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Francesco Nicassio

Researcher, Center Coordinator, Principal Investigator
Senior Researcher Tenured - Principal Investigator
Istituto Italiano di Tecnologia
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
2022
Carvelli A., Setti A., Desideri F., Galfre S.G., Biscarini S., Santini T., Colantoni A., Peruzzi G., Marzi M.J., Capauto D., Di Angelantonio S., Ballarino M., Nicassio F., Laneve P., Bozzoni I.
A multifunctional locus controls motor neuron differentiation through short and long noncoding RNAs
EMBO Journal, vol. 41, (no. 13)
DOI 10.15252/embj.2021108918
2022
Tordonato C., Marzi M.J., Di Fiore P.P., Nicassio F.
microRNAs transcriptional profiling of mammary stem cells isolated by PKH26 staining and FACS sorting
Methods in Cell Biology, vol. 170, pp. 59-79
DOI 10.1016/bs.mcb.2022.02.007
Book Chapter Book Series
2022
Ugolini C., Mulroney L., Leger A., Castelli M., Criscuolo E., Williamson M.K., Davidson A.D., Almuqrin A., Giambruno R., Jain M., Frige G., Olsen H., Tzertzinis G., Schildkraut I., Wulf M.G., Correa I.R., Ettwiller L., Clementi N., Clementi M., Mancini N., Birney E., Akeson M., Nicassio F., Matthews D.A., Leonardi T.
Nanopore ReCappable sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs
Nucleic Acids Research, vol. 50, (no. 6), pp. 3475-3489
DOI 10.1093/nar/gkac144
2022
Brancato V., Brentari I., Coscujuela Tarrero L., Furlan M., Nicassio F., Denti M.A.
News from around the RNA world: new avenues in RNA biology, biotechnology and therapeutics from the 2022 SIBBM meeting
Biology Open, vol. 11, (no. 10)
DOI 10.1242/bio.059597
2022
Simeone I., Rubolino C., Noviello T.M.R., Farinello D., Cerulo L., Marzi M.J., Nicassio F.
Prediction and pan-cancer analysis of mammalian transcripts involved in target directed miRNA degradation
Nucleic Acids Research, vol. 50, (no. 4), pp. 2019-2035
DOI 10.1093/nar/gkac057
Article Journal
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Scientific Talks
2022
Marzi M.J., Giuliani B., Fuentes P.B., Nicassio F.
A functional map of LncRNAs involved in Adaptation pathways of Breast Cancer Cells
EACR 2022
Conference
2022
nicassio f.
Dissecting tumor and molecular heterogeneity by new sequencing technologies
FILLING THE GAPS IN THE ALPS: THE 5000GENOMI@VDA PROJECT
Workshop/Symposium
2022
Nicassio F.
Killing miR-softly: new clues to TDMD
4th International Conference on the Long and the Short of Non-Coding RNAs
Conference
2022
Nicassio F.
ncRNAs in transcriptional and epigenetic reprogramming of breast cancer cell
RNA2022 -THE MULTIPLE FACETS OF RNA IN DEVELOPMENT AND DISEASE
Conference
2022
Nicassio F.
New insights into miRNA biology and human cancer
Vall Hebron Institut d’Oncologia (VHIO)
Institute
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Organized Events
2022
Bozzoni I., Denti M., Gustincich S., Nicassio F.
The RNA World 3.0
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