Single nucleus RNA-sequencing reveals altered intercellular communication and dendritic cell activation in nonobstructive hypertrophic cardiomyopathy

Abstract

End stage, nonobstructive hypertrophic cardiomyopathy (HCM) is an intractable condition with no disease-specific therapies. To gain insights into the pathogenesis of nonobstructive HCM, we performed single nucleus RNA-sequencing (snRNA-seq) on human HCM hearts explanted at the time of cardiac transplantation and organ donor hearts serving as controls. Differential gene expression analysis revealed 64 differentially expressed genes linked to specific cell types and molecular functions. Analysis of ligand-receptor pair gene expression to delineate potential intercellular communication revealed significant reductions in expressed ligand-receptor pairs affecting the extracellular matrix, growth factor binding, peptidase regulator activity, platelet-derived growth factor binding and protease binding in the HCM tissue. Changes in Integrin-beta1 receptor expression were responsible for many changes related to extracellular matrix interactions, by increasing in dendritic, smooth muscle and pericyte cells while decreasing in endothelial and fibroblast cells, suggesting potential mechanisms for fibrosis and microvascular disease in HCM and a potential role for dendritic cells. In contrast, there was an increase in ligand-receptor pair expression associated with adenylate cyclase binding, calcium channel molecular functions, channel inhibitor activity, ion channel inhibitor activity, phosphatase activator activity, protein kinase activator activity and titin binding, suggesting important shifts in various signaling cascades in nonobstructive, end stage HCM.

Common and Distinctive Intercellular Communication Patterns in Human Obstructive and Nonobstructive Hypertrophic Cardiomyopathy

“…Of the 26 clusters, 14 were assigned as cardiomyocytes, 5 were assigned as fibroblasts, 2 were assigned as endotheliial cells with single clusters of neurons, smooth muscle cells, pericytes, dendritic cells and leukocytes, for a total of 8 unique cell types. Cardiomyocyte and fibroblast diversity in the human heart likely reflects cell subtypes in different physiological states and has been previously reported in multiple studies [10][11][12][13][14]. No clusters specific to a single condition were observed (Fig.…”

“…The 22 datasets for control (6), obstructive HCM (10) and nonobstructive HCM (6) samples have been previously described [12][13][14]. The datasets are available from the Gene Expression Omnibus (GEO) database under accession numbers GSE161921, GSE174691 and GSE181764.…”

“…The final dataset thus consisted of 26 clusters. Cell type assignment for each cluster was performed as described previously [12][13][14]. Briefly, clusters were assessed for expression of cell type-specific gene markers, differentially expressed genes queried against panglaoDB [16], gene ontology (GO) using GOStats [17] and Ingenuity Pathway Analysis [18].…”

“…To determine the relationships between cell types represented by nuclei in different clusters and between cells represented by nuclei within a cluster, we performed trajectory analysis using Monocle3 [19]. Previous analysis of relationships between cellular subtypes in obstructive HCM normal tissue and between cellular subtypes in nonobstructive HCM and normal tissue by trajectory analysis did not reveal any significant differences between each type of HCM and normal tissue trajectories, although many genes were differentially expressed between conditions along the trajectories [13,14]. Similarly, in this work no differences were seen in trajectories between obstructive and nonobstructive HCM (data not shown), although differences were seen in gene expression along the trajectory paths.…”

“…We have previously defined the cellular diversity of the human heart IVS [12] and have delineated important changes in communication between the cells of the IVS in obstructive HCM, through mechanisms involving integrin-1 (ITGB1) and the extracellular matrix (ECM) [13]. We have also performed a separate study comparing the snRNA-seq profiles of nonobstructive HCM IVS tissue with normal IVS tissue and have found an increase in dendritic cell communication [14]. To date, no direct comparisons of single cell gene expression patterns in obstructive and nonobstructive HCM exist.…”