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Synthetic Lethal Phenotype Identification through Cancer Evolution Analysis

Periodic Reporting for period 4 - SPICE (Synthetic Lethal Phenotype Identification through Cancer Evolution Analysis)

Reporting period: 2020-04-01 to 2021-03-31

Human cancer is still a widely spread disease. Despite a significant decreased mortality for certain tumor types over the last two decades, it remains among the most common cause of death worldwide. In the last fifteen years, enormous progress in DNA sequencing technology and genome editing has revolutionized cancer genomic research and changed expectations of precision medicine, whereby tumor cells DNA alterations are exploited for patients’ treatment selection. Especially, the use of Next Generation Sequencing (NGS) allowed the scientific community to sequence thousands of tumor samples and to compare their DNA with their healthy counterparts widening the agnostic search for cancer vulnerabilities towards precision medicine in oncology. The SPICE research project has been designed to identify biomarkers of cancer progression and to nominate those vulnerabilities through a combination of computational genomics and experimental efforts. Mapping DNA alterations to the disruption of genes that accelerate disease progression potentially allows for the nomination of new drug targets for patients with advanced disease. Specifically, the search for drug targets was based on the concept of synthetic lethality, where the concomitant disruption of specific pairs (or combinations) of genes is fatal for the cell itself, while the disruption of one single gene is not. In practice, such gene combinations can be exploited by selecting a treatment to intentionally disrupt one gene, in presence of the alteration of a second gene in tumor cells; this can lead to a selective effect on tumor cells only while sparing all healthy cells. This approach could enormously reduce toxic effects typical of chemotherapeutic drugs and improve the quality of life of cancer patients. In order to enhance the chances to nominate these drug targets, in this project we implemented unbiased searches of biomarkers and synthetic lethal gene pairs using computational and mathematical methods to learn from the genomes of thousands of patients’ cancer samples and experimentally validated the most promising findings using state of the art techniques, including the use of genome editing and organoid technologies through collaborative efforts.

The project was designed to address specific clinical questions in the setting of lethal prostate cancers, a genetically and clinically heterogeneous disease with high incidence in the population. While advances in targeted therapy have recently led to more effective management of metastatic disease, prostate cancer still results in the second cause of cancer death in men. Significant effort was also dedicated to chemotherapy-resistant urothelial carcinoma. From a technical perspective, the project aimed at the development of computational approaches to be applicable across cancer, both for the refined analysis of genomic lesions and the inference of tumor evolution and disease progression biomarker identification, and for the nomination of potential synthetic lethal combinations. These approaches together with the results of the large-scale computations performed on thousands of tumors across more than twenty-five tumor types have been made available to the research community.
We achieved significant results both in terms of technological and analytical solutions and in terms of relevant biomedical discoveries. The team led the development of innovative solutions for the analysis of tumor genomes that proved successful in multiple tumor types and settings, including tissue and liquid biopsy-based analyses. Those solutions include the ability to characterize gene lesions at the single allele level, to quantify the ‘amount of tumor DNA’ from sequencing data (using structural changes, single nucleotide variants or DNA biochemical changes), and to perform ultra-fast computations for the identification of cancer vulnerabilities. The application of those approaches to thousands of tumor genomes led to the generation of a large collection of highly processed genomic data and of comprehensive lists of potential synthetic lethal combinations per tumor type.

Furthermore, through the application of those approaches, we provided major contributions to the clinically-relevant definition of common and aggressive tumor types. Specifically, we were able to describe the landscape of clonal evolution of chemotherapy-resistant urothelial carcinoma and the genomic and epigenetics features characteristic of prostate cancer trans-differentiation from adenocarcinoma to neuroendocrine disease. In this specific disease setting, through our well-established collaborative network, we provided major contributions to the field by suggesting neuroendocrine biomarkers relevant both for tissue and liquid biopsy based assays and by studying the profiles of human derived organoids in pre-clinical studies. All the above-mentioned results have been published and the relevant material made available to the research community. In the context of synthetic lethality, we coupled the agnostic search of genomic lesion combination results with extensive experimental work using ad hoc engineered single clones of prostate and of bladder cancer cells. This work led to the novel identification of a prostate cancer phenotype with therapeutic potential and to the nomination of drugs with higher sensitivity in the presence of a common genomic loss in bladder cancer. These lines of work are in their final stages and will soon be submitted for publication. Further, we contributed to the development of two innovative strategies to increase the specificity of genome editing systems (Hit and go strategy and evoCas9 strategy). Although at a limited rate due to the 2020 pandemic, dissemination of results has been pursued throughout the SPICE project through presentations at conferences and international collaborative meetings, including as part of AACR conferences, of World Congress of the International union of Physiological Sciences, and of Scientific Foundations Symposia.
The strength of the SPICE project relied on the highly interdisciplinary and continuous interactions within the team and with collaborators both at the host institution and outside. We had long series of regular project and sub-project meetings that solicited scientific synergies that proved successful as in the setting of genome editing. We made some discoveries that are likely to impact the clinical setting, as in the case of neuroendocrine prostate cancer diagnosis, and developed tools, now publicly available, that can be leveraged by other pre-clinical investigators to pursue cancer type specific questions. Altogether, the SPICE project moved forward the field of cancer genomics.
Schematics of the SPICE project