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Cinciripini PM, Wetter DW, Wang J, Yu R, Kypriotakis G, Kumar T, Robinson JD, Cui Y, Green CE, Bergen AW, Kosten TR, Scherer SE, Shete S. Deep sequencing of candidate genes identified 14 variants associated with smoking abstinence in an ethnically diverse sample. Sci Rep 2024; 14:6385. [PMID: 38493193 PMCID: PMC10944542 DOI: 10.1038/s41598-024-56750-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
Despite the large public health toll of smoking, genetic studies of smoking cessation have been limited with few discoveries of risk or protective loci. We investigated common and rare variant associations with success in quitting smoking using a cohort from 8 randomized controlled trials involving 2231 participants and a total of 10,020 common and 24,147 rare variants. We identified 14 novel markers including 6 mapping to genes previously related to psychiatric and substance use disorders, 4 of which were protective (CYP2B6 (rs1175607105), HTR3B (rs1413172952; rs1204720503), rs80210037 on chr15), and 2 of which were associated with reduced cessation (PARP15 (rs2173763), SCL18A2 (rs363222)). The others mapped to areas associated with cancer including FOXP1 (rs1288980) and ZEB1 (rs7349). Network analysis identified significant canonical pathways for the serotonin receptor signaling pathway, nicotine and bupropion metabolism, and several related to tumor suppression. Two novel markers (rs6749438; rs6718083) on chr2 are flanked by genes associated with regulation of bodyweight. The identification of novel loci in this study can provide new targets of pharmacotherapy and inform efforts to develop personalized treatments based on genetic profiles.
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Affiliation(s)
- Paul M Cinciripini
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - David W Wetter
- Department of Department of Population Health Sciences, University of Utah and Huntsman Cancer Institute, Salt Lake City, Utah, 84112, USA
| | - Jian Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Robert Yu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - George Kypriotakis
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Tapsi Kumar
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jason D Robinson
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yong Cui
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Charles E Green
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX, 77030, USA
| | | | - Thomas R Kosten
- Department of Psychiatry, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Steven E Scherer
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sanjay Shete
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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Ingersoll MA, Lutze RD, Kelmann RG, Kresock DF, Marsh JD, Quevedo RV, Zuo J, Teitz T. KSR1 knockout mouse model demonstrates MAPK pathway's key role in cisplatin- and noise-induced hearing loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566316. [PMID: 38014104 PMCID: PMC10680565 DOI: 10.1101/2023.11.08.566316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Hearing loss is a major disability in everyday life and therapeutic interventions to protect hearing would benefit a large portion of the world population. Here we found that mice devoid of the protein kinase suppressor of RAS 1 (KSR1) in their tissues (germline KO mice) exhibit resistance to both cisplatin- and noise-induced permanent hearing loss compared to their wild-type KSR1 littermates. KSR1 is expressed in the cochlea and is a scaffold protein that brings in proximity the mitogen-activated protein kinase (MAPK) proteins BRAF, MEK and ERK and assists in their activation through a phosphorylation cascade induced by both cisplatin and noise insults in the cochlear cells. Deleting the KSR1 protein tempered down the MAPK phosphorylation cascade in the cochlear cells following both cisplatin and noise insults and conferred hearing protection of up to 30 dB SPL in three tested frequencies in mice. Treatment with dabrafenib, an FDA-approved oral BRAF inhibitor, downregulated the MAPK kinase cascade and protected the KSR1 wild-type mice from both cisplatin- and noise-induced hearing loss. Dabrafenib treatment did not enhance the protection of KO KSR1 mice, as excepted, providing evidence dabrafenib works primarily through the MAPK pathway. Thus, either elimination of the KSR1 gene expression or drug inhibition of the MAPK cellular pathway in mice resulted in profound protection from both cisplatin- and noise-induce hearing loss. Inhibition of the MAPK pathway, a cellular pathway that responds to damage in the cochlear cells, can prove a valuable strategy to protect and treat hearing loss.
