BIOSKETCH
Since 2012, Dr Marzi has been working "non-coding Genome" laboratory, headed by Dr. Francesco Nicassio, now coordinator of the Center for Genomic Science at IIT@SEMM in Milan.
With a Master Degree in Pharmaceutical Biotechnology and a PhD in Molecular Medicine, the scientific career of Dr.Marzi has been characterised by a general interest in the role of non-coding RNAs (microRNAs, lncRNAs) and their ability to modify the expression of genes, shaping cell fate (Marzi et al. J Cell Biol 2012). To this purpose, he acquired familiarity with both computational and experimental approaches, exploiting several genome-wide approaches (small RNA-seq, RNA-seq, ATAC-seq, ChIP-seq), novel technologies and bioinformatics to dissect regulatory gene networks involved in cell differentiation, stem cell biology and cancer (Muller, Marzi et al., Front. Bioeng. Biotechnol. 2014; Marzi et al. Clinical Chemistry 2016). Furthermore, Dr. Marzi contributed to establish in the last few years fruitful collaborations with other laboratories, developing additional lines of research including the analysis of the transcriptional programs governing the development and differentiation of the central nervous system.
Contributing more than ten publications in high impact journals and an international patent on "Cancer Biomarkers" and their clinical use (Bianchi et al. EMBO Mol Med 2011), Dr. Marzi developed within the noncoding Genome lab at IIT two mail lines of research (see Project section):
EDUCATION
RESEARCH EXPERIENCE
miRNA Degradation Mechanisms and their interplay with RNA Targets
Project Outline
MicroRNAs are small molecules that regulate negatively gene expression, by promoting the degradation of their targets. Thus, it is not surprising that micoRNAs play a crucial role in several physiological and pathological contexts, including cancer biology. The alteration of the normal expression level of microRNAs (i.e. over- or under-expression) leads to aberrant expression of the targets and, for this reason, several mechanisms evolved to maintain the correct homeostasis of microRNAs. Recently, our lab and others discovered a new mechanism controlling microRNAs degradation, which was named Target-Dependent miRNA degradation (TDMD). TDMD is a process by which some peculaliar targets, showing special features in terms of binding (i.e. a stronger compared to canonical targets), are able not only to elude the control of their cognate microRNA but also to promote the degradation of microRNAs. In other words, the TDMD mechanism reduce the intracellular levels and activity of some microRNAs.
Our lab is currently investigating the involvement of TDMD transcripts in human disease, with an emphasis on cancer, with the aim of defining the role played by TDMD transcripts in modulating miRNA functions (CARIPLO funded project) and the possible clinical applications of TDMD in human tumors.
Project Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that function as guide molecules in RNA silencing. The miRNA:target interaction usually occurs at the 5′ end of the miRNA (the ‘seed’ region). In the last few years, it has emerged that there is a special class of targets which bind the miRNA not only through the seed, but also through a second region of complementarity at the 3′ end of the miRNA. The extended complementarity forces the miRNA out of Ago2, where it becomes accessible to enzymatic degradation.
Our lab was involved in the identification of one of the first endogenous target capable of triggering miRNA degradation (Ghini, Rubolino et al. Nat Commun 2018).However, we still miss how many of such transcripts could exist and the potential impact of TDMD mechanism in human cancer.
We are currently developing new bioinformatics pipelines, based on combined sequence alignment and feature selection approaches, to select for TDMD interactions in order to build a high confidence database that can be exploited to forster additional research lines and to isolate the best candidates that will be further investigated in order to unveal their clinical utility in the management of tumors.
Non-coding elements in epigenetic and transcriptional plasticity
Project Outline
Among the millions of cells constituting a tumor, there are often a few that can survive treatment and cause tumor relapse and metastatic dissemination. Through genetic events, such as mutations, and non-genetic (“epigenetic")mechanisms, these cells adapt to challenging environmental conditions and make the tumor progress. Current therapies, such as chemotherapy, are severely hindered by the difficulty dealing with these “adaptive responses”.
In our lab, we investigate the non-coding elements that contribute, both at RNA level (ncRNAs) and DNA level (“enhancers"), to shaping the "adaptive responses" that allow cancer cells to survive, disseminate and metastasize.
We predict that a targeted therapy based on these regulators should be successful in eradicating cancer cells surviving chemotherapy.
Project Abstract
Epigenetic plasticity (i.e., transcriptional heterogeneity) has emerged as a new hallmark of cancer, as it can give cells the ability to adapt to challenging environmental conditions, such as cancer therapy or metastasis formation. At the mechanistic level, adaptation is regulated by the complex interplay between dynamic regulatory elements (such as enhancers) and their target genes, which ultimately determine the cell response. Unfortunately, only a tiny fraction of the hundreds of thousands of regulatory elements in our genome has been characterized.
With this project, we mainly aim to identify enhancer-gene and lncRNA-gene interactions that are functionally relevant for breast cancer adaptative processes.
So far, we have been focusing on triple-negative breast cancer, an aggressive tumor sub-type characterised by extensive heterogeneity and few therapeutic options. We have already developed several experimental models with high epigenetic plasticity and employed cutting-edge genomic approaches (including NET-Cage, single cell ATAC sequencing and Nanopore sequencing) to identify the regulatory elements (~600 lncRNAs and ~1000 enhancers) that are putatively involved in adaptive responses (e.g. response to chemotherapy, cancer stem cells).
We are currently investigating the functional and transcriptional impact of perturbing each of these regions. Our innovative strategy combines CRISPR interference with single cell RNA sequencing by assigning a unique transcribed barcode to each sgRNA. In this way, single-cell RNA-seq profiles can be used to investigate which cell programs are affected by each individual perturbation. With this approach, we want to identify the cis- and -trans regulatory networks that control cancer cells ability to adapt to therapy.
In the long term, our study will allow us to identify diagnostic targets and therapeutic markers and improve the patients' survival rate.
This project is supported by a ROCHE individual grant to Dr. Marzi.
GRANTs
PATENTs
PUBLICATIONs
Total: 12
First Author: 6 Last Author: 1
h-index: 9
Citations: 486 (Scopus)
Total Impact Factor: 102.4
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.
