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Elling CL, Gomez HZ, Lee NK, Hirsch SD, Santos-Cortez RLP. The A2ml1-Knockout mouse as an animal model for non-syndromic otitis media. Int J Pediatr Otorhinolaryngol 2024; 181:111980. [PMID: 38759260 PMCID: PMC11175999 DOI: 10.1016/j.ijporl.2024.111980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/25/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Inflammation and infection of the middle ear, known as otitis media (OM), is a leading cause of hearing loss and the most frequently diagnosed disease in children worldwide. Traditionally, mouse models for OM rely on inducing acute infection through inoculation of the middle ear, e.g. with the human otopathogen non-typeable Haemophilus influenzae (NTHi), and with very few genetic models with spontaneous or chronic OM. A2ML1 variants, including loss-of-function variants, were associated with susceptibility to OM in humans, but no animal model has been reported for A2ml1-related OM. Here, we report our middle ear findings in a mouse line with a CRISPR-induced knockout (KO) of A2ml1. METHODS Mice were X-rayed prior to harvest to determine if there are craniofacial or skeletal abnormalities. Tissue from mouse middle ears, as well as other upper respiratory mucosal tissues, were harvested. The harvested middle ear bullae were examined under microscope and submitted for histologic preparation to study phenotypic indications of OM. RNA samples isolated from middle ear tissue were assayed for expression of genes correlated with A2ML1 expression in humans. RESULTS Data from a total of 119 mice (35 wildtype, 40 heterozygous, 44 homozygous) are presented here, with each analyses being performed on subsets of these mice. There were no significant craniofacial differences by genotype (n = 22). Findings in mice with the A2ml1-KO indicated an increased incidence of OM (n=29; odds ratio = 11; CI: 1.1, 573.6; Fisher exact two-sided p = 0.02) with tympanic membrane perforations or thickening, as well as cases of middle ear effusion, inflammatory cells, or fluid from histologic sections. Dsp was upregulated in the middle ear tissues of homozygous mice (Wilcoxon test p = 0.001). CONCLUSION Thus far, our results in this A2ml1-KO mouse line indicate spontaneous occurrence of OM and dysregulation of Dsp in the middle ear as a potential disease mechanism for A2ml1-related OM.
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Affiliation(s)
- Christina L Elling
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Helen Z Gomez
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Nam K Lee
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Scott D Hirsch
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Regie Lyn P Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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2
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Zhang X, Tang C, Lian J, Jiang Y. A2ML1 Inhibits Esophageal Squamous Cell Carcinoma Progression and Serves as a Novel Prognostic Biomarker. Can J Gastroenterol Hepatol 2023; 2023:5557546. [PMID: 37954860 PMCID: PMC10637849 DOI: 10.1155/2023/5557546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023] Open
Abstract
Studies have established a correlation between α2-macroglobulin-like 1 (A2ML1) and the prognosis of lung, pancreatic, and breast cancers; however, research on its involvement in the pathogenesis of esophageal carcinoma remains limited. Therefore, in this study, we aimed to investigate the role of A2ML1 in the progression of esophageal squamous cell carcinoma (ESCC). Immunohistochemical staining was employed to assess the expression level of A2ML1 protein in both tumor and adjacent normal tissues of patients with ESCC. The Kaplan-Meier method, along with univariate and multivariate Cox risk ratio analyses, was used to determine survival rates and prognostic factors. Furthermore, two human ESCC cell lines, KYSE30 and KYSE150, were used to assess the effect of A2ML1 overexpression on cell proliferation and apoptosis. A human apoptosis antibody kit was also used to analyze the downstream action proteins of A2ML1, and a nude mouse xenotransplantation model was used to evaluate the effect of A2ML1 on ESCC tumorigenesis in vivo. The protein level of A2ML1 in ESCC tissues was significantly lower than that in normal esophageal tissues, and higher A2ML1 protein levels were associated with smaller ESCC tumor sizes and improved tumor-specific survival rates. Multivariate analysis established A2ML1 as a novel independent prognostic factor for ESCC. Moreover, A2ML1 overexpression significantly inhibited ESCC cell proliferation and promoted apoptosis. A2ML1 consistently inhibited tumor growth in mouse models. Furthermore, the human apoptotic antibody kit results showed increased expression of the proliferation-inhibiting protein p21 downstream of KYSE150 cells overexpressing A2ML1. Our findings demonstrate that a correlation exists between A2ML1 and ESCC prognosis and that A2ML1 plays an antitumor role in ESCC progression. This study underscores the potential of A2ML1 as a novel biomarker for predicting the prognosis of ESCC.
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Affiliation(s)
- Xiaoyun Zhang
- Department of Medical Laboratory, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Nanjing, Jiangsu 223300, China
| | - Chaogui Tang
- Department of Medical Laboratory, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Nanjing, Jiangsu 223300, China
| | - Jianchun Lian
- Department of Medical Laboratory, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Nanjing, Jiangsu 223300, China
| | - Yuzhang Jiang
- Department of Medical Laboratory, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Nanjing, Jiangsu 223300, China
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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] [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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Nielsen NS, Zarantonello A, Harwood SL, Jensen KT, Kjøge K, Thøgersen IB, Schauser L, Karlsen JL, Andersen GR, Enghild JJ. Cryo-EM structures of human A2ML1 elucidate the protease-inhibitory mechanism of the A2M family. Nat Commun 2022; 13:3033. [PMID: 35641520 PMCID: PMC9156758 DOI: 10.1038/s41467-022-30758-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/12/2022] [Indexed: 12/26/2022] Open
Abstract
A2ML1 is a monomeric protease inhibitor belonging to the A2M superfamily of protease inhibitors and complement factors. Here, we investigate the protease-inhibitory mechanism of human A2ML1 and determine the structures of its native and protease-cleaved conformations. The functional inhibitory unit of A2ML1 is a monomer that depends on covalent binding of the protease (mediated by A2ML1’s thioester) to achieve inhibition. In contrast to the A2M tetramer which traps proteases in two internal chambers formed by four subunits, in protease-cleaved monomeric A2ML1 disordered regions surround the trapped protease and may prevent substrate access. In native A2ML1, the bait region is threaded through a hydrophobic channel, suggesting that disruption of this arrangement by bait region cleavage triggers the extensive conformational changes that result in protease inhibition. Structural comparisons with complement C3/C4 suggest that the A2M superfamily of proteins share this mechanism for the triggering of conformational change occurring upon proteolytic activation. A2ML1 is a human protease inhibitor belonging to the A2M protein family. In this study, the authors determine structures of A2ML1 before and after protease inhibition and investigate its mechanism of action.
