Non-coding RNAs in immunity and disease: a genome wide study

During past decades, genome-wide studies have revealed that mammalian genome is widespreadly transcribed and this led to the identification and isolation of novel classes of non-coding RNAs (ncRNAs) that influence gene expression by epigenetic mechanisms.The regulatory ncRNAs can be classified into long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) increasingly recognised to play a role in both physiological and pathological conditions. Despite the function of lncRNAs and miRNAs is the subject of intense studies, the molecular mechanism governing their expression and actions in immune cell function remains to be elucidated. Based on these premises, the purpose of this study is to provide a comprehensive identification and characterization of the role of ncRNAs in immune cell populations under both physiological and pathological conditions. In particular, the study is focused on three main goals:(A) Identification and characterization of the role of lncRNAs in resting and activated human monocytes and neutrophils;(B) Analysis of the expression of lncRNAs was extended to monocytes of patients affected by Systemic Sclerosis (SSc). In fact, several observations suggest that monocytes are likely to play a pathogenetic role in SSc disease;(C) Identification and characterization of the role of miRNAs in Large Granular Lymphocyte Leukaemia (LGLL).(A) The results of this study show that TLR4 activation is able to modulate the expression of lncRNAs in both monocytes and neutrophils. Most importantly, a subset of lncRNAs selectively expressed and modulated by LPS in a cell specific manner was identified. In silico analysis of the putative function of differentially expressed lncRNAs was performed, and suggests that lncRNAs regulate innate immune cells functions such as cytokines and chemokines biosynthesis, cell death, chromatin remodelling and signal transduction. Finally, we started to characterize the function of LINC00085 and AC002480.3. Although further studies must be performed in order to fully understand the role of these lncRNAs, our results indicate that LINC00085 controls the expression of miR-99b, while AC002480.3 has a role in the regulation of IL-6 production.(B) Monocytes have been recently indicated as crucial players in the pathogenesis of SSc. To identify the lncRNAs expressed and modulated in monocytes from SSc patients compared to healthy donors, RNA-seq analysis was performed. Our results show that all the progressive subset of SSc (ncSSc, lcSSc and dcSSc), are characterized by altered expression of lncRNAs in monocytes. Additionally, a detailed analysis of the expression levels of lncRNAs led to the identification of three groups of ncRNAs, specifically modulated in ncSSc rather than lcSS, or dcSSc and that can be used as biomarker for SSc development and progression. Finally, by performing in silico analysis of lncRNA function we show that they are involved in the regulation of key biological processes for the development of SSc, such as the differentiation from monocyte into myofibroblast, and the establishment of the interferon signature that characterizes the SSc.(C) The role of miRNAs in the pathogenesis of LGLL, was examined. By using high-throughput analysis, we initially characterized the profile of miRNAs expressed in T-LGLs, revealing a previously undescribed differential expression of miRNAs in T-LGL from leukemic patients compared to normal cytotoxic T lymphocytes. Interestingly, we identify a strong correlation among the miRNAs expression profiles, the T-LGL phenotype and the activation levels of STAT3.In summary, we have described that the expression of lncRNAs is modulated in LPS-activated human monocytes and neutrophils. In addition, our results show, for the first time, that ncRNA expression levels are deregulated in immune cells involved in the pathogenesis of SSc (monocytes) and T-LGLL. The results we have found suggest that these ncRNAs could be considered new biomarkers for SSc and T-LGLL.