The Genomic Basis of Noise-induced Hearing Loss: A Literature Review Organized by Cellular Pathways

Royce Ellen Clifford, Michael E Hoffer, Rick Rogers

Research output: Contribution to journalReview article

9 Citations (Scopus)

Abstract

Objective: Using Reactome, a curated Internet database, noise-induced hearing loss studies were aggregated into cellular pathways for organization of the emerging genomic and epigenetic data in the literature. Data Sources: PubMed and Reactome.org, a relational data base program systematizing biological processes into interactive pathways and subpathways based on ontology, cellular constituents, gene expression, and molecular components. Study Selection: Peer-reviewed population and laboratory studies for the previous 15 years relating genomics and noise and hearing loss were identified in PubMed. Criteria included p values <0.05 with correction for multiple genes, a fold change of >1.5, or duplicated studies. Data Extraction and Synthesis: One-hundred fifty-eight unique HGNC identifiers from 77 articles met the selection criteria, and were uploaded into the analysis program at http://reactome.org. These genes participated in a total of 621 cellular interactions in 21 of 23 pathways. Cellular response to stress with its attenuation phase, particularly in response to heat stress, detoxification of ROS, and specific areas of the immune system are predominant pathways identified as significantly overrepresented (p values <0.1e-5 and false discovery rates <0.01). Conclusion: Twenty-one of 23 of the designated pathways in Reactome have significant influence on noise-induced hearing loss, signifying a confluence of molecular pathways in reaction to acoustic trauma; however, cellular response to stress, including heat shock response, and other small areas of immune response were highly overrepresented. Yet-to-be-explored genomics areas include miRNA, lncRNA, copy number variations, RNA sequencing, and human genome-wide association study.

Original languageEnglish (US)
Pages (from-to)e309-e316
JournalOtology and Neurotology
Volume37
Issue number8
DOIs
StatePublished - Sep 1 2016

Fingerprint

Noise-Induced Hearing Loss
Heat-Shock Response
Genomics
PubMed
Long Noncoding RNA
Databases
RNA Sequence Analysis
Biological Phenomena
Information Storage and Retrieval
Genome-Wide Association Study
Human Genome
MicroRNAs
Hearing Loss
Epigenomics
Internet
Patient Selection
Noise
Immune System
Gene Expression
Population

Keywords

  • Cellular pathways
  • Genomics
  • Noise-induced hearing loss
  • Reactome
  • Sensorineural hearing loss

ASJC Scopus subject areas

  • Medicine(all)
  • Otorhinolaryngology
  • Sensory Systems
  • Clinical Neurology

Cite this

The Genomic Basis of Noise-induced Hearing Loss : A Literature Review Organized by Cellular Pathways. / Clifford, Royce Ellen; Hoffer, Michael E; Rogers, Rick.

In: Otology and Neurotology, Vol. 37, No. 8, 01.09.2016, p. e309-e316.

Research output: Contribution to journalReview article

@article{a755e067069f496e8e4bbac0c3c050c9,
title = "The Genomic Basis of Noise-induced Hearing Loss: A Literature Review Organized by Cellular Pathways",
abstract = "Objective: Using Reactome, a curated Internet database, noise-induced hearing loss studies were aggregated into cellular pathways for organization of the emerging genomic and epigenetic data in the literature. Data Sources: PubMed and Reactome.org, a relational data base program systematizing biological processes into interactive pathways and subpathways based on ontology, cellular constituents, gene expression, and molecular components. Study Selection: Peer-reviewed population and laboratory studies for the previous 15 years relating genomics and noise and hearing loss were identified in PubMed. Criteria included p values <0.05 with correction for multiple genes, a fold change of >1.5, or duplicated studies. Data Extraction and Synthesis: One-hundred fifty-eight unique HGNC identifiers from 77 articles met the selection criteria, and were uploaded into the analysis program at http://reactome.org. These genes participated in a total of 621 cellular interactions in 21 of 23 pathways. Cellular response to stress with its attenuation phase, particularly in response to heat stress, detoxification of ROS, and specific areas of the immune system are predominant pathways identified as significantly overrepresented (p values <0.1e-5 and false discovery rates <0.01). Conclusion: Twenty-one of 23 of the designated pathways in Reactome have significant influence on noise-induced hearing loss, signifying a confluence of molecular pathways in reaction to acoustic trauma; however, cellular response to stress, including heat shock response, and other small areas of immune response were highly overrepresented. Yet-to-be-explored genomics areas include miRNA, lncRNA, copy number variations, RNA sequencing, and human genome-wide association study.",
keywords = "Cellular pathways, Genomics, Noise-induced hearing loss, Reactome, Sensorineural hearing loss",
author = "Clifford, {Royce Ellen} and Hoffer, {Michael E} and Rick Rogers",
year = "2016",
month = "9",
day = "1",
doi = "10.1097/MAO.0000000000001073",
language = "English (US)",
volume = "37",
pages = "e309--e316",
journal = "Otology and Neurotology",
issn = "1531-7129",
publisher = "Lippincott Williams and Wilkins",
number = "8",