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Affiliation(s)
- Nadia Sukusu Nielsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alessandra Zarantonello
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,Cordeliers Research Center, Sorbonne University, Paris, France
| | | | | | - Katarzyna Kjøge
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Ida B Thøgersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | | | - Gregers R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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5
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Jamieson SE, Fakiola M, Tang D, Scaman E, Syn G, Francis RW, Coates HL, Anderson D, Lassmann T, Cordell HJ, Blackwell JM. Common and Rare Genetic Variants That Could Contribute to Severe Otitis Media in an Australian Aboriginal Population. Clin Infect Dis 2021; 73:1860-1870. [PMID: 33693626 PMCID: PMC8599203 DOI: 10.1093/cid/ciab216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/09/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Our goal was to identify genetic risk factors for severe otitis media (OM) in Aboriginal Australians. METHODS Illumina® Omni2.5 BeadChip and imputed data were compared between 21 children with severe OM (multiple episodes chronic suppurative OM and/or perforations or tympanic sclerosis) and 370 individuals without this phenotype, followed by FUnctional Mapping and Annotation (FUMA). Exome data filtered for common (EXaC_all ≥ 0.1) putative deleterious variants influencing protein coding (CADD-scaled scores ≥15] were used to compare 15 severe OM cases with 9 mild cases (single episode of acute OM recorded over ≥3 consecutive years). Rare (ExAC_all ≤ 0.01) such variants were filtered for those present only in severe OM. Enrichr was used to determine enrichment of genes contributing to pathways/processes relevant to OM. RESULTS FUMA analysis identified 2 plausible genetic risk loci for severe OM: NR3C1 (Pimputed_1000G = 3.62 × 10-6) encoding the glucocorticoid receptor, and NREP (Pimputed_1000G = 3.67 × 10-6) encoding neuronal regeneration-related protein. Exome analysis showed: (i) association of severe OM with variants influencing protein coding (CADD-scaled ≥ 15) in a gene-set (GRXCR1, CDH23, LRP2, FAT4, ARSA, EYA4) enriched for Mammalian Phenotype Level 4 abnormal hair cell stereociliary bundle morphology and related phenotypes; (ii) rare variants influencing protein coding only seen in severe OM provided gene-sets enriched for "abnormal ear" (LMNA, CDH23, LRP2, MYO7A, FGFR1), integrin interactions, transforming growth factor signaling, and cell projection phenotypes including hair cell stereociliary bundles and cilium assembly. CONCLUSIONS This study highlights interacting genes and pathways related to cilium structure and function that may contribute to extreme susceptibility to OM in Aboriginal Australian children.
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Affiliation(s)
- Sarra E Jamieson
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia
| | | | - Dave Tang
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia
| | - Elizabeth Scaman
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia
| | - Genevieve Syn
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia
| | - Richard W Francis
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia
| | - Harvey L Coates
- Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia
| | - Denise Anderson
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia
| | - Timo Lassmann
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia
| | - Heather J Cordell
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Jenefer M Blackwell
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia
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6
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Mulay A, Chowdhury MMK, James CT, Bingle L, Bingle CD. The transcriptional landscape of the cultured murine middle ear epithelium in vitro. Biol Open 2021; 10:258492. [PMID: 33913472 PMCID: PMC8084567 DOI: 10.1242/bio.056564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/10/2021] [Indexed: 11/24/2022] Open
Abstract
Otitis media (OM) is the most common paediatric disease and leads to significant morbidity. Although understanding of underlying disease mechanisms is hampered by complex pathophysiology, it is clear that epithelial abnormalities underpin the disease. The mechanisms underpinning epithelial remodelling in OM remain unclear. We recently described a novel in vitro model of mouse middle ear epithelial cells (mMEECs) that undergoes mucociliary differentiation into the varied epithelial cell populations seen in the middle ear cavity. We now describe genome wide gene expression profiles of mMEECs as they undergo differentiation. We compared the gene expression profiles of original (uncultured) middle ear cells, confluent cultures of undifferentiated cells and cells that had been differentiated for 7 days at an air liquid interface (ALI). >5000 genes were differentially expressed among the three groups of cells. Approximately 4000 genes were differentially expressed between the original cells and day 0 of ALI culture. The original cell population was shown to contain a mix of cell types, including contaminating inflammatory cells that were lost on culture. Approximately 500 genes were upregulated during ALI induced differentiation. These included some secretory genes and some enzymes but most were associated with the process of ciliogenesis. The data suggest that the in vitro model of differentiated murine middle ear epithelium exhibits a transcriptional profile consistent with the mucociliary epithelium seen within the middle ear. Knowledge of the transcriptional landscape of this epithelium will provide a basis for understanding the phenotypic changes seen in murine models of OM. Summary: This paper presents a genome wide transcriptional analysis of murine middle ear epithelial cells as they undergo differentiation to a mucociliary phenotype representative of the native middle ear epithelium.
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Affiliation(s)
- Apoorva Mulay
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2RX, UK
| | - Md Miraj K Chowdhury
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2RX, UK
| | - Cameron T James
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2RX, UK
| | - Lynne Bingle
- Oral and Maxillofacial Pathology, Department of Clinical Dentistry, University of Sheffield, Sheffield S10 2TA, UK
| | - Colin D Bingle
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2RX, UK.,The Florey Institute for Host Pathogen Interactions, University of Sheffield, Sheffield S102TN, UK
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Harwood SL, Nielsen NS, Jensen KT, Nielsen PK, Thøgersen IB, Enghild JJ. α 2-Macroglobulin-like protein 1 can conjugate and inhibit proteases through their hydroxyl groups, because of an enhanced reactivity of its thiol ester. J Biol Chem 2020; 295:16732-16742. [PMID: 32978260 PMCID: PMC7864068 DOI: 10.1074/jbc.ra120.015694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/18/2020] [Indexed: 11/08/2022] Open
Abstract
Proteins in the α-macroglobulin (αM) superfamily use thiol esters to form covalent conjugation products upon their proteolytic activation. αM protease inhibitors use theirs to conjugate proteases and preferentially react with primary amines (e.g. on lysine side chains), whereas those of αM complement components C3 and C4B have an increased hydroxyl reactivity that is conveyed by a conserved histidine residue and allows conjugation to cell surface glycans. Human α2-macroglobulin-like protein 1 (A2ML1) is a monomeric protease inhibitor but has the hydroxyl reactivity-conveying histidine residue. Here, we have investigated the role of hydroxyl reactivity in a protease inhibitor by comparing recombinant WT A2ML1 and the A2ML1 H1084N mutant in which this histidine is removed. Both of A2ML1s' thiol esters were reactive toward the amine substrate glycine, but only WT A2ML1 reacted with the hydroxyl substrate glycerol, demonstrating that His-1084 increases the hydroxyl reactivity of A2ML1's thiol ester. Although both A2ML1s conjugated and inhibited thermolysin, His-1084 was required for the conjugation and inhibition of acetylated thermolysin, which lacks primary amines. Using MS, we identified an ester bond formed between a thermolysin serine residue and the A2ML1 thiol ester. These results demonstrate that a histidine-enhanced hydroxyl reactivity can contribute to protease inhibition by an αM protein. His-1084 did not improve A2ML1's protease inhibition at pH 5, indicating that A2ML1's hydroxyl reactivity is not an adaption to its acidic epidermal environment.
