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Francesco Nicassio

Researcher, Center Coordinator, Principal Investigator
Researcher - Principal Investigator - Center Coordinator
Genomic Science
Research center
About
Since 2012, I have been heading the "Noncoding Genome" group at the Center of Genomic Science (CGS-IIT@SEMM) in Milan, one of the 11 research centers of the Istituto Italiano di Tecnologia (IIT). At the moment the "Noncoding Genome" lab consists of 9 people (6 post docs, 2 PhD students, 1 research fellow). Since 2017 I have been appointed as Center Coordinator, supervising, directing and managing scientific activities of 4 research groups and related infrastructure (32 people). The mission of the Center is to acquire, develop and apply genomic technologies towards a better understanding of biological processes and diseases, with emphasis on Cancer and RNA biology. The center also benefits with the close ties with European Institute of Oncology (IEO-hospital, in Milano), one of the largest cancer hospitals, which hosts our lab spaces and provide complementary infrastructure as well access to clinical data and biological samples for cancer studies. Scientific interests are centered on the exploitation of genomic approaches to the study of the dynamics of non-coding RNAs (microRNAs and long noncoding RNAs) and the control of gene expression and cell behaviour. The research activity is based on the integration of Experimental models with Computational methodologies, pointing out the reciprocal regulation of coding and non-coding RNAs. In the years, I have obtained wide experience in using high-throughput experimental and -omics approaches, including total RNA sequencing, small RNA sequencing and, more recently, single-cell RNA sequencing and Nanopore direct RNA sequencing. I have long time experience in the mechanisms controlling transcriptional plasticity and in microRNA biology with many contribution to the field, such as i) a combined mode of action of co-expressed miRNAs, a mechanism that had until then only hypothesized by in silico analyses [Marzi et al. J. Cell Biol 2012]; ii) the development of one of the first computational tools for exploring miRNA post-transcriptional modifications in cancer datasets from NGS data [Isomirage, Muller et al. Front Bioeng Biotechnol. 2014]; iii) the role of miRNA as Serum markers [Bianchi and Nicassio EMBO Mol Med. 2011; Montani, Marzi et al JNCI 2015; Marzi et al. Clin. Chem 2015]; the regulation of the microprocessor complex [Spadotto et al. Nucleic Acids Res. 2020; Marinaro et al., EMBO Rep 2017]; iv) the mechanisms controlling transcriptional plasticity, stem-cell identity and differentiation, in particular in breast cancer and the role of noncoding RNAs [Bonetti et al. Oncogene 2019; Santoro et al. Cell Reports 2019; Rossi et al Nat. Comm 2019; Culurgioni et al Nat. Comm. 2019; Pons et al Stem Cell Reports 2017 and 2019]; and v) the modes and mechanisms of miRNA degradation, to whose characterization my lab has recently given a fundamental contribution [Marzi, Ghini et al. Genome Res. 2016] and highlighting the involvement of a novel mechanism, termed Target-Dependent miRNA degradation [Ghini, Rubolino et al Nat Comm.2018].
Education

Title: PhD in Life Science
Institute: Open University, London (U.K.)
Location: Milan
Country: Italy
From: 2001 To: 2005

Title: Corso di Specializzazione post-laurea "POSTGEN - post-genomic technologies integration systems"
Institute: Università degli studi di Milano
Location: Milan
Country: Italy
From: 2001 To: 2002

Title: Laurea (vecchio ordin.) in Scienze Biologiche
Institute: Università degli studi di Milano
Location: Bari
Country: Italy
From: 1995 To: 2000

Experience External

Title: Scientific Advisor
Institute: Istituto Europeo di Oncologia (IEO)
Location: Milan
Country: Italy
From: 2012 To: 2014

Title: Scientist
Institute: Istituto Europeo di Oncologia (IEO)
Location: Milan
Country: Italy
From: 2011 To: 2011

Title: post-doctoral fellow
Institute: IFOM - FIRC Institute for Molecular Oncology
Location: Milan
Country: Italy
From: 2005 To: 2010

Title: PhD student
Institute: IFOM - FIRC Institute for Molecular Oncology
Location: Milan
Country: Italy
From: 2001 To: 2005

Title: Research Fellow
Institute: Istituto Europeo di Oncologia (IEO)
Location: Milan
Country: Italy
From: 2000 To: 2020

Skills

Manager Activities
- managing budget, personnel and facilities for the entire centre

Research Activities
- Coordinating research activity of the ‘noncoding genome lab
- scientific direction of CGS
- Securing funding
- Networking and scientific liaisons at national and international level

Teaching
- Teaching (sporadic activity) for PhD students enrolled at European School of Molecular Medicine (SEMM) - Milan

All Publications
2021
Tordonato C., Marzi M.J., Giangreco G., Freddi S., Bonetti P., Tosoni D., Di Fiore P.P., Nicassio F.
miR-146 connects stem cell identity with metabolism and pharmacological resistance in breast cancer
Journal of Cell Biology, vol. 220, (no. 5)
Article Journal
2020
Bonetti P., Climent M., Panebianco F., Tordonato C., Santoro A., Marzi M.J., Pelicci P.G., Ventura A., Nicassio F.
Correction: Dual role for miR-34a in the control of early progenitor proliferation and commitment in the mammary gland and in breast cancer (Oncogene, (2019), 38, 3, (360-374), 10.1038/s41388-018-0445-3)
Oncogene, vol. 39, (no. 10)
2020
Mazzara P.G., Muggeo S., Luoni M., Massimino L., Zaghi M., Valverde P.T.-T., 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
Nature Communications, vol. 11, (no. 1)
2020
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 Research, vol. 48, (no. 1), pp. 96-115
2020
Ceol A., Montanari P., Bartolini I., Ceri S., Ciaccia P., Patella M., Masseroli M.
Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks
BMC Bioinformatics
Scientific Talks
2020
Nicassio F.
microRNA degradation in physiology and disease
Fourth International and Sixteenth Iranian Genetics Congress
Conference
2019
Nicassio F., Simeone I., Rubolino C., Marzi M.
microRNA degradation in human physiology and pathology
3rd International Conference on the Long and the Short of Non-Coding RNAs
Conference
2019
Nicassio F.
microRNA degradation in human physiology and pathology
Center for Genetic Regulation, Barcelona
Institute
2019
Nicassio F.
microRNA degradation in human physiology and pathology
Hellenic Society for Computational Biology and Bioinformatics HSCBB meeting
Conference
2019
Nicassio F.
microRNA degradation in human physiology and pathology
EMBL Symposium: The Non-Coding Genome
Workshop/Symposium