Non-coding Genome - Francesco Nicassio

The Non-coding Genome Group studies the function and regulation of non-coding transcripts, focusing on the molecular mechanisms in control of gene expression regulation and how they shape the identity and properties of human stem cells during cancer evolution

WHAT? understanding the role played by ncRNAs in transcriptional/epigenetic plasticity

WHERE? physiology (development) and human (cancer) disease, focusing on cancer evolution (drug resistance, metastasis)

HOW? integration of Experimental models with Computational and –omics methodologies

Cancer organoids recapitulate cancer cell growth in vitro within a 3D environment. Able to copycat the 3D spatial tissue organization and catch the genetic and phenotypic heterogeneity of their tissue of origin, organoids represent a more reliable platform than 2D cultures for studying cancer progression and drug resistance mechanisms. We aim at investigating the role non-coding RNAs and DNA elements play in the adaptive response of breast cancer cells following anticancer therapies and in the context of  tumor organoids  We will use cutting-edge genomic approaches to achieve a high-resolution characterization of the transcriptional/epigenetic landscape of breast cancer organoids. We will focus on the evolutionary trajectories of the different tumour subpopulations that will be characterized both in basal conditions (homeostasis) and in response to anticancer treatments, stimulating adaptive response mechanisms. The goal will be to gain insight into the genetic and epigenetic factors that hinder the success of established anticancer therapies.

SARS-CoV-2 is a positive single-stranded RNA virus which interacts at different stages with the host proteins of infected cells. These interactions are necessary for the host to recognize and block the replication of the virus. But, at the same time, the virus requires host proteins to translate, transcribe and replicate its genetic material. In order to identify the host proteins that interact with SARS-CoV-2 RNA, we adopted the RNA-protein interaction detection coupled to mass spectrometry (RaPID-MS) technology, which allows the purification and identification by MS-based proteomics of the proteins associated to a specific RNA of interest expressed in mammalian cells. In particular, we conducted the analysis on the more structured regions of SARS-CoV-2 RNA and retrieved several proteins specifically associated with each region. Overall, our data revealed a list of proteins associated to SARS-CoV-2 RNA that will be further characterized to understand their role in SARS-CoV-2 infection and viral replication.

Long non-coding RNAs (lncRNAs) are emerging as promising novel diagnostic and therapeutic molecules. These transcripts provide a flexible and dynamic mechanism of gene expression regulation. Emerging evidence suggests a role for lncRNAs as key components in adaptation pathways. In breast cancer, transcriptional adaptation has been described to occur, in particular during the acquisition of chemoresistance. Unfortunately, the mechanisms behind cancer adaptation and the role lncRNAs play are still to be clarified. We are currently characterizing the role of a group of lncRNAs during adaptive responses in triple-negative breast cancer cells by means of CRISPRinterference. We are functionalizing lncRNAs in a classic-drop out screening during proliferation, drug response and in vivo tumorigenesis. In parallel, we are characterizing the transcriptomic response of lncRNAs modulation by single cell-RNAseq in a CROP-seq like setting.  With this work, we will bring novel knowledge into the regulatory framework played by lncRNAs in cancer cell plasticity.