Transcriptional regulation profiling reveals disrupted lipid metabolism in failing hearts with a pathogenic phospholamban mutation

Abstract

Background: The R14del mutation in the phospholamban (PLN) gene is associated with various types of cardiomyopathies and increases the risk of developing life-threatening ventricular arrhythmias. In this study, we focused on a homogeneous Dutch founder cohort of genetic cardiomyopathy due to PLN R14del mutation and aimed to study the influence of epigenetic changes from a multi-dimensional perspective. Results: Using cardiac tissue of PLN R14del patients and donors, we identified differentially acetylated promoters and enhancers (H3K27ac ChIPseq), annotated enriched transcription factor (TF) binding motifs located in those regions, and identified differentially expressed genes (RNA-seq). In line with the fibrofatty replacement in PLN R14del hearts at the histological level, our integrative analysis detected the downregulation of key TF regulators in fatty acid oxidation (FAO) metabolisms and their downstream target in PLN R14del hearts as compared to controls. We further examined heart tissue using immunofluorescence staining (IF) and to confirm the mitochondrial lipid abnormalities in the PLN R14del hearts. Furthermore, we observed the accumulation and deformation of lipid droplets and a disrupted morphology of mitochondria, the key organelle where FAO takes place, in PLN R14del heart using transmission electron microscopy (TEM). Conclusion: Using multi-omics approaches, we successfully obtained a unique list of chromatin regions and genes, including TF-coding genes, which played important roles in the metabolism-related signalling in PLN R14del hearts.

Targeting lipid metabolism as a new therapeutic strategy for inherited cardiomyopathies

“…Disease-specific gene sets, some of which are involved in lipid metabolism, were found to be differentially changed between DCM and HCM, such as the up-regulated APOE and the down-regulated GPT in DCM, as well as the up-regulated APOLD1 and the down-regulated STARD13 and PON3 in HCM. In line with these findings, we also demonstrated that KLF15, an important transcription factor regulating lipid metabolism (68), was significantly up-regulated in HCM hearts carrying mutated MYBPC3 and down-regulated in DCM hearts carrying mutated PLN when compared to non-failing donor hearts (16,38). Besides the transcriptional level, proteins involved in metabolic pathways, including lipid transfer and fatty acid biosynthetic process, also showed DCM-and HCM-specific changes (69).…”

“…PPARA is a key regulator in modulating fatty acid uptake and FAO; PPARD enhances the utilization of lipids and glucose; and PPARY increases fatty acid uptake, triglyceride formation, and lipid storage (80). Notably, multiple studies from us and others have shown suppressed PPARA expressions in DCM and HCM hearts carrying different genetic variants (16,81,82). Additionally, the interaction between PPARA and KLF15 showed a significant impact on cardiac lipid metabolism (83).…”

“…This suggests a tight relationship between TTN variants and metabolic alterations. In addition, murine and human DCM hearts carrying a PLN variant showed suppressed mitochondrial fatty acid metabolism at mRNA and protein levels ( 16 , 17 ). Suppressed metabolic genes and mitochondrial enzyme activities were also observed in 2D and 3D human induced pluripotent stem cell-derived cardiomyocytes harboring a mutated PLN gene ( 18 ).…”

Phospholamban R14del disease: The past, the present and the future

“…In addition, mitochondrial dysfunction could also, at least in part, be related to Ca 2+ dysregulation, most likely through impaired ER/ mitochondrial compartment contacts (67). Consequent defects in mitochondrial function including metabolic dysfunction, oxidative stress and lipid accumulation can also contribute to PLN-R14del disease (46,52,53,67). Since the majority of these changes are closely interconnected, it is still unclear as to which one represents the initial trigger causing the disease.…”

“…Concomitantly, a prospective randomized controlled clinical trial (PHOspholamban RElated CArdiomyopathy intervention Study, iPHORECAST) is currently evaluating the efficacy of the antifibrotic agent eplerenone in the prevention or delay in progression of disease ( www.clinicaltrials.gov , register number NCT01857856) ( 45 ). Accumulation of lipid droplets, impaired fatty acid oxidation and mitochondrial integrity disruption have also been observed in PLN-R14del patient hearts ( 46 ). Another characteristic of PLN-R14del disease is the presence of aggregates that are mainly observed in the perinuclear region ( 47 , 48 ).…”