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Hanssen F, Garcia MU, Folkersen L, Pedersen A, Lescai F, Jodoin S, Miller E, Seybold M, Wacker O, Smith N, Gabernet G, Nahnsen S. Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery. NAR Genom Bioinform 2024; 6:lqae031. [PMID: 38666213 PMCID: PMC11044436 DOI: 10.1093/nargab/lqae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
DNA variation analysis has become indispensable in many aspects of modern biomedicine, most prominently in the comparison of normal and tumor samples. Thousands of samples are collected in local sequencing efforts and public databases requiring highly scalable, portable, and automated workflows for streamlined processing. Here, we present nf-core/sarek 3, a well-established, comprehensive variant calling and annotation pipeline for germline and somatic samples. It is suitable for any genome with a known reference. We present a full rewrite of the original pipeline showing a significant reduction of storage requirements by using the CRAM format and runtime by increasing intra-sample parallelization. Both are leading to a 70% cost reduction in commercial clouds enabling users to do large-scale and cross-platform data analysis while keeping costs and CO2 emissions low. The code is available at https://nf-co.re/sarek.
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Affiliation(s)
- Friederike Hanssen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, 72076 Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard-Karls University of Tübingen, Tübingen 72076, Baden-Württemberg, Germany
| | - Maxime U Garcia
- Seqera Labs, Carrer de Marià Aguilò, 28, Barcelona 08005, Spain
- Barntumörbanken, Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Visionsgatan 4, Solna 17164, Sweden
- National Genomics Infrastructure, SciLifeLab, SciLifeLab, Tomtebodavägen 23, Solna 17165, Sweden
| | | | | | - Francesco Lescai
- Department of Biology and Biotechnology ”L. Spallanzani”, University of Pavia, via Ferrata, 9, Pavia, 27100 PV, Italy
| | - Susanne Jodoin
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
| | - Edmund Miller
- Department of Biological Sciences and Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX 75080, USA
| | - Matthias Seybold
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
| | - Oskar Wacker
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
| | - Nicholas Smith
- Department of Informatics, Technical University of Munich, Boltzmannstr. 3, Garching, 85748 Bavaria, Germany
| | - Gisela Gabernet
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Department of Pathology, Yale School of Medicine, 300 George, New Haven, CT 06510, USA
| | - Sven Nahnsen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, 72076 Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard-Karls University of Tübingen, Tübingen 72076, Baden-Württemberg, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard-Karls University of Tübingen, Tübingen 72076, Baden-Württemberg, Germany
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Liu P, Xue X, Zhang C, Zhou H, Ding Z, Wang L, Jiang Y, Shen WD, Yang S, Wang F. Transcriptional-profile changes in the medial geniculate body after noise-induced tinnitus. Exp Biol Med (Maywood) 2024; 249:10057. [PMID: 38562529 PMCID: PMC10984379 DOI: 10.3389/ebm.2024.10057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Tinnitus is a disturbing condition defined as the occurrence of acoustic hallucinations with no actual sound. Although the mechanisms underlying tinnitus have been explored extensively, the pathophysiology of the disease is not completely understood. Moreover, genes and potential treatment targets related to auditory hallucinations remain unknown. In this study, we examined transcriptional-profile changes in the medial geniculate body after noise-induced tinnitus in rats by performing RNA sequencing and validated differentially expressed genes via quantitative polymerase chain reaction analysis. The rat model of tinnitus was established by analyzing startle behavior based on gap-pre-pulse inhibition of acoustic startles. We identified 87 differently expressed genes, of which 40 were upregulated and 47 were downregulated. Pathway-enrichment analysis revealed that the differentially enriched genes in the tinnitus group were associated with pathway terms, such as coronavirus disease COVID-19, neuroactive ligand-receptor interaction. Protein-protein-interaction networks were established, and two hub genes (Rpl7a and AC136661.1) were identified among the selected genes. Further studies focusing on targeting and modulating these genes are required for developing potential treatments for noise-induced tinnitus in patients.
