Abstract Body (Do not enter title and authors here): Background: The LMNA gene codes for lamin A/C, a nuclear structural protein with wide expression. Pathogenic Variants (PVs) in LMNA lead to a variety of clinical presentations called laminopathies, though the phenotype, severity, and rate of progression varies with the specific variant.
Research Question: Do cardiomyocytes with the highly penetrant and severely pathogenic LMNA^R541C display unique gene and pathway dysregulation compared to other LMNA PVs.
Approach: Induced pluripotent stem cells (IPSCs) derived from a patient with LMNA^R541C were compared to the same cell line that was CRISPR-corrected to wild-type LMNA. A paraellel experiment compared a standard control iPSC line (PGP1) with and without CRISPR-knock-in of heterozygous LMNA^R541C. IPSCs were differentiated to ventricular cardiomyocytes (iCMs) and matured for at least 30 days. Total RNA was isolated for RNAseq. Differential expression analysis was performed with DESeq2, and pathway analysis was performed with GSVA. Pathway significance was assessed with limma. Ingenuity Pathway Analysis (IPA) was also used to identify enriched pathways and gene networks.
Results: Differential expression analysis identified 3699 and 330 significant genes after multiple testing correction in the CRISPR-corrected and knock-in experiments, respectively. A subset of 123 genes were consistently dysregulated in the same manner compared to controls across experiments.
Pathway analysis using the MSIG Hallmark database identified consistent dysregulation of the G2M checkpoint and oxidative phosphorylation pathways, as well as 8 other pathways. Additionally, N=673 enriched pathways were detected using the GO Biological Process (BP) database. Comparing these results to 3 previously published LMNA mouse model experiments identified N=2 conserved pathways in the Hallmark database (oxidative phosphorylation and G2M checkpoint), and 12 pathways in the BP database.
Conclusion: Previous analysis of cardiomyocytes with LMNA^R541C identified physiological changes in LMNA production, sarcomere formation, and electrophysiology. The current experiments identify a subset of 123 genes as potential drug targets to counteract LMNA^R541C mutations. The identified dysregulated pathways may also provide treatment options beyond genes identified as differentially expressed, as a subset were also identified as differentially expressed in previous mouse LMNA experiments.