Single Nuclei Sequencing Reveals Novel Insights Into the Regulation of Cellular Signatures in Children With Dilated Cardiomyopathy

Abstract

Background: Dilated cardiomyopathy (DCM) is a leading cause of death in children with heart failure. The outcome of pediatric heart failure treatment is inconsistent and large cohort studies are lacking. Progress may be achieved through personalized therapy that takes age- and disease-related pathophysiology, pathology and molecular fingerprints into account. We present snRNA-seq from pediatric DCM patients as the next step in identifying cellular signatures. Methods: We performed single nuclei RNA sequencing with heart tissues from six children with DCM with an age of 0.5, 0.75, 5, 6, 12 and 13 years. Unsupervised clustering of 18,211 nuclei led to the identification of 14 distinct clusters with 6 major cell types. Results: The number of nuclei in fibroblast clusters increased with age in DCM patients, a finding that was confirmed by histological analysis and was consistent with an age-related increase in cardiac fibrosis quantified by cardiac magnetic resonance imaging. Fibroblasts of DCM patients over 6 years of age showed a profoundly altered gene expression pattern with enrichment of genes encoding fibrillary collagens, modulation of proteoglycans, switch in thrombospondin isoforms and signatures of fibroblast activation. Additionally, a population of cardiomyocytes with a high pro-regenerative profile was identified in infant DCM patients, but was absent in > 6-year-old children. This cluster showed high expression of cell cycle activators such as cyclin D family members, increased glycolytic metabolism and antioxidative genes and alterations in ß-adrenergic signaling genes. Conclusions: Novel insights into the cellular transcriptomes of hearts from pediatric DCM patients provide remarkable age-dependent changes in the expression patterns of fibroblast and cardiomyocyte genes with less fibrotic but enriched pro-regenerative signatures in infants.

Single Cell Transcriptomics Reveals Cell Type Specific Diversification in Human Heart Failure

“…Interesting, ANKRD1 expression was recently found to be enriched in cardiomyocytes from patients with adolescent versus pediatric DCM. 20 Pseudotime trajectory analysis identified three highly differentiated cardiomyocyte states (MYL7, ACTA1, NPPA/NPPB) in donor hearts. Surprisingly, we observed a two highly differentiated cardiomyocyte state in DCM marked by ADGRL3 and NPPA/NPPB expression.…”

“…6,7 While considerable interest exists, only limited data is available to decipher how the cellular and transcriptional landscape of the heart is impacted by disease. 20,21…”

“…Current scRNAseq datasets exploring human heart failure are small and lack the sample size necessary to elucidate the impact of disease on common and rare cardiac cell types. 20,21 scRNAseq data provided greater depth at the expense of biased cell recovery. For example, within myeloid cells, scRNAseq data was biased towards monocytes and intermediate macrophage populations with fewer resident macrophages recovered.…”

ExpressHeart: Web Portal to Visualize Transcriptome Profiles of Non-Cardiomyocyte Cells

“…Compared to traditional bulk RNA sequencing technologies, scRNA-seq identifies and characterizes sub-cell types/intermediate cellular states, even for rare cell types/cellular states with a limited number of cells. In recent years, increasingly, more studies have employed scRNA-seq or single-nucleus RNA-seq (snRNA-seq) to investigate the transcriptional features of the nonCM populations, broadening our knowledge on the molecular functions of the nonCM cells [8][9][10][11][12][13][14][15][16][17][18][19][20]. For example, Skelly et al employing scRNA-seq, comprehensively characterized gene expression profiles of nonCMs in mouse hearts at a single-cell level, which provides a comprehensive view of the diversity and specific molecular features, as well as intercellular communication, for different nonCM cell types [9].…”

A word on netting of angiotensin-converting enzyme inhibitor therapy in hypoplastic left heart syndrome following stage-I

“…The next step for a structured approach is the subsequent translation of the accumulated knowledge into an improved prescription of cardiovascular drugs. Novel diagnostic tools as receptor genotyping 29,30 or based on single cell analysis 31,32 will play a key role in the management of accurate and tailored pharmacological therapy in paediatric cardiovascular diseases.…”