumya S. Jamuar
- Genetics Service, Department of Pediatrics, KK Women’s and Children’s Hospital and Pediatric ACP, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, King Chulalongkorn Memorial Hospital and Chulalongkorn University, Bangkok, Thailand
| | - William A. Gahl
- National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, United States
| | | | - Olaf Bodamer
- Division of Genetics and Genomics, Harvard Medical School, Boston Children's Hospital, Boston, MA, United States
| | - Manuel Posada
- Rare Diseases Research Institute (IIER), SpainUDP, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Domenica Taruscio
- National Center for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy
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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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Taruscio D, Salvatore M, Lumaka A, Carta C, Cellai LL, Ferrari G, Sciascia S, Groft S, Alanay Y, Azam M, Baynam G, Cederroth H, Cutiongco-de la Paz EM, Dissanayake VHW, Giugliani R, Gonzaga-Jauregui C, Hettiarachchi D, Kvlividze O, Landoure G, Makay P, Melegh B, Ozbek U, Puri RD, Romero V, Scaria V, Jamuar SS, Shotelersuk V, Roccatello D, Gahl WA, Wiafe SA, Bodamer O, Posada M. Undiagnosed diseases: Needs and opportunities in 20 countries participating in the Undiagnosed Diseases Network International. Front Public Health 2023; 11:1079601. [PMID: 36935719 PMCID: PMC10017550 DOI: 10.3389/fpubh.2023.1079601] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction Rare diseases (RD) are a health priority worldwide, overall affecting hundreds of millions of people globally. Early and accurate diagnosis is essential to support clinical care but remains challenging in many countries, especially the low- and medium-income ones. Hence, undiagnosed RD (URD) account for a significant portion of the overall RD burden. Methods In October 2020, the Developing Nations Working Group of the Undiagnosed Diseases Network International (DNWG-UDNI) launched a survey among its members, belonging to 20 countries across all continents, to map unmet needs and opportunities for patients with URD. The survey was based on questions with open answers and included eight different domains. Conflicting interpretations were resolved in contact with the partners involved. Results All members responded to the survey. The results indicated that the scientific and medical centers make substantial efforts to respond to the unmet needs of patients. In most countries, there is a high awareness of RD issues. Scarcity of resources was highlighted as a major problem, leading to reduced availability of diagnostic expertise and research. Serious equity in accessibility to services were highlighted both within and between participating countries. Regulatory problems, including securing informed consent, difficulties in sending DNA to foreign laboratories, protection of intellectual property, and conflicts of interest on the part of service providers, remain issues of concern. Finally, most respondents stressed the need to strengthen international cooperation in terms of data sharing, clinical research, and diagnostic expertise for URD patients in low and medium income countries. Discussion The survey highlighted that many countries experienced a discrepancy between the growing expertise and scientific value, the level of awareness and commitment on the part of relevant parties, and funding bodies. Country-tailored public health actions, including general syllabus of medical schools and of the education of other health professionals, are needed to reduce such gaps.
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Affiliation(s)
- Domenica Taruscio
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Domenica Taruscio
| | - Marco Salvatore
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Aimè Lumaka
- Reference Center for Rare and Undiagnosed Diseases, University of Kinshasa, Kinshasa, Democratic Republic of Congo
- Service de Génétique Humaine, University Hospitals of Liège, Liège, Belgium
| | - Claudio Carta
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Laura L. Cellai
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Gianluca Ferrari
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Savino Sciascia
- Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) With Nephrology and Dialysis Unit, San Giovanni Bosco Hub Hospital, University of Turin, Turin, Italy
| | - Stephen Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Yasemin Alanay
- ACURARE-Rare and Undiagnosed Diseases Center, Acibadem University, Istanbul, Turkey
| | - Maleeha Azam
- COMSATS University Islamabad, Islamabad, Pakistan
| | - Gareth Baynam
- Rare Care, Clinical Centre of Expertise for Rare and Undiagnosed Diseases, Perth Children's Hospital, Perth, WA, Australia
| | | | - Eva Maria Cutiongco-de la Paz
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | | | - Roberto Giugliani
- House of Rares, Medical Genetics Service, HCPA, Department Genetics UFRGS and DASA, Porto Alegre, Brazil
| | - Claudia Gonzaga-Jauregui
- International Laboratory for Human Genome Research, Universidad Nacional Autonoma de Mexico, Juriquilla, Queretaro, Mexico
| | - Dineshani Hettiarachchi
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Oleg Kvlividze
- Georgian Foundation for Genetic and Rare Diseases (GeRaD), School of Medicine, New Vision University, Tbilisi, Georgia
| | - Guida Landoure
