Our LJI CCHI was first funded in April of 2019 and has been highly impactful in human immunology research in the past < 4 years, particularly in the areas of COVID and COVID vaccines. Crotty and Sette published the first major paper on virus-specific T cell and antibody responses in COVID cases ( > 3,000 citations) and went on to collaboratively publish several more of the most influential T cell, B cell, and immune memory papers on COVID and COVID vaccines. The adaptive immune system is important for control of most viral infections. The three fundamental components of the adaptive immune system are B cells (the source of antibodies), CD4+ T cells, and CD8+ T cells. The armamentarium of B cells, CD4+ T cells, and CD8+ T cells has differing roles in different viral infections, and in vaccines, and thus it has been critical to directly study adaptive immunity to SARS2 (SARS2) to understand COVID. The COVID pandemic has been a historic disaster, with over 1 million American deaths and millions of deaths and billions of infections around the world, counterweighted by the exceptionally efficient development of COVID vaccines which had remarkable efficacy and have saved over 15 million lives in less than two years. In 2023 COVID remains a major American public health problem and global health problem, with COVID being the #3 cause of death in the USA in 2022, and in the USA there were over 1.6 million confirmed new cases of COVID in the month of January 2023 alone. Improvements in controlling COVID remain somewhat impaired by our limited understanding of immune memory and upper airways immunity to SARS2. The overarching focus connecting the three Projects in this LJI CCHI renewal proposal is immune memory, with emphasis on COVID, highlighted by three overall LJI CCHI themes: (1) understanding immune memory in humans from blood samples, rich in complexities; (2) understanding human upper airways T and B cell biology and memory; and (3) COVID immunobiology, including breakthrough infections, differences between COVID vaccines, and immunity relatedness to other respiratory viral infections of humans. These three themes are explored in depth in Projects 1-3 and the Clinical Core.
Our LJI CCHI was first funded in April of 2019 and it has been highly impactful in human immunology research in the past < 4 years, particularly during the COVID pandemic in the areas of COVID and COVID vaccines immune responses. The adaptive immune system is important for control of most viral infections. Improvements in controlling COVID remain somewhat impaired by our limited understanding of immune memory and upper airways immunity to SARS2, and the overarching focus connecting the three Projects in this LJI CCHI renewal proposal is immune memory, with emphasis on COVID and upper airways protective immunity.
Our U19 Center consists of two Cores and three Projects:
ADMINISTRATIVE CORE
CROTTY, SHANE P, Core Lead
The purpose of Core A (Administrative Core) is to provide administrative, fiscal, and information technology (IT) support to all projects within the CCHI. The Core will be based at LJI, the CCHI’s home institution and will be utilized equally by all projects. The Administrative Core provides a central focus for the program. The Administrative Core of the CCHI will facilitate interactions between the projects and with the National Institutes of Health. The goal of this core is to provide programmatic direction and promote interaction between the investigators. It will be the responsibility of the Administrative Core to assure access to core facilities by all Projects funded by this application.
CLINICAL STUDIES CORE
SETTE, ALESSANDRO, Core Lead
The success of the entire program is contingent upon successful accrual of human samples. The purpose of Core B (Clinical Core) is to provide a centralized resource for the accrual of human lymph node (LN), head and neck, nasopharyngeal swab (NP), peripheral blood mononuclear cells (PBMC), and sera and/or plasma samples. This Core will also ensure the quality and uniformity of handling samples received. In addition to recruitment goals, the goal of this Core is to design, establish, and maintain IRB approval while overseeing the quality control of coded clinical information and donor samples. These functions are crucial to provide a strong foundation for the studies described in the three proposed projects. The Core will be based at LJI at the John and Susan Major Center for Clinical Investigation, the CCHI’s home institution. The Clinical Core will work closely with subcontracts (Liverpool, U.K. and UCSD) to enable the acquisition of additional samples for Projects 1 and 3.
IMPLICATIONS of LONG GERMINAL CENTERS (GC) for T and B CELL MEMORY and MUCOSAL IMMUNITY
CROTTY, SHANE P, Project Lead
COVID remains a major killer and disruptor worldwide. We made fundamental contributions to the understanding of COVID and T and B cell immune memory after SARS2 infection and COVID vaccines. Those studies predominantly examined human blood. In Project 1 we now aim to complement those fundamental findings with studies of T and B cell memory of URT lymphoid tissue and nasal epithelium. Mechanistic studies, particularly in humans, are essential to inform on URT immune memory and the roles of long GCs in adaptive immune responses, but are currently sparse or nonexistent given the complexities for such experiments. Here we address these important knowledge gaps, synergizing with Project 2 and 3. We will do so through a series of experiments. Additionally, there are striking data demonstrating that (1) long GCs can exist after acute SARS2 infection, (2) long GCs can exist after a protein immunization, and (3) long GCs can exist after mRNA vaccination. The recent recognition of these long GCs to acute antigens significantly changes our understanding of immune responses, and long GCs appear to have great value for protective immunity and immune memory. We hypothesize that long GCs have broad impacts on adaptive immunity, including memory B cell affinity maturation, memory B cell functional properties, the functionality and durability of memory follicular helper T (TFH) cells, and characteristics of mucosal immunity in the upper airways. All of those attributes are directly examined in this Project. In both components (analyses of long GCs and analyses of URT immune memory), we will study multiple human cohorts, with particular focus on COVID-19 breakthrough infections and COVID-19 vaccinations.