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Affiliation(s)
- Peng Liu
- Medical School of Chinese PLA, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
| | - Xinmiao Xue
- Medical School of Chinese PLA, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
| | - Chi Zhang
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
| | - Hanwen Zhou
- Medical School of Chinese PLA, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
| | - Zhiwei Ding
- Medical School of Chinese PLA, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
| | - Li Wang
- Medical School of Chinese PLA, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
| | - Yuke Jiang
- Medical School of Chinese PLA, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
| | - Wei-Dong Shen
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
| | - Shiming Yang
- Medical School of Chinese PLA, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Fangyuan Wang
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
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Perez-Carpena P, Lopez-Escamez JA, Gallego-Martinez Á. A Systematic Review on the Genetic Contribution to Tinnitus. J Assoc Res Otolaryngol 2024; 25:13-33. [PMID: 38334885 PMCID: PMC10907330 DOI: 10.1007/s10162-024-00925-6] [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] [Received: 08/13/2023] [Accepted: 12/31/2023] [Indexed: 02/10/2024] Open
Abstract
PURPOSE To assess the available evidence to support a genetic contribution and define the role of common and rare variants in tinnitus. METHODS After a systematic search and quality assessment, 31 records including 383,063 patients were selected (14 epidemiological studies and 17 genetic association studies). General information on the sample size, age, sex, tinnitus prevalence, severe tinnitus distribution, and sensorineural hearing loss was retrieved. Studies that did not include data on hearing assessment were excluded. Relative frequencies were used for qualitative variables to compare different studies and to obtain average values. Genetic variants and genes were listed and clustered according to their potential role in tinnitus development. RESULTS The average prevalence of tinnitus estimated from population-based studies was 26.3% for any tinnitus, and 20% of patients with tinnitus reported it as an annoying symptom. One study has reported population-specific differences in the prevalence of tinnitus, the white ancestry being the population with a higher prevalence. Genome-wide association studies have identified and replicated two common variants in the Chinese population (rs2846071; rs4149577) in the intron of TNFRSF1A, associated with noise-induced tinnitus. Moreover, gene burden analyses in sequencing data from Spanish and Swede patients with severe tinnitus have identified and replicated ANK2, AKAP9, and TSC2 genes. CONCLUSIONS The genetic contribution to tinnitus is starting to be revealed and it shows population-specific effects in European and Asian populations. The common allelic variants associated with tinnitus that showed replication are associated with noise-induced tinnitus. Although severe tinnitus has been associated with rare variants with large effect, their role on hearing or hyperacusis has not been established.
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Affiliation(s)
- Patricia Perez-Carpena
- Otology and Neurotology Group CTS495, Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, Ibs.GRANADA, Universidad de Granada, Granada, Spain.
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain.
- Department of Otolaryngology, Instituto de Investigación Biosanitaria Ibs.GRANADA, Hospital Universitario Virgen de Las Nieves, Granada, Spain.
| | - Jose A Lopez-Escamez
- Otology and Neurotology Group CTS495, Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, Ibs.GRANADA, Universidad de Granada, Granada, Spain.
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain.
- Meniere's Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, NSW, Australia.
