Researcher - Principal Investigator - Center Coordinator
Noncoding Genome in Development and Disease
Jan-Dec 2000 Research Fellow in Pier Paolo Di Fiore's Group at IEO, Milan (IT)
The last decades have witnessed a tremendous development in next generation sequencing technologies. Both genome and transcriptome of virtually any cell in any condition can now be characterized easily and quickly. Such unprecedented power of analysis should have revealed the molecular basis of cell identity, behavior and disease by now, but nature always finds ways to surprise us.
Which of the thousands of identified ncRNAs play important roles? How do they work exactly? What mechanisms regulate them? These questions have not been answered yet and are still being addressed by many scientists worldwide.
The aim of my research is to provide a critical and original contribution towards the understanding of the role played by non-coding RNAs in shaping the cell transcriptome, both in physiology and (cancer) disease. To reach this goal, I investigate modes and mechanisms of action of ncRNAs within specific biological contexts, exploiting a combination of high-throughput genomic approaches, in silico analysis and sophisticated experimental models.
The “Noncoding Genome” lab studies the function and regulation of non-coding transcripts (miRNAs and long non-coding RNAs), with a particular emphasis on how regulatory RNAs shape the identity and properties of mammalian cells in cancer stem cells and during cancer evolution (therapy resistance, metastatic spread). We use a modern scientific approach based on the integration of Experimental models, reproducing cancer alterations, with Computational methodologies, applying cutting-edge analyses and state-of-the art technological platforms.
1. miRNA Degradation Mechanisms and their interplay with RNA Targets
MicroRNAs (miRNAs) are an evolutionary conserved class of small (18-25nt) non-coding RNAs that function in post-transcriptional gene silencing by binding to target RNAs. Levels of miRNAs are frequently altered in human disease, leading to target deregulation and pathological consequences. Mechanisms of miRNA degradation have been only recentry described (Marzi, Ghini, et al. Genome Res 2016).
It has recently been shown that targets with extended complementarity can induce miRNA degradation through a mechanism known as TDMD, Target-Directed miRNA Degradation. In 2018, the existence of endogenous TDMD transcripts in mammalian cells has been proved by our lab (Ghini, Rubolino et al. Nat Comm 2018) and others, thus establishing the existence of TDMD in mammalian genomes. However, the number of endogenous TDMD-targets and their possible impact on physiopathology in humans are yet to be defined.
Our lab is currently investigating the involvement of TDMD transcripts in human disease with the aim of:
- defining the role played by TDMD transcripts in modulating miRNA functions (CARIPLO funded project)
- elucidating the way degradation mechanisms function in physiology and disease (i.e. cancer – AIRC funded project)
2. Breast Cancer and Cancer Stem Cells: the role of non-coding RNAs
Despite treatment, some cancers progress by tumor re-initiation, metastasis development or acquisition of therapy resistance. Subpopulations of cancer cells with tumor-initiating capacity and known as cancer stem cells (CSCs) or tumor-initiating cells (TICs) have been implicated in such processes. In breast cancer, tumors may display a variable degree of stemness, which is related to the number of cancer cells with stem properties, acquired through transcriptional and metabolic reprogramming, governed by mechanisms that have yet to be established. So far, the role of ncRNAs in this context has been only marginally explored (Tordonato et al. Front. Genet. 2014).
We are investigating how TICs are originated in cancer, which the transcriptional mechanisms that sustain their identity and what the contribute of miRNAs and non-coding RNAs, using the mammary gland and breast cancer as a model (Bonetti et al. Oncogene 2019, Santoro A. et al. Cell Reports 2019, Culurgioni et al. Nat. Comm. 2018).
Through the combination of human transcripts high-resolution analysis (high-coverage strand-specific RNA sequencing) and the use of sophisticated biological models reproducing TIC properties, we have managed to isolate a subset of long non coding RNAs (TIC-lncRNAs) extremely relevant as potential novel markers or therapeutic targets for cancer treatment.
Our lab is currently searching for TIC-lncRNAs that are critical for the identity and maintenance of breast TICs with the aim of:
- characterizing underlying molecular mechanisms
- mapping TICs epigenetic and transcriptional landscape in aggressive breast tumors and metastasis
- isolating non-coding elements that functions as determinants of the transcriptional and epigenetic plasticity of cancer cells
3. Noncoding Elements and Transcriptional plasticity in advanced (breast) cance.
Cancer cells have the ability of adapting their phenotype in response to challenging environmental conditions by reshaping their transcriptome, a process that has been termed as ‘transcriptional plasticity’. In breast cancer, there is increasing evidence that transcriptional reprogramming and cancer cell plasticity are associated with aggressive behavior [i.e. metastatic spread, resistance to chemotherapy, cancer stem cell properties ] and lead to a profound reshaping of the transcriptome at the level of both coding genes and noncoding RNAs.
Our aim is to define the regulatory framework of plastic cancer cells at the level of coding genes, enhancers and lncRNAs, and to highlight the direct involvement of lncRNAs in the modulation of transcriptional and epigenetic plasticity.
Breast cancer is our model system, with in vitro and in vivo tailored models that reproduce the transcriptional reprogramming of cancer cells during
- adaptation to chemotherapy (i.e. paclitaxel, doxorubicin);
- inter-conversion of Mammary Stem Cell (MaSC)-like cells (CD44high/CD24low) and more differentiated cells (CD44low/CD24high);
- epithelial-to-mesenchymal (EMT) transition in breast epithelial cells.
4. Astrocyte-mediated Circadian Clock in Neurodegeneration and Brain Ageing - in collaboration with Davide De Pietri Tonelli (IIT - Central Lab)
Animals have an internal timekeeping mechanism that influences cellular metabolic pathways, organ functions and behaviours by precisely regulating circadian rhythms of gene expression. In mammals, the circadian system is centered on the brain and is organized in a hierarchy of multiple oscillators at organ, cellular and molecular level.
