In Silico Transcriptome-based Screens Identify Epidermal Growth Factor Receptor Inhibitors as Therapeutics for Noise-induced Hearing Loss

Noise-Induced Hearing Loss (NIHL) represents a widespread disease for which no therapeutics have been approved by the Food and Drug Administration (FDA). Addressing the conspicuous void of efficacious in vitro or animal models for high throughput pharmacological screening, we utilized an in silico transcriptome-oriented drug screening strategy, unveiling 22 biological pathways and 64 promising small molecule candidates for NIHL protection. Afatinib and zorifertinib, both inhibitors of the Epidermal Growth Factor Receptor (EGFR), were validated for their protective efficacy against NIHL in experimental zebrafish and murine models. This protective effect was further confirmed with EGFR conditional knockout mice and EGF knockdown zebrafish, both demonstrating protection against NIHL. Molecular analysis using Western blot and kinome signaling arrays on adult mouse cochlear lysates unveiled the intricate involvement of several signaling pathways, with particular emphasis on EGFR and its downstream pathways being modulated by noise exposure and Zorifertinib treatment. Administered orally, Zorifertinib was successfully detected in the perilymph fluid of the inner ear in mice with favorable pharmacokinetic attributes. Zorifertinib, in conjunction with AZD5438 – a potent inhibitor of cyclin dependent kinase 2 – produced synergistic protection against NIHL in the zebrafish model. Collectively, our findings underscore the potential application of in silico transcriptome-based drug screening for diseases bereft of efficient screening models and posit EGFR inhibitors as promising therapeutic agents warranting clinical exploration for combatting NIHL. Highlights In silico transcriptome-based drug screens identify pathways and drugs against NIHL. EGFR signaling is activated by noise but reduced by zorifertinib in mouse cochleae. Afatinib, zorifertinib and EGFR knockout protect against NIHL in mice and zebrafish. Orally delivered zorifertinib has inner ear PK and synergizes with a CDK2 inhibitor.

[1]  J. Loscalzo,et al.  Repurposing Drugs for the Treatment of COVID-19 and Its Cardiovascular Manifestations , 2023, Circulation research.

[2]  Yan Zhang,et al.  Profiling mouse cochlear cell maturation using 10× Genomics single-cell transcriptomics , 2022, Frontiers in Cellular Neuroscience.

[3]  E. Aikawa,et al.  In silico Drug Screening Approach Using L1000-Based Connectivity Map and Its Application to COVID-19 , 2022, Frontiers in Cardiovascular Medicine.

[4]  Jun-Sub Kim.  Repurposing Drugs for the Treatment of COVID-19 , 2021, Journal of Biotechnology and Bioindustry.

[5]  R. Mccullumsmith,et al.  Strategies to identify candidate repurposable drugs: COVID-19 treatment as a case example , 2021, Translational Psychiatry.

[6]  Maxim V. Kuleshov,et al.  KEA3: improved kinase enrichment analysis via data integration , 2021, Nucleic Acids Res..

[7]  B. Zhu,et al.  Histone deacetylase 2 polymorphisms associated with noise-induced hearing loss in Chinese workers , 2021, Environmental Science and Pollution Research.

[8]  Taosheng Chen,et al.  BRAF inhibition protects against hearing loss in mice , 2020, Science Advances.

[9]  A. Ryan,et al.  Noise Exposures Causing Hearing Loss Generate Proteotoxic Stress and Activate the Proteostasis Network , 2020, Cell reports.

[10]  R. Mccullumsmith,et al.  Oxytocin’s anti-inflammatory and proimmune functions in COVID-19: a transcriptomic signature-based approach , 2020, Physiological genomics.

[11]  J. Meller,et al.  Signature-based approaches for informed drug repurposing: targeting CNS disorders , 2020, Neuropsychopharmacology.

[12]  S. Eyles,et al.  Lovastatin protects against cisplatin-induced hearing loss in mice , 2020, Hearing Research.

[13]  K. Stępnik,et al.  In Silico Studies on Triterpenoid Saponins Permeation through the Blood–Brain Barrier Combined with Postmortem Research on the Brain Tissues of Mice Affected by Astragaloside IV Administration , 2020, International journal of molecular sciences.

[14]  Eduard Bentea,et al.  Kinase network dysregulation in a human induced pluripotent stem cell model of DISC1 schizophrenia. , 2019, Molecular omics.

[15]  C. L. Le Prell.  Otoprotectants: From Research to Clinical Application , 2019, Seminars in Hearing.

[16]  Jacqueline K. White,et al.  Mouse screen reveals multiple new genes underlying mouse and human hearing loss , 2019, PLoS biology.

[17]  J. Sarkaria,et al.  Brain Distribution of a Panel of Epidermal Growth Factor Receptor Inhibitors Using Cassette Dosing in Wild-Type and Abcb1/Abcg2-Deficient Mice , 2019, Drug Metabolism and Disposition.