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Affiliation(s)
- Matthew A. Ingersoll
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Richard D. Lutze
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Regina G. Kelmann
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Daniel F. Kresock
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Jordan D. Marsh
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Rene V. Quevedo
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Jian Zuo
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Tal Teitz
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA
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Gregory GE, Munro KJ, Couper KN, Pathmanaban ON, Brough D. The NLRP3 inflammasome as a target for sensorineural hearing loss. Clin Immunol 2023; 249:109287. [PMID: 36907540 DOI: 10.1016/j.clim.2023.109287] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/08/2023] [Accepted: 02/24/2023] [Indexed: 03/14/2023]
Abstract
Sensorineural hearing loss is the most common type of hearing loss in adults and occurs due to damage of the inner ear caused by a range of factors including ageing, excessive noise, toxins, and cancer. Auto-inflammatory disease is also a cause of hearing loss and there is evidence that inflammation could contribute to hearing loss in other conditions. Within the inner ear there are resident macrophage cells that respond to insults and whose activation correlates with damage. The NLRP3 inflammasome is a multi-molecular pro-inflammatory protein complex that forms in activated macrophages and may contribute to hearing loss. The aim of this article is to discuss the evidence for the NLRP3 inflammasome and associated cytokines as potential therapeutic targets for sensorineural hearing loss in conditions ranging from auto-inflammatory disease to tumour-induced hearing loss in vestibular schwannoma.
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Affiliation(s)
- Grace E Gregory
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK; Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK; The Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
| | - Kevin J Munro
- Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester, UK; Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Kevin N Couper
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK; The Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
| | - Omar N Pathmanaban
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK; Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK; The Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK; Department of Neurosurgery, Manchester Centre for Clinical Neurosciences, Salford Royal Hospital NHS Foundation Trust, Salford, UK.
| | - David Brough
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK; Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK; The Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK.
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4
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Wang H, Sun R, Xu N, Wang X, Bao M, Li X, Li J, Lin A, Feng J. Untargeted metabolomics of the cochleae from two laryngeally echolocating bats. Front Mol Biosci 2023; 10:1171366. [PMID: 37152899 PMCID: PMC10154556 DOI: 10.3389/fmolb.2023.1171366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023] Open
Abstract
High-frequency hearing is regarded as one of the most functionally important traits in laryngeally echolocating bats. Abundant candidate hearing-related genes have been identified to be the important genetic bases underlying high-frequency hearing for laryngeally echolocating bats, however, extensive metabolites presented in the cochleae have not been studied. In this study, we identified 4,717 annotated metabolites in the cochleae of two typical laryngeally echolocating bats using the liquid chromatography-mass spectroscopy technology, metabolites classified as amino acids, peptides, and fatty acid esters were identified as the most abundant in the cochleae of these two echolocating bat species, Rhinolophus sinicus and Vespertilio sinensis. Furthermore, 357 metabolites were identified as significant differentially accumulated (adjusted p-value <0.05) in the cochleae of these two bat species with distinct echolocating dominant frequencies. Downstream KEGG enrichment analyses indicated that multiple biological processes, including signaling pathways, nervous system, and metabolic process, were putatively different in the cochleae of R. sinicus and V. sinensis. For the first time, this study investigated the extensive metabolites and associated biological pathways in the cochleae of two laryngeal echolocating bats and expanded our knowledge of the metabolic molecular bases underlying high-frequency hearing in the cochleae of echolocating bats.
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Affiliation(s)
- Hui Wang
- College of Life Science, Jilin Agricultural University, Changchun, China
- *Correspondence: Hui Wang, ; Jiang Feng,
| | - Ruyi Sun
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Ningning Xu
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Xue Wang
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Mingyue Bao
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Xin Li
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Jiqian Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- College of Life Science, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- *Correspondence: Hui Wang, ; Jiang Feng,
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5
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Kaderbay A, Berger F, Bouamrani A, Bidart M, Petre G, Baguant A, Giraud L, Schmerber S. Perilymph metabolomic and proteomic MALDI-ToF profiling with porous silicon chips: a proof-of-concept study. Hear Res 2022; 417:108457. [DOI: 10.1016/j.heares.2022.108457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 01/16/2022] [Accepted: 01/27/2022] [Indexed: 11/30/2022]
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Key Signaling Pathways Regulate the Development and Survival of Auditory Hair Cells. Neural Plast 2021; 2021:5522717. [PMID: 34194486 PMCID: PMC8214483 DOI: 10.1155/2021/5522717] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/01/2021] [Accepted: 05/31/2021] [Indexed: 01/16/2023] Open
Abstract
The loss of auditory sensory hair cells (HCs) is the most common cause of sensorineural hearing loss (SNHL). As the main sound transmission structure in the cochlea, it is necessary to maintain the normal shape and survival of HCs. In this review, we described and summarized the signaling pathways that regulate the development and survival of auditory HCs in SNHL. The role of the mitogen-activated protein kinase (MAPK), phosphoinositide-3 kinase/protein kinase B (PI3K/Akt), Notch/Wnt/Atoh1, calcium channels, and oxidative stress/reactive oxygen species (ROS) signaling pathways are the most relevant. The molecular interactions of these signaling pathways play an important role in the survival of HCs, which may provide a theoretical basis and possible therapeutic interventions for the treatment of hearing loss.
