Education
Università degli Studi di Milano, Milan, Italy
Universita’ degli Studi di Milano, Milan, Italy
Liceo Scientifico “G. Marconi”, Pesaro (PU), Italy
Working Experience
11/2019-present Bioinformatician in Dr. Nicassio’s laboratory , IIT, Milan, Italy
04/2018-04/2019 Master student in Dr. Tiana’s laboratory of Theoretical Biophysics, Università degli Studi, Milan, Italy
Internship in Dr. Giorgetti's laboratory, Friedrich Miescher Institute, Basel, Switzerland
Lay summary
Nanopore sequencing is a novel technology that permits to sequence single DNA or RNA molecules. In particular, for the first time, it allows to directly sequence full-length RNA molecules without intermediate steps (retrotranscription or amplification), therefore making it possible to profile transcriptomes at an unprecedented level of detail.
As such, Nanopore sequencing is a very promising tool. In our lab we are using Nanopore and breast cancer models to gain insight into the transcriptional landscape of cancer cells and to see how it changes and adapts in response to chemoterapy.
Impact
Single molecule sequencing through Nanopore constitutes a new frontier in genomic studies, in particular in the field of cancer. Our knowledge of genome organization and regulation will be profoundly affected by this unprecedented ability to investigate genomic sequences directly.
The project
TNBC is an aggressive subtype of breast cancer that does not express the genes for estrogen receptor (ER), progesterone receptor (PR) and the growth factor receptor HER2/neu. Most hormone therapies target those receptors and this is why TNBC cannot be treated with standard methods. Furthermore, TNBC exhibits a certain grade of plasticity when subjected to chemotherapy, but little is known of the regulatory mechanisms responsible for this behavior. Recently, non-coding RNAs (ncRNAs) have been shown to provide an additional layer of gene expression control through various mechanisms. An important class of ncRNAs are microRNA primary transcripts (pri-miRNAs), which act as precursors in miRNA biogenesis but could also exert other functions as cis- or trans-acting regulatory ncRNAs.
The aims of my project are:
- leveraging full-length, direct RNA Nanopore sequencing to profile the transcriptional landscape of cancer cells;
- gaining new insights into the mechanisms linked to the processing of transcripts and to potential functions of pri-miRNAs.
We are using Nanopore direct RNA sequencing to profile chromatin-associated and cytoplasmic RNAs in breast cancer cells prior to and after chemotherapy treatment. Nanopore generates long genomic reads that need to be analysed and quantified in order to identify lncRNA and pri-miRNA transcripts. Consequently we are developing specific bioinformatic pipelines to filter and cluster the genomic data, dealing with the experimental and systematic bias that could eventually occur.
We expect to unambiguosly identify and quantify the expression of pri-miRNAs, lncRNAs and their processing intermediates.
These data will allow us to compare naive tumour cells with cells subjected to chemo-treatment and detect the influence of any possible sequence rearrangement on the development of drug resistance.
L’Istituto Italiano di Tecnologia (IIT) è una fondazione di diritto privato - cfr. determinazione Corte dei Conti 23/2015 “IIT è una fondazione da inquadrare fra gli organismi di diritto pubblico con la scelta di un modello di organizzazione di diritto privato per rispondere all’esigenza di assicurare procedure più snelle nella selezione non solo nell’ambito nazionale dei collaboratori, scienziati e ricercatori ”.
IIT è sotto la vigilanza del Ministero dell'Istruzione, dell'Università e della Ricerca e del Ministero dell'Economia e delle Finanze ed è stato istituito con la Legge 326/2003. La Fondazione ha l'obiettivo di promuovere l'eccellenza nella ricerca di base e in quella applicata e di favorire lo sviluppo del sistema economico nazionale. La costruzione dei laboratori iniziata nel 2006 si è conclusa nel 2009.
Lo staff complessivo di IIT conta circa 1440 persone. L’area scientifica è rappresentata da circa l’85% del personale. Il 45% dei ricercatori proviene dall’estero: di questi, il 29% è costituito da stranieri provenienti da oltre 50 Paesi e il 16% da italiani rientrati. Oggi il personale scientifico è composto da circa 60 principal investigators, circa 110 ricercatori e tecnologi di staff, circa 350 post doc, circa 500 studenti di dottorato e borsisti, circa 130 tecnici. Oltre 330 posti su 1400 creati su fondi esterni. Età media 34 anni. 41% donne / 59 % uomini.
Nel 2015 IIT ha ricevuto finanziamenti pubblici per circa 96 milioni di euro (80% del budget), conseguendo fondi esterni per 22 milioni di euro (20% budget) provenienti da 18 progetti europei, 17 finanziamenti da istituzioni nazionali e internazionali, circa 60 progetti industriali
La produzione di IIT ad oggi vanta circa 6990 pubblicazioni, oltre 130 finanziamenti Europei e 11 ERC, più di 350 domande di brevetto attive, oltre 12 start up costituite e altrettante in fase di lancio. Dal 2009 l’attività scientifica è stata ulteriormente rafforzata con la creazione di dieci centri di ricerca nel territorio nazionale (a Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) e internazionale (MIT ed Harvard negli USA) che, unitamente al Laboratorio Centrale di Genova, sviluppano i programmi di ricerca del piano scientifico 2015-2017.
Istituto Italiano di Tecnologia (IIT) is a public research institute that adopts the organizational model of a private law foundation. IIT is overseen by Ministero dell'Istruzione, dell'Università e della Ricerca and Ministero dell'Economia e delle Finanze (the Italian Ministries of Education, Economy and Finance). The Institute was set up according to Italian law 326/2003 with the objective of promoting excellence in basic and applied research andfostering Italy’s economic development. Construction of the Laboratories started in 2006 and finished in 2009.
IIT has an overall staff of about 1,440 people. The scientific staff covers about 85% of the total. Out of 45% of researchers coming from abroad 29% are foreigners coming from more than 50 countries and 16% are returned Italians. The scientific staff currently consists of approximately 60 Principal Investigators, 110 researchers and technologists, 350 post-docs and 500 PhD students and grant holders and 130 technicians. External funding has allowed the creation of more than 330 positions . The average age is 34 and the gender balance proportion is 41% female against 59% male.
In 2015 IIT received 96 million euros in public funding (accounting for 80% of its budget) and obtained 22 million euros in external funding (accounting for 20% of its budget). External funding comes from 18 European Projects, other 17 national and international competitive projects and approximately 60 industrial projects.
So far IIT accounts for: about 6990 publications, more than 130 European grants and 11 ERC grants, more than 350 patents or patent applications, 12 up start-ups and as many which are about to be launched. The Institute’s scientific activity has been further strengthened since 2009 with the establishment of 11 research nodes throughout Italy (Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) and abroad (MIT and Harvard University, USA), which, along with the Genoa-based Central Lab, implement the research programs included in the 2015-2017 Strategic Plan.