}

TY - JOUR

T1 - The Genomic Basis of Noise-induced Hearing Loss

T2 - A Literature Review Organized by Cellular Pathways

AU - Clifford, Royce Ellen

AU - Hoffer, Michael E

AU - Rogers, Rick

PY - 2016/9/1

Y1 - 2016/9/1

N2 - Objective: Using Reactome, a curated Internet database, noise-induced hearing loss studies were aggregated into cellular pathways for organization of the emerging genomic and epigenetic data in the literature. Data Sources: PubMed and Reactome.org, a relational data base program systematizing biological processes into interactive pathways and subpathways based on ontology, cellular constituents, gene expression, and molecular components. Study Selection: Peer-reviewed population and laboratory studies for the previous 15 years relating genomics and noise and hearing loss were identified in PubMed. Criteria included p values <0.05 with correction for multiple genes, a fold change of >1.5, or duplicated studies. Data Extraction and Synthesis: One-hundred fifty-eight unique HGNC identifiers from 77 articles met the selection criteria, and were uploaded into the analysis program at http://reactome.org. These genes participated in a total of 621 cellular interactions in 21 of 23 pathways. Cellular response to stress with its attenuation phase, particularly in response to heat stress, detoxification of ROS, and specific areas of the immune system are predominant pathways identified as significantly overrepresented (p values <0.1e-5 and false discovery rates <0.01). Conclusion: Twenty-one of 23 of the designated pathways in Reactome have significant influence on noise-induced hearing loss, signifying a confluence of molecular pathways in reaction to acoustic trauma; however, cellular response to stress, including heat shock response, and other small areas of immune response were highly overrepresented. Yet-to-be-explored genomics areas include miRNA, lncRNA, copy number variations, RNA sequencing, and human genome-wide association study.

AB - Objective: Using Reactome, a curated Internet database, noise-induced hearing loss studies were aggregated into cellular pathways for organization of the emerging genomic and epigenetic data in the literature. Data Sources: PubMed and Reactome.org, a relational data base program systematizing biological processes into interactive pathways and subpathways based on ontology, cellular constituents, gene expression, and molecular components. Study Selection: Peer-reviewed population and laboratory studies for the previous 15 years relating genomics and noise and hearing loss were identified in PubMed. Criteria included p values <0.05 with correction for multiple genes, a fold change of >1.5, or duplicated studies. Data Extraction and Synthesis: One-hundred fifty-eight unique HGNC identifiers from 77 articles met the selection criteria, and were uploaded into the analysis program at http://reactome.org. These genes participated in a total of 621 cellular interactions in 21 of 23 pathways. Cellular response to stress with its attenuation phase, particularly in response to heat stress, detoxification of ROS, and specific areas of the immune system are predominant pathways identified as significantly overrepresented (p values <0.1e-5 and false discovery rates <0.01). Conclusion: Twenty-one of 23 of the designated pathways in Reactome have significant influence on noise-induced hearing loss, signifying a confluence of molecular pathways in reaction to acoustic trauma; however, cellular response to stress, including heat shock response, and other small areas of immune response were highly overrepresented. Yet-to-be-explored genomics areas include miRNA, lncRNA, copy number variations, RNA sequencing, and human genome-wide association study.

KW - Cellular pathways

KW - Genomics

KW - Noise-induced hearing loss

KW - Reactome

KW - Sensorineural hearing loss

UR - http://www.scopus.com/inward/record.url?scp=84983251094&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84983251094&partnerID=8YFLogxK

U2 - 10.1097/MAO.0000000000001073

DO - 10.1097/MAO.0000000000001073

M3 - Review article

C2 - 27518140

AN - SCOPUS:84983251094

VL - 37

SP - e309-e316

JO - Otology and Neurotology

JF - Otology and Neurotology

SN - 1531-7129

IS - 8

ER -