Predictive literature analysis and in vitro evaluation of Adenine base editors targeting the LMNA-Q493X mutation in murine fibroblasts

Abstract

Cardiac laminopathies (LMNA-DCM) are an LMNA-associated subgroup of dilated cardiomyopathy (DCM), and one of the most common types of familial DCM. LMNA is a gene coding for A-type lamins, which are proteins integral to the structure known as the nuclear lamina. They contribute to nuclear integrity, as well as mechanotransduction and genetic regulation. Currently, there is no cure available for cardiac laminopathies. Gene editing to correct LMNA-DCM-causing mutations has provided an approach that could cure laminopathies. However, the heterogenous nature of LMNA mutations and limited data on the safety of targeting them still poses a challenge. We therefore performed an in-depth literature analysis, collecting potential base editors for the treatment of cardiac laminopathies. We then used available data to predict the compatibility, efficiency, and safety of these editors in targeting the patient-derived LMNA-Q493X mutation. After selecting the editors predicted to be the most safe and effective, we constructed them along with their sgRNAs, into lentiviral transfer vectors which we used to produce the lentiviral treatments. We subsequently treated primary murine liver fibroblasts from wildtype (LMNA WT/WT), heterozygous- (LMNA WT/Q493X) or homozygous mutant (LMNA Q493X/Q493X) mice and evaluated the rate of transduction. Following this treatment, levels of LMNA/C, LMNA and LMNC transcripts were quantified. We found that lentiviral particles transduced the cell cultures with varying success, showing lower efficiency of transduction in highly dense cultures. We additionally showed that SpRYCas9-ABE9 with sgRNA3, as predicted by the data analysis, was most consistent in restoring the evaluated transcript levels in vitro. Therefore, this study does not only contribute to the depth and quantity of available data on gene editing in cardiac laminopathies. It additionally sets a precedent for the use of predictive literature analyses in streamlining of the adaptation of gene therapy approaches. This facilitates the realization of gene therapy as a viable treatment option for all individuals suffering from cardiac laminopathies.