While we have learned a tremendous amount about human immune responses in recent years, many studies of human immunology examine the system in a static state of health or disease. However, to truly define how a complex system works, dissect the components that interact with each other under dynamic conditions, and gain actionable knowledge of how the system effectively resets (or not) during and after disease, the system must be perturbed. Thus, the central theme of this Program is that by capturing perturbations of the human immune system and performing high resolution studies of key immune cell types and immune reactions in flux we will gain new mechanistic insights into the functional connections driving productive or pathological immune responses in humans. To address this central theme, we propose 3 Projects to: 1) test the hypothesis that post acute sequelae of COVID-19 (PASC) is associated with incomplete clearance of SARS- CoV-2 and/or reactivation of latent viruses, resulting in chronic inflammation and durable immune dysregulation; 2) utilize chronic and cured HCV infection as a human model system for defining the impact of both natural and precision immune perturbation on overall host fitness and health; and 3) define mechanisms of human vaccine- induced immune memory using precision immune perturbation through PD-1 pathway blockade. Each Project captures a key immune perturbation with a major common feature of known timing and nature of the perturbation including viral infection leading to PASC (Project 1), viral cure in a long-standing chronic infection (Project 2), and vaccination in the context of precision disruption of a single immune pathway, PD-1 (Project 3). As a result, we “capture the human experiment” through focused profiling of the human immune system around these key perturbations. These Projects are supported by an administrative Core and two scientific Cores that enable robust human cohort development, management and sample collection (Core B) and high dimensional, highly standardized, large scale and integrated immune landscape profiling for all patients and subjects studied (Core C). This latter effort will allow common themes, immunotypes and cross-disease immune mechanisms to be identified and leverages the interactions across our interconnected Projects. Thus, this highly interactive IPSG CCHI U19 Program will allow us to make major mechanistic advances in our understanding of human antiviral immunity.
The inability to perturb, and then study the effects of specific immune pathways in humans has been a major limitation to alleviating the morbidity and mortality associated with infectious disease. In this Cooperative Center for Human Immunology, we “capture the human experiment” through focused profiling of the human immune system following key immune perturbations where the timing and nature of the perturbation can be carefully controlled or documented. Specifically, we will investigate persistent immune defects following acute viral infection with SARS-CoV-2 that contribute to Post-Acute Sequelae of COVID-19, long lasting defects developed during chronic HCV infection that persist even beyond cure, and alterations in vaccine responses in the context of precision PD-1-targeted immunotherapy.
Our Center consists of three Cores and three Projects
CORE A: ADMINISTRATIVE CORE
CHUNG, RAYMOND T, Core Lead
The purpose of Core A is to provide administrative support to the Program Leaders, to the Principal Investigators of the Projects and Cores, and to the scientific personnel of the Projects and Cores of the Immune Perturbation Study Group (IPSG). Core A will be located in Dr. Chung’s laboratory/office complex at the Liver Center and Gastrointestinal Division of Massachusetts General Hospital. The main goals of Core A are to manage and oversee the scientific efforts of the Projects and to coordinate scientific and administrative interactions. Thus, the specific tasks of Core A will be: (a) to facilitate interactions between Program Investigators, Scientific Advisors and administrative personnel, (b) to plan and coordinate the External Scientific Advisory Group (ESAG) meeting as well as meetings between Program scientists, (c) to organize and coordinate travel for scientific advisors, visiting scientists and Program Investigators, (d) to assist in the organization of the annual External Scientific Advisory Group Meeting and Scientific Symposium, (e) to facilitate resource sharing including assisting in the speedy execution of material transfer agreements (MTA) and (f) to assist the Program Directors and Principal Investigators in preparation of progress reports, financial reports and manuscripts for publication. Core A will also be responsible for the resolution of any potential conflicts.
