Clin Exp Otorhinolaryngol.  2023 May;16(2):115-124. 10.21053/ceo.2022.01235.

Identification and Characterization of mRNA and lncRNA Expression Profiles in Age-Related Hearing Loss

• Kim J
• Lee B
• Lee S
• Kim JT
• Kim BC
• Cho HH

• KMID: 2542352
• DOI: http://doi.org/10.21053/ceo.2022.01235

Abstract

Objectives
. Age-related hearing loss (ARHL), or presbycusis, is caused by disorders of sensory hair cells and auditory neurons. Many studies have suggested that the accumulation of mitochondrial DNA damage, the production of reactive oxygen species, noise, inflammation, and decreased antioxidant function are associated with subsequent cochlear senescence in response to aging stress. Long non-coding RNA (lncRNA) has been reported to play important roles in various diseases. However, the function of lncRNA in ARHL remains unclear. In this study, we analyzed the common expression profiles of messenger RNA (mRNA) and lncRNA through ARHL-related RNA-sequencing datasets.
Methods
. We selected and downloaded three different sets of RNA-sequencing data for ARHL. We performed differential expression analysis to find common mRNA and lncRNA profiles in the cochleae of aged mice compared to young mice. Gene Ontology (GO) analysis was used for functional exploration. Real-time quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was performed to validate mRNAs and lncRNAs. In addition, we performed trans target prediction analysis with differentially expressed mRNAs and lncRNAs to understand the function of these mRNAs and lncRNAs in ARHL.
Results
. We identified 112 common mRNAs and 10 common lncRNAs in the cochleae of aged mice compared to young mice. GO analysis showed that the 112 upregulated mRNAs were enriched in the defense response pathway. When we performed qRT-PCR with 1 mM H2O2-treated House Ear Institute-Organ of Corti 1 (HEI-OC1) cells, the qRT-PCR results were consistent with the RNA-sequencing analysis data. lncRNA-mRNA networks were constructed using the 10 common lncRNAs and 112 common mRNAs in ARHL.
Conclusion
. Our study provides a comprehensive understanding of the common mRNA and lncRNA expression profiles in ARHL. Knowledge of ARHL-associated mRNAs and lncRNAs could be useful for better understanding ARHL and these mRNAs and lncRNAs might be a potential therapeutic target for preventing ARHL.

Keyword

Presbycusis; Hearing Loss; Long Noncoding RNA; Messenger RNA

Figure

• 

  Fig. 1. Identification of differentially expressed messenger RNA (mRNA) profiles in age-related hearing loss. A Venn diagram (A) and heatmap (B) showing the number of significantly differentially expressed mRNA profiles in the cochleae of aged mice compared to young mice. Red indicates upregulation and blue represents downregulation. Significantly enriched Gene Ontology terms of upregulated (C) and downregulated (D) mRNAs. MHC, major histocompatibility complex.

• 

  Fig. 2. Bar graphs representing the upregulated differentially expressed messenger RNAs (mRNAs) (A) and downregulated differentially expressed mRNAs (B) in the cochleae of aged mice. (C) Validation of five differentially expressed mRNAs in H2O2-treated House Ear Institute-Organ of Corti 1 (HEI-OC1) cells using quantitative polymerase chain reaction. Statistical significance is indicated by asterisks (*P<0.05, **P<0.01, ***P<0.001).

• 

  Fig. 3. Identification of differentially expressed long non-coding RNA (lncRNA) profiles in age-related hearing loss. A Venn diagram (A) and heatmap (B) showing the number of the differentially expressed lncRNA profiles in the cochleae of aged mice compared to young mice. Red indicates upregulation and blue represents downregulation. (C) The identified lncRNAs in their genomic context. Genomic information was visualized with the Gviz package.

• 

  Fig. 4. Bar graphs representing the upregulated differentially expressed long non-coding RNAs (lncRNAs) (A) and downregulated differentially expressed lncRNAs (B) in the cochleae of aged mice. (C) Validation of 10 differentially expressed lncRNAs in H2O2-treated House Ear InstituteOrgan of Corti 1 (HEI-OC1) cells using quantitative polymerase chain reaction. Statistical significance is indicated by asterisks (*P<0.05, **P<0.01, ***P<0.001). NS, not significant.

• 

  Fig. 5. Construction of the long non-coding RNA (lncRNA)-messenger RNA (mRNA) network for age-related hearing loss, consisting of upregulated lncRNAs and downregulated lncRNAs with their trans-target differentially expressed mRNA. The diamonds and circles represent lncRNA and mRNAs. Red nodes represent upregulated lncRNAs or mRNAs, and blue nodes represent downregulated lncRNAs or mRNAs.

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