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Affiliation(s)
- Seandean Lykke Harwood
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; General Research Technologies, Novo Nordisk A/S, Måløv, Denmark
| | - Nadia Sukusu Nielsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | | | - Ida B Thøgersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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Jiang F, Wu C, Wang M, Wei K, Zhou G, Wang J. Multi-omics analysis of tumor mutation burden combined with immune infiltrates in melanoma. Clin Chim Acta 2020; 511:306-318. [PMID: 33164879 DOI: 10.1016/j.cca.2020.10.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND In multiple malignancies, whether tumor mutation burden (TMB) correlated with increased survival or promotion of immunotherapy remained a debate. Our aim was to analyze the prognosis of TMB and the possible connection with immune infiltration of the skin cutaneous melanoma (SKCM). METHODS We gathered somatic mutation data from the 472 SKCM patients using the Cancer Genome Atlas (TCGA) database and analyzed the mutation profiles using ""maftools" package. TMB was determined and samples were divided into high and low TMB groups. We undertook differential analysis to determine the profiles of expression between two groups using the "limma" package and established the 10 Hub TMB signature from a batch survival study. Gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene Set Enrichment Analysis (GSEA) were performed in order to test considerably enriched pathways between the two groups. The connections of 10 TMB-related signature mutants with immune infiltration in SKCM were further assessed based on the TIMER database. We used the CIBERSORT package to measure the amount of 22 immune fractions between low and high TMB groups, and Wilcoxon's rank-sum amounts estimated the significant difference. In addition, the Cox regression model and survival analysis were used to determine the prognostic importance of immune cells. Finally, we estabilished a multivaried Cox results Tumor Mutation Burden Prognostic Index (TMBPI) and built a Receiver Operating Characteristic (ROC) curve to check the predictive accuracy. RESULTS Single nucleotide polymorphism (SNP) was more frequent than insertion or deletion and C > T was SKCM's most frequently single nucleotide variants (SNV). Higher TMB levels provided poor survival outcomes, associated with tumor stage, age, and gender. In addition, 224 differentially expressed genes were obtained and Venn diagram established the top 25 immune-related genes. GSEA observed that patients in high TMB groups associated with nucleotide excision repair, pyrimidine metabolism, basal transcription factors, spliceosome, RNA polymerase, and RNA degradation in cancers. 10 hub TMB-related immune genes were also established and 10 signature mutants were correlated with lower immune infiltrates. In addition, the infiltration levels of macrophages M1 and macrophages M2 in the low-TMB group were lower. Eventually, the TMBPI was developed and the AUC of ROC curve was 0.604. CONCLUSIONS High TMB contributed to low survival outcomes and may prevent SKCM immune infiltration. The 10 hub immune signature TMB-related mutants conferred lower immune cell infiltration that required further confirmation.
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Affiliation(s)
- Feng Jiang
- Neonatal Department, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
| | - Chuyan Wu
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Ming Wang
- Plastic Surgery Department, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Ke Wei
- Medical Department, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Guoping Zhou
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jimei Wang
- Neonatal Department, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China.
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9
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Brinkmann J, Lissewski C, Pinna V, Vial Y, Pantaleoni F, Lepri F, Daniele P, Burnyte B, Cuturilo G, Fauth C, Gezdirici A, Kotzot D, Güleç EY, Iotova V, Schanze D, Ramond F, Havlovicová M, Utine GE, Simsek-Kiper PO, Stoyanova M, Verloes A, De Luca A, Tartaglia M, Cavé H, Zenker M. The clinical significance of A2ML1 variants in Noonan syndrome has to be reconsidered. Eur J Hum Genet 2020; 29:524-527. [PMID: 33082526 DOI: 10.1038/s41431-020-00743-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 09/22/2020] [Accepted: 09/30/2020] [Indexed: 12/22/2022] Open
Abstract
The RASopathies are a group of clinically and genetically heterogeneous developmental disorders caused by dysregulation of the RAS/MAPK signalling pathway. Variants in several components and regulators of this pathway have been identified as the pathogenetic cause. In 2015, missense variants in A2ML1 were reported in three unrelated families with clinical diagnosis of Noonan syndrome (NS) and a zebrafish model was presented showing heart and craniofacial defects similar to those caused by a NS-associated Shp2 variant. However, a causal role of A2ML1 variants in NS has not been confirmed since. Herein, we report on 15 individuals who underwent screening of RASopathy-associated genes and were found to carry rare variants in A2ML1, including variants previously proposed to be causative for NS. In cases where parental DNA was available, the respective A2ML1 variant was found to be inherited from an unaffected parent. Seven index patients carrying an A2ML1 variant presented with an alternate disease-causing genetic aberration. These findings underscore that current evidence is insufficient to support a causal relation between variants in A2ML1 and NS, questioning the inclusion of A2ML1 screening in diagnostic RASopathy testing.
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Affiliation(s)
- Julia Brinkmann
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Christina Lissewski
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Valentina Pinna
- Medical Genetics Section, IRCCS Fondazione Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Yoann Vial
- Department of Genetics, Hopital Robert Debré, Assistance Publique des Hopitaux de Paris (AP-HP), Paris, France.,Inserm U1131, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Francesca Pantaleoni
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Francesca Lepri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Paola Daniele
- Medical Genetics Section, IRCCS Fondazione Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Birute Burnyte
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Goran Cuturilo
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,University Children's Hospital, Belgrade, Serbia
| | - Christine Fauth
- Division of Human Genetics, Medizinische Universität Innsbruck, Innsbruck, Austria
| | - Alper Gezdirici
- Health Sciences University, Istanbul Kanuni Sultan Suleyman Research and Training Hospital, Section of Medical Genetics, Istanbul, Turkey
| | - Dieter Kotzot
- Division of Human Genetics, Medizinische Universität Innsbruck, Innsbruck, Austria
| | - Elif Yılmaz Güleç
- Health Sciences University, Istanbul Kanuni Sultan Suleyman Research and Training Hospital, Section of Medical Genetics, Istanbul, Turkey
| | - Violeta Iotova
- Department of Pediatrics, Medical University of Varna, Varna, Bulgaria
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Francis Ramond
- Department of Genetics, Hôpital Nord, Saint Etienne University Hospital, Lyon, France
| | - Markéta Havlovicová
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Gulen Eda Utine
- Department of Pediatric Genetics, Hacettepe University, Ankara, Turkey
| | | | - Milena Stoyanova
- Department of Medical Genetics, Varna Medical University, Varna, Bulgaria
| | - Alain Verloes
- Department of Genetics, Hopital Robert Debré, Assistance Publique des Hopitaux de Paris (AP-HP), Paris, France
| | - Alessandro De Luca
- Medical Genetics Section, IRCCS Fondazione Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Hélène Cavé
- Department of Genetics, Hopital Robert Debré, Assistance Publique des Hopitaux de Paris (AP-HP), Paris, France.,Inserm U1131, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany.
