A regulatory crosstalk in Down syndrome: competing mRNA-miRNA network

Down syndrome (DS) - also known as Trisomy 21 - is a genetic disorder caused by an extra copy of all or part of human chromosome 21 (HSA21). DS is a complex genetic condition characterized by over 80 clinically different phenotypes of variable penetrance and expressivity. Individuals with DS show alterations - both structural and functional - affecting distinct organs and systems, which suggest that a perturbation of embryogenesis occurs in individuals with Down syndrome, due to Trisomy 21. Large-scale gene expression studies have revealed a more complex scenario, highlighting a global transcriptional deregulation, extended also to genes mapping outside the DS Critical Region (DSCR) on HSA21, as well as on the other chromosomes. In this context, it is clear that direct and/or indirect interactions between gene products of HSA21 and those from the other chromosomes can better explain the complexity of the clinical manifestations of the disorder. Recent studies have pointed out a previously unexpected role of non-coding RNA (ncRNAs), such as pseudogenes and lincRNAs, on gene expression regulation. In particular, a new crosstalk mediated by the competition for the binding to specific miRNAs has been demonstrated between messenger RNAs and ncRNAs. Such a regulatory crosstalk represents a new and interesting "RNA language" through which different mRNAs regulate each other by competing for miRNAs' availability. Given these recent findings and considering that Trisomy 21-induced gene imbalance perturbs the entire transcriptome and occurs throughout the embryogenesis, the above-described regulatory crosstalk may be altered by HSA21 trisomy in DS fetuses. The pathological overexpression of HSA21 genes may perturb gene expression during embryogenesis through the alteration of the crosstalk mediated by the interaction with specific miRNAs. In turn, it would cause typical multisystem clinical manifestations of Down syndrome. Thus, the aim of this PhD project is to deeply explore the global gene deregulation, and the potential role of microRNAs' "sponges" played by HSA21 genes that are overexpressed in DS during embryonic development. Taking advantage of publicly available mRNA and miRNA expression datasets of human embryos (4-6 weeks), a regulatory miRNA/mRNA network in these crucial weeks of the human embryonic development was established. A significant fraction of genes within the network belong to developmental-related pathways. Afterwards, HSA21 genes overexpressed in DS embryos that belong to this network were identified using RNA-Seq datasets from DS and euploid matched chorionic villi. HUNK gene was computationally selected as the best candidate to be an HSA21-derived miRNAs' sponge. Experimental studies confirmed that the overexpression of its 3'UTR induces an increased expression of genes involved in embryonic development, including BCL2, CLIC5, EPHA5, ERBB4, HIPK2, MECP2, ONECUT2, and WNT5A, and a reduction of the expression of correlated miRNAs, including miR-17, miR-20a, miR-20b, miR-128 and miR-200c. Although further studies are still in progress, the results of both the computational and the experimental studies strongly suggest that the overexpression of HSA21 genes may perturb the physiologic regulatory miRNA/mRNA network during DS embryos' development. This would explain, at least in part, the multisystemic nature of the alterations the typically occur in individuals with the syndrome.