Comparative Transcriptomic Analysis of Archival Human Vestibular Schwannoma Tissue from Patients with and without Tinnitus

Abstract

Vestibular schwannoma (VS) is an intracranial tumor that commonly presents with tinnitus and hearing loss. To uncover the molecular mechanisms underlying VS-associated tinnitus, we applied next-generation sequencing (Illumina HiSeq) to formalin-fixed paraffin-embedded archival VS samples from nine patients with tinnitus (VS-Tin) and seven patients without tinnitus (VS-NoTin). Bioinformatic analysis was used to detect differentially expressed genes (DEG; i.e., ≥two-fold change [FC]) while correcting for multiple comparisons. Using RNA-seq analysis, VS-Tin had significantly lower expression of GFAP (logFC = −3.04), APLNR (logFC = −2.95), PREX2 (logFC = −1.44), and PLVAP (logFC = −1.04; all p < 0.01) vs. VS-NoTin. These trends were validated by using real-time RT-qPCR. At the protein level, immunohistochemistry revealed a trend for less PREX2 and apelin expression and greater expression of NLRP3 inflammasome and CD68-positive macrophages in VS-Tin than in VS-NoTin, suggesting the activation of inflammatory processes in VS-Tin. Functional enrichment analysis revealed that the top three protein categories—glycoproteins, signal peptides, and secreted proteins—were significantly enriched in VS-Tin in comparison with VS-NoTin. In a gene set enrichment analysis, the top pathway was allograft rejection, an inflammatory pathway that includes the MMP9, CXCL9, IL16, PF4, ITK, and ACVR2A genes. Future studies are needed to examine the importance of these candidates and of inflammation in VS-associated tinnitus.

Metastasis Associated in Colorectal Cancer 1 (MACC1) mRNA Expression Is Enhanced in Sporadic Vestibular Schwannoma and Correlates to Deafness

“…Large tumors may be associated with good hearing function, while some patients with small tumors may suffer from high hearing impairment, suggesting an alternative mechanism besides tumor compression of the nerve [ 32 , 44 , 45 , 46 ]. Recently, it has been shown that NLR family pyrin domain containing 3 (NLRP3) inflammasome activation in VS is correlated with VS-induced hearing loss [ 47 , 48 ]. Tumor necrosis factor (TNF) receptors activate NFκB, which induces increased transcription of NLRP3 [ 49 ].…”

“…Interestingly, these genes have been identified in the transcriptome list of MACC1. Therefore, invasive tumor growth in conjunction with inflammasome activation could be an explanation for an over-proportional hearing loss in some cases with small tumors [ 35 , 47 , 48 , 51 ]. Although the evaluation of invasiveness was out of the scope of this study, MACC1 has been shown to correlate with further invasiveness of tumor cells [ 2 ] and therefore might be relevant for hearing impairment caused by tumor invasiveness.…”