PI: Maria Luisa Appetecchia
Other IRE Principal Collaborators Involved: Toietta Gabriele, Soddu Silvia, Monteonofrio Laura, Puliani Giulia

Project duration: 24 months

Project code: PNRR-TR1-2023-12377062

This project aims to address two of the main gaps in the Gastro-entero-pancreatic neuroendocrine neoplasms (GEP-NEN) field: dissect the heterogeneity of GEP-NENs and the lack of research models.

GEP-NENs are a rare group of neoplasms originating from the diffuse endocrine system of gastrointestinal tract and pancreas.

Tumor heterogeneity is a common phenomenon in GEP-NENs. Besides inter-tumor heterogeneity related to the different site of origin, intra-tumor heterogeneity is also present as confirmed by single-cell sequencing. In clinical practice, the selection of therapeutic strategies depends on histological features, surgical resectability, and expression of somatostatin receptors (SSTRs). However, patients with similar clinical and pathological features may have significantly different prognosis and treatment response.

Recently, spatial transcriptomics has emerged as a highly sensitive and accurate high-throughput technology to measure gene expression while preserving the spatial information of tumor cells and their microenvironment. This opens a new scenario for dissecting GEP-NEN heterogeneity and understanding key steps of GEP-NEN development, progression, metastatization and identification of novel biomarkers.

At present, a few cell lines and in vivo models are available, but they only partially recapitulate the different biological and clinical features of GEP-NENs. Genetically modified mouse and rat models have been useful to better characterize the role of somatic mutations related to familial GEP-NEN; however, GEP-NEN phenotypes vary with mice strain while tumor latency and incomplete penetrance complicate drug screenings. Thus, further pre-clinical models are needed. For this aspect we will create a living biobank by collecting fresh samples of GEP-NENs patients undergoing surgery, allowing us to generate 2D or 3D cell models to study GEP-NEN biology, development, progression and therapeutic strategies.

The IRE is a referral center for NENs and is the leading unit of the interdisciplinary team proposing this project which is composed also by the Centro cardiologico Monzino in Milan, the Univeristy of Chieti and the ARNAS Garibaldi in Catania.

Beside the intrinsic restriction due to the rarity of these tumors, the identification of more effective therapeutic strategies for GEP-NENs has been limited, at least in part, by: i) their intra- and inter- tumor heterogeneity; ii) the incomplete understanding of their biology; iii) the lack of cell and animal research models. Our hypothesis is that high resolution definition of the GEP-NEN landscape through spatial transcriptomics and proteomics, together with the generation of a living biobank, will shed light on these heterogeneous tumors with the potential in identify novel biomarkers and test actionable targets/pathways for patients with nonresectable, SSTR-negative, relapsing, and/or metastatic diseases.

For achieve these goals, our unit at IRE will use a relatively large cohort of clinically well-annotated FFPE GEP-NENs available in our biobank to perform spatial transcriptomics. The same samples will be analyzed for proteomic studies at the centro cardiologico Monzino. The ARNAS Garibaldi Hospital, together with IRE, will collect fresh samples from patients undergoing surgery for GEP-NEN treatment. These samples will be used to create the living biobank of 2D or 3D cell culture. Lastly, the University of Chieti will perform the pharmacological in vitro studies on the obtained research models.

With this project we expect to:

1. profile a cohort of GEP-NENs by using spatial transcriptomics and proteomics to accurately map their heterogeneity and explore the biological underpinnings;
2. create a living biobank to provide the researchers with GEP-NEN models for genetic, epigenetic, proteomics, and pharmacological studies;
3. perform functional studies in in vitro models, to test new therapeutic strategies.

This project will thus uncover new biomarkers and therapeutic vulnerabilities.