- Faculté de Médecine et d'Odontostomatologie, l'Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Prince Makay
- Reference Center for Rare and Undiagnosed Diseases, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Béla Melegh
- Department of Medical Genetics, School of Medicine, University of Pécs, Pécs, Hungary
| | - Ugur Ozbek
- ACURARE-Rare and Undiagnosed Diseases Center, Acibadem University, Istanbul, Turkey
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Vanessa Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Saumya S. Jamuar
- Singhealth Duke-NUS Genomic Medicine Centre, KK Women's and Children's Hospital, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, King Chulalongkorn Memorial Hospital and Chulalongkorn University, Bangkok, Thailand
| | - Dario Roccatello
- Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) With Nephrology and Dialysis Unit, San Giovanni Bosco Hub Hospital, University of Turin, Turin, Italy
| | - William A. Gahl
- National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, United States
| | | | - Olaf Bodamer
- Division of Genetics and Genomics, Harvard Medical School, Boston Children's Hospital, Boston, MA, United States
| | - Manuel Posada
- Rare Diseases Research Institute (IIER), SpainUDP, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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5
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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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6
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Albao DS, Cutiongco-de la Paz EM, Mercado ME, Lirio A, Mariano M, Kim S, Yangco A, Melegrito J, Wad-Asen K, Gauran II, Francisco MA, Santos-Acuin C, David-Padilla C, Murphy EJ, Paz-Pacheco E, Seielstad M. Methylation changes in the peripheral blood of Filipinos with type 2 diabetes suggest spurious transcription initiation at TXNIP. Hum Mol Genet 2020; 28:4208-4218. [PMID: 31691802 DOI: 10.1093/hmg/ddz262] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 09/23/2019] [Accepted: 10/15/2019] [Indexed: 11/14/2022] Open
Abstract
While much work has been done in associating differentially methylated positions (DMPs) to type 2 diabetes (T2D) across different populations, not much attention has been placed on identifying its possible functional consequences. We explored methylation changes in the peripheral blood of Filipinos with T2D and identified 177 associated DMPs. Most of these DMPs were associated with genes involved in metabolism, inflammation and the cell cycle. Three of these DMPs map to the TXNIP gene body, replicating previous findings from epigenome-wide association studies (EWAS) of T2D. The TXNIP downmethylation coincided with increased transcription at the 3' UTR, H3K36me3 histone markings and Sp1 binding, suggesting spurious transcription initiation at the TXNIP 3' UTR as a functional consequence of T2D methylation changes. We also explored potential epigenetic determinants to increased incidence of T2D in Filipino immigrants in the USA and found three DMPs associated with the interaction of T2D and immigration. Two of these DMPs were located near MAP2K7 and PRMT1, which may point towards dysregulated stress response and inflammation as a contributing factor to T2D among Filipino immigrants.
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Affiliation(s)
- Dominic S Albao
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Ermita, Manila 1000, Philippines.,National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Diliman, Quezon City 1101, Philippines.,Philippine Genome Center, University of the Philippines System, Diliman, Quezon City 1101, Philippines
| | - Eva Maria Cutiongco-de la Paz
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Ermita, Manila 1000, Philippines.,Philippine Genome Center, University of the Philippines System, Diliman, Quezon City 1101, Philippines
| | - Maria Elizabeth Mercado
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Ermita, Manila 1000, Philippines.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alvin Lirio
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Ermita, Manila 1000, Philippines.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Margarette Mariano
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Sarah Kim
- Division of Endocrinology, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ariane Yangco
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Ermita, Manila 1000, Philippines
| | - Jodelyn Melegrito
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Ermita, Manila 1000, Philippines
| | - Kate Wad-Asen
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Ermita, Manila 1000, Philippines
| | - Iris Ivy Gauran
- School of Statistics, University of the Philippines Diliman, Diliman, Quezon City 1101, Philippines
| | - Marie Angeline Francisco
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Ermita, Manila 1000, Philippines.,National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Diliman, Quezon City 1101, Philippines.,Philippine Genome Center, University of the Philippines System, Diliman, Quezon City 1101, Philippines
| | | | - Carmencita David-Padilla
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Ermita, Manila 1000, Philippines
| | - Elizabeth J Murphy
- Division of Endocrinology, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Elizabeth Paz-Pacheco
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of the Philippines Manila, Ermita, Manila 1000, Philippines
| | - Mark Seielstad