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10
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Bootpetch TC, Hafrén L, Elling CL, Baschal EE, Manichaikul AW, Pine HS, Szeremeta W, Scholes MA, Cass SP, Larson ED, Chan KH, Ishaq R, Prager JD, Shaikh RS, Gubbels SP, Yousaf A, Wine TM, Bamshad MJ, Yoon PJ, Jenkins HA, Nickerson DA, Streubel SO, Friedman NR, Frank DN, Einarsdottir E, Kere J, Riazuddin S, Daly KA, Leal SM, Ryan AF, Mattila PS, Ahmed ZM, Sale MM, Chonmaitree T, Santos-Cortez RLP. Multi-omic studies on missense PLG variants in families with otitis media. Sci Rep 2020; 10:15035. [PMID: 32929111 PMCID: PMC7490366 DOI: 10.1038/s41598-020-70498-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Otitis media (OM), a very common disease in young children, can result in hearing loss. In order to potentially replicate previously reported associations between OM and PLG, exome and Sanger sequencing, RNA-sequencing of saliva and middle ear samples, 16S rRNA sequencing, molecular modeling, and statistical analyses including transmission disequilibrium tests (TDT) were performed in a multi-ethnic cohort of 718 families and simplex cases with OM. We identified four rare PLG variants c.112A > G (p.Lys38Glu), c.782G > A (p.Arg261His), c.1481C > T (p.Ala494Val) and c.2045 T > A (p.Ile682Asn), and one common variant c.1414G > A (p.Asp472Asn). However TDT analyses for these PLG variants did not demonstrate association with OM in 314 families. Additionally PLG expression is very low or absent in normal or diseased middle ear in mouse and human, and salivary expression and microbial α-diversity were non-significant in c.1414G > A (p.Asp472Asn) carriers. Based on molecular modeling, the novel rare variants particularly c.782G > A (p.Arg261His) and c.2045 T > A (p.Ile682Asn) were predicted to affect protein structure. Exploration of other potential disease mechanisms will help elucidate how PLG contributes to OM susceptibility in humans. Our results underline the importance of following up findings from genome-wide association through replication studies, preferably using multi-omic datasets.
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Affiliation(s)
- Tori C Bootpetch
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lena Hafrén
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Christina L Elling
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Erin E Baschal
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ani W Manichaikul
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Harold S Pine
- Department of Otolaryngology, University of Texas Medical Branch, Galveston, TX, USA
| | - Wasyl Szeremeta
- Department of Otolaryngology, University of Texas Medical Branch, Galveston, TX, USA
| | - Melissa A Scholes
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, USA
| | - Stephen P Cass
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eric D Larson
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kenny H Chan
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, USA
| | - Rafaqat Ishaq
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Jeremy D Prager
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, USA
| | - Rehan S Shaikh
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Samuel P Gubbels
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ayesha Yousaf
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Todd M Wine
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Patricia J Yoon
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, USA
| | - Herman A Jenkins
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Sven-Olrik Streubel
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, USA
| | - Norman R Friedman
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, USA
| | - Daniel N Frank
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - 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
| | - 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
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Saima Riazuddin
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Kathleen A Daly
- Department of Otolaryngology, Head and Neck Surgery, University of Minnesota, Minneapolis, MN, USA
| | - Suzanne M Leal
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Allen F Ryan
- Division of Otolaryngology, Department of Surgery, UCSD School of Medicine and VA Medical Center, La Jolla, CA, USA
| | - Petri S Mattila
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Zubair M Ahmed
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Michele M Sale
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Tasnee Chonmaitree
- Division of Infectious Diseases, Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Regie Lyn P Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Center for Children's Surgery, Children's Hospital Colorado, Aurora, CO, USA.
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11
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Folino F, Ruggiero L, Capaccio P, Coro I, Aliberti S, Drago L, Marchisio P, Torretta S. Upper Respiratory Tract Microbiome and Otitis Media Intertalk: Lessons from the Literature. J Clin Med 2020; 9:jcm9092845. [PMID: 32887458 PMCID: PMC7563526 DOI: 10.3390/jcm9092845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Otitis media (OM) is one of the most common diseases occurring during childhood. Microbiological investigations concerning this topic have been primarily focused on the four classical otopathogens (Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pyogenes) mainly because most of the studies have been conducted with culture-dependent methods. In recent years, the introduction of culture-independent techniques has allowed high-throughput investigation of entire bacterial communities, leading to a better comprehension of the role of resident flora in health and disease. The upper respiratory tract (URT) is a region of major interest in otitis media pathogenesis, as it could serve as a source of pathogens for the middle ear (ME). Studies conducted with culture-independent methods in the URT and ME have provided novel insights on the pathogenesis of middle ear diseases through the identification of both possible new causative agents and of potential protective bacteria, showing that imbalances in bacterial communities could influence the natural history of otitis media in children. The aim of this review is to examine available evidence in microbiome research and otitis media in the pediatric age, with a focus on its different phenotypes: acute otitis media, otitis media with effusion and chronic suppurative otitis media.
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Affiliation(s)
- Francesco Folino
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (I.C.); (S.A.); (P.M.)
- Correspondence:
| | - Luca Ruggiero
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Pasquale Capaccio
- Department of Otolaryngology and Head and Neck Surgery, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (P.C.); (S.T.)
- Department of Biomedical Surgical Dental Science, University of Milan, 20122 Milan, Italy
| | - Ilaria Coro
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (I.C.); (S.A.); (P.M.)
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Stefano Aliberti
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (I.C.); (S.A.); (P.M.)
- Internal Medicine Department, Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Lorenzo Drago
- Laboratory of Clinical Microbiology, Department of Biomedical Science for Health, University of Milan, 20122 Milan, Italy;
| | - Paola Marchisio
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (I.C.); (S.A.); (P.M.)
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Sara Torretta
- Department of Otolaryngology and Head and Neck Surgery, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (P.C.); (S.T.)
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
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12
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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] [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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13
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Giese APJ, Ali S, Isaiah A, Aziz I, Riazuddin S, Ahmed ZM. Genomics of Otitis Media (OM): Molecular Genetics Approaches to Characterize Disease Pathophysiology. Front Genet 2020; 11:313. [PMID: 32391049 PMCID: PMC7191070 DOI: 10.3389/fgene.2020.00313] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 03/16/2020] [Indexed: 12/21/2022] Open
Abstract
Otitis media (OM) is an infective and inflammatory disorder known to be a major cause of hearing impairment across all age groups. Both acute and chronic OM result in substantial healthcare utilization related to antibiotic prescription and surgical procedures necessary for its management. Although several studies provided evidence of genetics playing a significant role in the susceptibility to OM, we had limited knowledge about the genes associated with OM until recently. Here we have summarized the known genetic factors that confer susceptibility to various forms of OM in mice and in humans and their genetic load, along with associated cellular signaling pathways. Spotlighted in this review are fucosyltransferase (FUT) enzymes, which have been implicated in the pathogenesis of OM. A comprehensive understanding of the functions of OM-associated genes may provide potential opportunities for its diagnosis and treatment.
