The development of Next-Generation Sequencing (NGS) technologies has added a new method to investigate the role of genes in several diseases, including breast cancer (BC). For example, RNA-Seq is mainly used to analyze the continuously changing cellular transcriptome and finding the pathways enriched/inhibited by the differently expressed genes. Small RNA-Seq is a very similar method allowing the detection of other classes of RNA such as small non-coding RNA (miRNA, piRNA, tRNA). In particular, microRNAs (miRNA) are a small non-coding RNA that regulate gene expression at the post-transcriptional level by binding to the 3'UTR (untranslated region) of target mRNAs, causing their degradation or translation inhibition. Several studies correlated an altered expression of these sncRNAs with the onset and /or progression of different diseases, including cancer. They can be used as biomarkers, playing a key role in the diagnosis, prognosis and prediction of response to specific therapies. Moreover, many studies have focused on the possibility of developing new therapeutic strategies based on microRNAs modulation and their potential use in the personalized management of cancer. Furthermore, also Piwi-interacting RNA (piRNA) is a class of small non-coding RNA molecules expressed in animal cells that are associated with both epigenetic and post-transcriptional gene silencing of retrotransposons and other genetic elements. They are distinct from miRNA in size (26–31 nt rather than 21–24 nt), lack of sequence conservation, and increased complexity. The aim of my research project was to understand the carcinogenic mechanisms and pathways modulated by these mRNAs and smallRNAs, since the clarification of the roles played by these molecules in cancer might provide new opportunities to develop novel strategies for diagnosing and treating this disease using bioinformatics tools and created it. Furthermore, a tool has been created that allows the analysis of smallRNAs by integrating various software to facilitate the use of this technology and to better explore the expected results
