Deep profiling of natural killer cells in health and disease

Natural killer (NK) cells are innate immune cells with a crucial role in the early anti- viral and anti-cancer immune responses. In this thesis, I present two distinct projects in which the phenotype and function of NK cells are deeply profiled—the first in healthy individuals, and the second in individuals chronically infected with HIV-1. Understanding the intracellular signaling pathways that govern NK cell responses to target cells is crucial for designing optimal NK cell based therapeutics. NK cells are a highly diverse cell type, with many identified functional subsets. Studying this diversity requires the use of high-parameter, single cell approaches. Many previous studies of NK cell signaling with defined receptor stimulation rely on antibody crosslinking of the targeted receptors. This approach is limited in its ability to re-create the stimuli encountered by NK cells in vivo. The latent HIV-1 reservoir represents a major barrier to achieving a long-term antiretroviral therapy (ART)-free remission or cure for HIV-1. NK cells have been shown to be involved in preventing HIV-1 infection and, in those who are infected, delaying time to progression to AIDS. However, their role in limiting HIV-1 persistence on long term ART is still uncharacterized. In Chapter 1, I provide relevant background information and summarize relevant literature for these two projects. In Chapter 2, I provide a proof of concept and application of a system we developed to simultaneously profile the phenotype and signaling response of NK cells to defined target cells. I show that I can measure the breadth of the NK cell signaling response in bulk NK cells. I also identify a memory-like phenotype of NK cells that has lower signaling responses across the board. In Chapter 3, I present a study in which we deeply profiled the NK cell receptor and ligand repertoire in patients chronically infected with HIV-1. We found that the NK cell receptor and ligand repertoires did not change across three longitudinal samples over one year—a median of 25 weeks and 50 weeks after the initial sampling. To determine the features of the receptor-ligand repertoire that associate with markers of HIV-1 persistence, we performed a LASSO normalized regression. This analysis revealed that the NK cell ligands CD58, HLA-B, and CRACC, as well as the killer cell immunoglobulin-like receptors (KIRs) KIR2DL1, KIR2DL3, and KIR2DS4 were robustly predictive of markers of HIV-1 persistence, as measured by total HIV-1 cell-associated DNA, HIV-1 cell-associated RNA, and single copy HIV-RNA assays. To characterize the roles of cell populations defined by multiple markers, we augmented the LASSO analysis with FlowSOM clustering. This analysis found that an immature NK cell phenotype (CD16+CD56dimCD57-LILRB1-NKG2C-) was associated with lower HIV-1 cell associated DNA. Finally, we found that surface expression of HLA-Bw6 measured by CyTOF was associated with lower HIV-1 persistence. Genetic analysis revealed that this was driven by lower HIV-1 persistence in HLA-Bw4/6 heterozygotes. In Chapter 4, I discuss the impact of these studies on their respective fields, and how these results may most effectively be followed up in future studies. Deep profiling of NK cell biology has yielded unprecedented understanding of how NK cells are involved in maintaining health and responding to disease. In this thesis, I lay out two studies that demonstrate the value of this approach to understanding basic NK cell biology and to mapping out the relationship of NK cells to the persistence of HIV on therapy. These studies advance our understanding of the role NK cells play in responding to dangerous cells and putting a check on infectious disease

Advisor: Bendall Sean
Blish Catherine
Krams Sheri Michele 
Mallick Parag
Sunwoo John B.