[18]  Lei Dong,et al.  Weighted gene co-expression network analysis and connectivity map identifies lovastatin as a treatment option of gastric cancer by inhibiting HDAC2. , 2019, Gene.

[19]  R. E. Stevens,et al.  Streamlining nonclinical drug development using the FDA 505(b)(2) new drug application regulatory pathway. , 2019, Drug Discovery Today.

[20]  Jill P. Mesirov,et al.  A Curated Resource for Phosphosite-specific Signature Analysis* , 2018, Molecular & Cellular Proteomics.

[21]  D. Raible,et al.  The Inner Ear Heat Shock Transcriptional Signature Identifies Compounds That Protect Against Aminoglycoside Ototoxicity , 2018, Front. Cell. Neurosci..

[22]  A. Edge,et al.  ERBB2 signaling drives supporting cell proliferation in vitro and apparent supernumerary hair cell formation in vivo in the neonatal mouse cochlea , 2018, The European journal of neuroscience.

[23]  Wei-ping Zhou,et al.  Gene expression profiling coupled with Connectivity Map database mining reveals potential therapeutic drugs for Hirschsprung disease. , 2018, Journal of pediatric surgery.

[24]  K. Graydon,et al.  Global burden of hearing impairment and ear disease. , 2018, The Journal of laryngology and otology.

[25]  A. Kurabi,et al.  Screening Mammalian Cochlear Hair Cells to Identify Critical Processes in Aminoglycoside-Mediated Damage , 2018, Front. Cell. Neurosci..

[26]  Charles Gawad,et al.  High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor , 2018, PLoS genetics.

[27]  E. Mufson,et al.  Impact of age on acute post-TBI neuropathology in mice expressing humanized tau: a Chronic Effects of Neurotrauma Consortium study , 2018, Brain injury.

[28]  Michael R. Taylor,et al.  CDK2 inhibitors as candidate therapeutics for cisplatin- and noise-induced hearing loss , 2018, The Journal of experimental medicine.

[29]  Fabian J Theis,et al.  SCANPY: large-scale single-cell gene expression data analysis , 2018, Genome Biology.

[30]  Jaeki Min,et al.  Progress in the Development of Preventative Drugs for Cisplatin-Induced Hearing Loss , 2018, Journal of medicinal chemistry.

[31]  Terry K. Smith,et al.  Direct and indirect approaches to identify drug modes of action , 2018, IUBMB life.

[32]  Blake S Wilson,et al.  Global hearing health care: new findings and perspectives , 2017, The Lancet.

[33]  J. Ahn,et al.  Activity and safety of AZD3759 in EGFR-mutant non-small-cell lung cancer with CNS metastases (BLOOM): a phase 1, open-label, dose-escalation and dose-expansion study. , 2017, The Lancet. Respiratory medicine.

[34]  Jarek Meller,et al.  Abnormalities of signal transduction networks in chronic schizophrenia , 2017, npj Schizophrenia.

[35]  Sarah M. Theodoroff,et al.  Audiologic characteristics in a sample of recently-separated military Veterans: The Noise Outcomes in Servicemembers Epidemiology Study (NOISE Study) , 2017, Hearing Research.

[36]  Lavinia Sheets.  Excessive activation of ionotropic glutamate receptors induces apoptotic hair-cell death independent of afferent and efferent innervation , 2017, Scientific Reports.

[37]  Kayla Hill,et al.  Inhibitors of Histone Deacetylases Attenuate Noise-Induced Hearing Loss , 2016, Journal of the Association for Research in Otolaryngology.

[38]  Gert Vriend,et al.  New ways to boost molecular dynamics simulations , 2015, J. Comput. Chem..

[39]  Leslie D. Liberman,et al.  Dynamics of cochlear synaptopathy after acoustic overexposure , 2015, Journal of the Association for Research in Otolaryngology.

[40]  C. Betsholtz,et al.  Reverse genetic screening reveals poor correlation between morpholino-induced and mutant phenotypes in zebrafish. , 2015, Developmental cell.

[41]  A. Butte,et al.  A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors. , 2013, Cancer discovery.

[42]  M. Bellingham,et al.  A method for the three-dimensional reconstruction of Neurobiotin™-filled neurons and the location of their synaptic inputs , 2013, Front. Neural Circuits.

[43]  Chun-Ming Tsai,et al.  Phase III study of afatinib or cisplatin plus pemetrexed in patients with metastatic lung adenocarcinoma with EGFR mutations. , 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[44]  F. Iorio,et al.  Transcriptional data: a new gateway to drug repositioning? , 2013, Drug discovery today.

[45]  K. Fukushima,et al.  Time Courses of Changes in Phospho- and Total- MAP Kinases in the Cochlea after Intense Noise Exposure , 2013, PloS one.

[46]  Kurt Yankaskas,et al.  Prelude: Noise-induced tinnitus and hearing loss in the military , 2013, Hearing Research.

[47]  L. Di,et al.  Demystifying brain penetration in central nervous system drug discovery. Miniperspective. , 2013, Journal of medicinal chemistry.