| | - Álvaro Gallego-Martinez
- Otology and Neurotology Group CTS495, Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, Ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
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Yélamos Lorente MÁ, Perez-Carpena P, Lopez-Escamez JA. A Systematic Review on Heritability of Sudden Sensorineural Hearing Loss. Laryngoscope 2024. [PMID: 38270208 DOI: 10.1002/lary.31308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/26/2024]
Abstract
OBJECTIVE To assess the evidence supporting the heritability and genetic basis of sudden sensorineural hearing loss (SSNHL). DATA SOURCE Records were extracted from PubMed, Scopus, and Cochrane databases. REVIEW METHODS The protocol was registered on PROSPERO (CRD42022357389) and includes a systematic review on the genetic contribution to SSNHL. The search strategy yielded 1.483 articles from electronic databases. After quality assessment, 34 records were selected, including 369.650 patients with SSNHL from nine prevalence studies, two familial aggregation studies, one twin study, and 22 genetic studies. The prevalence of SSNHL was calculated from data on its incidence from population-based studies (period prevalence). To evaluate the heritability of SSNHL, the sibling recurrence risk ratio (λs) was calculated, by comparing the prevalence of SSNHL among siblings within the same generation to the estimated prevalence in the overall population. Genetic variants were grouped, based on the pathological mechanism related to SSNHL. RESULTS The prevalence of SSNHL ranged from 0.1% to 0.0003% in America to 0.12%-0.0093% in Asia. The estimated sibling recurrence risk ratio for SSNHL (λs = 20.8-83.3) supports a significant familial aggregation. Although several genetic variants were reported to be associated with SSHL in controlled studies, neither was replicated in an independent cohort. CONCLUSIONS Evidence supporting heritability of SSNHL is limited to epidemiological studies showing prevalence differences across different populations and familial aggregation. Genetic studies are of low quality and they lack replication cohort to confirm their findings. According to its low prevalence, exome or genome sequencing familial-based studies are needed to identify rare genetic variants in SSNHL. LEVEL OF EVIDENCE NA Laryngoscope, 2024.
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Affiliation(s)
- Mª Á Yélamos Lorente
- Division of Otolaryngology, Department of Surgery, University of Granada, Granada, Spain
- Family and Community Medicine, Zaidin Sur Health Center (Granada), San Cecilio University Hospital, Granada, Spain
| | - Patricia Perez-Carpena
- Division of Otolaryngology, Department of Surgery, University of Granada, Granada, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Jose A Lopez-Escamez
- Division of Otolaryngology, Department of Surgery, University of Granada, Granada, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, Granada, Spain
- Meniere's Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, New South Wales, Australia
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Escalera-Balsera A, Parra-Perez AM, Gallego-Martinez A, Frejo L, Martin-Lagos J, Rivero de Jesus V, Pérez-Vázquez P, Perez-Carpena P, Lopez-Escamez JA. Rare Deletions or Large Duplications Contribute to Genetic Variation in Patients with Severe Tinnitus and Meniere Disease. Genes (Basel) 2023; 15:22. [PMID: 38254912 PMCID: PMC10815708 DOI: 10.3390/genes15010022] [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] [Received: 11/20/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Meniere disease (MD) is a debilitating disorder of the inner ear defined by sensorineural hearing loss (SNHL) associated with episodes of vertigo and tinnitus. Severe tinnitus, which occurs in around 1% of patients, is a multiallelic disorder associated with a burden of rare missense single nucleotide variants in synaptic genes. Rare structural variants (SVs) may also contribute to MD and severe tinnitus. In this study, we analyzed exome sequencing data from 310 MD Spanish patients and selected 75 patients with severe tinnitus based on a Tinnitus Handicap Inventory (THI) score > 68. Three rare deletions were identified in two unrelated individuals overlapping the ERBB3 gene in the positions: NC_000012.12:g.56100028_56100172del, NC_000012.12:g.56100243_56101058del, and NC_000012.12:g.56101359_56101526del. Moreover, an ultra-rare large duplication was found covering the AP4M1, COPS6, MCM7, TAF6, MIR106B, MIR25, and MIR93 genes in another two patients in the NC_000007.14:g.100089053_100112257dup region. All the coding genes exhibited expression in brain and inner ear tissues. These results confirm the contribution of large SVs to severe tinnitus in MD and pinpoint new candidate genes to get a better molecular understanding of the disease.
