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

Krishna Bommakanti; Richard Seist; Phanidhar Kukutla; Murat Cetinbas; Shelley Batts; Ruslan I Sadreyev; Anat Stemmer-Rachamimov; Gary J Brenner; Konstantina M Stankovic

doi:10.3390/jcm12072642

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

J Clin Med. 2023 Apr 1;12(7):2642. doi: 10.3390/jcm12072642.

Authors

Krishna Bommakanti^{1

2}, Richard Seist^{1

3

4}, Phanidhar Kukutla⁵, Murat Cetinbas⁶, Shelley Batts³, Ruslan I Sadreyev⁶, Anat Stemmer-Rachamimov⁷, Gary J Brenner⁵, Konstantina M Stankovic^{1

3

8

9}

Affiliations

¹ Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA 02114, USA.
² Department of Head and Neck Surgery, University of California Los Angeles, Los Angeles, CA 90095, USA.
³ Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA.
⁴ Department of Otorhinolaryngology-Head and Neck Surgery, Paracelsus Medical University, 5020 Salzburg, Austria.
⁵ Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
⁶ Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
⁷ Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
⁸ Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA.
⁹ Wu Tsai Neuroscience Institute, Stanford University, Stanford, CA 94305, USA.

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.

Keywords: bioinformatic analysis; functional enrichment analysis; gene set enrichment analysis; inflammation; tinnitus; vestibular schwannoma.

Abstract

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