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Affiliation(s)
- Arnaud P J Giese
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Saadat Ali
- The Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Amal Isaiah
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Ishrat Aziz
- Department of Biotechnology, Virtual University of Pakistan, Lahore, Pakistan
| | - Saima Riazuddin
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Zubair M Ahmed
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
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14
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Geng R, Wang Q, Chen E, Zheng QY. Current Understanding of Host Genetics of Otitis Media. Front Genet 2020; 10:1395. [PMID: 32117425 PMCID: PMC7025460 DOI: 10.3389/fgene.2019.01395] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022] Open
Abstract
The pathogenesis of otitis media (OM), an inflammatory disease of the middle ear (ME), involves interplay between many different factors, including the pathogenicity of infectious pathogens, host immunological status, environmental factors, and genetic predisposition, which is known to be a key determinant of OM susceptibility. Animal models and human genetics studies have identified many genes and gene variants associated with OM susceptibility: genes that encode components of multiple signaling pathways involved in host immunity and inflammatory responses of the ME mucosa; genes involved in cellular function, such as mucociliary transport, mucin production, and mucous cell metaplasia; and genes that are essential for Eustachian tube (ET) development, ME cavitation, and homeostasis. Since our last review, several new mouse models with mutations in genes such as CCL3, IL-17A, and Nisch have been reported. Moreover, genetic variants and polymorphisms in several genes, including FNDC1, FUT2, A2ML1, TGIF1, CD44, and IL1-RA variable number tandem repeat (VNTR) allele 2, have been identified as being significantly associated with OM. In this review, we focus on the current understanding of the role of host genetics in OM, including recent discoveries and future research prospects. Further studies on the genes identified thus far and the discovery of new genes using advanced technologies such as gene editing, next generation sequencing, and genome-wide association studies, will advance our understanding of the molecular mechanism underlying the pathogenesis of OM and provide new avenues for early screening and developing effective preventative and therapeutic strategies to treat OM.
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Affiliation(s)
- Ruishuang Geng
- College of Special Education, Binzhou Medical University, Yantai, China
| | - Qingzhu Wang
- College of Special Education, Binzhou Medical University, Yantai, China.,Department of Otolaryngology, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Eileen Chen
- Department of Otolaryngology, Case Western Reserve University, Cleveland, OH, United States
| | - Qing Yin Zheng
- Department of Otolaryngology, Case Western Reserve University, Cleveland, OH, United States
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15
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Baschal EE, Larson ED, Bootpetch Roberts TC, Pathak S, Frank G, Handley E, Dinwiddie J, Moloney M, Yoon PJ, Gubbels SP, Scholes MA, Cass SP, Jenkins HA, Frank DN, Yang IV, Schwartz DA, Ramakrishnan VR, Santos-Cortez RLP. Identification of Novel Genes and Biological Pathways That Overlap in Infectious and Nonallergic Diseases of the Upper and Lower Airways Using Network Analyses. Front Genet 2020; 10:1352. [PMID: 32010199 PMCID: PMC6979043 DOI: 10.3389/fgene.2019.01352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
Previous genetic studies on susceptibility to otitis media and airway infections have focused on immune pathways acting within the local mucosal epithelium, and outside of allergic rhinitis and asthma, limited studies exist on the overlaps at the gene, pathway or network level between the upper and lower airways. In this report, we compared [1] pathways identified from network analysis using genes derived from published genome-wide family-based and association studies for otitis media, sinusitis, and lung phenotypes, to [2] pathways identified using differentially expressed genes from RNA-sequence data from lower airway, sinus, and middle ear tissues, in particular cholesteatoma tissue compared to middle ear mucosa. For otitis media, a large number of genes (n = 1,806) were identified as differentially expressed between cholesteatoma and middle ear mucosa, which in turn led to the identification of 68 pathways that are enriched in cholesteatoma. Two differentially expressed genes CR1 and SAA1 overlap in middle ear, sinus, and lower airway samples and are potentially novel genes for otitis media susceptibility. In addition, 56 genes were differentially expressed in both tissues from the middle ear and either sinus or lower airways. Pathways that are common in upper and lower airway diseases, whether from published DNA studies or from our RNA-sequencing analyses, include chromatin organization/remodeling, endocytosis, immune system process, protein folding, and viral process. Taken together, our findings from genetic susceptibility and differential tissue expression studies support the hypothesis that the unified airway theory wherein the upper and lower respiratory tracts act as an integrated unit also applies to infectious and nonallergic airway epithelial disease. Our results may be used as reference for identification of genes or pathways that are relevant to upper and lower airways, whether common across sites, or unique to each disease.
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Affiliation(s)
- Erin E Baschal
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Eric D Larson
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Tori C Bootpetch Roberts
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Shivani Pathak
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Gretchen Frank
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Elyse Handley
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Jordyn Dinwiddie
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Molly Moloney
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Patricia J Yoon
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Samuel P Gubbels
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Melissa A Scholes
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Stephen P Cass
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Herman A Jenkins
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Daniel N Frank
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ivana V Yang
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - David A Schwartz
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Vijay R Ramakrishnan
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Regie Lyn P Santos-Cortez
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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16
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Mittal R, Sanchez-Luege SV, Wagner SM, Yan D, Liu XZ. Recent Perspectives on Gene-Microbe Interactions Determining Predisposition to Otitis Media. Front Genet 2019; 10:1230. [PMID: 31850076 PMCID: PMC6901973 DOI: 10.3389/fgene.2019.01230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/06/2019] [Indexed: 01/15/2023] Open
Abstract
A comprehensive understanding about the pathogenesis of otitis media (OM), one of the most common pediatric diseases, has the potential to alleviate a substantial disease burden across the globe. Advancements in genetic and bioinformatic detection methods, as well as a growing interest in the microbiome, has enhanced the capability of researchers to investigate the interplay between host genes, host microbiome, invading bacteria, and resulting OM susceptibility. Early studies deciphering the role of genetics in OM susceptibility assessed the heritability of the phenotype in twin and triplet studies, followed by linkage studies, candidate gene approaches, and genome-wide association studies that have helped in the identification of specific loci. With the advancements in techniques, various chromosomal regions and genes such as FBXO11, TGIF1, FUT2, FNDC1, and others have been implicated in predisposition to OM, yet questions still remain as to whether these implicated genes truly play a causative role in OM and to what extent. Meanwhile, 16S ribosomal RNA (rRNA) sequencing, microbial quantitative trait loci (mbQTL), and microbial genome-wide association studies (mGWAS) have mapped the microbiome of upper airways sites and therefore helped in enabling a more detailed study of interactions between host polymorphisms and host microbiome composition. Variants of specific genes conferring increased OM susceptibility, such as A2ML1, have also been shown to influence the microbial composition of the outer and middle ear in patients with OM, suggesting their role as mediators of disease. These interactions appear to impact the colonization of known otopathogens (Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis), as well as Neisseria, Gemella, Porphyromonas, Alloprevotella, and Fusobacterium populations that have also been implicated in OM pathogenesis. Meanwhile, studies demonstrating an increased abundance of Dolosigranulum and Corynebacterium in healthy patients compared to those with OM suggest a protective role for these bacteria, thereby introducing potential avenues for future probiotic treatment. Incorporating insights from these genetic, microbiome, and host-pathogen studies will allow for a more robust, comprehensive understanding of OM pathogenesis that can ultimately facilitate in the development of exciting new treatment modalities.
