Tommaso Leonardi

Researcher
Computational RNA Biology

Research Lines

Genomic Science

Center

CGS@SEMM Milano

Contacts

Via Adamello 16, 20139, Milano
+39 (02) 943 750 69

About

My long-standing scientific interest is in the field of non-coding RNA genomics. I started approaching the field during my masters, in the laboratories of Dr Stefano Pluchino (Clinical Neuroscience Department, University of Cambridge) and Prof John Mattick (University of Queensland). I was then awarded an EMBL pre-doctoral fellowship and consequently obtained a PhD in bioinformatics from the University of Cambridge in the laboratory of Dr Anton Enright (EMBL-EBI). After completing my PhD I did a postdoc in the laboratory of Prof Tony Kouzarides at the Gurdon Institute, where I conducted research as a computational scientist in the field of epitranscriptomics. In 2019 I joined the Center for Genomic Science of the Italian Institute of Technology, where I now lead a small team that focuses on computational RNA biology.

Over the last several years my research has primarily focused on the broad topic of non-coding RNA biology with the ambitious aim of providing novel insights into their functions. One of my main research areas at the time was the study of ncRNAs in cell-to-cell communication. Through collaborations with experimental groups at the department of clinical neuroscience (Pluchino laboratory, University of Cambridge) I led the bioinformatics analyses for several studies that characterised the role of exosomes in the transfer of inflammatory molecules (Cossetti et al., Mol Cell 2014), metabolic enzymes (Iraci et al., Nat Chem Bio 2017) and microRNAs. Subsequently, my main research focus shifted toward long ncRNAs: in fact, the main scientific contribution stemming from my doctoral studies is the discovery and characterisation of a group of long ncRNAs that are positionally conserved in the mouse and human genomes relative to orthologous protein coding genes (Amaral, Leonardi et al, Genome Biology 2018). This study allowed to define the new class of “topological anchor point RNAs” (tapRNAs), a group of functionally related lncRNAs associated with the boundaries of chromatin loops and Topological Associated Domains (TADs). Our study also showed that these RNAs have important regulatory functions, being often found de-regulated and/or mutated in cancers and affecting malignant cell phenotypes. It is becoming increasingly clear that long-range chromatin interactions play a central role in the organisation and regulation of the genome and this work showed for the first time a link between chromatin topology, non-coding loci and regulation of gene expression.

In parallel to the application of existing methods to biologically relavant problems, I have always had a strong interest in the development of new technologies and algorithms, for example contributing to the development of a novel RNA sequencing method (captureSeq) that allowed us to provide a comprehensive characterisation of the human and mouse non-coding transcriptomes (Clark et al, Nat Meth 2015; Bussotti et al, Gen Res 2016). More recently, I have focused on the development of accurate and efficient methods for the analysis of Nanopore direct RNA-Seq data. This line of work resulted in the development of Nanocompore, a comparative algorithm that allows single molecule detection of RNA modifications from Nanopore data (Leger et al, bioRxiv 2019).

 

Education

PhD

Biological Science, EMBL-European Bioinformatics Institute, University of Cambridge, Cambridge, UK (2016)
Thesis title: Insights into the function of non-coding RNAs
Supervisors: Dr Anton Enright and Dr Stefano Pluchino

Master degree

Medical, molecular and cellular biotechnologies, University Vita-Salute San Raffaele, Milan, Italy (2011)
Thesis title: The inflammatory fingerprint of Neural Stem Cells
Supervisor: Dr Stefano Pluchino

Undergraduate degree

Medical biotechnology, University Vita-Salute San Raffaele, Milan, Italy (2009)
Thesis title: Molecular mechanism of interaction between the serin protease Matriptase-2 and its sub-
strate Hemojuvelin
Supervisors: Prof Clara Camaschella and Dr Laura Silvestri


Work experience

  • Researcher, Center for Genomic Science, Italian Institute of Technology, Milan ('19-present)
  • Postdoctoral scientist, Gurdon Institute, Kouzarides lab, Cambridge ('17-'18)
  • Postdoctoral fellow (bridging), EMBL-EBI, Enright lab, Hinxton ('16-17')
  • Predoctoral fellow, EMBL-EBI, Enright lab, Hinxton ('12-16')
  • Masters student, Cambridge Centre for Brain Repair, Pluchino lab, Cambridge ('10-12')
  • Visiting student, Prof John Mattick lab, Insitute for Molecular Bioscience, University of Queensland, Brisbane, Australia ('11)
  • Undergraduate intern, Unit of Iron Metabolism, Silvestri lab. Vita-Salute San Raffale University, Milan, Italy ('09-'10)

Projects

My main research focus is the development of algorithms, software and data-analysis strategies to study the function, evolution and regulation of RNA molecules, with a particular interest on the application and development of methods based on Nanopore direct RNA-Sequencing. By designing and creating dedicated tools I aim to leverage the potential of this technology to dissect the transcriptional output of complex loci, quantify isoform expression and determine non genomically encoded transcript features, such as epitranscriptional modifications or polyA tail length.

