Perimatrix of middle ear cholesteatoma: A granulation tissue with a specific transcriptomic signature

Abstract

Objectives/Hypothesis To establish comprehensive transcriptomic profiles of cholesteatoma perimatrix tissue and granulation tissue from chronic otitis media (COM) that did not develop cholesteatoma, which can indicate molecular pathways involved in the cholesteatoma perimatrix pathology and invasiveness. Study Design Retrospective Case Series. Methods Transcriptome data were obtained from cholesteatoma perimatrix tissue and COM granulation tissue by an Illumina iScan microarray. Differentially expressed genes (DEGs) were subsequently analyzed using both bioinformatical functional annotation and network analysis. Expression of candidate genes (MMP9 and LCN2) was validated by quantitative reverse transcription‐polymerase chain reaction (qRT‐PCR) on a larger group of samples. Results Analysis of the transcriptome led to the identification of 169 differentially expressed genes between investigated tissues. Bioinformatic analysis suggested that most significant biological processes involving DEGs were previously described in cholesteatoma pathology. Network analysis identified ERBB2, TFAP2A, and TP63 as major hubs of the DEGs molecular network. Furthermore, it was observed that the cellular component most significantly enriched in DEGs was extracellular space containing 47 DEGs. Using qRT‐PCR, it was confirmed that mRNA levels of the major extracellular hub (MMP9) are increased, whereas its interacting molecule (LCN2) mRNA levels were decreased in cholesteatoma perimatrix tissue compared to COM granulation tissue. Conclusions The current study approach offers an overall look at molecular mechanisms that describe the cholesteatoma entity by focusing exclusively on the perimatrix processes in comparison to COM granulation tissue. The observed differences in gene expression between cholesteatoma perimatrix and COM granulation tissue could suggest novel markers potentially influenced by the perimatrix–matrix molecular interplay, which is not present in COM without cholesteatoma. Level of Evidence NA Laryngoscope, 130:E220–E227, 2020

Identification of Novel Genes and Biological Pathways That Overlap in Infectious and Nonallergic Diseases of the Upper and Lower Airways Using Network Analyses

“…This is the first report using RNA-Seq in OM patients with middle ear cholesteatoma compared to middle ear mucosal tissue as a control. Previous studies have used either skin or granulation tissue as control tissue in cholesteatoma studies (Kwon et al, 2006;Klenke et al, 2012;Macias et al, 2013;Gao et al, 2018a;Jovanovic et al, 2019). In our study, 1,806 genes were differentially expressed between cholesteatoma and mucosa samples ( Supplementary Table 7; Figure 1).…”

“…Overall, based on DEGs, 32 pathways (38%) overlap between the upper and lower airways, and 27 pathways were common to all three phenotypes (OM, CRS, and Lower; Supplementary Figure 5; Supplementary Table 5). Notably about half of these 27 pathways that were common in OM, CRS, and Lower also overlap with DEGs identified in previous microarray and RNA-Seq studies (Liu et al, 2004;Kwon et al, 2006;Lee et al, 2006;Payne et al, 2008;Raju et al, 2008;Stankovic et al, 2008;Rostkowska-Nadolska et al, 2011;Klenke et al, 2012;Macias et al, 2013;Wang et al, 2016;Ramakrishnan et al, 2017;Wang et al, 2017;Gao et al, 2018a;Gao et al, 2018b;Kato et al, 2018;Langelier et al, 2018;Ninomiya et al, 2018;Okada et al, 2018;Jovanovic et al, 2019;Walter et al, 2019;Yao et al, 2019). The common pathways from Part 2 RNA-Seq data that were identified in the transcriptome literature are apoptosis, cell adhesion, cell cycle, cell proliferation, chromatin organization/remodeling, Table 6).…”

Non‐coding RNA and cholesteatoma

“…14 These discrepancies warrant further ex vivo validation in cholesteatoma tissue on a larger number of samples to confirm the in vitro observations especially by taking into account the complex perimatrix-matrix molecular interplay which has been suggested to play a major role in cholesteatoma. 6…”

“…cholesteatoma, [2][3][4][5][6] no discrete pharmacological targets have been identified yet. To identify master regulators of these pathways and provide pharmacologic targets for medical management of cholesteatoma, we need to look beyond the protein-coding genes and into the universe of noncoding RNA (ncRNA) molecules (Table 1).…”

Panel 4: Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures

“…A small number of studies have used transcriptomics to study human gene expression in otitis media (e.g. [160]). Pathogen transcriptomes were reported by one study of nasopharyngeal aspirates [71].…”