Laboratory of functional genomics

The research activity of the lab revolves around 3 major research areas.

Chronic lymphocytic leukemia (CLL), the most common adult leukemia in the western world, is a fascinating disease for at least four different reasons. The first is that the tumor and the host co-exist for several years, even without therapy. Several studies, including some from our group, have uncovered the many and complex interactions undergoing between the host microenvironment and the tumor and mediating progressive adaptation and disruption of the host defenses (see references 1-4, among the others). 

The second is that while several recurrently mutated genes have been identified, none of them is predominant or pathognomonic, leaving the question of leukemogenesis still unanswered. The third is that in a small and still unpredictable percentage of patients the disease evolves into an aggressive lymphoma, a condition known as Richter’s syndrome, with a dire prognosis. The lab has established unique patient-derived xenograft models of this conditions that have been extensively used to model therapy (see references 5-7). The fourth and final reason is that today CLL is effectively treated with small molecules that inhibit oncogenic pathways or that drive apoptosis, without chemoimmunotherapy. 

Currently, there are two main CLL – RS projects ongoing in the lab:

The first one is funded by an Italian Association for Cancer Research Investigator Grant is dedicated to the study on the connections between the B cell receptor (BCR), which is the driving force in the disease and NOTCH1, which is the most common single gene abnormality in the disease. The hypothesis behind this project is that oncogenic signaling in CLL and RS cells, as driven through BCR and NOTCH1 acts directly through the up-regulation of the metabolic capabilities of the cancer cell. Hence, the combination of drugs that target oncogenic pathways with drugs that inhibit central metabolism of cancer cells may show synergistic effects. We have focused on Nicotinamide Phosphorybosyl Transferase (NAMPT), the main NAD biosynthetic enzyme in CLL and RS cells. Our data so far show that NAMPT is upregulated through BCR signaling and that drugs that target NAMPT and the BCR induce apoptosis in vitro and in vivo in RS patient derived xenograft models (see Figure 1).

We are now trying to pinpoint the role of NOTCH1 in the system, by building models expressing a set BCR, with or without NOTCH1 mutations. These models will be instrumental in understanding the molecular connections between the pathways and to identify therapeutic vulnerabilities.

Reference scientist: Amelia Fascì

The second one is a collaboration with a novel pharma company dedicated to understanding the role of WNT/planar cell polarity (WNT/PCP) signaling pathway in CLL. The choice of this pathway stems from very encouraging results obtained using antibodies targeting ROR1, which is one of the receptors. This pathway is important in regulating homing to the leukemic niche and hence in generating therapy resistance. For this reason, we have embarked in a project to study the other ligands of this family, namely ROR2, RYK and PTK7.

Reference scientist: Matilde Micillo

We have exploited the concept of liquid biopsy, extensively used to monitor tumor relapse, in the feld of transplantation, to monitor rejection. To do so, we set-up an assay to measure donor-derived cell free DNA (dd-cfDNA, see Figure 2). Research showed that dd-cfDNA values correlate with the state of the transplanted organ and can therefore be predictive of the occurrence of rejection episodes. The lab has devised an innovative monitoring system based on HLA-DRB1 and HLA-DQB1 mismatches between donor and recipient and a strictly quantitative droplet digital PCR assay. Preliminary results obtained in cohorts of heart and lung recipients are encouraging (see references 8,9). Reference Scientist: Monica Sorbini.

Research showed that dd-cfDNA values ​​correlate with the state of the transplanted organ and can therefore be predictive of the occurrence of rejection episodes. The lab has devised an innovative monitoring system based on HLA-DRB1 and HLA-DQB1 mismatches between donor and recipient and a strictly quantitative droplet digital PCR assay. This assay was recently patented and acquired by GenDX, a leading diagnostic company in the field of transplantation, for development into a diagnostic kit. Preliminary results obtained in cohorts of heart and lung recipients are encouraging (see references 8,9).

Reference Scientist: Monica Sorbini

My clinical activity provides diagnosis and genetic counseling to patients who have received a solid organ transplant or are at risk of receiving one. This activity was started thanks to an Excellence Grant awarded to the Department of Medical Sciences in late 2018 and is now an integral part of the diagnostic offer of the Service of Immunogenetics and Transplant Biology of the Città della Salute e della Scienza Hospital. 

In many instances, the impact of genetic damage on the phenotype remains unknown, particularly in the presence of previously unreported mutations or of diseases with unclear pathogenetic mechanisms. Part of the lab activities are being dedicated to design easy and ready to use genome editing approaches to generate experimental models to better understand the impact of specific mutations on the phenotype or genotype-phenotype correlations (see reference 10).