CORE B: CLINICAL CORE
KIM, ARTHUR Y, Core Lead
Translational research is critically dependent on availability of adequate specimens from well-defined clinical cohorts of patients. This Clinical Core builds and maintains such cohorts and facilitates a broad array of studies in human immunology. During the past three cycles of our consortium, we successfully recruited and enrolled over two thousand subjects, leveraging two paradigm-shifting therapeutic advances of this century: effective direct-acting antivirals (DAAs) against hepatitis C virus (HCV) and immune checkpoint inhibitors (ICIs), particularly targeting the PD-1 axis, for cancer. These developments allowed unique opportunities to study the scars left by human chronic viral infection and to explore the reversal of T-cell exhaustion and resetting of immunity. We can further capitalize on “the human experiment” by dissecting immune mechanisms in humans where a single immune pathway involved in the germinal center response can be interrogated by capturing standard of care vaccination in patients receiving αPD-1. Finally, during the last cycle a global immunological challenge in the COVID-19 pandemic spurred a third major advance of this century: the introduction of SARS- CoV-2 mRNA vaccines. While their biology and clinical courses differ, SARS-CoV-2 and HCV are each RNA viruses where immune responses and outcomes can be compared. Moreover, we can dissect differences between immune responses to vaccination for Flu and SARS-CoV-2. Samples collected by the Clinical Core will allow examination of three areas of immunobiology: 1) investigation of persisting virus and immune dysfunction in post-acute sequelae of PASC; 2) interrogation of immune scarring after cure of a persisting infection, and 3) dissection of an immunoregulatory pathway associated with persisting infections for its role in vaccine-induced adaptive immune memory. Integration of findings across these areas is a distinct advantage of this Immune Perturbation Study Group (IPSG), empowered by this Clinical Core and its relevant cohorts and large numbers of well-annotated samples. By supporting the studies described in the Projects and the Immune Health Core, this Core will facilitate a novel and integrated examination of human immune responses to viral pathogens and to their vaccines in the context of three key perturbations: PASC, HCV infection and specific immune manipulation via αPD-1.
CORE C: IMMUNE MONITORING CORE
GREENPLATE, ALLISON RAE, Core Lead
This CCHI U19 Program aims to determine how perturbations of the human immune system leads to do durable changes that impact future immune responses. Core C of this Immune Perturbation Study Group Program application will be central to the scientific efforts of this consortium. A unique and comprehensive pipeline has been created alongside an expansive repository of existing samples and background data to measure and analyze high dimensional immune landscapes using quantification of all circulating immune cell types with activation status, serology and systemic inflammation over the course of different perturbations outlined in the Projects. This pipeline will be maintained and expanded to include additional longitudinal samples from subjects with post-acute sequalae of COVID-19 (Project 1), subjects cured of HCV (Project 2), and subjects receiving vaccines during anti-PD-1 therapy (Project 3). This concerted effort will maintain high throughput of immune phenotyping to catalyze scientific efforts across the consortium, including analyzing samples accrued by Core B. Thus, Core C provides a central and integrative service that will allow studies in the different Projects to inter- relate around immune landscapes during immune perturbation.
