Biology Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/2749
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Item SYSTEMS IMMUNOLOGY OF IMMUNE IMPRINTS INDUCED BY ACUTE VIRAL INFECTIONS(2023) Liu, Can; Johnson, Philip L.F.; Tsang, John S.; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Upon encountering perturbations such as viral infections, the immune system initiates a cascade of molecular and cellular responses. These alterations may persist even after recovery, resulting in enhanced or diminished response to subsequent stimuli compared to the naïve state. Such persistent changes, referred to as immune imprints or long-term non-specific memory, indicate an incomplete resolution from immunological perturbations. The primary focus of this dissertation is to systemically investigate the immune imprints resulting from acute infections and how they shape the baseline immune status to future heterologous challenges.First, we employed cutting-edge single-cell multi-omics and computational approaches to assess the immune response during the COVID-19 disease course and severity correlates at an unprecedented resolution. We identified gene expression profiles – apoptosis in plasmacytoid dendritic cells and IL-15-linked increase of fatty acid (FA) metabolism in CD56dimCD16hi NK cells – as primary correlates of disease severity. This increase of FA signature with disease severity was also concomitant with an attenuated inflammation, indicating a dysfunctional or exhaustion-like state of these NK cells. While the depressed inflammation signature in severe patients was also found in different cell types near hospitalization, it increased temporally at later time points, indicating a critical late-stage juncture in the disease course. Next, we took the opportunity of the period following the first wave of COVID-19 pandemic to study immune imprints in human cohorts who had recovered from COVID-19 before widespread vaccination and reinfection occurred. We demonstrated that individuals who recovered from mild COVID-19, exhibit distinct immune signatures through single-cell transcriptomic profiling. Male recoverees also showed heightened responses to the seasonal influenza vaccine compared to healthy individuals without a history of COVID-19 and female recoverees. These sex dimorphic imprints highlight the interplay between intrinsic factors like sex and non-intrinsic factors such as prior SARS-CoV-2 infection, in shaping an individual's immune system over time. Lastly, we also investigated the immune imprints after acute viral infection using a controlled experimental mouse model of influenza infection. After examining cellular and gene expression profiles in various organs after the infection, we found persistent changes in both adaptive and innate immune components across multiple organs. Moreover, these changes affected subsequent local IL-17 inflammatory response and secondary heterologous vaccinations in anatomically distinct organs. Together, both human and mouse studies here are important pieces toward an improved understanding of long-term immune imprints after perturbations, which can be leveraged to develop more effective and personalized vaccines and disease treatments.Item Systems Approaches to Immunology in Acute COVID19, Monogenic Immune Disorders, and Childhood Development(2022) Rachmaninoff, Nicholas; Johnson, Philip F; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In recent years advances in immune profiling technologies have allowed us to generate data at anunprecedented scale, and interrogate human immune systems in ways that were not previously possible. In this dissertation, I use these approaches in three different contexts. First, I explore how the cells of the immune system respond to acute COVID-19 infection and how this depends on the severity of the disease. Using CITEseq, simultaneous profiling of surface markers and RNA in peripheral blood mononuclear cells, I identify differentially expressed gene expression programs associated with COVID-19 infection and gene expression programs associated with disease severity. In addition, I explore how phenotypes of memory Tcells including the clonal nature and exhaustion signatures are associated with severity of COVID-19 infection. Second, I address what it means to be immunologically healthy through a multi-omics study of a cohort of patients at the NIH clinical center with various monogenic Immune disorders. I identify supervised and unsupervised axes of immune health that can separate disease from healthy controls, and additionally track changes to the immune system as people age, showing the parallels between disease associated inflammation and aging associated inflammation. I verify the utility of these metrics in several contexts outside of the original cohort and show that the signatures reflect broad changes to various cells of the immune system. Last, I explore the development of the immune system in childhood and the maintenance of temporally stable gene expression patterns. In a cohort of children that was tracked longitudinally over six years in Nicaragua, I utilize whole blood transcriptomics to explore both how the immune system changes as children grow older and which aspects of the immune system show large amounts of individuality or persistent inter-subject variation in their levels. I show that persistent inter-subject variation in gene expression and cellular frequencies is quite pronounced throughout childhood and attempt to identify when certain aspects of the immune system begin to stabilize in terms of their levels for an individual.Item ROLES OF PLASMA MEMBRANE WOUNDING AND REPAIR IN B CELL ANTIGEN CAPTURE AND PRESENTATION(2022) van Haaren, Jurriaan Jan Hein; Song, Wenxia W; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The B cell-mediated humoral immune responses play a crucial role in neutralizing pathogens and unwanted foreign substances. B cells become activated upon