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Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Sebastian V Sanchez-Luege
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Shannon M Wagner
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States.,Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States.,Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States
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17
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The SLC26A4 c.706C>G (p.Leu236Val) Variant is a Frequent Cause of Hearing Impairment in Filipino Cochlear Implantees. Otol Neurotol 2019; 39:e726-e730. [PMID: 30113565 DOI: 10.1097/mao.0000000000001893] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
HYPOTHESIS Variants in SLC26A4 are an important cause of congenital hearing impairment in the Philippines. BACKGROUND Cochlear implantation is a standard rehabilitation option for congenital hearing impairment worldwide, but places a huge cost burden in lower-income countries. The study of risk factors such as genetic variants that may help determine genetic etiology of hearing loss and also predict cochlear implant outcomes is therefore beneficial. METHODS DNA samples from 29 GJB2-negative Filipino cochlear implantees were Sanger-sequenced for the coding exons of SLC26A4. Exome sequencing was performed to confirm results. RESULTS Four cochlear implantees with bilaterally enlarged vestibular aqueducts (EVA) were homozygous for the pathogenic SLC26A4 c.706C>G (p.Leu236Val) variant, which has a minor allele frequency of 0.0015 in Filipino controls. In patients with the SLC26A4 variant there was no association between cochlear implant outcome and age at implantation or duration of implant. There was also no association between the occurrence of the SLC26A4 variant and postsurgical audiometric thresholds and parents' evaluation of aural/oral performance of children (PEACH) scores. On the other hand, the SLC26A4 variant increased presurgical median audiometric thresholds (p = 0.01), particularly at 500 to 2000 Hz. CONCLUSION The SLC26A4 c.706C>G (p.Leu236Val) variant is a frequent cause of congenital hearing impairment in Filipinos and is associated with bilateral EVA and increased presurgical audiometric thresholds, but does not adversely affect post-implant outcomes.
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18
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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] [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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19
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Dewan KK, Taylor-Mulneix DL, Campos LL, Skarlupka AL, Wagner SM, Ryman VE, Gestal MC, Ma L, Blas-Machado U, Faddis BT, Harvill ET. A model of chronic, transmissible Otitis Media in mice. PLoS Pathog 2019; 15:e1007696. [PMID: 30970038 PMCID: PMC6476515 DOI: 10.1371/journal.ppat.1007696] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 04/22/2019] [Accepted: 03/11/2019] [Indexed: 12/15/2022] Open
Abstract
Infection and inflammation of the middle ears that characterizes acute and chronic otitis media (OM), is a major reason for doctor visits and antibiotic prescription, particularly among children. Nasopharyngeal pathogens that are commonly associated with OM in humans do not naturally colonize the middle ears of rodents, and experimental models in most cases involve directly injecting large numbers of human pathogens into the middle ear bullae of rodents, where they induce a short-lived acute inflammation but fail to persist. Here we report that Bordetella pseudohinzii, a respiratory pathogen of mice, naturally, efficiently and rapidly ascends the eustachian tubes to colonize the middle ears, causing acute and chronic histopathological changes with progressive decrease in hearing acuity that closely mimics otitis media in humans. Laboratory mice experimentally inoculated intranasally with very low numbers of bacteria consistently have their middle ears colonized and subsequently transmit the bacterium to cage mates. Taking advantage of the specifically engineered and well characterized immune deficiencies available in mice we conducted experiments to uncover different roles of T and B cells in controlling bacterial numbers in the middle ear during chronic OM. The iconic mouse model provides significant advantages for elucidating aspects of host-pathogen interactions in otitis media that are currently not possible using other animal models. This natural model of otitis media permits the study of transmission between hosts, efficient early colonization of the respiratory tract, ascension of the eustachian tube, as well as colonization, pathogenesis and persistence in the middle ear. It also allows the combination of the powerful tools of mouse molecular immunology and bacterial genetics to determine the mechanistic basis for these important processes.
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Affiliation(s)
- Kalyan K. Dewan
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| | - Dawn L. Taylor-Mulneix
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Laura L. Campos
- University of Colorado Hospital, Aurora, Colorado, United States of America
| | - Amanda L. Skarlupka
- Department of Microbiology, Franklin College of Arts and Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Shannon M. Wagner
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Valerie E. Ryman
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Monica C. Gestal
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Longhua Ma
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Uriel Blas-Machado
- Department of Pathology, Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Brian T. Faddis
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Eric T. Harvill
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
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20
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Blanc F, Ayache D, Calmels MN, Deguine O, François M, Leboulanger N, Lescanne E, Marianowski R, Nevoux J, Nicollas R, Tringali S, Tessier N, Franco-Vidal V, Bordure P, Mondain M. Management of otitis media with effusion in children. Société française d'ORL et de chirurgie cervico-faciale clinical practice guidelines. Eur Ann Otorhinolaryngol Head Neck Dis 2019; 135:269-273. [PMID: 29759911 DOI: 10.1016/j.anorl.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Société française d'ORL et de chirurgie cervico-faciale clinical practice guidelines concern the management of otitis media with effusion (OME) in children under the age of 12 years. They are based on extensive review of MEDLINE and Cochrane Library publications in English or French from 1996 to 2016 concerning the methods of diagnosis and assessment of otitis media with effusion, as well as the efficacy of tympanostomy tubes and medical and surgical treatments of OME.
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Affiliation(s)
- F Blanc
- Service d'ORL, hôpital Gui-de-Chauliac, CHU de Montpellier, 34000 Montpellier, France.
