An antisense lncRNA mediated mechanism controls desmoplakin gene expression

Abstract Funding Acknowledgements Type of funding sources: Public Institution(s). Main funding source(s): Department of Innovation, Research and University of the Autonomous Province of Bolzano-South Tyrol (Italy). Background Desmosomal genes are established as definitive genes for Arrhythmogenic Cardiomyopathy (ACM). The desmoplakin encoding gene, DSP, is amongst the most frequently mutated genes in ACM patients. While rare genetic variants within desmosomal genes can cause ACM, common variants might also affect cardiac conduction traits in the general population. Purpose 1) To explore the association between common genetic variants in ACM desmosomal genes (DSC2, DSG2, PKP2, JUP, DSP) and cardiac conduction traits. 2) To investigate the effect of a lncRNA, identified from downstream analyses, on DSP gene expression. Methods P-wave, PR, QRS and QT intervals were measured using standard 12-lead electrocardiograms (ECG) in 4295 participants to the Cooperative Health Research in South Tyrol (CHRIS) study (data release 2). Samples were genotyped using the Illumina HumanOmniExpressExome array and imputed on the 1000 Genome Phase 1 panel. We conducted a genetic association study on 3458 variants within the linkage disequilibrium blocks that encompass desmosomal genes, assuming an additive genetic model, at 1.9x10-4 statistical significance. Mendelian Randomization (MR) analyses integrating ECG traits and Genotype-Tissue Expression (GTEx) database transcription levels were performed. A specific GapmeR was used to downregulate the antisense RP3-512B11.3 lncRNA expression in human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs). hiPSC-CMs lysates were analyzed by digital droplet PCR and Wes™ immunoassay system. Results The rs2744389 variant in DSP gene is associated with a shorter QRS interval (-1.10 ms per effect allele copy; p=3.5x10-6). In the GTEx database, rs2744389 is identified as an expression quantitative trait locus for the antisense lncRNA. MR results support a causal effect of the lncRNA on QRS. To assess the hypothesis that the lncRNA regulates DSP gene expression, we identified a Gapmer able to downregulate the lncRNA expression by approximately 60% in hiPSC-CMs. The lncRNA downregulation led to a significant increase of DSP expression, both at mRNA and protein level, compared to hiPSC-CMs treated with a negative control Gapmer (DSP/RPP30: 16.39±3.32 vs 11.84±1.79; p=0.0313), (Desmoplakin/total protein: 2.44±0.29 vs 1.66±0.11; p=0.0156). Conclusions Starting with the identification of an association between a common genetic variant in DSP gene and a significantly shorter QRS interval in a general population sample, we further unrevealed a new mechanism regulating DSP expression through an antisense lncRNA. While requiring further evidence, these findings might pave the way to a potentially novel therapeutic approach for DSP mutations carriers characterized by desmoplakin protein deficit, as for example patients affected by ACM, but also by dilated cardiomyopathy, cardiocutaneous diseases such as the Carvajal syndrome, and some cancer conditions.