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Marwan Ali, Arun Balasubramaniam, Mark Maienschein-Cline, Shreya Wadhwa, Dhara Shah, Kyung-No Son, Sushma Kalmodia, Vinay Kumar Aakalu; Non-coding RNA Expression in Inflammatory Dacryoadenitis. Invest. Ophthalmol. Vis. Sci. 2018;59(9):107.
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Inflammatory dacryoadenitis (ID) is an important cause of morbidity and may be associated with inflammatory disorders [e.g. sarcoidosis, IgG4 related disease (IgG4RD)]. Advances in understanding of non-coding RNA [microRNA (miRNA), small nuclear RNA(snRNA) and small nucleolar RNAs (snoRNAs)], have revealed their importance in transcriptional regulation and pathogenesis of disease. We investigated the role of non-coding RNA levels in a pilot study using samples of ID [sarcoidosis, idiopathic chronic dacryoadenitis (ICD), IgG4RD and sclerosing dacryoadenitis (SD)].
Formalin fixed paraffin embedded lacrimal gland (LG) specimens obtained under an IRB approved protocol. RNA extraction and sequencing were performed using the Maxwell® RSC RNA FFPE Kit and the Illumina NextSeq500 platform. Patient samples included: 2 patient LG controls, 1 patient with SD, 1 patient with sarcoidosis [with biologic replicate (BR)], 2 IgG4RD patients (1 with one sample and 1 patient with 2 BR), 4 patients with ICD (one with BR).Adapter and quality-trimmed raw reads were mapped against the human reference genome using bwa aln, and quantified against small non-coding RNA annotations from Ensembl using featureCounts. Differential expression between groups was computed using edgeR, and p-values were adjusted for multiple testing using the false discovery rate (FDR) correction. Differentially expressed miRNAs were determined at a 0.05 FDR threshold.
Non-coding RNA data were quantified against annotations from Ensembl (miRNA, snRNA, snoRNA). We found 600-700 of these RNAs on average per sample (appx. 1/3 were miRNAs); 1497 were seen at least once in any sample. The number of non-coding RNAs that were differentially expressed varied by comparison, but as many as 50 were found. Some differentially expressed miRNAs (e.g. MIR142) have roles in inflammatory disorders.
Our study indicates that non-coding RNA expression patterns may be useful in differentiating control tissue from ID. Future, larger studies to compare amongst individual disease types and understand the pathologic importance of these RNAs will be needed.
This is an abstract that was submitted for the 2018 ARVO Annual Meeting, held in Honolulu, Hawaii, April 29 - May 3, 2018.
Figure 1: P Principle Coordinate (PC) Analysis of small non-coding RNA expression in lacrimal gland tissue samples. Notable is the clustering of expression patterns amongst ICD, sarcoidosis, and IgG4RD samples. SD and control samples did not overlap considerably with any of the disease sample gene expression patterns.
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