The Whole Transcriptome Sequencing Profile of Serum-Derived Exosomes and Potential Pathophysiology of Age-Related Hearing Loss.

Objectives

To systematically analyze the expression profiles of long non-coding RNAs (lncRNAs) in serum-derived exosomes from patients with age-related hearing loss (ARHL), and to further identify key regulatory lncRNAs involved in the pathogenesis and progression of ARHL.

Methods

Peripheral blood samples were collected from patients with ARHL and age-matched normal-hearing controls. Serum was separated and exosomes were extracted. The exosomes were identified by nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), and Western blot. Subsequently, total RNA was extracted from the purified exosomes for lncRNA transcriptome sequencing. Based on the sequencing results, we identified differentially expressed lncRNAs and mRNAs and conducted multi-dimensional functional analysis, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome pathway database (Reactome), and Disease Ontology (DO). Finally, four key mRNAs (THAP2, ZNF225, MED12, and RNF141) and four differentially expressed lncRNAs (DE-lncRNAs), namely MSTRG.150961.7, ENSG00000273015, MSTRG.336598.1, and ENSG00000273493, were experimentally verified by quantitative real-time polymerase chain reaction (RT-qPCR) technology.

Results

Exosomes were successfully isolated from serum and confirmed by particle size, morphological examination, and the expression of exosome-labeled proteins. A total of 2874 DE-lncRNAs were identified, among which 988 were downregulated and 1886 were upregulated. Similarly, 2132 DE-mRNAs were detected, among which 882 were downregulated and 1250 were upregulated. GO analysis revealed significant enrichment in biological processes such as "phospholipid binding", "phosphatidylinositol binding", "phosphatase binding", "phosphatidylinositol bisphosphate binding", "phosphatidylinositol-4,5-bisphosphate binding", "phosphatidylinositol-3,5-bisphosphate phosphatase activity". KEGG is significantly enriched in signaling pathways including "Wnt signaling pathway", "Hippo signaling pathway", "Cushing syndrome", and "Nucleocytoplasmic transport". The functional annotations of Reactome were significantly enriched in biomolecular pathways including "tRNA processing", "Cellular response to heat stress", "Extra-nuclear estrogen signaling", "Metabolism of non-coding RNA", and "CTNNB1 T41 mutants aren't phosphorylated". DO is significantly enriched in diseases or pathological conditions such as "hepatitis", "bacterial infectious disease", "cystic fibrosis", and "vasculitis".

Conclusions

THAP2, ZNF225, MED12, and RNF141 may serve as potential candidate biomarker for ARHL. Additionally, lncRNA MSTRG.150961.7, lncRNA MSTRG.336598.1, and lncRNA ENSG00000273493 may play significant roles in the pathogenesis of this condition.