PROJECT 1: DURABLE IMPACT of COVID on INNATE and ADAPTIVE IMMUNITY
LOCCI, MICHELA, Project Lead
At least 7 million people have died from COVID-19 with > half the world likely infected and a staggering burden of Post-Acute Sequelae of COVID-19 (PASC) affecting ~20M Americans with long-term, often crippling, symptoms including neurological symptoms (“brain fog”, memory and/or concentration disruptions), autonomic dysfunction, fatigue, flu-like symptoms, post-exertional malaise, and cardiovascular issues. PASC may develop in 50-70% of hospitalized and ~10-12% of non-hospitalized COVID-19 patients, with considerable personal, medical and economic burden. Although PASC is now well-described clinically, the immune mechanisms are poorly-understood and treatments are limited. One hypothesis is that persisting SARS-CoV-2 virus and/or antigen is involved. Alternative hypotheses that are not mutually exclusive include: (i) autoreactivity; (ii) persisting immune dysregulation; (iii) reactivation of latent viruses including EBV. Indeed, viral RNA/antigen is more likely to be found in PASC than healthy recovered individuals. Some groups have also reported EBV reactivation in PASC suggesting perhaps a connection between persisting SARS-CoV-2 and reactivation of other latent viruses. Persisting viral infections can cause immunopathogenesis and ongoing innate or adaptive immune stimulation. However, how SARS-CoV-2 persistence or reactivating latent viruses are involved and the role of persisting immune stimulation in PASC is unclear. We postulate that chronic stimulation of antigen-specific CD8 T cells, GC-dependent CD4 T cells and B cells, and/or myeloid cells occurs in PASC and drives pathogenesis, but also that these perturbations can be harnessed like immune biosensors to dissect disease mechanisms. Examining immune perturbations of chronic viral infections has been a hallmark of this CCHI U19 Program since its inception and is a strong foundation to address these questions. We hypothesize that PASC is associated with durable immune dysregulation linked to viral/antigen persistence, reactivation of latent viruses, and/or chronic inflammation. We will address these questions through deep interrogation of immune responses. In Aim 1, we will test whether altered CD8 T cell responses in PASC reflect exposure to persistent antigen, long-lasting inflammation or altered CD8 T cell activation during acute infection. In Aim 2, we will examine whether altered or misdirected germinal center (GC) responses in PASC implicate persisting antigen or “distraction” associated with altered inflammation and/or autoimmunity. In Aim 3, we will identify PASC-associated alterations in the myeloid cell compartment connected with changes in adaptive immune responses. This work will reveal new concepts about persisting/chronic infections with implications for therapeutics for PASC and possibly other post- acute infection sequelae. Project 1 capitalizes on a long history of expertise in our U19 Program on chronic viral infections and will thus draw on Project 2 and 3. Core B will generate samples used in this Project, and all aims of Project 1 will use Core C services. Projects 1, 2 and 3 will integrate their finding to understand shared features and mechanisms of chronic immune abnormalities after infection.
PROJECT 2: DURABLE IMPACT of HCV on INNATE and ADAPTIVE IMMUNITY
LAUER, GEORG MICHAEL, Project Lead
Chronic viral infections are associated with functional impairment of innate and adaptive immunity, including the development of T cell exhaustion. We and others recently showed that these functional defects persist even after cure of chronic viremia and are associated with irreversible molecular and epigenetic “scars”. With the rise of treatment options, ranging from antivirals to immunomodulatory therapies or even therapeutic vaccines, attention in biomedical research has shifted to understanding the long-term immune sequelae of chronic infection: how does the irreversible regulatory wiring within virus-specific exhausted T cells mediate dysfunction? How does chronic infection exposure impact bystander innate as well as adaptive responses and how durable are these effects? This is an important knowledge gap preventing the identification of regulatory pathways as well as relevant cell types that can be targeted to reverse long-lasting immune dysregulation in chronic infection. In Project 2, we focus on a fundamental, yet understudied aspect of persistent viral infection: the impact on existing as well as de novo antiviral responses, and we explore new strategies for modulating immune dysfunction. This problem is ideally studied in human cohorts since animal models cannot mimic the breadth and timescale of immune exposures in humans. Chronic HCV infection is a unique model system in humans to study fundamental principles of antiviral immunity – it can cause self-limited acute infection or progress to chronic disease in healthy adults and remains the only persistent virus that can be fully cured. Therefore, we propose to use HCV as a pathognomonic disease context to test our overarching hypothesis that chronic infection leads to broadly dysregulated innate and adaptive responses and that targeted modulation of key molecular pathways can rescue immune dysfunction. Specifically, we will 1) test whether reversal of known immune sequelae/”scars” in chronic infection through epigenetic reprogramming can rescue T cell exhaustion, 2) assess the impact of chronic infection and its cure on bystander T cell differentiation and function, and 3) test how altered innate myeloid responses following chronic viral infection (HCV) affects inflammatory setpoint and heterologous vaccine responses. Upon completion of this Project, we will have identified specific mechanistic interventions that can restore exhausted T cell function by reversing previously defined regulatory “scars”. We will also have delineated more broadly the immune sequelae of chronic infection on bystander innate and adaptive cells. These studies are intended to establish new paradigms for antiviral immunity in humans and will ultimately act as proof- of-concept for new intervention strategies that can enhance or modulate anti-viral immunity with high specificity. Importantly, this Project will closely interact with Projects 1 and 3, to compare and contrast the immune perturbation mediated by severe acute infection with long-term sequelae (Project 1) or αPD-1 immunotherapy (Project 3) to chronic infection followed by viral cure (Project 2). This will help us to develop an integrated understanding of how prior immune exposures alter antiviral immunity and overall host health.