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
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7
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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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8
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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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9
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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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10
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la Paz EMCD, Pedro M, Yarza TKL, Lagrana-Villagracia SM, Amoranto AJP, Jover EJM, Domine MTB, Chiong CM, Santos-Cortez RLP. Genetic counseling in an indigenous Filipino community with a high prevalence of A2ML1-related otitis media. J Community Genet 2018; 10:143-151. [PMID: 29949068 DOI: 10.1007/s12687-018-0368-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 01/05/2018] [Accepted: 05/08/2018] [Indexed: 11/29/2022] Open
Abstract
In this report, we describe the knowledge and beliefs on causes and management of otitis media of an indigenous Filipino community with a high prevalence of otitis media that is associated with an A2ML1 variant. Community lectures and individual genetic counseling were provided as intervention. Knowledge, beliefs, and health care-seeking behavior pertaining to otitis media were assessed pre- and post-genetic counseling. Twenty-five heads of households were interviewed. Beliefs regarding etiology of ear discharge varied widely, with swimming in the sea as the most commonly cited cause of ear discharge. During the post-counseling session, poor personal hygiene, dirty environment, and familial inheritance were mentioned as risk factors for otitis media or ear discharge. Knowledge about the genotypes for the A2ML1 variant and otitis media diagnoses within the household influenced beliefs on the role of hygiene and genetic susceptibility to otitis media and attitudes towards health care-seeking behavior. Genetic counseling was associated with variable improvement in knowledge on otitis media and in their understanding of genetic susceptibility to otitis media due to the A2ML1 variant. Language barriers, literacy level, cultural factors, and the complex nature of genetic information made genetic counseling in the particular population a challenge. Insights drawn from this experience recommend follow-up visits in the community.
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Affiliation(s)
- Eva Maria Cutiongco-de la Paz
- University of the Philippines (UP) Manila - National Institutes of Health (NIH), Pedro Gil St., 1000, Manila, Philippines.,Section of Genetics, Department of Pediatrics, UP College of Medicine - Philippine General Hospital (PGH), Taft Ave., Ermita, 1000, Manila, Philippines
| | - Melquiadesa Pedro
- Philippine National Ear Institute, UP Manila - NIH, Manila, Philippines
| | - Talitha Karisse L Yarza
- Philippine National Ear Institute, UP Manila - NIH, Manila, Philippines.,Newborn Hearing Screening Reference Center, UP Manila-NIH, Manila, Philippines
| | | | | | | | | | - Charlotte M Chiong
- Philippine National Ear Institute, UP Manila - NIH, Manila, Philippines.,Newborn Hearing Screening Reference Center, UP Manila-NIH, Manila, Philippines.,Department of Otorhinolaryngology, UP College of Medicine - PGH, Manila, Philippines
| | - Regie Lyn P Santos-Cortez
- Philippine National Ear Institute, UP Manila - NIH, Manila, Philippines. .,Department of Otolaryngology, University of Colorado School of Medicine, 12700 E. 19th Ave., Aurora, CO, 80045, USA. .,Center for Children's Surgery, Children's Hospital Colorado, 13623 E. 16th Ave., Aurora, CO, 80045, USA.
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11
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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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12
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Abstract
Genetics and genomic medicine in the Philippines.
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Affiliation(s)
- Carmencita D Padilla
- Department of PediatricsCollege of MedicineUniversity of the Philippines ManilaManilaPhilippines; Institute of Human GeneticsNational Institutes of HealthUniversity of the Philippines ManilaManilaPhilippines; Philippine Genome CenterUniversity of the Philippines SystemQuezon CityPhilippines
| | - Eva Maria Cutiongco-de la Paz
- Department of PediatricsCollege of MedicineUniversity of the Philippines ManilaManilaPhilippines; Institute of Human GeneticsNational Institutes of HealthUniversity of the Philippines ManilaManilaPhilippines; Philippine Genome CenterUniversity of the Philippines SystemQuezon CityPhilippines
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13
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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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14
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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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Chiong CM, Cutiongco-de la Paz EM, Reyes-Quintos MRT, Tobias CAM, Hernandez K, Santos-Cortez RLP. GJB2Variants and Auditory Outcomes among Filipino Cochlear Implantees. Audiol Neurotol Extra 2013. [DOI: 10.1159/000346271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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