 

Nanocompore

nanocompore workflow

We are actively continuing the development of Nanocompore, an algorithm for the identification of RNA modifications from Nanopore data. Nanocompore implements a comparative approach where the raw electrical signal for a sample of interest in compared, base by base, to the signal generated by a sample devoid of RNA modifications, e.g. a knock-out of an RNA modifying enzyme or an in vitro transcribed RNA. Our current work consists on the improvement of the statistical methods that underlie the algorithm and in the implementation of new functionality to detect and quantify RNA modifications at the level of individual RNA molecules.

 

RNA modification profile of 7SK

 

Through the application of Nanocompore we are starting to characterise the modifications repertoire of ncRNAs, shedding some light on their potential roles in the regulation of RNA structure and/or function.

 

Detection and quantification of Endogenous Retroviruses from Nanopore data

During the course of evolution it happened multiple times that retroviral particles infected the germline and became part of the human genome, with the result that ancient pro-viral genomes now account for approximately 5-8% of the genome of present day humans. In response to these insults we have evolved precise defence mechanisms, which in normal conditions control and regulate the expression and activity of these endogenous retroviruses (ERVs). However, when these mechanisms of control fail, the de-regulated expression of ERVs can interfere with the physiological processes of the cell and has the potential to lead to or contribute to the development of diseases such as cancer. Our research aims to provide an accurate characterization of ERV expression profiles in health and disease and to identify the molecular mechanisms responsible for their aberrant expression in cancer.

We have previously developed a computational method that allowed to de-convolute transposon‐driven transcription in spermatogenesis based on expression signal from Illumina short-read RNA-Seq datasets. We have then improved such method using the Markov Cluster Algorithm to accurately quantify expression of ERV families and preliminary data support the validity of the approach. At present, we are further refining ERV detection through the use of Nanopore direct RNA-Seq, which allows to sequence and quantify full-length transcripts derived from individual ERV insertions. The combination of these approaches will allow us to produce a database of ERV expression signatures, providing for the first time a consistent and accurate picture of the landscape of ERV expression in physiological and pathological conditions.

 

RNA modification profiling in viral genomes

In light of the current emergency caused by the SARS-CoV2 pandemic we are contributing to the world-wide research efforts by applying our expertise and research paradigms to obtain a better understanding of the biology of this RNA virus.

In particular, through the use of the Nanocompore algorithm we found that viral genomic and sub-genomic RNAs are heavily modified, suggesting that RNA modifications play a role in the complex interaction between the virus and its host. Our current work is exploring this possibility further, in the hope that a better knowledge of the viral regulatory mechanisms will provide new opportunities to develop effective therapeutic strategies.

Selected Publications

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IIT Publications

  • 2020
  • Furlan M.iit, Tanaka I.iit, Leonardi T.iit, de Pretis S.iit, Pelizzola M.iit
    DOI

    Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts

    Frontiers in Genetics, vol. 11
  • 2019
  • Leonardi T.iit
    DOI

    Bedparse: feature extraction from BED files

    The journal of open source software, vol. 4, (no. 34), pp. 1228
  • Leger A., Leonardi T.iit
    DOI

    pycoQC, interactive quality control for Oxford Nanopore Sequencing

    The journal of open source software, vol. 4, (no. 34), pp. 1236
  • Leger A., Amaral P.P., Pandolfini L., Capitanchik C., Capraro F., Barbieri I., Migliori V., Luscombe N.M., Enright A.J., Tzelepis K., Ule J., Fitzgerald T., Birney E., Leonardi T.iit, Kouzarides T.
    DOI

    RNA Modifications Detection by Comparative Nanopore Direct RNA Sequencing

    bioRxiv
  • Leonardi T.iit, Leger A., Amaral P., Che H., Pandolfini L., Santo Rosa H., Enright A.J., Fitzgerlad T., Birney E., Kouzarides T.
    DOI