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Lin HC, Ren Y, Lysaght AC, Kao SY, Stankovic KM. Proteome of normal human perilymph and perilymph from people with disabling vertigo. PLoS One 2019; 14:e0218292. [PMID: 31185063 PMCID: PMC6559673 DOI: 10.1371/journal.pone.0218292] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022] Open
Abstract
The vast majority of hearing loss, the most common sensory impairment, and vertigo, which commonly causes falls, both reflect underlying dysfunction of inner ear cells. Perilymph sampling can thus provide molecular cues to hearing and balance disorders. While such "liquid biopsy" of the inner ear is not yet in routine clinical practice, previous studies have uncovered alterations in perilymph in patients with certain types of hearing loss. However, the proteome of perilymph from patients with intact hearing has been unknown. Furthermore, no complete characterization of perilymph from patients with vestibular dysfunction has been reported. Here, using liquid-chromatography with tandem mass spectrometry, we analyzed samples of normal perilymph collected from three patients with skull base meningiomas and intact hearing. We identified 228 proteins that were common across the samples, establishing a greatly expanded proteome of the previously inferred normal human perilymph. Further comparison to perilymph obtained from three patients with vestibular dysfunction with drop attacks due to Meniere's disease showed 38 proteins with significantly differential abundance. The abundance of four protein candidates with previously unknown roles in inner ear biology was validated in murine cochleae by immunohistochemistry and in situ hybridization: AACT, HGFAC, EFEMP1, and TGFBI. Together, these results motivate future work in characterizing the normal human perilymph and identifying biomarkers of inner ear disease.
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Affiliation(s)
- Hsiao-Chun Lin
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, United States of America
- Eaton Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear, Boston, Massachusetts, United States of America
| | - Yin Ren
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, United States of America
- Eaton Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear, Boston, Massachusetts, United States of America
| | - Andrew C. Lysaght
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, United States of America
- Eaton Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear, Boston, Massachusetts, United States of America
- Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, United States of America
| | - Shyan-Yuan Kao
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, United States of America
- Eaton Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear, Boston, Massachusetts, United States of America
| | - Konstantina M. Stankovic
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, United States of America
- Eaton Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear, Boston, Massachusetts, United States of America
- Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, United States of America
- Harvard Program in Therapeutic Science, Harvard University, Boston, United States of America
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8
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McGuire JL, Depasquale EA, Funk AJ, O'Donnovan SM, Hasselfeld K, Marwaha S, Hammond JH, Hartounian V, Meador-Woodruff JH, Meller J, McCullumsmith RE. Abnormalities of signal transduction networks in chronic schizophrenia. NPJ SCHIZOPHRENIA 2017; 3:30. [PMID: 28900113 PMCID: PMC5595970 DOI: 10.1038/s41537-017-0032-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 07/07/2017] [Accepted: 07/31/2017] [Indexed: 12/11/2022]
Abstract
Schizophrenia is a serious neuropsychiatric disorder characterized by disruptions of brain cell metabolism, microstructure, and neurotransmission. All of these processes require coordination of multiple kinase-mediated signaling events. We hypothesize that imbalances in kinase activity propagate through an interconnected network of intracellular signaling with potential to simultaneously contribute to many or all of the observed deficits in schizophrenia. We established a workflow distinguishing schizophrenia-altered kinases in anterior cingulate cortex using a previously published kinome array data set. We compared schizophrenia-altered kinases to haloperidol-altered kinases, and identified systems, functions, and regulators predicted using pathway analyses. We used kinase inhibitors with the kinome array to test hypotheses about imbalance in signaling and conducted preliminary studies of kinase proteins, phosphoproteins, and activity for kinases of interest. We investigated schizophrenia-associated single nucleotide polymorphisms in one of these kinases, AKT, for genotype-dependent changes in AKT protein or activity. Kinome analyses identified new kinases as well as some previously implicated in schizophrenia. These results were not explained by chronic antipsychotic treatment. Kinases identified in our analyses aligned with cytoskeletal arrangement and molecular trafficking. Of the kinases we investigated further, AKT and (unexpectedly) JNK, showed the most dysregulation in the anterior cingulate cortex of schizophrenia subjects. Changes in kinase activity did not correspond to protein or phosphoprotein levels. We also show that AKT single nucleotide polymorphism rs1130214, previously associated with schizophrenia, influenced enzyme activity but not protein or phosphoprotein levels. Our data indicate subtle changes in kinase activity and regulation across an interlinked kinase network, suggesting signaling imbalances underlie the core symptoms of schizophrenia. A study by US scientists indicates that changes in the activity of key signaling proteins may underlie core symptoms of schizophrenia. Protein kinases mediate the activation of intracellular signaling events and analyses of the kinome, the complete set of protein kinases encoded in the genome, previously revealed significant changes in phosphorylation patterns in postmortem brain tissue from patients with schizophrenia. Based on these findings, Jennifer McGuire at the University of Cincinnati and colleagues investigated the upstream regulation of these proteins. They identified both established and novel proteins associated with schizophrenia in the anterior cingulate cortex, with JNK and AKT activity being the most disrupted in schizophrenia patients. Their findings highlight how subtle changes in the activity of a small number of signaling proteins can propagate and have major consequences for mental health.
