Nuclear Proteomics to Study Gene Expression Regulation in Cancer

A distinctive hallmark of our research activity is the unique combination of a strong technological attitude/imprint grounded on Mass Spectrometry (MS)- based quantitative proteomics, and a long-standing scientific focus on gene expression regulation in cancer, mediated by the synergism between different protein determinants on chromatin.

Thus, our investigation on the different layers of gene expression modulation in cancer is carried out using MS-based proteomics as the technology of choice, with the ambition of establishing innovative technological approaches that can offer original perspectives and new concepts to the epigenetics field. Our achievements comprise both the generation of new knowledge and the implementation of innovative proteomics methods to complement and extend more standard epigenomics approaches. The implementation of our MS-based platform is continuously carried out in synergy with the Proteomics Technological Unit in order to maintain state-of-art protein/peptide separation methods and high-resolution LC-MS/MS analysis.

Historically, our interest has focused on how gene expression regulation is achieved through the functional interplay between post-translational modifications (PTMs) - on both histones and non-histone proteins- and transcription factors (TFs) and chromatin modifiers. By combining classical molecular biology assays with proteomics, we investigate complementary aspects of the epigenetic control of transcription and chromatin and nuclear dynamics, addressing the following main questions:

• How do combinatorial histone PTM patterns – from single histone up to small chromatin regions - synergize with non-histone chromatin factors to enforce specific functional states on chromatin?
• Can we comprehensively detect and profile by MS histone PTMs in cancer patient samples (formalin-fixed paraffin-embedded (FFPE) tissues, frozen tissues and liquid biopsies), to define epigenetic signatures to be used as diagnostic tools for patient stratification?
• To which degree do PTMs, in particular K-acetylation and K/R-methylation, extend beyond histones to the cellular proteome, and how do they impinge on transcription and other nuclear processes?
• Can we investigate the in vivoactivity of histone-modifying enzymes in close-to-physiological conditions and comprehensively profile the effect of their pharmacological modulation?