Cancer Biology and Functional Genomics

Projects in this area aim to investigate dynamic aspects of genome, such as gene transcription, translation, regulation of gene expression, protein–protein and protein-DNA interactions, and their relationship with the mechanisms leading to cancer development and progression. 

To this end our projects are focused:

• to identify non-coding DNA regulatory regions functionally relevant in cancer and to dissect their mechanism of action
• to identify and characterize from both a molecular and functional point of view long non-coding RNA involved in cancer development and progression
• to understand the relationship between coding and non-coding genome and cancer cell biology
• to explore the mechanisms underlying cancer aggressiveness 
• to explore the mechanisms underlying cancer drug resistance
• to study changes in cellular metabolism during cancer progression.

Major experimental technologies:

• Chromatin Immunoprecipitaion (ChIP) for the characterization of the functional status of the genome and for the analysis of proteins-DNA binding.
• ChIP-Sequencing analysis, for the genome wide profile of chromatin status.
• CRISPR-Cas9- genome editing approaches for targeted and genome wide mutagenesis of coding and non-coding elements.
• RNA-sequencing for gene expression profile.
• Luminex-based technology for high sensitivity multiplex analytes determination.
• Flow-cytometry.
  • RNA-Immunoprecipitation (RIP-Seq) for proteins-RNA interaction analysis.
  • Chromosome conformation capture (3C) to characterize the tridimensional interactions of distant genomic regions.
  • Chromatin Isolation by RNA purification (ChiRP) for the identification of RNA binding to genomic regions.
• Primary cell cultures derived from human tumor and normal tissues.

List of active projects

• Assessing the function of non-coding genome in the metastatic progression of melanoma.
• Characterization of DNA regulatory regions responsible for the aberrant reactivation of Runx2 expression in cancer.
• A CRISPR-Cas9 approach for the identification of genetic determinants of immunotherapy resistance in lung cancer.
• Molecular dissection of Cadherin 6 (CDH6) function in aggressive thyroid tumors.
• From epigenetic drugs to target therapies: improving HDACi based anti-cancer therapies by dissecting the functional relation between HADC and RUNX2.
• RAINs: Novel RUNX2 associated lncRNAs in cancer.
• Novel aspects in the long-non coding RNA (lncRNA) NEAT1 biological function in tumors.
• Characterization of E2F7 role in aggressive thyroid cancer.
• Mapping lncRNAs associated to transcription activator chromatin remodeling complexes.
• Discovery of novel lncRNAs involved in T cell differentiation and Anaplastic Large Cell Lymphomas classification.
• Characterization of SIRT1 pathway in Non-Hodgkin lymphomas.
• SIRT1 regulation in diffuse large B-cell lymphomas: epigenetic modifications as therapeutic targets.
• Characterization of Resveratrol metabolites anti-inflammatory and anti-tumoral potential.
• Investigating Aicda expression and activity in mature B-cell lymphomas.
• Profiling the molecular bases of the metabolitic switch in cancer: a challenge to overcome drug resistance.