Researcher - 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.
With the advent of genomic sequencing, genomes were indeed found to contain long stretches of DNA that do not codify for any protein. Almost all of this apparently functionless DNA is transcribed instead into RNAs molecules of different lengths and collectively known as non-coding RNAs (ncRNAs).
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.
microRNA 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.
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)
LONG NON-CODING RNAS AND STEMNESS PROGRAMME (TIC-lncRNAs)
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, in particular, TICs have been shown to sustain tumor re-growth at local (relapse) or distant sites (metastasis) and to contribute to the emergence of therapy resistance. TICs are thought to originate from tumor cells upon activation of a ‘stemness’ programme, a transcriptional programme much similar to that acting in normal tissue on adult stem cells (Bonetti et al. Oncogene 2018, Culurgioni et al. Nat. Comm. 2018).
The ‘stemness’ programme is established and mantained through a series of molecular mechanisms, some of them involving regulatory non-coding RNAs. So far, the role of ncRNAs in this context has been only marginally explored (Tordonato et al. Front. Genet. 2014).
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
EPIGENETIC AND TRANSCRIPTIONAL DETERMINANTS OF CANCER CELL PLASTICITY AT SINGLE-CELL RESOLUTION
Different cellular mechanisms acting at epigenetic, transcriptional and post-transcriptional level have been postulated to account for the intrinsic heterogeneity of cancer, this being the main cause of imprecise diagnosis and failure in identifying therapeutic regimens that effectively tackle the disease.
Following recent developments in single cell technologies, our lab is working on producing high-resolution, genome-wide blueprints of the transcriptional and epigenetic mechanisms that regulate plasticity programmes, with the aim of:
- solving the complexity of intrinsic heterogeneity of cancer
- revealing the molecular underpinnings of plasticity (genetic /transcriptional and phenotypic) in tumor cells
- paving the way to the development of new therapies for targeting carcinomas
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
▪ 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 2018
▪ 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
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