The research line in Genomic Science applies modern genomic technologies towards a better understanding of complex biological processes and diseases, with particular emphasis on Cancer.Our line is located within the IFOM-IEO Campus in Milan, one of the largest and most vibrant cancer research communities in Europe. Our laboratories provide state-of-the art technological platforms for functional genomics, and benefits from all the infrastructure, technological platforms and didactic activities already present in the IFOM-IEO Campus. Our PhD program is integrated with that of SEMM, the European School of Molecular Medicine.
Our mission is to identify changes in the genome that underlie the development of cancer, as well as its susceptibility to therapeutic intervention. Our general aim is to reduce pathological traits into their molecular components, which might correspond to disease markers or potential targets for pharmacological intervention. We will exploit these molecular markers and targets in order to build up strategic programs for disease prevention, early detection and treatment.
The recent development of novel technological platforms has increased the range of applications for genomic analyses to new areas of investigation. We are interested in exploiting these novel technologies to gain insight into the mechanisms of gene regulation and into the biology of cancer evolution.
In order to solve the challenge of intra-sample heterogeneity at the single cell level, we are using single-cell sequencing with the Chromium 10X Genomics platform, a robust and standardized microfluidic technology for single cell analysis that is well established in our institute. Several ongoing projects use this technology to characterize heterogeneous cell populations, measuring transcripts (scRNA-seq) directly or together with surface marker detection (cell hashing + scRNA-seq), mapping chromatin accessibility and active regulatory regions (ATAC-seq), or measuring genomic alterations at DNA level (scCNV-seq).
In addition, we have set up approaches that combine single-cell transcriptome profiling with either DNA or RNA barcodes at single cell level (CROP-seq, Perturb-seq) that will be used in: i) pooled CRISPR screening, directly linking sgRNA expression to transcriptome responses in thousands of individual cells, thus facilitating high-throughput functional dissection of complex regulatory mechanisms and heterogeneous cell populations; ii) tracing transcriptional patterns over time, useful to resolve adaptive transcriptional mechanisms of cancer cells.
Finally, we are developing applications that use Nanopore sequencing (Oxford Nanopore Technologies) to natively sequence full-length RNA molecules (direct RNA-Seq). We are applying this technique for the identification of RNA modifications and the profiling of nascent RNA (through RNA metabolic labelling).
Moreover, some fully operational facilities are available, responsible for the routine use of Sequencing applications (Illumina, Nanopore, 10X Genomics) to perform a broad range of analysis of DNA and RNA and provide technical support to the research groups for routine use of genomic application and development of tailored protocols. DNA analysis includes: Whole Genome Analysis, Targeted DNA Analysis, Chromatin-immunoprecitipation (ChIP), Chromatin-Accessibility (ATACseq), Methylation analysis, and Single Cell Copy Number Variation (CNV). RNA applications include: whole-transcriptome Analysis (RNAseq), Analysis of Small RNAs (sRNAseq), Nascent RNA analysis (4sU/TT-seq); Epitranscriptomics (Methylated RNA), immunoprecipated RNA (RIP/RAP), Single Cell transcriptomics (sc-RNA) and single molecule direct RNA sequencing (dRNAseq)
Our research line includes four units
We study the function and regulation of non-coding transcripts (miRNAs and long non-coding RNAs), with a particular emphasis on how regulatory RNAs shape the identity and properties of mammalian cells in cancer stem cells and during cancer evolution (therapy resistance, metastatic spread)
We combine genetically modified mouse models (GEMMs) that faithfully recapitulate tumor progression with forward and reverse genetic screenings for the identification of transcriptional and epigenomic alterations causally involved in cancer.
We apply an interdisciplinary approach combining mathematical modeling and genomics to study the dynamics of transcription (including RNA synthesis, processing and degradation), and how these are affected by RNA modifications and chromatin regulation in cancer.
we develop computational methods and algorithms to study the function and regulation of RNA molecules, with a particular focus on the development of analytical strategies based on Nanopore direct RNA sequencing (dsRNAseq)
- We have applied new tailored approaches based on in vivo RNA labeling and high-throughput sequencing to the study of miRNA degradation mechanisms, thus highlighting the importance of decay dynamics in the regulation of the miRNA pool (DOI).
- We have developed a computational tool (termed IsomiRage) able to identify, analyse and classify miRNA isoforms (called “isomiRs” from NGS data (DOI).
- Identification of compensatory RNApolII loading on promoters explains the selective efficacy of Brd4 inhibitors in Myc driven cancers. (DOI1, DOI2).
- Discovery of a mechanism of transcriptional regulation, which reinforces Myc dependent transcription and allows integration of chemical and physical cues, directly on promoters and enhancers, to regulate cell division. (DOI).
- We develop experimental and computational methods to quantify the kinetic rates governing the main steps in the RNA life cycle (RNA synthesis, processing and degradation), collectively defining the dynamics of each transcript (DOI1, DOI2).
- We use an interdisciplinary approach – based on metabolic labelling of nascent RNA, epitranscriptome profiling and their integrative analysis through mathematical modeling - to study the functional role of RNA dynamics in tumors with high-levels of the MYC oncogene (DOI1, DOI2).
- Dr. Ana Marques, University of Lausanne - Lausanne, Switzerland
- Dr. Davide De Petri Tonelli, IIT - Genova, Italy
- Dr. Tiziana Bonaldi, IEO - Milan, Italy
- Prof. Johannes Zuber, Research Institute of Molecular Biology (IMP) - Vienna, Austria
- Prof. Pier Giuseppe Pelicci, IEO – Milan, Italy
- Dr. Bruno Amati, IEO – Milan, Italy
- Dr. Benedetto Grimaldi, IIT – Genova, Italy