Bioinformatics design of MiniPromoters for targeted delivery of expression
Year: 2018
Type: other
Abstract: Gene therapy has re-emerged as a viable treatment for rare genetic disorders. Key to recent progress in the field is non-insertional gene delivery using adeno-associated virus (AAV) vectors. Limited by the restricted payload capacity of AAV vectors, most AAV-based gene therapies use small, ubiquitous promoters. As a result, off-target expression of the therapeutic gene can occur, which may in turn have undesired side effects. In this context, designing selective promoters that restrict the expression of the therapeutic genes to the clinically relevant cells is an important research goal. In the past, we have shown the capacity to design compact, selective promoter sequences ( i.e. MiniPromoters) for targeting specific cells within the brain and eye. The design of a MiniPromoter was a manual process involving three steps: 1) literature search for a gene with restricted expression patterns in the target cells; 2) identification of the cis -regulatory regions (CRRs) of that gene ( i.e. promoter and enhancers); and 3) assembly of a subset of the gene’s CRRs into a MiniPromoter sequence. We are developing the OnTarget software to automate the design of MiniPromoters. It has three main components: 1) a Data Repository linking thousands of public processed experiments (CAGE, GRO-seq, ATAC-seq, DNase-seq, ChIP-seq, Hi-C, etc.) from multiple human primary cells, tissues and cell lines with in-house data collections (JASPAR, MANTA, allele-specific binding events, etc.); 2) a Selection Module for identifying and selecting CRRs of human genes in cell/tissue-specific contexts; and 3) a Design Module for fine-tuning the identified CRRs and modifying transcription factor binding sites within these CRRs in order to modulate the amount of delivered expression. We have applied the OnTarget software to design different MiniPromoters driving cell type-specific expression patterns, including ganglion cells (based on CRRs of the NEFL and NEFM genes), bipolar cells (based on PCP2 ), or neurons from the locus coeruleus (based on DBH ). We anticipate that OnTarget will simplify and improve the design of promoters for targeted delivery of gene therapies while limiting off-target side effects for patients.
Institution: University of British Columbia
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W4416514399