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Francesco Nicassio

Researcher, Center Coordinator, Principal Investigator
Senior Researcher Tenured - Principal Investigator
Genomic Science
Research center
About

Francesco Nicassio is Senior Researcher at IIT, Principal Investigator of the Genomic Science research line. Scientific interests are centered on the exploitation of genomic approaches to the study of mechanisms in control of gene expression dynamics provided by non-coding RNAs (microRNAs and long noncoding RNAs) and their impact on cell behaviour and human disease, with emphasis on Cancer.

He graduated in Biology at the University of Bari, then moved in Milan at the European Institute of Oncology (IEO- Milan), as a student enrolled in the Open University PhD program in Life Science, awarded in 2005. He moved to IFOM in Milan for post-doc in Pier Paolo Di Fiore’s lab (2005-2010), identifying novel genes and transcriptional signatures deregulated in human cancers and useful for the prognostic stratification of breast and lung cancer patients.  He worked as Scientist of the Molecular Medicine Program with prof Di Fiore (2011-2012) and, jointly with clinicians at the European Institute of Oncology (IEO- Milan), he developed one of the first signatures of circulating miRNAs, effective in identifying asymptomatic early-stage lung cancers and developing into a clinical grade test to be used in large-scale cancer screenings. Since 2012, he joined the Center of Genomic Science at Istituto Italiano di Tecnologia (IIT), as Researcher and leading his own scientific group, focusing on microRNAs and regulatory non-coding RNAs. Since 2017 is the Coordinator of the Center of Genomic Science (CGS) of IIT@SEMM in Milan, supervising, directing and managing scientific activities of CGS and related infrastructure (approx. 30 people).  In 2022, he has been tenured as Senior Researcher. 

He is recognized for the key contribution in the field of non-coding RNAs, in particular for characterizing the function and regulation of microRNAs in the gene expression regulatory network. After pioneering the exploitation of circulating microRNAs for diagnostic purposes in cancer, he has recently brought to attention the mechanisms of miRNA degradation, highlighting the involvement of a novel mechanism, termed Target-Dependent miRNA degradation (TDMD), to whose discovery his lab decisively contributed. Recently, he has implemented technological platform for RNA research in IIT and developed ad hoc tools for their application to human disease and clinical research.

Our platforms include i. Nanopore Sequencing, a single-molecule sequencing platform allowing multi-modal analysis of transcripts, mapping isoforms, RNA processing events and the study of RNA modifications; ii. Single-Cell Multi-omics, which combine transcriptional and epigenetic analysis at single-cell resolution, useful to deconvolve the cellular and molecular heterogeneity and characterize gene-regulatory networks (GRNs) within sub-populations; iii. a CRISPR-based platform, to perform genetic screens aimed at identifying molecular targets effective in cancer phenotypes, including growth, migration, drug tolerance and tumour initiation in vivo. 

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

Top Publications
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
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
Article Journal
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)
2019
Bonetti P., Climent M., Panebianco F., Tordonato C., Santoro A., Marzi M.J., Pelicci P.G., Ventura A., Nicassio F.
Dual role for miR-34a in the control of early progenitor proliferation and commitment in the mammary gland and in breast cancer
Oncogene, vol. 38, (no. 3), pp. 360-374
2018
Ghini F., Rubolino C., Climent M., Simeone I., Marzi M.J., Nicassio F.
Endogenous transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation
Nature Communications, vol. 9, (no. 1)
All Publications
2024
Maestri S., Furlan M., Mulroney L., Coscujuela Tarrero L., Ugolini C., Dalla Pozza F., Leonardi T., Birney E., Nicassio F., Pelizzola M.
Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing
Briefings in Bioinformatics
Article Journal
2023
Giambruno R., Zacco E., Ugolini C., Vandelli A., Mulroney L., DOnghia M., Giuliani B., Criscuolo E., Castelli M., Clementi N., Clementi M., Mancini N., Bonaldi T., Gustincich S., Leonardi T., Tartaglia G., Nicassio F.
Discovering host protein interactions specific for SARS-CoV-2 RNA genome
Molecular Therapy - Nucleic Acids
Article in Press Journal
2023
Lattanzi G., Strati F., Diaz-Basabe A., Perillo F., Amoroso C., Protti G., Rita Giuffre M., Iachini L., Baeri A., Baldari L., Cassinotti E., Ghidini M., Galassi B., Lopez G., Noviello D., Porretti L., Trombetta E., Messuti E., Mazzarella L., Iezzi G., Nicassio F., Granucci F., Vecchi M., Caprioli F., Facciotti F.
iNKT cell-neutrophil crosstalk promotes colorectal cancer pathogenesis
Mucosal Immunology
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)
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
Book Chapter Book Series
Scientific Talks
2023
Nicassio F.
Applications and limitations of human small RNA biology in the clinic
InteRNAt - summer school
School (Summer school, ...)
2023
Nicassio F.
Cellular and molecular heterogeneity in human cancer
Kick off meeting GIULIa Project
Workshop/Symposium
2023
Nicassio F.
Coding and Noncoding RNAs in Cancer Mechanisms
Department of Cellular, Computational and Integrative Biology (CIBIO) University of Trento, Italy
Institute
2023
Nicassio F.
Interplay of coding and noncoding RNAs in cancer mechanisms
ABCD 2023 • The Biennial Congress of the Italian Association of Cell Biology and Differentiation
Conference
2023
Nicassio F.
Interplay of Coding and Noncoding RNAs in Cancer Mechanisms
Centre de Biologie Intégrative, Toulouse
Institute
Organized Events
2023
Peano C., Nicassio F., Carninci P.
Single-molecule Sequencing Technologies & Applications
2023
De Leo F., Nicassio F., Leonardi T., Fosso B., Picardi E., Pesole G.
Training course in computational methods for epitranscriptomics
2022
De Pietri Tonelli D., Nicassio F., Tartaglia GG.
Co-coordinator of the “RNA Collaborative Seminar Series” by the RNA society (USA)
2022
Bozzoni I., Denti M., Gustincich S., Nicassio F.
The RNA World 3.0
2022
Bozzoni I., Dente C., Gustincich S., Nicassio F.
The RNA World 3.0 - SIBBM 2022 - Frontiers in Molecular Biology