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Affiliation(s)
- Jennifer L McGuire
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA.
| | - Erica A Depasquale
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Adam J Funk
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA
| | - Sinead M O'Donnovan
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA
| | - Kathryn Hasselfeld
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA
| | - Shruti Marwaha
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH, USA
| | - John H Hammond
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
| | - Vahram Hartounian
- Psychiatry & Neuroscience, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.,James J. Peters VA Medical Center, Mental Illness Research Education and Clinical Center (MIRECC), Bronx, NY, USA
| | - James H Meador-Woodruff
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
| | - Jarek Meller
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Departments of Environmental Health, Electrical Engineering & Computing Systems and Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Robert E McCullumsmith
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA
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Identifying novel genes and biological processes relevant to the development of cancer therapy-induced mucositis: An informative gene network analysis. PLoS One 2017; 12:e0180396. [PMID: 28678827 PMCID: PMC5498049 DOI: 10.1371/journal.pone.0180396] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 05/30/2017] [Indexed: 12/20/2022] Open
Abstract
Mucositis is a complex, dose-limiting toxicity of chemotherapy or radiotherapy that leads to painful mouth ulcers, difficulty eating or swallowing, gastrointestinal distress, and reduced quality of life for patients with cancer. Mucositis is most common for those undergoing high-dose chemotherapy and hematopoietic stem cell transplantation and for those being treated for malignancies of the head and neck. Treatment and management of mucositis remain challenging. It is expected that multiple genes are involved in the formation, severity, and persistence of mucositis. We used Ingenuity Pathway Analysis (IPA), a novel network-based approach that integrates complex intracellular and intercellular interactions involved in diseases, to systematically explore the molecular complexity of mucositis. As a first step, we searched the literature to identify genes that harbor or are close to the genetic variants significantly associated with mucositis. Our literature review identified 27 candidate genes, of which ERCC1, XRCC1, and MTHFR were the most frequently studied for mucositis. On the basis of this 27-gene list, we used IPA to generate gene networks for mucositis. The most biologically significant novel molecules identified through IPA analyses included TP53, CTNNB1, MYC, RB1, P38 MAPK, and EP300. Additionally, uracil degradation II (reductive) and thymine degradation pathways (p = 1.06-08) were most significant. Finally, utilizing 66 SNPs within the 8 most connected IPA-derived candidate molecules, we conducted a genetic association study for oral mucositis in the head and neck cancer patients who were treated using chemotherapy and/or radiation therapy (186 head and neck cancer patients with oral mucositis vs. 699 head and neck cancer patients without oral mucositis). The top ranked gene identified through this association analysis was RB1 (rs2227311, p-value = 0.034, odds ratio = 0.67). In conclusion, gene network analysis identified novel molecules and biological processes, including pathways related to inflammation and oxidative stress, that are relevant to mucositis development, thus providing the basis for future studies to improve the management and treatment of mucositis in patients with cancer.