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Affiliation(s)
- Alba Escalera-Balsera
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
| | - Alberto M. Parra-Perez
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
| | - Alvaro Gallego-Martinez
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
| | - Lidia Frejo
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
- Meniere’s Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, NSW 2065, Australia
| | - Juan Martin-Lagos
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Department of Otorhinolaryngology, Hospital Clinico Universitario San Cecilio, 18016 Granada, Spain
| | | | - Paz Pérez-Vázquez
- Servicio de Otorrinolaringología, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain;
| | - Patricia Perez-Carpena
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
- Department of Otorhinolaryngology, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
| | - Jose A. Lopez-Escamez
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
- Meniere’s Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, NSW 2065, Australia
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Sandeep P, Sharma P, Luhach K, Dhiman N, Kharkwal H, Sharma B. Neuron navigators: A novel frontier with physiological and pathological implications. Mol Cell Neurosci 2023; 127:103905. [PMID: 37972804 DOI: 10.1016/j.mcn.2023.103905] [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: 09/12/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023] Open
Abstract
Neuron navigators are microtubule plus-end tracking proteins containing basic and serine rich regions which are encoded by neuron navigator genes (NAVs). Neuron navigator proteins are essential for neurite outgrowth, neuronal migration, and overall neurodevelopment along with some other functions as well. The navigator proteins are substantially expressed in the developing brain and have been reported to be differentially expressed in various tissues at different ages. Over the years, the research has found neuron navigators to be implicated in a spectrum of pathological conditions such as developmental anomalies, neurodegenerative disorders, neuropathic pain, anxiety, cancers, and certain inflammatory conditions. The existing knowledge about neuron navigators remains sparse owing to their differential functions, undiscovered modulators, and unknown molecular mechanisms. Investigating the possible role of neuron navigators in various physiological processes and pathological conditions pose as a novel field that requires extensive research and might provide novel mechanistic insights and understanding of these aspects.
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Affiliation(s)
- Parth Sandeep
- Department of Pharmacology, Amity Institute of Pharmacy, Amity University, Uttar Pradesh, Noida, India
| | - Poonam Sharma
- Department of Pharmacology, Amity Institute of Pharmacy, Amity University, Uttar Pradesh, Noida, India
| | - Kanishk Luhach
- Department of Pharmacology, Amity Institute of Pharmacy, Amity University, Uttar Pradesh, Noida, India
| | - Neerupma Dhiman
- Amity Institute of Pharmacy, Amity University, Uttar Pradesh, Noida, India
| | - Harsha Kharkwal
- Amity Natural and Herbal Product Research, Amity Institute of Phytochemistry and Phytomedicine, Amity University, Uttar Pradesh, India
| | - Bhupesh Sharma
- Department of Pharmacology, Amity Institute of Pharmacy, Amity University, Uttar Pradesh, Noida, India.
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Lazzeri G, Biagioni F, Ferrucci M, Puglisi-Allegra S, Lenzi P, Busceti CL, Giannessi F, Fornai F. The Relevance of Autophagy within Inner Ear in Baseline Conditions and Tinnitus-Related Syndromes. Int J Mol Sci 2023; 24:16664. [PMID: 38068993 PMCID: PMC10706730 DOI: 10.3390/ijms242316664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/07/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Tinnitus is the perception of noise in the absence of acoustic stimulation (phantom noise). In most patients suffering from chronic peripheral tinnitus, an alteration of outer hair cells (OHC) starting from the stereocilia (SC) occurs. This is common following ototoxic drugs, sound-induced ototoxicity, and acoustic degeneration. In all these conditions, altered coupling between the tectorial membrane (TM) and OHC SC is described. The present review analyzes the complex interactions involving OHC and TM. These need to be clarified to understand which mechanisms may underlie the onset of tinnitus and why the neuropathology of chronic degenerative tinnitus is similar, independent of early triggers. In fact, the fine neuropathology of tinnitus features altered mechanisms of mechanic-electrical transduction (MET) at the level of OHC SC. The appropriate coupling between OHC SC and TM strongly depends on autophagy. The involvement of autophagy may encompass degenerative and genetic tinnitus, as well as ototoxic drugs and acoustic trauma. Defective autophagy explains mitochondrial alterations and altered protein handling within OHC and TM. This is relevant for developing novel treatments that stimulate autophagy without carrying the burden of severe side effects. Specific phytochemicals, such as curcumin and berberin, acting as autophagy activators, may mitigate the neuropathology of tinnitus.
