RNA Sequencing and Pathways Analyses of Middle Ear Epithelia From Patients With Otitis Media

Abstract

Objectives Otitis media (OM) is the most common pediatric diagnosis in the United States. However, our understanding of the molecular pathogenesis of OM remains relatively poor. Investigation of molecular pathways involved in OM may improve the understanding of this disease process and elucidate novel therapeutic targets. In this study, RNA sequencing (RNA‐Seq) was used to discern cellular changes associated with OME compared to healthy middle ear epithelium (MEE). Study Design Ex vivo case‐control translational. Methods Middle ear epithelia was collected from five pediatric patients diagnosed with OME undergoing tympanostomy tube placement and five otherwise healthy pediatric patients undergoing cochlear implantation. Specimens underwent RNA‐Seq and pathways analyses. Results A total of 1,292 genes exhibited differential expression in MEE from OME patients compared to controls including genes involved in inflammation, immune response to bacterial OM pathogens, mucociliary clearance, regulation of proliferation and transformation, and auditory cell differentiation. Top networks identified in OME were organismal injury and abnormalities, cell morphology, and auditory disease. Top Ingenuity canonical pathways identified were axonal guidance signaling, which contains genes associated with auditory development and disease and nicotine degradation II and III pathways. Associated upstream regulators included β‐estradiol, dexamethasone, and G‐protein‐coupled estrogen receptor‐1 (GPER1), which are associated with otoprotection or inflammation during insult. Conclusions RNA‐Seq demonstrates differential gene expression in MEE from patients with OME compared to healthy controls with important implications for infection susceptibility, hearing loss, and a role for tobacco exposure in the development and/or severity of OME in pediatric patients. Level of Evidence 4 Laryngoscope, 131:2590–2597, 2021

The FUT2 Variant c.461G>A (p.Trp154*) Is Associated With Differentially Expressed Genes and Nasopharyngeal Microbiota Shifts in Patients With Otitis Media

“…Contributes to composition of mucous barrier as part of host defense against infection (Kesimer et al, 2009) • Upregulated in middle ear epithelia of OM patients as compared to normal controls (Stabenau et al, 2021) In conclusion, we propose that the mechanistic effects of the FUT2 c.461G>A variant on OM susceptibility are two-fold:…”

Association of e-Cigarette Exposure with Pediatric Otitis Media Recurrence

“…[26][27][28][29]31 These studies suggest that particulate matter, nicotine and other chemicals in TP and SHS play a role, with that of nicotine corroborated by dysregulated nicotine metabolism in the ME of pediatric patients with chronic OM. 44 Despite strong evidence for the contribution of tobacco exposure to pediatric OM, the association of EE with OM has never, to our knowledge, been examined. The cross-sectional analysis herein represents the first epidemiologic evidence of the contribution of EE exposure to recurring OM in children.…”

Pepsinogen/Proton Pump Co‐Expression in Barrett's Esophageal Cells Induces Cancer‐Associated Changes

“…RNA isolation, sequencing, and pathways analyses of BAR‐T expressing ATP4A , ATP4B , and/or PGA5 were performed at the Genomic Science and Precision Medicine Center (GSPMC at MCW) as previously described 8,12 …”

“…RNA isolation, sequencing, and pathways analyses of BAR-T expressing ATP4A, ATP4B, and/or PGA5 were performed at the Genomic Science and Precision Medicine Center (GSPMC at MCW) as previously described. 8,12 Transmission Electron Microscopy BAR-T expressing ATP4A, ATP4B, and/or PGA5 were cultured to near confluence and analyzed by transmission electron microscopy (TEM) as previously described. 11…”