Year: 2023
Type: dissertation
Abstract: This dissertation presents three manuscripts that originated from my work on the ageing liver. The first two manuscripts concentrate on integrative multi-omics ap-proaches, such as scATAC-seq and scRNA-seq, spatial transcriptomics, CUT&RUN sequencing and lipidomics. They reveal distinct ageing signatures within the murine liver, mainly in hepatocytes. The third manuscript introduces a new methodology for the analysis of spatial sequencing data, which was developed with the ageing liver as an intended application. \n \nThe first manuscript, "Single-cell resolution unravels spatial alterations in metabo-lism, transcriptome, and epigenome of ageing liver", establishes how spatial loca-tion and microenvironmental changes impact the ageing trajectories of hepatocytes within liver tissue. Through the integration of spatial transcriptomics, single-cell ATAC- and RNA-seq, lipidomics, and functional assays, the study elucidates zonation-specific and age-related changes in the epigenome, transcriptome, and metabolic states. We identified a zonation-dependent shift in the epigenome and show that changing microenvironments within a tissue exert strong influences on their resident cells that can shape epigenetic, metabolic and phenotypic outputs. From a functional perspective, periportal hepatocytes exhibited diminished mitochondrial fitness, whereas pericentral hepatocytes demonstrated an increased accumulation of large lipid droplets. \n \nThe second manuscript, "Ageing is associated with increased chromatin accessibil-ity and reduced polymerase pausing in liver", examines the chromatin landscape of the ageing liver by using CUT&RUN for RNA polymerase mapping, integrated with ATAC-seq, RNA-seq, and NET-seq. The study reveals an increase in chromatin accessi-bility at promoter regions as a characteristic of ageing, which is not accompanied by a corresponding increase in transcriptional output. Ageing is also found to be associated with a decrease in promoter-proximal pausing of RNA Polymerase II. Our observations suggest that alterations in transcriptional regulation associated with ageing may be due to decreased stability of the pausing complex. \n \nThe third manuscript, "Dimension reduction by spatial components analysis im-proves pattern detection in multivariate spatial data", introduces SPACO, a new statistical approach designed to enhance pattern recognition in multivariate spatial sequencing data. SPACO stands out by focusing on gene co-regulation and maximising local covariance. It provides a more sensitive and accurate test for the identification of genes with a spatial expression pattern. Moreover, the use of spatial components for gene denoising by SPACO boosts the effective linkage of histological observations with gene expression patterns, even in high-noise conditions.
Author: Kleinenkuhnen, Niklas Peter
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7002373747