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Affiliation(s)
- Gloria Lazzeri
- Human Anatomy, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, PI, Italy; (G.L.); (M.F.); (P.L.); (F.G.)
| | - Francesca Biagioni
- IRCCS, Istituto di Ricovero e Cura a Carattere Scientifico, Neuromed, 86077 Pozzilli, IS, Italy; (F.B.); (S.P.-A.); (C.L.B.)
| | - Michela Ferrucci
- Human Anatomy, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, PI, Italy; (G.L.); (M.F.); (P.L.); (F.G.)
| | - Stefano Puglisi-Allegra
- IRCCS, Istituto di Ricovero e Cura a Carattere Scientifico, Neuromed, 86077 Pozzilli, IS, Italy; (F.B.); (S.P.-A.); (C.L.B.)
| | - Paola Lenzi
- Human Anatomy, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, PI, Italy; (G.L.); (M.F.); (P.L.); (F.G.)
| | - Carla Letizia Busceti
- IRCCS, Istituto di Ricovero e Cura a Carattere Scientifico, Neuromed, 86077 Pozzilli, IS, Italy; (F.B.); (S.P.-A.); (C.L.B.)
| | - Francesco Giannessi
- Human Anatomy, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, PI, Italy; (G.L.); (M.F.); (P.L.); (F.G.)
| | - Francesco Fornai
- Human Anatomy, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, PI, Italy; (G.L.); (M.F.); (P.L.); (F.G.)
- IRCCS, Istituto di Ricovero e Cura a Carattere Scientifico, Neuromed, 86077 Pozzilli, IS, Italy; (F.B.); (S.P.-A.); (C.L.B.)
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Singh A, Smith PF, Zheng Y. Targeting the Limbic System: Insights into Its Involvement in Tinnitus. Int J Mol Sci 2023; 24:9889. [PMID: 37373034 DOI: 10.3390/ijms24129889] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Tinnitus is originally derived from the Latin verb tinnire, which means "to ring". Tinnitus, a complex disorder, is a result of sentient cognizance of a sound in the absence of an external auditory stimulus. It is reported in children, adults, and older populations. Patients suffering from tinnitus often present with hearing loss, anxiety, depression, and sleep disruption in addition to a hissing and ringing in the ear. Surgical interventions and many other forms of treatment have been only partially effective due to heterogeneity in tinnitus patients and a lack of understanding of the mechanisms of tinnitus. Although researchers across the globe have made significant progress in understanding the underlying mechanisms of tinnitus over the past few decades, tinnitus is still deemed to be a scientific enigma. This review summarises the role of the limbic system in tinnitus development and provides insight into the development of potential target-specific tinnitus therapies.
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Affiliation(s)
- Anurag Singh
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
- Brain Health Research Centre, University of Otago, Dunedin 9016, New Zealand
- The Eisdell Moore Centre for Research in Hearing and Balance Disorders, University of Auckland, Auckland 1023, New Zealand
| | - Paul F Smith
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
- Brain Health Research Centre, University of Otago, Dunedin 9016, New Zealand
- The Eisdell Moore Centre for Research in Hearing and Balance Disorders, University of Auckland, Auckland 1023, New Zealand
| | - Yiwen Zheng
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
- Brain Health Research Centre, University of Otago, Dunedin 9016, New Zealand
- The Eisdell Moore Centre for Research in Hearing and Balance Disorders, University of Auckland, Auckland 1023, New Zealand
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