Cellular individuality across the spectrum of heart diseases with implications for new therapeutic targets

Heart failure (HF) is a leading cause of death and disability globally. HF represents the common end- stage of most heart conditions, during which the heart is unable to generate sufficient output of blood for the metabolic demands of the body and intracardiac pressures increase. Different heart diseases display specific molecular pathophysiologies, but common pathways are also present that drive development and progression of HF. Specifically, the negative remodelling of the heart muscle that occurs gradually during prolonged load includes activation of a fetal gene expression program in heart muscle cells, immune cell activation, fibroblast activation, and increased fibrosis. However, both the molecular mechanisms of many underlying heart diseases and negative remodelling remain incompletely understood with limited therapeutic options beyond neurohormonal antagonists. The aims of this thesis were to (a) comprehensively investigate cell type-specific mechanisms involved in underlying heart diseases and negative remodeling in human hearts and (b) explore mechanisms linking the immunological mediator TSLP to HF mortality, as identified in a previous genetic study from the group.In Paper I, we sought to develop a protocol for single cell isolation from frozen human hearts. However, a range of protocols was unable to isolate intact cells. Instead, we developed a protocol for isolation of single nuclei and show that nuclear transcriptomes are highly representative of the overall cellular and cytoplasmic transcriptome in human heart cells. By application of this protocol to human hearts and single nuclei RNA sequencing (snRNAseq) we developed a transcriptional atlas of the cell types and molecular profiles of the human heart. In Paper II, we greatly expanded this atlas to >100 human hearts with specific heart diseases and hearts without evidence of heart disease (controls). Compared to control hearts, the largest number of transcriptional differences were observed in dil