Our Three-Year Planning (2025-2027) for Research

Over the past 20 years, the introduction of next-generation technologies for the study of the genome, transcriptome, metagenome and epigenome has expanded our knowledge of cancer pathogenesis, allowing the development of targeted therapies. This revolution has led to the identification of specific subgroups of patients able to respond to particular treatments and to a significant improvement in survival. However, there are neoplasms, often with a low incidence, for which progress has been minimal. Even in case of success, there is great variability in the response to treatments, both in terms of efficacy and duration over time. This clinical heterogeneity is a consequence of a marked biological and molecular heterogeneity due to the presence in the tumor of cellular subpopulations with different biological characteristics (epithelial, mesenchymal, inflammatory phenotype, stem cells, etc.) and with heterogeneous genetic and epigenetic alterations. These variations are also patient-specific and influenced by interactions with the microenvironment, including through exosomes, small vesicles of 40-150 nm actively released by tumor and stromal cells. The challenge of oncology for the next few years will therefore be to identify the molecular, cellular and exosomal determinants of this heterogeneity to develop predictive biomarkers.

Neoplasms will be characterized at the genomic, transcriptomic, metagenomic, epigenomic, and immunophenotypic levels through the analysis of tumor tissue, healthy tissue, germline, liquid biopsy, exosomes, and stem cells isolated from fresh biopsy and post-surgical tumor tissue. We will employ next-generation technologies such as DNA microarrays, real-time and digital PCR (for the analysis of mRNA and microRNA expression and mutations in circulating DNA), multicolor flow cytometry, Next Generation Sequencing (e.g., Targeted Sequencing, Copy Number Variation, RNA-seq, ChIP-seq, single-cell RNA-seq), and Nanoparticle Tracking Analysis for exosomes.

Advanced statistical and bioinformatic analyses will be used to correlate the data with the clinical-pathological characteristics of the tumor and life styles (e.g., diet, exposure to pollutants). This will allow for the characterization of tumor cell subpopulations and the stem cell component, as well as the tumor microenvironment (including exosomes), which are at the root of tumor heterogeneity and are associated with varying risks of disease development, progression, prognosis, and response to conventional and biological/molecular treatments.

Biomolecular mechanisms will also be studied in primary cell lines, stem cells, and organoids isolated from tumor tissue (ex vivo), peripheral blood (whole blood, serum, and plasma) of each patient, and in mouse models generated through orthotopic injection of tumor and stem cells (cell- and patient-derived xenografts, CDX-PDX). This will be achieved through gene expression manipulations (siRNA, shRNA, CRISPR-Cas9, expression vectors), the use of exosomes, including engineered ones, and interactions with pharmacologically active molecules.

i) To identify the biological mechanisms associated with patient-specific and intratumoral tumor heterogeneity through the study of genomic, transcriptomic, metagenomic, epigenomic, and immunophenotypic profiles of tissues, liquid biopsies (including exosomes), and cancer stem cells.

ii) To identify prognostic and predictive biomarkers of response to conventional drugs, molecular therapies, and immunotherapy, both in tissue and in liquid biopsy samples.

iii) To identify novel molecular targets specific to metastatic cells and the stem cell component, as well as their related recurrences/metastases, with the aim of developing innovative personalized therapies.

i) Identification of mutational, transcriptional, epigenetic, and immunophenotypic profiles of neoplasms in different patients and of tumor cell subpopulations (at single-cell resolution and in exosomes);

ii) Identification of novel effectors/regulators specific to cancer stem cells, useful for diagnostic and prognostic purposes and as potential new therapeutic targets;

iii) Characterization of the molecular mechanisms involved in the development of distant metastases;

iv) Development and analytical/clinical validation of diagnostic, prognostic, and predictive biomarker panels through the analysis of nucleic acids and proteins in tumor tissues and blood (liquid biopsy);

v) Development of an engineered diet as an adjuvant to therapy;

vi) Design of innovative, patient-specific therapeutic strategies involving the use of conventional pharmacological agents and novel biopharmaceuticals, with a translational perspective toward Phase I clinical trials.