antigen binding of their B cell receptor (BCR), and then internalize and process antigen for presentation on their MHCII for T cell recognition. acquiring T cell signaling through antigen presentation is essential for B cell differentiation into high-affinity antibody-producing cells and memory B cells. In vivo, Antigen encountered by B cells is often tightly associated with the surface of pathogens and/or antigen-presenting cells. When B cells engage surface-associated antigen, BCR signaling induces reorganization of the cytoskeleton, causing spreading and contraction of the B cell on the antigen-presenting surface. This allows the B cell to engage more antigen and gather the antigen into a central cluster for internalization. Internalization of surface-associated antigen has been shown to require myosin-generated forces and the exocytosis of lysosomal enzymes. However, the mechanism that initiates lysosomal exocytosis remains unknown.This research explored a possible mechanism for the triggering of lysosomal exocytosis of B cells during interaction with surface-associated antigen. We showed that BCR interaction with antigen tethered to beads, to planar lipid-bilayers (PLBs) or expressed on the surface of live cells causes permeabilization of the B cell plasma membrane (PM), an event that required strong BCR-antigen affinity, BCR signaling, and activation of non-muscle myosin IIA (NMIIA). Moreover, we showed that B cell PM permeabilization triggers a repair response that includes the exocytosis of lysosomes at the site of antigen interaction. Importantly, we showed that B cells undergoing PM permeabilization and subsequent repair internalize more antigen; and better activate T cells compared to unpermeabilized B cells. Thus, our research reveals a novel mechanism for B cells to capture surface-associated antigen: antigen affinity-dependent binding of the BCR indices localized B cell PM permeabilization and lysosome exocytosis as a repair response, which facilitates antigen internalization and presentation through the extracellular release of lysosomal hydrolases. In addition, we explored the molecular mechanism required for B cell PM permeabilization in response to surface-associated antigen. We showed that B cells that undergo PM permeabilization in response to PLB-associated antigen spread over the PLB at a faster rate and to a larger area in comparison to cells that remain intact. Furthermore, we showed that B cells that undergo PM permeabilization recruit more NMIIA at a faster rate, and display a higher level of NMIIA organization at the immune synapse. We additionally discovered a 2o B cell spreading and NMIIA recruitment event, approximately 25-30 minutes after antigen engagement, that facilitates B cell PM permeabilization. Thus, B cell PM permeabilization requires the engagement of a large amount of antigen through B cell spreading on the presenting surface, as well as strong NMIIA recruitment and organization at the immune synapse. This research suggests that B cell PM permeabilization in response to surface-associated antigen plays an important role in distinguishing B cells with various levels of BCR activation, providing novel insights into the mechanisms responsible for affinity differentiation during B cell activation.Item SEX-SPECIFIC EFFECTS OF PATERNAL DEPRIVATION ON HYPOTHALAMIC NEUROIMMUNE RESPONSE AND GENERAL ANXIETY-LIKE BEHAVIOR IN PEROMYSCUS CALIFORNICUS (CALIFORNIA MICE)(2021) Walker, Shakeera; Glasper, Erica R; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Early-life stress (ELS) can induce anxiety-like behaviors and social deficits in male and female rodent models via neuroinflammation. The California mouse (Peromyscus californicus) is a rodent model for paternal deprivation (PD), a form of ELS. The paternal California mouse is essential in offspring development; his absence impairs emotional regulation and induces sex-specific deficits in social behaviors and neuroplasticity. We determined to what extent PD induced sex-specific social and anxiety-like behaviors in adult California mice during the three-chamber social interaction test and the novelty-suppressed feeding test. We also assessed the neuroinflammatory response to PD in the same mice after an acute physical stressor. We demonstrated that female California mice displayed social avoidance, while PD males exhibited stress-induced eating in novel anxiogenic environments. PD also increased hypothalamic interleukin-1β, but only in adult males. Taken together, PD resulted in sex-dependent stress-coping behaviors, which may underlie sex differences in neuroinflammatory responses in adulthood.Item Structural Basis for Clonal Diversity of the Public T Cell Response to Dominant Epitopes from Cytomegalovirus and Influenza(2016) Yang, Xinbo; Mariuzza, Roy A; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)A diverse T cell receptor (TCR) repertoire is a prerequisite for effective viral clearance. However, knowledge of human TCR repertoire to defined viral antigens is limited. Recent advances in high-throughput sequencing (HTS) and single-cell sorting have revolutionized the study of human TCR repertoires to different types of viruses. In collaboration with the laboratory of Dr. Nan-ping Weng (National Institute on Aging, NIH), we applied unique molecular identifier (UMI)-labelled HTS, single-cell paired TCR analysis, surface plasmon resonance, and X-ray crystallography to exhaustively interrogate CD8+ TCR repertoires specific for cytomegalovirus (CMV) and influenza A (Flu) in HLA-A2+ humans. Our two CMV-specific TCR-pMHC structures and two Flu-specific TCR-pMHC structures provide a plausible explanation for the much higher diversity of CMV-specific than Flu-specific TCR repertoires in humans. Our comprehensive biochemical and structural portrait of two different anti-viral T cell responses may contribute to the future development of predictors of immunity or disease at the individual level.