title: Variation analysis of transcriptome changes reveals cochlear genes and their associated functions in cochlear susceptibility to acoustic overstimulation.
abstract: Individual variation in the susceptibility of the auditory system to acoustic overstimulation has been well-documented at both the functional and structural levels. However, the molecular mechanism responsible for this variation is unclear. The current investigation was designed to examine the variation patterns of cochlear gene expression using RNA-seq data and to identify the genes with expression variation that increased following acoustic trauma. This study revealed that the constitutive expressions of cochlear genes displayed diverse levels of gene-specific variation. These variation patterns were altered by acoustic trauma; approximately one-third of the examined genes displayed marked increases in their expression variation. Bioinformatics analyses revealed that the genes that exhibited increased variation were functionally related to cell death, biomolecule metabolism, and membrane function. In contrast, the stable genes were primarily related to basic cellular processes, including protein and macromolecular syntheses and transport. There was no functional overlap between the stable and variable genes. Importantly, we demonstrated that glutamate metabolism is related to the variation in the functional response of the cochlea to acoustic overstimulation. Taken together, the results indicate that our analyses of the individual variations in transcriptome changes of cochlear genes provide important information for the identification of genes that potentially contribute to the generation of individual variation in cochlear responses to acoustic overstimulation.
authors.affiliation: Center for Hearing and Deafness, University at Buffalo, NY, 14214, USA. Electronic address: qits-002@163.com.
authors.forename: Shuzhi
authors.initials: S
authors.lastname: Yang
authors.affiliation: Center for Hearing and Deafness, University at Buffalo, NY, 14214, USA. Electronic address: qunfengcai@gmail.com.
authors.forename: Qunfeng
authors.initials: Q
authors.lastname: Cai
authors.affiliation: Next-Generation Sequencing and Expression Analysis Core, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, 14263, USA. Electronic address: jbard@buffalo.edu.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Bard
authors.affiliation: Next-Generation Sequencing and Expression Analysis Core, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, 14263, USA. Electronic address: jjamison@buffalo.edu.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Jamison
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY, 14263, USA. Electronic address: Jianmin.Wang@RoswellPark.org.
authors.forename: Jianmin
authors.initials: J
authors.lastname: Wang
authors.affiliation: Center for Hearing and Deafness, University at Buffalo, NY, 14214, USA. Electronic address: yangwp301@126.com.
authors.forename: Weiping
authors.initials: W
authors.lastname: Yang
authors.affiliation: Center for Hearing and Deafness, University at Buffalo, NY, 14214, USA. Electronic address: bhu@buffalo.edu.
authors.forename: Bo Hua
authors.initials: BH
authors.lastname: Hu
mesh_terms: D000161:Acoustic Stimulation; D000818:Animals; D003051:Cochlea / Q000378:metabolism* / Q000502:physiology; D019295:Computational Biology; D004423:Ear / Q000502:physiology; D016057:Evoked Potentials, Auditory, Brain Stem / Q000502:physiology; D005260:Female; D020869:Gene Expression Profiling; D014644:Genetic Variation; D018698:Glutamic Acid / Q000378:metabolism; D006198:Hair Cells, Auditory / Q000378:metabolism; D006317:Hearing Loss, Noise-Induced / Q000503:physiopathology; D046911:Macromolecular Substances; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D008808:Mice, Inbred CBA; D009622:Noise / Q000009:adverse effects*; D009925:Organ of Corti / Q000378:metabolism; D012313:RNA / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D046911:Macromolecular Substances; D018698:Glutamic Acid; D012313:RNA
keywords: Cochlea; Gene; Glutamate; Noise; RNA-sequence; Susceptibility