[48]  R. Salvi,et al.  Noise induced changes in the expression of p38/MAPK signaling proteins in the sensory epithelium of the inner ear. , 2011, Journal of proteomics.

[49]  Philip Griebel,et al.  Peptide arrays for kinome analysis: New opportunities and remaining challenges , 2011, Proteomics.

[50]  Yanli Wang,et al.  Identifying Compound-Target Associations by Combining Bioactivity Profile Similarity Search and Public Databases Mining , 2011, J. Chem. Inf. Model..

[51]  K. Campbell,et al.  Anti-epileptic drugs delay age-related loss of spiral ganglion neurons via T-type calcium channel , 2011, Hearing Research.

[52]  B. Lonsbury-Martin,et al.  Noise-induced changes in gene expression in the cochleae of mice differing in their susceptibility to noise damage , 2011, Hearing Research.

[53]  S. Green,et al.  Functional Role of Neurotrophin-3 in Synapse Regeneration by Spiral Ganglion Neurons on Inner Hair Cells after Excitotoxic Trauma In Vitro , 2011, The Journal of Neuroscience.

[54]  B. Canlon,et al.  Differential activation of mitogen-activated protein kinases and brain-derived neurotrophic factor after temporary or permanent damage to a sensory system , 2010, Neuroscience.

[55]  Rickie R. Davis,et al.  Exposure to hazardous workplace noise and use of hearing protection devices among US workers--NHANES, 1999-2004. , 2009, American journal of industrial medicine.

[56]  D. Raible,et al.  Identification of FDA-Approved Drugs and Bioactives that Protect Hair Cells in the Zebrafish (Danio rerio) Lateral Line and Mouse (Mus musculus) Utricle , 2009, Journal of the Association for Research in Otolaryngology.

[57]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[58]  M. Moasser.  Targeting the function of the HER2 oncogene in human cancer therapeutics , 2007, Oncogene.

[59]  W. Mann,et al.  Akt and c-Jun N-Terminal Kinase Are Regulated in Response to Moderate Noise Exposure in the Cochlea of Guinea Pigs , 2007, ORL.

[60]  L. Rybak,et al.  Mechanisms of cisplatin-induced ototoxicity and prevention , 2007, Hearing Research.

[61]  Yu Xue,et al.  GPS: a comprehensive www server for phosphorylation sites prediction , 2005, Nucleic Acids Res..

[62]  Mitsuru Sugawara,et al.  Survival of Adult Spiral Ganglion Neurons Requires erbB Receptor Signaling in the Inner Ear , 2004, The Journal of Neuroscience.

[63]  A. Groves,et al.  Generation of Pax2‐Cre mice by modification of a Pax2 bacterial artificial chromosome , 2004, Genesis.

[64]  R. Salvi,et al.  Expression of heregulin and ErbB/Her receptors in adult chinchilla cochlear and vestibular sensory epithelium , 2002, Hearing Research.

[65]  M. Liberman,et al.  Dynamics of Noise-Induced Cellular Injury and Repair in the Mouse Cochlea , 2002, Journal of the Association for Research in Otolaryngology.

[66]  N. Hakuba,et al.  Exacerbation of Noise-Induced Hearing Loss in Mice Lacking the Glutamate Transporter GLAST , 2000, The Journal of Neuroscience.

[67]  F. Ribaupierre,et al.  Spatial expression patterns of epidermal growth factor receptor gene transcripts in the postnatal mammalian cochlea , 2000, Hearing Research.

[68]  F. de Ribaupierre,et al.  Tissue-specific levels and cellular distribution of epidermal growth factor receptors within control and neomycin-damaged neonatal rat Organ of Corti. , 1999, Journal of neurobiology.

[69]  G. Moonen,et al.  Expression of Growth Factors and Their Receptors in the Postnatal Rat Cochlea , 1998, Neurochemical Research.

[70]  Jean-Luc Puel,et al.  Excitotoxicity and repair of cochlear synapses after noise‐trauma induced hearing loss , 1998, Neuroreport.

[71]  K. Henry.  Cochlear damage resulting from exposure to four different octave bands of noise at three ages. , 1984, Behavioral neuroscience.

[72]  Daniel Eisenberg,et al.  Economic Impact of Hearing Loss and Reduction of Noise-Induced Hearing Loss in the United States. , 2017, Journal of speech, language, and hearing research : JSLHR.

[73]  R. DorsettChristopher,et al.  Traumatic Brain Injury Induces Alterations in Cortical Glutamate Uptake without a Reduction in Glutamate Transporter-1 Protein Expression , 2017 .

[74]  Zhiyong Lu,et al.  A survey of current trends in computational drug repositioning , 2016, Briefings Bioinform..

[75]  D. Gerrard,et al.  Effects of AMP-activated protein kinase (AMPK) signaling and essential amino acids on mammalian target of rapamycin (mTOR) signaling and protein synthesis rates in mammary cells. , 2014, Journal of dairy science.