| | - D Ayache
- Service d'ORL, fondation Rothschild, 75019 Paris, France
| | - M N Calmels
- Service d'ORL, hôpital Purpan, CHU de Toulouse, 31059 Toulouse, France
| | - O Deguine
- Service d'ORL, hôpital Purpan, CHU de Toulouse, 31059 Toulouse, France
| | - M François
- Service d'ORL, hôpital Robert-Debré, AP-HP, 75019 Paris, France
| | - N Leboulanger
- Service d'ORL, hôpital Necker, AP-HP, 75015 Paris, France
| | - E Lescanne
- Service d'ORL, CHU de Tours, 37000 Tours, France
| | | | - J Nevoux
- Service d'ORL, hôpital Kremlin-Bicêtre, AP-HP, 94270 Le Kremlin-Bicêtre, France
| | - R Nicollas
- Service d'ORL pédiatrique, AP-HM La Timone, 13005 Marseille, France
| | - S Tringali
- Service d'ORL, CHU de Lyon, 69003 Lyon, France
| | - N Tessier
- Service d'ORL, hôpital Robert-Debré, AP-HP, 75019 Paris, France
| | | | - P Bordure
- Service d'ORL, CHU de Nantes, 44093 Nantes, France
| | - M Mondain
- Service d'ORL, hôpital Gui-de-Chauliac, CHU de Montpellier, 34000 Montpellier, France
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21
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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] [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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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] [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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23
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Broekaert IJ, Becker K, Gottschalk I, Körber F, Dötsch J, Thiele H, Altmüller J, Nürnberg P, Hünseler C, Cirak S. Mutations in plasmalemma vesicle-associated protein cause severe syndromic protein-losing enteropathy. J Med Genet 2018; 55:637-640. [PMID: 29661969 DOI: 10.1136/jmedgenet-2018-105262] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/19/2018] [Accepted: 03/22/2018] [Indexed: 11/03/2022]
Abstract
BACKGROUND Protein-losing enteropathy (PLE) is characterised by gastrointestinal protein leakage due to loss of mucosal integrity or lymphatic abnormalities. PLE can manifest as congenital diarrhoea and should be differentiated from other congenital diarrhoeal disorders. Primary PLEs are genetically heterogeneous and the underlying genetic defects are currently emerging. OBJECTIVES We report an infant with fatal PLE for whom we aimed to uncover the underlying pathogenic mutation. METHODS We performed whole exome sequencing (WES) for the index patient. Variants were classified based on the American College of Medical Genetics and Genomics guidelines. WES results and our detailed clinical description of the patient were compared with the literature. RESULTS We discovered a novel homozygous stop mutation (c.988C>T, p.Q330*) in the Plasmalemma Vesicle-Associated Protein (PLVAP) gene in a newborn with fatal PLE, facial dysmorphism, and renal, ocular and cardiac anomalies. The Q330* mutation is predicted to result in complete loss of PLVAP protein expression leading to deletion of the diaphragms of endothelial fenestrae, resulting in plasma protein extravasation and PLE. Recently, another single homozygous stop mutation in PLVAP causing lethal PLE in an infant was reported. CONCLUSIONS Our findings validate PLVAP mutations as a cause of syndromic PLE. Prenatal anomalies, severe PLE and syndromic features may guide the diagnosis of this rare disease.
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Affiliation(s)
| | - Kerstin Becker
- Department of Pediatrics, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Ingo Gottschalk
- Department of Gynecology, University Hospital Cologne, Cologne, Germany
| | - Friederike Körber
- Department of Radiology, University Hospital Cologne, Cologne, Germany
| | - Jörg Dötsch
- Department of Pediatrics, University Hospital Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | | | - Sebahattin Cirak
- Department of Pediatrics, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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Simon F, Haggard M, Rosenfeld RM, Jia H, Peer S, Calmels MN, Couloigner V, Teissier N. International consensus (ICON) on management of otitis media with effusion in children. Eur Ann Otorhinolaryngol Head Neck Dis 2018; 135:S33-S39. [PMID: 29398506 DOI: 10.1016/j.anorl.2017.11.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 11/28/2017] [Accepted: 11/30/2017] [Indexed: 12/31/2022]
Abstract
Otitis media with effusion (OME) is a common childhood disease defined as the presence of liquid in the middle ear without signs or symptoms of acute ear infection. Children can be impacted mainly with hearing impairment and/or co-occurring recurrent acute otitis media (AOM) thus requiring treatment. Although many meta-analyses and national guidelines have been issued, management remains difficult to standardize, and use of surgical and medical treatments continue to vary. We convened an international consensus conference as part of the 2017 International Federation of Oto-rhino-laryngological Societies Congress, to identify best practices in OME management. Overall, regional differences were minor and consensual management was obtained on several important issues. At initial assessment, although a thorough medical examination is necessary to seek reflux, allergy or nasal obstruction symptoms; an age-appropriate auditory test is the only assessment required in children without abnormal history. Non-surgical treatments poorly address the underlying problem of an age-dependent dysfunctional Eustachian tube; auto-inflation seems to be the only beneficial, low-risk and low-cost non-surgical therapy. There was a clear international recommendation against using steroids, antibiotics, decongestants or antihistamines to treat OME, because of side-effects, cost issues and no convincing evidence of long-term effectiveness. Decisions to insert tympanostomy ventilation tubes should be based on an auditory test but also take into account the child's context and overall hearing difficulties. Tubes significantly improve hearing and reduce the number of recurrent AOM with effusion while in place. Adjuvant adenoidectomy should be considered in children over four years of age, and in those with significant nasal obstruction or infection.
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Affiliation(s)
- F Simon
- Department of Pediatric Otolaryngology, hôpital Necker-Enfants-Malades, Paris-Descartes University, AP-HP, 149, rue de Sèvres, 75015 Paris, France
| | - M Haggard
- Department of Psychology, Cambridge University, Downing Street, Cambridge CB2 3EB, United Kingdom
| | - R M Rosenfeld
- Department of Otolaryngology, SUNY Downstate Medical Center, 450, Clarkson avenue, MSC 126, Brooklyn, NY 11203, United States of America
| | - H Jia
- Department of Otolaryngology, Shanghai Ninth People's Hospital & Shanghai Jiaotong University School of Medicine, 639, Zhizaoju Road, Shanghai 200011, China
| | - S Peer
- Department of Pediatric Otolaryngology, Red Cross War Memorial Children's Hospital, University of Cape Town,, Rondebosch, Cape Town 7700, South Africa
| | - M-N Calmels
- Department of Otolaryngology, Purpan Hospital, Paul-Sabatier-Toulouse-3 University, CHU de Toulouse, 1, place du Dr-Baylac, 31059 Toulouse, France
| | - V Couloigner
- Department of Pediatric Otolaryngology, hôpital Necker-Enfants-Malades, Paris-Descartes University, AP-HP, 149, rue de Sèvres, 75015 Paris, France
| | - N Teissier
- Department of Pediatric Otolaryngology, hôpital Robert-Debré, Paris-Diderot University, AP-HP, 48, boulevard Sérurier, 75019 Paris, France.
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Hansen RD, Christensen AF, Olesen J. Family studies to find rare high risk variants in migraine. J Headache Pain 2017; 18:32. [PMID: 28255817 PMCID: PMC5334193 DOI: 10.1186/s10194-017-0729-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/27/2017] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Migraine has long been known as a common complex disease caused by genetic and environmental factors. The pathophysiology and the specific genetic susceptibility are poorly understood. Common variants only explain a small part of the heritability of migraine. It is thought that rare genetic variants with bigger effect size may be involved in the disease. Since migraine has a tendency to cluster in families, a family approach might be the way to find these variants. This is also indicated by identification of migraine-associated loci in classical linkage-analyses in migraine families. A single migraine study using a candidate-gene approach was performed in 2010 identifying a rare mutation in the TRESK potassium channel segregating in a large family with migraine with aura, but this finding has later become questioned. The technologies of next-generation sequencing (NGS) now provides an affordable tool to investigate the genetic variation in the entire exome or genome. The family-based study design using NGS is described in this paper. We also review family studies using NGS that have been successful in finding rare variants in other common complex diseases in order to argue the promising application of a family approach to migraine. METHOD PubMed was searched to find studies that looked for rare genetic variants in common complex diseases through a family-based design using NGS, excluding studies looking for de-novo mutations, or using a candidate-gene approach and studies on cancer. All issues from Nature Genetics and PLOS genetics 2014, 2015 and 2016 (UTAI June) were screened for relevant papers. Reference lists from included and other relevant papers were also searched. For the description of the family-based study design using NGS an in-house protocol was used. RESULTS Thirty-two successful studies, which covered 16 different common complex diseases, were included in this paper. We also found a single migraine study. Twenty-three studies found one or a few family specific variants (less than five), while other studies found several possible variants. Not all of them were genome wide significant. Four studies performed follow-up analyses in unrelated cases and controls and calculated odds ratios that supported an association between detected variants and risk of disease. Studies of 11 diseases identified rare variants that segregated fully or to a large degree with the disease in the pedigrees. CONCLUSION It is possible to find rare high risk variants for common complex diseases through a family-based approach. One study using a family approach and NGS to find rare variants in migraine has already been published but with strong limitations. More studies are under way.