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Bahrami SB, Tolg C, Peart T, Symonette C, Veiseh M, Umoh JU, Holdsworth DW, McCarthy JB, Luyt LG, Bissell MJ, Yazdani A, Turley EA. Receptor for hyaluronan mediated motility (RHAMM/HMMR) is a novel target for promoting subcutaneous adipogenesis. Integr Biol (Camb) 2017; 9:223-237. [PMID: 28217782 DOI: 10.1039/c7ib00002b] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hyaluronan, CD44 and the Receptor for Hyaluronan-Mediated Motility (RHAMM, gene name HMMR) regulate stem cell differentiation including mesenchymal progenitor differentiation. Here, we show that CD44 expression is required for subcutaneous adipogenesis, whereas RHAMM expression suppresses this process. We designed RHAMM function blocking peptides to promote subcutaneous adipogenesis as a clinical and tissue engineering tool. Adipogenic RHAMM peptides were identified by screening for their ability to promote adipogenesis in culture assays using rat bone marrow mesenchymal stem cells, mouse pre-adipocyte cell lines and primary human subcutaneous pre-adipocytes. Oil red O uptake into fat droplets and adiponectin production were used as biomarkers of adipogenesis. Positive peptides were formulated in either collagen I or hyaluronan (Orthovisc) gels then assessed for their adipogenic potential in vivo following injection into dorsal rat skin and mammary fat pads. Fat content was quantified and characterized using micro CT imaging, morphometry, histology, RT-PCR and ELISA analyses of adipogenic gene expression. Injection of screened peptides increased dorsal back subcutaneous fat pad area (208.3 ± 10.4 mm2versus control 84.11 ± 4.2 mm2; p < 0.05) and mammary fat pad size (45 ± 11 mg above control background, p = 0.002) in female rats. This effect lasted >5 weeks as detected by micro CT imaging and perilipin 1 mRNA expression. RHAMM expression suppresses while blocking peptides promote expression of PPARγ, C/EBP and their target genes. Blocking RHAMM function by peptide injection or topical application is a novel and minimally invasive method for potentially promoting subcutaneous adipogenesis in lipodystrophic diseases and a complementary tool to subcutaneous fat augmentation techniques.
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Affiliation(s)
- S B Bahrami
- Biological Systems and Engineering Division, BioSciences Area, Lawrence Berkeley National Laboratories, 977R225A, Berkeley, CA 94720, USA
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11
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Prevention of gentamicin ototoxicity with N-acetylcysteine and vitamin A. The Journal of Laryngology & Otology 2016; 130:440-6. [PMID: 27095551 DOI: 10.1017/s0022215116000992] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OBJECTIVE To investigate the use of systemic N-acetylcysteine and vitamin A in the prevention of gentamicin ototoxicity in rats. METHODS Forty-two Wistar rats were divided into four groups according to treatment: intratympanic saline, intratympanic gentamicin, intraperitoneal vitamin A after intratympanic gentamicin, and intraperitoneal N-acetylcysteine after intratympanic gentamicin. Signal-to-noise ratio and distortion product otoacoustic emissions were evaluated in all groups. RESULTS N-acetylcysteine had a significant protective effect at 1.5, 2, 3, 4, 6 and 8 kHz, whilst vitamin A had a significant protective effect at 2, 3, 4 and 6 kHz, as determined by the distortion product otoacoustic emission measurements. According to the signal-to-noise measurements, N-acetylcysteine had a significant protective effect at 1.5, 2, 3, 4, 6 and 8 kHz, whilst vitamin A had a significant protective effect at 3, 6 and 8 kHz. CONCLUSION Gentamicin-induced hearing loss in rats may be prevented by the concomitant use of vitamin A and N-acetylcysteine. Specifically, N-acetylcysteine appeared to have a more protective effect than vitamin A for a greater range of noise frequencies.
