LONG-TERM VISION OF THE PROJECT
Discovering new targets driving patho-biological processes in human ECs and functionally validate them in mouse models, in order to develop new therapeutic strategies (“from the bench to the bedside”).
• TARGET DISCOVERY by studying TEC heterogeneity. We utilized (amongst other techniques) unbiased multi-omics, including single cell analyses, in combination with state-of-the-art (meta-analysis) bioinformatics methods (BIOMEX, EC-GEM, EndoDB, etc.) as described in our studies: Rohlenova et al. Cell Metab 2020; Goveia et al. Cancer Cell 2020; Kalucka et al. Cell 2020. We have already identified multiple targets in TECs from lung cancer using this approach, which now need functional validation before proceeding to selection for drug development. By focusing on genes that, by analysing scRNA-seq datasets were found to be upregulated in proliferating ECs and were conserved in both patients and mouse models from different disorders that are characterized by excessive angiogenesis, and by combining the scRNAseq analyses with other complementary bioinformatics meta-analyses, we were able to identify previously unrecognized angiogenic targets (Cell Metab 2020; Cancer Cell 2020). As a next step, we will use similar approaches to identify targets, involved in EC heterogeneity in other human cancer types.
• “SMARTER” DISCOVERY & SELECTION OF TARGETS: An estimated third of the human coding genome contains (up to 6,000) “mystery” genes, lacking functional annotation and publications. We developed a novel Artificial Intelligence (AI)-based prototype tool (SCMYSTERYDENTIFIER) that uses classical classifier algorithms and single cell transcriptomics data to successfully predict immunosuppressive functions for “mystery” genes in ECs, never associated with alternative immunotherapy. Building further on this, we are developing an improved AI-based BRAIN-FOR-BIOTECH (BFBIO) tool that integrates multiple data modalities and graph neural networks to discover mystery immunosuppressive targets in ECs more accurately (BFBIO-V1.0).
• TARGET VALIDATION is a critical step in the process of drug development starting from target discovery to functionally characterizing a large number of candidates. Validation occurs at several levels. We developed a novel revolutionizing (“REVOLT”) strategy to generate EC-selective knockout mice. REVOLT is based on the combined use of: a) lipid nanoparticles with improved EC-selective targeting containing sgRNA; and b) endothelial Cas9 expressing mice. We will validate the role of target genes in vivo, by generating EC gene manipulated mice (using REVOLT) and phenotyping their tumor growth & response to traditional immunotherapy.