    Signal level RNA modifications detection in eukaryotic ncRNAs

    Oxford Nanopore Technologies London Calling Conference
  • Bernstock J.D., Peruzzotti-Jametti L., Leonardi T., Vicario N., Ye D., Lee Y.-J., Maric D., Johnson K.R., Mou Y., Van Den Bosch A., Winterbone M., Friedman G.K., Franklin R.J.M., Hallenbeck J.M., Pluchino S.
    DOI

    SUMOylation promotes survival and integration of neural stem cell grafts in ischemic stroke

    EBioMedicine, vol. 42, pp. 214-224
  • 2018
  • Amaral P.P., Leonardi T., Han N., Vire E., Gascoigne D.K., Arias-Carrasco R., Buscher M., Pandolfini L., Zhang A., Pluchino S., Maracaja-Coutinho V., Nakaya H.I., Hemberg M., Shiekhattar R., Enright A.J., Kouzarides T.
    DOI

    Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci

    Genome Biology, vol. 19, (no. 1)
  • Donegà M., Giusto E., Leonardi T., Alfaro-Cervello C., Pluchino S.
    DOI

    Group I metabotropic glutamate receptor signaling regulatesthe release of BDNF and LIF by neural stem cells

    Matters
  • Peruzzotti-Jametti L., Bernstock J.D., Vicario N., Costa A.S.H., Kwok C.K., Leonardi T., Booty L.M., Bicci I., Balzarotti B., Volpe G., Mallucci G., Manferrari G., Donega M., Iraci N., Braga A., Hallenbeck J.M., Murphy M.P., Edenhofer F., Frezza C., Pluchino S.
    DOI

    Macrophage-Derived Extracellular Succinate Licenses Neural Stem Cells to Suppress Chronic Neuroinflammation

    Cell Stem Cell, vol. 22, (no. 3), pp. 355-368.e13
  • 2017
  • Pathan M., Keerthikumar S., Chisanga D., Alessandro R., Ang C.-S., Askenase P., Batagov A.O., Benito-Martin A., Camussi G., Clayton A., Collino F., di Vizio D., Falcon-Perez J.M., Fonseca P., Fonseka P., Fontana S., Gho Y.S., Hendrix A., Nolte-'T Hoen E., Iraci N., Kastaniegaard K., Kislinger T., Kowal J., Kurochkin I.V., Leonardi T., Liang Y., Llorente A., Lunavat T.R., Maji S., Monteleone F., Overbye A., Panaretakis T., Patel T., Peinado H., Pluchino S., Principe S., Ronquist G., Royo F., Sahoo S., Spinelli C., Stensballe A., Thery C., van Herwijnen M.J.C., Wauben M., Welton J.L., Zhao K., Mathivanan S.
    DOI

    A novel community driven software for functional enrichment analysis of extracellular vesicles data

    Journal of Extracellular Vesicles, vol. 6, (no. 1)
  • Iraci N., Gaude E., Leonardi T., Costa A.S.H., Cossetti C., Peruzzotti-Jametti L., Bernstock J.D., Saini H.K., Gelati M., Vescovi A.L., Bastos C., Faria N., Occhipinti L.G., Enright A.J., Frezza C., Pluchino S.
    DOI

    Extracellular vesicles are independent metabolic units with asparaginase activity

    Nature Chemical Biology, vol. 13, (no. 9), pp. 951-955
  • Giusto E., Donegà M., Dumitru C.A., Foschi G., Casalini S., Bianchi M., Leonardi T., Russo A., Occhipinti L.G., Biscarini F., Garcia R., Pluchino S.
    DOI

    Interfacing Polymers and Tissues: Quantitative Local Assessment of the Foreign Body Reaction of Mononuclear Phagocytes to Polymeric Materials

    Advanced Biosystems, vol. 1, (no. 4)
  • Davis M.P., Carrieri C., Saini H.K., van Dongen S., Leonardi T., Bussotti G., Monahan J.M., Auchynnikava T., Bitetti A., Rappsilber J., Allshire R.C., Shkumatava A., O'Carroll D., Enright A.J.
    DOI

    Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution

    EMBO Reports, vol. 18, (no. 7), pp. 1231-1247
  • 2016
  • Iraci N., Leonardi T., Gessler F., Vega B., Pluchino S.
    DOI

