Drug repurposing aims at finding a new therapeutic application of a drug already approved in clinics but for a different purpose. We developed three computational approaches for drug repurposing based on the analysis of transcriptional responses to drug treatment: Gene2Drug2 (http://gene2drug.tigem.it) , Mode of Action by Network Analysis (http://mantra.tigem.it) and Drug Set Enirchment Analysis (http://dsea.tigem.it). Gene2Drug identifies drugs to repurpose according to their ability to transcriptionally modulate genes belonging to a set of known disease-relevant pathways. Mantra is based on the hypothesis that if a drug induces a transcriptional response opposite to the one caused by the disease, then that drug might be potentially therapeutic. DSEA analyses the transcriptional response of hit compounds from screening studies to detect those molecular pathways that are consistently up- or down- regulated by most of the compounds, thus helping to elucidate their mechanism of action. In this project, we aim at repositioning drugs for the treatment of rare genetic disorders, including CDKL5 Deficiency Disorder (CDD) using computational approaches to sift through thousands of drugs and select the most promising ones and to experimentally validate them. Cyclin-dependent kinase-like 5 disorder (CDD) represents a severe developmental encephalopathy caused by pathological mutations in the cyclin-dependent kinase-like 5 (CDKL5) transcript (OMIM 300203, 300672). No disease-modifying treatments have been identified, in part because of the incomplete knowledge of CDKL5 functio. The project consists of three Specific Aims: AIM 1 Identification of putative drugs based on the analysis of CDKL5 functional interactors. We will perform an in silico al study to establish CDKL5 functional interactors starting from publicly available databases of physical interactions to obtain a set of genes and pathways functionally related to CDKL5. The resulting set of genes, including CDKL5 functional interactors will be given in input to the Gene2Drug tool to generate a list of compounds able to transcriptionally modulate these genes, and thus potentially bypassing CDKL5 deficiency. AIM 2: Identification of putative compounds able to reverse the CDD gene signature. Two relevant human cell lines will be edited by deletion of CDKL5 and will be transcriptionally profiled to obtain a list of differentially expressed genes (DEGs) against wild-type controls. DEGs will be analysed to identify dysregulated pathways and then given as input to the MANTRA tool to search for FDA approved drugs and research compounds able to reverse the DEGs and thus making CDKL5 KO cells more transcriptionally similar to their WT counterparts, and thus potentially reversing or ameliorating the CDKL5 deficiency. AIM 3 Experimental Validation. The list of candidate drugs from AIM1 and AIM2 will be experimentally and functionally validated in cell lines and in ex vivo cortical neurons in mice.

APPROCCI INTEGRATI COMPUTAZIONALI E SPERIMENTALI PER Il RIPOSIZIONAMENTO DI FARMACI PER LE MALATTIE GENETICHE RARE

1. Napolitano, F., Sirci, F., Carrella, D. & Di Bernardo, D. Drug-set enrichment analysis: a novel tool to investigate drug mode of action. Bioinformatics 32, 235-241 (2015). 2. Napolitano, F. et al. Gene2drug: A computational tool for pathway-based rational drug repositioning. Bioinformatics 34, 1498-1505 (2018). 3. Iorio, F. et al. Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc. Natl. Acad. Sci. U. S. A. 107, 14621-14626 (2010). 4. Carrella, D. et al. Mantra 2.0: An online collaborative resource for drug mode of action and repurposing by network analysis. Bioinformatics 30, (2014). 5. Belcastro, V. et al. Reverse engineering and analysis of genome-wide gene regulatory networks from gene expression profiles using high-performance computing. IEEE/ACM Trans. Comput. Biol. Bioinforma. 9, 668-678 (2012).

CDKL5 Deficiency Disorder

Malattia da deficit di CDKL5