University of Cambridge
Spatially-resolved multiomic profiling of the human heart in adulthood and development
Abstract
dc:description.abstractThe human heart is composed of a multitude of cell types that must work in a coordinated fashion to achieve tissue and organ functions. Single-cell genomics is a powerful framework for characterising cell and tissue biology, including functional gene programmes, regulatory networks, and cell-cell interactions. This thesis contributes to our understanding of cardiac cellular diversity and function by generating two spatially-resolved cell atlases, encompassing the heart in adulthood and development. Chapter 1 summarises cardiac development, cardiac innervation, and the cardiac conduction system, before providing a brief review of the strengths and weaknesses of the technologies used. The combined experimental and computational methods used in both atlases are detailed in Chapter 2. This is followed by Chapter 3 which presents a spatio-temporally resolved cell atlas using 23 human hearts ranging from 4-20 post conception weeks. We integrate cell type annotations with spatial transcriptomic data to map cells in space and define multicellular niches, exploring the foetal sinoatrial node niche and its innervation. We leverage the temporal dimension of our dataset to characterise the maturing cardiomyocyte subsets and the gene regulatory networks that underlie these processes. We leveraged somatic mutations called in both RNA- and ATAC-seq reads and used mutational profiles to infer cell type lineage divergence. Finally, we generated similar data from hearts with Trisomy 21 and use a variety of approaches to draw comparisons with our euploid atlas, finding that formation of the compact myocardium is impaired in this condition. Chapters 4 and 5 present the findings of our study on the cellular niches of the adult heart, findings which have now been published. Chapter 4 describes the characterisation of the cell types of the cardiac conduction system (CCS). Although they represent a tiny fraction of the cardiac cellulome, we hypothesised that CCS cells could be enriched through careful dissection and would be transcriptionally distinguishable from working cardiomyocytes. We generated paired single-nucleus RNA- and ATAC-seq data from sinoatrial and atrioventricular node (SAN, AVN) samples from healthy hearts. Using the single-nucleus data we profiled the human CCS cell types for the first time, including the pacemaker cells of the SAN and AVN, as well as the specialist conduction cell types of the atrioventricular bundle and Purkinje cells. We defined their gene regulatory networks, ion channel profiles, and diverse repertoire of G-protein-coupled receptors. Inspired by this diversity, we developed a computational package, drug2cell, which uses the ChEMBL database of drug-target interactions to infer drug-impacted cell types in single-cell RNA-seq data. Chapter 5 is dedicated to the spatial analysis of the adult heart including the detection of multicellular niches. It describes the approach used to define these niches, which combined unbiased matrix factorisation with expert human structural annotation. In the nodal niches a novel population of nerve growth factor-expressing glial cells was detected, which co-localised with the pacemaker cells. The analysis showed that the histologically-defined SAN can be decomposed into transcriptionally distinct core and peripheral zones, each with differing cellular constituents. Finally, we also define a ventricular myocardial-stress niche enriched for activated fibroblasts and stressed cardiomyocytes, cell states which are expanded in cardiomyopathies. The thesis concludes with a discussion of its strengths and limitations, as well as a perspective on future research directions in Chapter 6.
Degree
thesis:*- Name dc:type.qualificationname
- Doctor of Philosophy (PhD)
- Level dc:type.qualificationlevel
- Doctoral
- Grantor dc:publisher.institution
- University of Cambridge
- Year dc:date.issued
- 2024
Author and committee
dc:creator, dc:contributor.*- Author dc:creator
-
- Cranley, John
- Advisor dc:contributor.advisor
-
- Teichmann, sarah
Subjects
dc:subject × 4Rights
dc:rightsIdentifiers
dc:identifier.*- DOI dc:identifier.doi
- https://doi.org/10.17863/CAM.116013
- OAI identifier oai:identifier
- oai:www.repository.cam.ac.uk:1810/380362