    Focus on extracellular vesicles: Physiological role and signalling properties of extracellular membrane vesicles

    International Journal of Molecular Sciences, vol. 17, (no. 2)
  • Bussotti G., Leonardi T., Clark M.B., Mercer T.R., Crawford J., Malquori L., Notredame C., Dinger M.E., Mattick J.S., Enright A.J.
    DOI

    Improved definition of the mouse transcriptome via targeted RNA sequencing

    Genome Research, vol. 26, (no. 5), pp. 705-716
  • 2015
  • Fuster-Matanzo A., Gessler F., Leonardi T., Iraci N., Pluchino S.
    DOI

    Acellular approaches for regenerative medicine: On the verge of clinical trials with extracellular membrane vesicles? Extracellular vesicles and regenerative medicine

    Stem Cell Research and Therapy, vol. 6, (no. 1)
  • Lener T., Gimona M., Aigner L., Borger V., Buzas E., Camussi G., Chaput N., Chatterjee D., Court F.A., del Portillo H.A., O'Driscoll L., Fais S., Falcon-Perez J.M., Felderhoff-Mueser U., Fraile L., Gho Y.S., Gorgens A., Gupta R.C., Hendrix A., Hermann D.M., Hill A.F., Hochberg F., Horn P.A., de Kleijn D., Kordelas L., Kramer B.W., Kramer-Albers E.-M., Laner-Plamberger S., Laitinen S., Leonardi T., Lorenowicz M.J., Lim S.K., Lotvall J., Maguire C.A., Marcilla A., Nazarenko I., Ochiya T., Patel T., Pedersen S., Pocsfalvi G., Pluchino S., Quesenberry P., Reischl I.G., Rivera F.J., Sanzenbacher R., Schallmoser K., Slaper-Cortenbach I., Strunk D., Tonn T., Vader P., van Balkom B.W.M., Wauben M., El Andaloussi S., Thery C., Rohde E., Giebel B.
    DOI

    Applying extracellular vesicles based therapeutics in clinical trials - An ISEV position paper

    Journal of Extracellular Vesicles, vol. 4, (no. 1)
  • Smith J.A., Leonardi T., Huang B., Iraci N., Vega B., Pluchino S.
    DOI

    Extracellular vesicles and their synthetic analogues in aging and age-associated brain diseases

    Biogerontology, vol. 16, (no. 2), pp. 147-185
  • Clark M.B., Mercer T.R., Bussotti G., Leonardi T., Haynes K.R., Crawford J., Brunck M.E., Cao K.-A.L., Thomas G.P., Chen W.Y., Taft R.J., Nielsen L.K., Enright A.J., Mattick J.S., Dinger M.E.
    DOI

    Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

    Nature Methods, vol. 12, (no. 4), pp. 339-342
  • 2014
  • Cossetti C., Iraci N., Mercer T.R., Leonardi T., Alpi E., Drago D., Alfaro-Cervello C., Saini H.K., Davis M.P., Schaeffer J., Vega B., Stefanini M., Zhao C., Muller W., Garcia-Verdugo J.M., Mathivanan S., Bachi A., Enright A.J., Mattick J.S., Pluchino S.
    DOI

    Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells

    Molecular Cell, vol. 56, (no. 2), pp. 193-204
  • 2013
  • Hill A.F., Pegtel D.M., Lambertz U., Leonardi T., O'Driscoll L., Pluchino S., Ter-Ovanesyan D., Nolte-'t Hoen EN.
    DOI

    ISEV position paper: extracellular vesicle RNA analysis and bioinformatics.

    Journal of Extracellular Vesicles, vol. 23, (no. 2)
  • 2012
  • Cossetti C., Smith J.A., Iraci N., Leonardi T., Alfaro-Cervello C., Pluchino S.
    DOI

    Extracellular membrane vesicles and immune regulation in the brain

    Frontiers in Physiology, vol. 3 MAY
  • Cossetti C., Mercer T.R., Alpi E., Leonardi T., Drago D., Iraci N., Alfaro-Cervello C., Dinger M.E., Dietmann S., Crawford J., Caddeo C., Garcia Verdugo M., Bachi A., Mattick J.S., Pluchino S.

    Neural stem cells sort protein and RNA cargoes for export with exosomes in response to inflammation

    Journal of Neuroimmunology, vol. 253, (no. 1-2), pp. 127