Integrated Proteomic Profiling of Inner Ear and Systemic Fluids Following Noise-Induced Hearing Loss in Rats

Abstract Noise-induced hearing loss (NIHL) arises from acute or prolonged exposure to loud sounds, yet early diagnosis remains difficult as some individuals show minimal changes in standard audiometry. This study presents the first comparative mass spectrometry-based proteomic analysis of perilymph, cochlear-derived cerebrospinal fluid (CSF), whole blood, and plasma in Sprague–Dawley rats following acute noise exposure, to identify molecular signatures of NIHL. Rats were exposed to 110 dB noise for 1 h under anesthesia, inducing an approximately 40 dB threshold shift measured by cochlear nerve Compound Action Potential (CAP). Nano LC–MS/MS in data-independent acquisition (DIA) mode followed by peptide- and protein-level filtering, identified 310 proteins in perilymph, 396 in CSF, 1688 in blood, and 281 in plasma. Differential expression analysis revealed 50, 79, 281, and 49 significantly changed proteins, respectively. A shared inflammatory response was observed, highlighted by consistent upregulation of IGHM across all fluids. Cochlear samples showed enrichment of metabolic and injury-related proteins, including PGAM2 and ALDOA, while systemic samples exhibited changes in fibrinogen chains, IGFBP5, and apolipoproteins. KEGG pathway analysis indicated involvement of metabolic, immune, and lipid-regulatory pathways. Targeted PRM validation confirmed selected protein changes. These findings demonstrate coordinated local and systemic responses to noise trauma, supporting the potential of peripheral biomarkers for early NIHL detection.