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Dorsett CR, McGuire JL, Niedzielko TL, DePasquale EAK, Meller J, Floyd CL, McCullumsmith RE. Traumatic Brain Injury Induces Alterations in Cortical Glutamate Uptake without a Reduction in Glutamate Transporter-1 Protein Expression. J Neurotrauma 2016; 34:220-234. [PMID: 27312729 DOI: 10.1089/neu.2015.4372] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We hypothesize that the primary mechanism for removal of glutamate from the extracellular space is altered after traumatic brain injury (TBI). To evaluate this hypothesis, we initiated TBI in adult male rats using a 2.0 atm lateral fluid percussion injury (LFPI) model. In the ipsilateral cortex and hippocampus, we found no differences in expression of the primary glutamate transporter in the brain (GLT-1) 24 h after TBI. In contrast, we found a decrease in glutamate uptake in the cortex, but not the hippocampus, 24 h after injury. Because glutamate uptake is potently regulated by protein kinases, we assessed global serine-threonine protein kinase activity using a kinome array platform. Twenty-five kinome array peptide substrates were differentially phoshorylated between LFPI and controls in the cortex, whereas 19 peptide substrates were differentially phosphorylated in the hippocampus (fold change ≥ ± 1.15). We identified several kinases as likely to be involved in acute TBI, including protein kinase B (Akt) and protein kinase C (PKC), which are well-characterized modulators of GLT-1. Exploratory studies using an inhibitor of Akt suggest selective activation of kinases in LFPI versus controls. Ingenuity pathway analyses of implicated kinases from our network model found apoptosis and cell death pathways as top functions in acute LFPI. Taken together, our data suggest diminished activity of glutamate transporters in the prefrontal cortex, with no changes in protein expression of the primary glutamate transporter GLT-1, and global alterations in signaling networks that include serine-threonine kinases that are known modulators of glutamate transport activity.
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Affiliation(s)
- Christopher R Dorsett
- 1 Biological and Biomedical Sciences Doctoral Program, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Jennifer L McGuire
- 2 Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati , Cincinnati, Ohio
| | - Tracy L Niedzielko
- 3 Department of Physical Medicine and Rehabilitation, University of Alabama at Birmingham , Birmingham, Alabama
| | - Erica A K DePasquale
- 2 Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati , Cincinnati, Ohio
| | - Jaroslaw Meller
- 4 Departments of Environmental Health, Electrical Engineering & Computing Systems, and Biomedical Informatics, University of Cincinnati College of Medicine , Cincinnati, Ohio.,5 Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center , Cincinnati, Ohio
| | - Candace L Floyd
- 3 Department of Physical Medicine and Rehabilitation, University of Alabama at Birmingham , Birmingham, Alabama
| | - Robert E McCullumsmith
- 2 Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati , Cincinnati, Ohio
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Reyes-Gibby CC, Wang J, Silvas MRT, Yu R, Yeung SCJ, Shete S. MAPK1/ERK2 as novel target genes for pain in head and neck cancer patients. BMC Genet 2016; 17:40. [PMID: 26872611 PMCID: PMC4752805 DOI: 10.1186/s12863-016-0348-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/05/2016] [Indexed: 01/23/2023] Open
Abstract
Background Genetic susceptibility plays an important role in the risk of developing pain in individuals with cancer. As a complex trait, multiple genes underlie this susceptibility. We used gene network analyses to identify novel target genes associated with pain in patients newly diagnosed with squamous cell carcinoma of the head and neck (HNSCC). Results We first identified 36 cancer pain-related genes (i.e., focus genes) from 36 publications based on a literature search. The Ingenuity Pathway Analysis (IPA) analysis identified additional genes that are functionally related to the 36 focus genes through pathway relationships yielding a total of 82 genes. Subsequently, 800 SNPs within the 82 IPA-selected genes on the Illumina HumanOmniExpress-12v1 platform were selected from a large-scale genotyping effort. Association analyses between the 800 candidate SNPs (covering 82 genes) and pain in a patient cohort of 1368 patients with HNSCC (206 patients with severe pain vs. 1162 with non-severe pain) showed the highest significance for MAPK1/ERK2, a gene belonging to the MAP kinase family (rs8136867, p value = 8.92 × 10−4; odds ratio [OR] = 1.33, 95 % confidence interval [CI]: 1.13–1.58). Other top genes were PIK3C2G (a member of PI3K [complex], rs10770367, p value = 1.10 × 10−3; OR = 1.46, 95 % CI: 1.16–1.82), TCRA (the alpha chain of T-cell receptor, rs6572493, p value = 2.84 × 10−3; OR = 0.70, 95 % CI: 0.55–0.88), PDGFC (platelet-derived growth factor C, rs6845322, p value = 4.88 × 10−3; OR = 1.32, 95 % CI: 1.09–1.60), and CD247 (a member of CD3, rs2995082, p value = 7.79 × 10−3; OR = 0.76, 95 % CI: 0.62–0.93). Conclusions Our findings provide novel candidate genes and biological pathways underlying pain in cancer patients. Further study of the variations of these candidate genes could inform clinical decision making when treating cancer pain. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0348-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cielito C Reyes-Gibby
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, U.S.A..
| | - Jian Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, U.S.A..
| | - Mary Rose T Silvas
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, U.S.A..
| | - Robert Yu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, U.S.A..
| | - Sai-Ching J Yeung
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, U.S.A..
| | - Sanjay Shete
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, U.S.A.. .,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, U.S.A.