Recent studies suggest that astrocytes (the most abundant cell type in the brain) actively participate in the modulation of physiological and circadian behavioral processes in invertebrates (“astroclock”) (Barca-Mayo O. et al. Nat. Comm. 2017 ).
Based on the hypothesis that the astroclock maintains neural rhythmic behaviour and, in so doing, slows down brain ageing and the associated decline of cognitive functions and peripheral metabolic abnormalities, our lab aims at:
- investigating the molecular and functional mechanisms used by the astroclock
- clarifying the transcriptional and post-transcriptional mechanisms controlling astrocyte-to-neuron communication and the astroclock
- identifying molecular targets valuable as potential new drugs in disorders related with ageing and in age-related brain neuropathology and altered metabolism
▪ Mazzara, P.G., Muggeo, S., Luoni, M., Luoni M., Massimino L., Zaghi Mattia, Tajalli-Tehrani Valverde P., Brusco S., Marzi M.J., Palma C., Colasante G., Iannielli A., Paulis M., Cordiglieri C., Giannelli S.G., Podini P., Gellera C., Taroni F., Nicassio F., Rasponi M.& Broccoli V. Frataxin gene editing rescues Friedreich’s ataxia pathology in dorsal root ganglia organoid-derived sensory neurons. Nat Commun 11, 4178 (2020). https://doi.org/10.1038/s41467-020-17954-3
▪ Spadotto V, Giambruno R, Massignani E, Mihailovich M, Maniaci M, Patuzzo F, Ghini F, Nicassio F, Bonaldi T. PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis. Nucleic Acids Res. 2020;48(1):96-115. doi:10.1093/nar/gkz1051
▪ Panebianco F, Climent M, Malvindi MA, Pompa PP, Bonetti P, Nicassio F. “Delivery of biologically active miR-34a in normal and cancer mammary epithelial cells by synthetic nanoparticles” Nanomedicine. 2019 Apr 25; 19:95-105. doi: 10.1016/j.nano.2019.03.013
▪ Bonetti P, Climent M, Panebianco F, Tordonato C, Santoro A, Marzi MJ, Pelicci PG, Ventura A, Nicassio F. "Dual role from miR-34a in the control of early progenitor proliferation and commitment in the mammary gland and in breast cancer" Oncogene 2019
▪ Santoro A, Vlachou T, Luzi L, Melloni G, Mazzarella L, D'Elia E, Aobuli X, Pasi CE, Reavie L, Bonetti P, Punzi S, Casoli L, Sabò A, Moroni MC, Dellino GI, Amati B, Nicassio F, Lanfrancone L, Pelicci PG. "p53 Loss in Breast Cancer Leads to Myc Activation, Increased Cell Plasticity, and Expression of a Mitotic Signature with Prognostic Value" Cell Reports 2019
▪ Ghini F, Rubolino C, Climent M, Simeone I, Marzi MJ, Nicassio F. "Endogenous Transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation" Nature Communications 2018
▪ Culurgioni S, Mari S, Bonetti P, Gallini S, Bonetto G, Brennich M, Round A, Nicassio F, Mapelli M. “Insc:LGN tetramers promote asymmetric divisions of mammary stem cells” Nature Communications 2018
▪ Pons-Espinal M, de Luca E, Marzi MJ, Beckervordersandforth R, Armirotti A, Nicassio F, Fabel K, Kempermann G, De Pietri Tonelli D. “Synergic Functions of miRNAs Determine Neuronal Fate of Adult Neural Stem Cells” Stem Cell Reports 2017
▪ Marinaro F, Marzi MJ, Hoffmann N, Amin H, Pelizzoli R, Niola F, Nicassio F, De Pietri Tonelli D. “MicroRNA-independent functions of DGCR8 are essential for neocortical development and TBR1 expression” EMBO Reports 2017
▪ Marzi MJ, Montani F, Carletti RM, Dezi F, Dama E, Bonizzi G, Sandri MT, Rampinelli C, Bellomi M, Maisonneuve P, Spaggiari L, Veronesi G, Bianchi F, Di Fiore PP, Nicassio F. “Optimization and Standardization of Circulating MicroRNA Detection for Clinical Application: The miR-Test Case” Clinical Chemistry 2016
▪ Marzi MJ, Ghini F, Cerruti B, de Pretis S, Bonetti P, Giacomelli C, Gorski MM, Kress T, Pelizzola M, Muller H, Amati B, Nicassio F. “Degradation dynamics of microRNAs revealed by a novel pulsechase approach” Genome Research 2016
▪ Muller H., Marzi M.J., Nicassio F. “IsomiRage: From Functional Classification to Differential Expression of miRNA Isoforms” Front. Bioeng. Biotechnol. 2014
2019 - AIRC (Italian Association for Cancer Research) Investigator Grant Award “Target-directed miRNA degradation mechanism: role and implications in breast cancer”
2015 - AIRC (Italian Association for Cancer Research) Investigator Grant Award “MicroRNA degradation dynamics in human cancer”
2014 - CARIPLO Foundation Grant for Biomedical Research on ageing-related illnesses “Role of the astrocyte-mediated circadian clock in neurodegeneration and brain aging”
2013 - AIRC (Italian Association for Cancer Research) Investigator Grant Award “Noncoding RNAs as modifiers of stem cell properties in breast cancer: a whole genome approach”
2011- Fondazione Umberto Veronesi Research Grant Award “Identification of circulating non-coding RNAs as biomarkers for tumor diagnosis by “next-generation sequencing”
2010 - Istituto Regina Elena Award for the best oral presentation at the 52th Annual Meeting of the Italian Cancer Society