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Matteo Marzi

Post Doc
Post Doc

Research Line

Genomic Science




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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):

  1. miRNA Degradation Mechanisms and their interplay with RNA Targets
  2. Non-coding elements in epigenetic and transcriptional plasticity
    • ROCHE funded project


  • 2011 “Phd in Molecular Medicine” (4 years degree at the European School of Molecular Medicine, within the IFOM-IEO-CAMPUS)
  • 2006: “Laurea magistrale in Biotecnologie Farmaceutiche” (5 years degree; final mark 110 cum laude) at the University of Milan
  • 2000: “Diploma di maturita’ scientifica” (High School; final mark 99/100) at Liceo Scientifico Leonardo da Vinci, Milan



  • 2012-to present: Post-doctoral Fellowship at Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT)
  • 2010-2012: Post-doctoral Fellowship at the Molecular Medicine Program, European Institute of Oncology (IEO). 
  • 2007-2010: PhD studentship in Molecular Medicine (European School of Molecular Medicine, SEMM) at IFOM-IEO campus, Pier Paolo Di Fiore’s group. 
  • 2005-2006: Research training for Biotechnology Degree at the Centre of Excellence for Neurodegenerative Diseases (CEND), University of Milano,Adriana Maggi's lab. 


miRNA Degradation Mechanisms and their interplay with RNA Targets

Project Outline


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).

We are now 




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.


lnc and enhancer screen part1





  • Winner of a 2018 Roche individual grant "Roche per la ricerca" as Principal Investigator
  • Winner of a 2016 Cariplo individual grant "Ricerca Biomedica condotta da Giovani Ricercatori 2016"as Principal Investigator.
  • Winner of a 2014 AIRC/Fondazione Cariplo individual grant "TRIDEO" (Transforming IDeas in Oncological research award) as Principal Investigator




Total: 12

First Author: 6 Last Author: 1

h-index: 9 

Citations: 486 (Scopus)

Total Impact Factor: 102.4


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