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Curhan SG, Stankovic KM, Eavey RD, Wang M, Stampfer MJ, Curhan GC. Carotenoids, vitamin A, vitamin C, vitamin E, and folate and risk of self-reported hearing loss in women. Am J Clin Nutr 2015; 102:1167-75. [PMID: 26354537 PMCID: PMC4625586 DOI: 10.3945/ajcn.115.109314] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/04/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Higher intake of certain vitamins may protect against cochlear damage from vascular compromise and oxidative stress, thereby reducing risk of acquired hearing loss, but data are limited. OBJECTIVE We prospectively examined the relation between carotenoids, vitamin A, vitamin C, vitamin E, and folate intake and risk of self-reported hearing loss in women. DESIGN This prospective cohort study followed 65,521 women in the Nurses' Health Study II from 1991 to 2009. Baseline and updated information obtained from validated biennial questionnaires was used in Cox proportional hazards regression models to examine independent associations between nutrient intake and self-reported hearing loss. RESULTS After 1,084,598 person-years of follow-up, 12,789 cases of incident hearing loss were reported. After multivariable adjustment, we observed modest but statistically significant inverse associations between higher intake of β-carotene and β-cryptoxanthin and risk of hearing loss. In comparison with women in the lowest quintile of intake, the multivariable-adjusted RR of hearing loss among women in the highest quintile was 0.88 (95% CI: 0.81, 0.94; P-trend < 0.001) for β-carotene and 0.90 (95% CI: 0.84, 0.96; P-trend < 0.001) for β-cryptoxanthin. In comparison with women with folate intake 200-399 μg/d, very low folate intake (<200 μg/d) was associated with higher risk (RR: 1.19; 95% CI: 1.01, 1.41), and higher intake tended to be associated with lower risk (P-trend = 0.04). No significant associations were observed for intakes of other carotenoids or vitamin A. Higher vitamin C intake was associated with higher risk; in comparison with women with intake <75 mg/d, the RR among women with vitamin C intake ≥1000 mg/d (mainly supplemental) was 1.22 (95% CI: 1.06, 1.42; P-trend = 0.02). There was no significant trend between intake of vitamin E intake and risk. CONCLUSION Higher intakes of β-carotene, β-cryptoxanthin, and folate, whether total or from diet, are associated with lower risk of hearing loss, whereas higher vitamin C intake is associated with higher risk.
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Affiliation(s)
- Sharon G Curhan
- Channing Division of Network Medicine and Harvard Medical School, Boston MA
| | - Konstantina M Stankovic
- Eaton-Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Boston, MA; Department of Otology and Laryngology, Harvard Medical School, Boston, MA; Program in Speech and Hearing Bioscience and Technology, Division of Health Science and Technology, Harvard and Massachusetts Institute of Technology, Boston, MA
| | - Roland D Eavey
- Vanderbilt Bill Wilkerson Center for Otolaryngology and Communication Sciences, Vanderbilt University School of Medicine, Nashville, TN; and
| | - Molin Wang
- Channing Division of Network Medicine and Departments of Biostatistics and Epidemiology, Harvard School of Public Health, Boston, MA
| | - Meir J Stampfer
- Channing Division of Network Medicine and Epidemiology, Harvard School of Public Health, Boston, MA
| | - Gary C Curhan
- Channing Division of Network Medicine and Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Epidemiology, Harvard School of Public Health, Boston, MA, Harvard Medical School, Boston MA
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Reyes-Gibby CC, Wang J, Yeung SCJ, Shete S. Informative gene network for chemotherapy-induced peripheral neuropathy. BioData Min 2015; 8:24. [PMID: 26269716 PMCID: PMC4534051 DOI: 10.1186/s13040-015-0058-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/04/2015] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Host genetic variability has been implicated in chemotherapy-induced peripheral neuropathy (CIPN). A dose-limiting toxicity for chemotherapy agents, CIPN is also a debilitating condition that may progress to chronic neuropathic pain. We utilized a bioinformatics approach, which captures the complexity of intracellular and intercellular interactions, to identify genes for CIPN. METHODS Using genes pooled from the literature as a starting point, we used Ingenuity Pathway Analysis (IPA) to generate gene networks for CIPN. RESULTS We performed IPA core analysis for genes associated with platinum-, taxane- and platinum-taxane-induced neuropathy. We found that IL6, TNF, CXCL8, IL1B and ERK1/2 were the top genes in terms of the number of connections in platinum-induced neuropathy and TP53, MYC, PARP1, P38 MAPK and TNF for combined taxane-platinum-induced neuropathy. CONCLUSION Neurotoxicity is common in cancer patients treated with platinum compounds and anti-microtubule agents and CIPN is one of the debilitating sequela. The bioinformatic approach helped identify genes associated with CIPN in cancer patients.