IMMUNE MEMORY to SARS2 in a CHANGING LANDSCAPE
SETTE, ALESSANDRO, Project Lead
SARS-CoV-2 (SARS2) remains a fundamental threat to global health and a leading cause of death. Here, we will address a number of important outstanding questions in the field of T cell memory to SARS2. Accordingly, we’ve established novel donor cohorts, including the Multiple Vaccinations and Infections (MVI) Cohort, with over 450 donors enrolled in an ongoing longitudinal study (total of 8 years). These samples reflect the real-life evolution of memory responses, from donors with up to 5 distinct immunizations and up to 4 different infections. The Breakthrough Infection (BTI) Cohort includes donors who provided large blood donations (leukapheresis) during the Delta and Omicron waves, and on-going recruitment as new variant waves arise. The Discordant Pairs (DP) cohort enrolled people sharing living arrangements where one individual experienced BTI infection, while the other tested negative. First, we will determine the evolution of memory T cell responses over repeated exposures and vaccinations in a real-life study spanning several years, using a multifaceted approach. We hypothesize that a history of immunization plus infection is associated with broad responses against antigens beyond S (spike), indicating a qualitative advantage in T cell responses. We will also consider the alternative, that previous immunizations imprint T cell responses and a pre-existing S response inhibits development of T cell responses against other SARS2 antigens. We will also study long term evolution of T cell memory responses as a function of type and number of exposures. We hypothesize that we will observe progressive functional maturation of memory T cells. Alternatively, we might observe progressive exhaustion and loss of functionality. We will also measure T cell memory longevity as a function of type and number of exposures. Finally, we will assess the impact of age on real-life evolution of SARS2-specific memory T cells in the context of repeated vaccinations and reinfections, by comparing responses between donors aged 20-39, 40-59, and 60 and over. We will further determine memory T cell responses in the BTI cohort utilizing apheresis samples collected in a shorter pre/post-infection time frame, leveraging knowing the exposure window and variant wave of exposure. We will probe if broad responses are detected against antigens beyond S, or if a pre-existing S response inhibits development of responses to other antigens. Further, is the epitope repertoire modulated with new, variant- specific epitopes being recognized? We will also determine SARS2-specific T cell responses from donors in the DP cohort. To explain why SARS2 exposed donors do not develop overt infection, we hypothesize that they might be higher vaccine responders; might be associated with previous asymptomatic infections and/or high levels of pre-existing immunity; and/or might have experienced an abortive infection. Finally, we will test the hypothesis that BTIs are associated with selective expansion of different T cell memory subpopulations, defined by varied antigen sensitivity and cross-reactivity patterns, and defined by different methodologies.
FACTORS INFLUENCING TRM RESPONSES in UPPER AIRWAY TISSUE
VIJAYANAND, PANDURANGAN, Project Lead
The La Jolla CCHI team will investigate pathogen-specific memory T and B cell responses in the blood, and in lymphoid and non-lymphoid tissues in the upper airways, where many airborne infectious pathogens entry and replicate. In Project 3, we will focus on understanding the factors (smoking status, older age, diabetes, vaccination) associated with the magnitude, persistence and quality of pathogen-specific tissue-resident memory T cells (TRM cells) in the upper airway tissue. Upper airway TRM cells play important roles in protection against infection by airborne pathogens. Despite their importance, very little is known about the factors like vaccination routes, co-morbidities like age, diabetes, smoking status that influence the generation of pathogen/vaccine- specific TRM cells in human upper airway tissue. We have extensive expertise in understanding the biology of TRM cells, having shown their importance in driving anti-PD1 therapy T cell responses in human cancers. Here, we will examine the biology of infection-elicited and vaccine-elicited TRM cells in upper airway tissue samples obtained during routine surgery from 200 living donors. These donors are relatively fit for elective surgery and are enrolled in TARGET head and neck study, a prospective observational study that grows by ~20 cases/month at tertiary health centers, and now includes vaccination (TARGET vaccination) as an intervention prior to surgery. Our studies will expand well beyond SARS-CoV-2 to understand the diversity of TRM cells specific to viral (Influenza, respiratory syncytial virus, parainfluenza, metapneumovirus, varicella zoster virus, human papilloma virus), bacterial (pertussis) and fungal pathogens. Studies in Aim 1 will determine the correlation of three important immunomodulating co-morbidities (smoking, older age and diabetes) with features (frequency, phenotype and persistency) of pathogen/vaccine-specific TRM cells in the upper airway tissue. We will test the hypothesis that key co-morbidities like smoking, older age and diabetes are associated with defects in pathogen- specific TRM cell responses in airways. For studies in Aim 2, we will vaccinate donors 2-4 weeks prior to surgery and determine vaccine-responsive TRM cells in upper airway tissue. We hypothesize that parenteral (i.m.) vaccination can also induce/boost (pre-existing) TRM responses in the upper airways. This hypothesis is based on recent studies in model organisms and humans, which suggests that parental vaccination may induce/boost TRM responses in lungs. Because most donors would have had prior exposure to the antigens present in these vaccines by either infection or vaccination – a real-life scenario – our analysis will largely assess effects on pre- existing memory T cells. Overall, studies proposed in this Project that complement studies in Projects 1 & 2 will provide important insights into the nature of TRM responses in humans.
