Comparative transcriptome analysis of human conjunctiva between normal and conjunctivochalasis persons by RNA sequencing

Conjunctivochalasis (CCH) is a common ocular disease, especially in aged people. However, the molecular mechanism of CCH on transcriptional level has been unclear. In this study, we characterized the transcriptional landscape of human conjunctiva and compared the transcriptome between normal persons (n = 10) and CCH patients (n = 11). Illumina RNA sequencing (RNA-seq) was performed to obtain transcriptional data, and these data were analyzed using various bioinformatics methods, including read mapping, the analysis of gene expression, gene ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genomes (KEGG) metabolic pathway analysis. Additionally, expression patterns of 20 dysregupated genes were validated by qRT-PCR. RNA-seq result showed that clean ratios of 21 samples were more than 95% and more than 92% of all clean reads (32-41 million reads) were mapped to human genome sequence. There were 175 up-regulated genes and 582 down-regulated genes identified in CCH compared to normal persons. Among down-regulated genes in CCH, many genes were related with cell cycle and proliferation, such as BUB1, CCNB1, CCNB2 and CENPA, which might disturb cell growth and proliferation. In addition, several down-regulated genes were associated with keratinization and differentiation of epidermal cells, such as SPRR1A, SPRR1B, and CALML5. In over-expressed genes, CALML6 might play important roles on the development of CCH. The results of qRT-PCR confirmed the accuracy and credibility of RNA-Seq analysis. This study provided a lot of valuable information about pathogenic mechanism of CCH, which could be used to better study CCH in the future.