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Affiliation(s)
- Cielito C. Reyes-Gibby
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Jian Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Sai-Ching J. Yeung
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Sanjay Shete
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
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Gene network analysis shows immune-signaling and ERK1/2 as novel genetic markers for multiple addiction phenotypes: alcohol, smoking and opioid addiction. BMC SYSTEMS BIOLOGY 2015; 9:25. [PMID: 26044620 PMCID: PMC4456775 DOI: 10.1186/s12918-015-0167-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 05/12/2015] [Indexed: 01/09/2023]
Abstract
Background Addictions to alcohol and tobacco, known risk factors for cancer, are complex heritable disorders. Addictive behaviors have a bidirectional relationship with pain. We hypothesize that the associations between alcohol, smoking, and opioid addiction observed in cancer patients have a genetic basis. Therefore, using bioinformatics tools, we explored the underlying genetic basis and identified new candidate genes and common biological pathways for smoking, alcohol, and opioid addiction. Results Literature search showed 56 genes associated with alcohol, smoking and opioid addiction. Using Core Analysis function in Ingenuity Pathway Analysis software, we found that ERK1/2 was strongly interconnected across all three addiction networks. Genes involved in immune signaling pathways were shown across all three networks. Connect function from IPA My Pathway toolbox showed that DRD2 is the gene common to both the list of genetic variations associated with all three addiction phenotypes and the components of the brain neuronal signaling network involved in substance addiction. The top canonical pathways associated with the 56 genes were: 1) calcium signaling, 2) GPCR signaling, 3) cAMP-mediated signaling, 4) GABA receptor signaling, and 5) G-alpha i signaling. Conlusions Cancer patients are often prescribed opioids for cancer pain thus increasing their risk for opioid abuse and addiction. Our findings provide candidate genes and biological pathways underlying addiction phenotypes, which may be future targets for treatment of addiction. Further study of the variations of the candidate genes could allow physicians to make more informed decisions when treating cancer pain with opioid analgesics. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0167-x) contains supplementary material, which is available to authorized users.
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Sudden sensorineural hearing loss and polymorphisms in iron homeostasis genes: new insights from a case-control study. BIOMED RESEARCH INTERNATIONAL 2015; 2015:834736. [PMID: 25789325 PMCID: PMC4348611 DOI: 10.1155/2015/834736] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/15/2014] [Accepted: 01/06/2015] [Indexed: 12/19/2022]
Abstract
Background. Even if various pathophysiological events have been proposed as explanations, the putative cause of sudden hearing loss remains unclear. Objectives. To investigate and to reveal associations (if any) between the main iron-related gene variants and idiopathic sudden sensorineural hearing loss. Study Design. Case-control study. Materials and Methods. A total of 200 sudden sensorineural hearing loss patients (median age 63.65 years; range 10-92) were compared with 400 healthy control subjects. The following genetic variants were investigated: the polymorphism c.-8CG in the promoter of the ferroportin gene (FPN1; SLC40A1), the two isoforms C1 and C2 (p.P570S) of the transferrin protein (TF), the amino acidic substitutions p.H63D and p.C282Y in the hereditary hemochromatosis protein (HFE), and the polymorphism c.-582AG in the promoter of the HEPC gene, which encodes the protein hepcidin (HAMP). Results. The homozygous genotype c.-8GG of the SLC40A1 gene revealed an OR for ISSNHL risk of 4.27 (CI 95%, 2.65-6.89; P = 0.001), being overrepresented among cases. Conclusions. Our study indicates that the homozygous genotype FPN1 -8GG was significantly associated with increased risk of developing sudden hearing loss. These findings suggest new research should be conducted in the field of iron homeostasis in the inner ear.
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