PROJECT 3: DUARBLE IMPACT of PRECISION IMMUNOTHERAPY on VACCINE-INDUCED ADAPTIVE IMMUNE MEMORY
WHERRY, III, E. JOHN, Project Lead
Human immunology has changed radically in the past decade, accelerated, in part, by the COVID-19 pandemic. Despite this progress, we still lack knowledge of how to specifically induce optimal vaccine-induced T and B cell responses. One major gap in human immunology is the inability to precisely interrogate individual immune pathways in antigen-specific T and B cell responses through gain- or loss-of-function. Such studies have remained largely the domain of mouse immunology. However, humans are routinely treated with specific immune modifying therapeutics. Many of these same individuals also receive vaccines that allow examination of a specific adaptive immune response with known timing and well-defined antigens. Thus, it is now possible to capture the human experiment where the human immune system has been specifically perturbed by a therapeutic while another immune stimulus, such as a vaccine, is delivered. With well-designed patient cohorts selected for receipt of drugs that target a pathway of interest, key mechanistic gain- and loss-of-function type studies can be performed in humans. Here, we focus on the PD-1 inhibitory receptor pathway and vaccine-induced immunity. PD-1 is highly expressed in germinal centers (GC) by GC T follicular helper (TFH) cells, and the PD-1 ligands PD-L1 and PD-L2 are expressed by GC B cells. PD-1 is also upregulated by activated CD8 T cells during priming in humans. The role of the PD-1 pathway in human vaccine immunity, however, is largely unknown. Our preliminary data generated during the previous U19 cycle demonstrate the feasibility of this approach with promising data on effects of PD-1 on vaccine-induced TFH responses. Thus, the studies proposed will address a major gap in knowledge in human immunology: how does PD-1, expressed highly by vaccine induced immune cells, regulate vaccine-induced humoral and cellular immunity. We will test the central hypothesis that disruption of the PD-1 pathway through precision immunotherapy leads to changes in magnitude, differentiation state, repertoire, quality, and memory for GC-dependent TFH and B cell responses as well as GC-independent CD8 T cell responses. First, we will test whether loss of PD-1 signals alters the quality and/or magnitude of GC- associated CD4 T cell and B cell responses to vaccination. Second, we will ask whether loss of PD-1 signals alters CD8 T cell priming, repertoire and memory CD8 T cell differentiation following vaccination. This work will provide new insights into how a key immune regulatory pathway controls vaccine induced immunity using “mouse-like” loss-of-function studies in humans. This work will have implications for improving vaccines and for the fundamental regulation of immunological memory in humans. Moreover, this approach could be a platform for future studies capturing specific human immune perturbation to interrogate new immunobiology. By its nature Project 3 will be highly interactive with Project 1 and 2 and all Cores. Core B will generate samples used in this Project, and this Project will use Core C services. Projects 1, 2 and 3 will synergize and interact extensively to understand PD-1-based immune perturbation in humans.