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Affiliation(s)
- Rikke Dyhr Hansen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
| | - Anne Francke Christensen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
| | - Jes Olesen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
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Granath A. Recurrent Acute Otitis Media: What Are the Options for Treatment and Prevention? CURRENT OTORHINOLARYNGOLOGY REPORTS 2017; 5:93-100. [PMID: 28616364 PMCID: PMC5446546 DOI: 10.1007/s40136-017-0151-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Purpose of Review To survey current strategies for treatment and prevention of recurrent acute otitis media (rAOM). Recent Findings Treatment with systemic antibiotics is required in recurrent episodes of acute otitis media. A cautious attitude is recommended due to antibiotic resistance. Antibiotics also provide effective prophylaxis for rAOM. Topical treatment with ear drops is recommended in rAOM with otorrhea from tympanostomy tubes. Pneumococcal conjugated vaccines seem to have a moderate reductive effect on overall otitis media. The effect on rAOM is still unclear. Different administrations of immunoglobulins have not been effective against rAOM. Breastfeeding had a protective effect against rAOM. A recommendation against cigarette smoke exposure as a measure to prevent otitis seems warranted. An effect for adenoidectomy in children <2 years old with rAOM has been suggested. There is a strong genetic connection with rAOM. Probiotics and nasal spray with Streptococci might offer future opportunities as prophylaxis. Too little is known about complimentary treatments to give any recommendations. Summary Systemic antibiotics are still needed as treatment against episodes of AOM in rAOM children. There are several preventive measures that can be taken to reduce the burden of AOM but they all have a small-moderate effect. Systemic antibiotics provide effective prophylaxis in rAOM, but must be used with extreme caution due to the emerging antibiotic resistance.
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Affiliation(s)
- Anna Granath
- ENT-Department Karolinska University Hospital and Department of Clinical Science Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
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27
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Lin J, Hafrén H, Kerschner J, Jian-Dong L, Brown S, Zheng QY, Preciado D, Nakamura Y, Huang Q, Zhang Y. Panel 3: Genetics and Precision Medicine of Otitis Media. Otolaryngol Head Neck Surg 2017; 156:S41-S50. [PMID: 28372532 PMCID: PMC6211190 DOI: 10.1177/0194599816685559] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 12/01/2016] [Indexed: 12/31/2022]
Abstract
Objective The objective is to perform a comprehensive review of the literature up to 2015 on the genetics and precision medicine relevant to otitis media. Data Sources PubMed database of the National Library of Medicine. Review Methods Two subpanels were formed comprising experts in the genetics and precision medicine of otitis media. Each of the panels reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The entire panel met at the 18th International Symposium on Recent Advances in Otitis Media in June 2015 and discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members. Conclusion Many genes relevant to otitis media have been identified in the last 4 years in advancing our knowledge regarding the predisposition of the middle ear mucosa to commensals and pathogens. Advances include mutant animal models and clinical studies. Many signaling pathways are involved in the predisposition of otitis media. Implications for Practice New knowledge on the genetic background relevant to otitis media forms a basis of novel potential interventions, including potential new ways to treat otitis media.
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Affiliation(s)
- Jizhen Lin
- Department of Otolaryngology–Head and Neck Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hena Hafrén
- Departments of Otorhinolaryngology–Head and Neck Surgery, Helsinki University Hospital, Helsinki, Finland
| | - Joseph Kerschner
- Department of Otorhinolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Li Jian-Dong
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | - Steve Brown
- Medical Research Council Harwell Institute, Oxfordshire, UK
| | - Qing Y. Zheng
- Department of Otolaryngology–Head and Neck Surgery, Case Western University, Cleveland, Ohio, USA
| | - Diego Preciado
- Shiekh Zayed Institute for Pediatric Surgical Innovation, Pediatric Otolaryngology, Children’s National Health System, Washington, DC, USA
| | | | - Qiuhong Huang
- Department of Otolaryngology, Sun Yat-sen University, Guangzhou, China
| | - Yan Zhang
- Department of Otolaryngology, Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
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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] [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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29
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Ruben RJ. The trajectory of Pediatric Otolaryngology. Int J Pediatr Otorhinolaryngol 2016; 89:179-82. [PMID: 27401025 DOI: 10.1016/j.ijporl.2016.06.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Robert J Ruben
- Albert Einstein College of Medicine, Montefiore Medical Center, United States.
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30
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Genome-wide association study for acute otitis media in children identifies FNDC1 as disease contributing gene. Nat Commun 2016; 7:12792. [PMID: 27677580 PMCID: PMC5052699 DOI: 10.1038/ncomms12792] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 08/02/2016] [Indexed: 02/07/2023] Open
Abstract
Acute otitis media (AOM) is among the most common pediatric diseases, and the most frequent reason for antibiotic treatment in children. Risk of AOM is dependent on environmental and host factors, as well as a significant genetic component. We identify genome-wide significance at a locus on 6q25.3 (rs2932989, Pmeta=2.15 × 10−09), and show that the associated variants are correlated with the methylation status of the FNDC1 gene (cg05678571, P=1.43 × 10−06), and further show it is an eQTL for FNDC1 (P=9.3 × 10−05). The mouse homologue, Fndc1, is expressed in middle ear tissue and its expression is upregulated upon lipopolysaccharide treatment. In this first GWAS of AOM and the largest OM genetic study to date, we identify the first genome-wide significant locus associated with AOM. Acute otitis media (AOM) is an acute infection of middle ear mucosa and among the most common pediatric diseases. Here, the authors performed a genome-wide association study to link a variant in the FNDC1 locus on 6q25.3 and differential methylation status of the FNDC1 gene with predisposition to AOM.
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31
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Padilla CD, Cutiongco-de la Paz EM. Genetics and genomic medicine in the Philippines. Mol Genet Genomic Med 2016; 4:494-503. [PMID: 27652277 PMCID: PMC5023934 DOI: 10.1002/mgg3.247] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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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32
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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] [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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