Single cell analysis and methods to characterize peripheral blood immune cell types in disease and aging

In the past decade, RNA-sequencing (RNA-seq)-based genome-wide expression studies have contributed to major advances in understanding human biology and disease. However, for heterogeneous tissues such as peripheral blood, RNA-sequencing masks the expression of different populations of cells that may be important in understanding different conditions and disease progression. With the advent of single cell RNA-sequencing (scRNA-seq), it has become possible to study the gene expression of each single cell and to explore cellular heterogeneity in the context of disease and under the influence of medications or other substances. In this dissertation, I will present three projects that demonstrate how single cell sequencing methods can be used to characterize novel changes in the peripheral immune system in human disease and aging. I will also describe novel methodological approaches I created to analyze cell type composition and gene expression level changes. First, I investigated the cell type specific changes due to opioid use in human peripheral blood. Utilizing single cell transcriptomic methods, I identified a genome-wide suppression of antiviral gene expression across immune cell types of chronic opioid users, and similarly under acute exposure to morphine. Second, I investigated the immune cell type specific changes of gene expression and composition in the context of human aging and longevity. I developed novel approaches to measure and compare overall cell type composition between samples, and identified significant overall differences in immune cell type composition, including pro-inflammatory cell populations, between extreme longevity and younger ages. In addition, I generated cell type-specific signatures associated with longevity after accounting for age-related changes that demonstrate an upregulation in immune response and metabolic processes important in the activation of immune cells in extreme long lived individuals compared to normally aging individuals. Finally, I investigated whether aging of the immune system is accelerated in opioid-dependent individuals. I utilized the unique aging signatures generated in the aging project and discovered higher expression of aging signatures in specific cell types of opioid-dependent individuals, suggesting chronic opioid use causes premature aging of the immune system that may contribute to the increased susceptibility to infections in these individuals.2023-02-18T00:00:00