# data[].attributes.title
Uncovering the mechanisms and implications of BST2 antagonism by SARS-CoV-2

# data[].attributes.funder_divisions[]
National Institute of Allergy and Infectious Diseases (NIAID)

# data[].attributes.abstract
BST2/Tetherin is a key factor of the cellular intrinsic immune response that broadly restricts enveloped viruses. BST2 tethers nascent virions to the cell surface by embedding itself into cellular and viral membranes. Tethering not only limits viral release, but also facilitates adaptive immune recognition of the infecting virus. Tethered virions are opsonized by antibodies, which can be recognized by Fc receptors on both natural killer cells and macrophages, activating their ability to kill or phagocytose the infected cell. We have recently reported that SARS-CoV-2 is susceptible to BST2 restriction. However, the virus has evolved to use its Spike to downregulate BST2. Downregulation is achieved by an interaction between Spike and the extracellular domains of BST2, routing BST2 for lysosomal degradation in a Clathrin- and Ubiquitin-dependent manner. Remarkably, newly emerged variants of concern (VOC) have enhanced their ability to counteract BST2, suggesting that BST2 antagonism is a contributing factor to the host adaptation of SARS-CoV-2. Therefore, my long-term goal is to block the ability of SARS-CoV-2 to evade BST2 restriction. My overall objective is to understand the mechanism and implications of BST2 evasion by SARS-CoV-2. My central hypothesis is that mutations accumulated in the Spike of SARS-CoV-2 allow for more efficient counteraction of BST2, increasing virion release and reducing the susceptibility of SARS-CoV-2 to BST2-dependent antibody-mediated cellular responses. I will achieve my overall objective by exploring these two specific aims: (1) elucidate the mechanism of enhancement of BST2 antagonism across VOC, and (2) identify the driving pressures of BST2 antagonism. This work is significant as it will (1) fill the critical gap in knowledge of how SARS-CoV-2 evades BST2 restriction, and how VOC enhance this activity; (2) define the extent to which evasion of BST2 allows for evasion of antibody-mediated responses, and how this translates to vaccine efficacy; and (3) provide proof-of-concept for the design of antivirals to disable SARS-CoV- 2 antagonism of BST2 with the goal of both blocking viral replication and enhancing clearance of infected cells. The support provided by this F31 award will enhance my education by (1) facilitating my training in Surface Plasmon Resonance by Dr. Jermaine Jenkins and the URMC Structural Biology Core Facility (see letter of support), (2) allowing me to travel to the University of Wisconsin-Madison to gain hands-on training from my co- sponsor, Dr. David Evans (see co-sponsor statement), who developed assays to measure Fc receptor-mediated killing of infected cells, which we are proposing to use here, and (3) expanding my experience in scientific writing and communication as I publish my findings and present at both national and international conferences.

# data[].attributes.title
Interrogating stress and viral shedding in a migratory bat model

# data[].attributes.funder_divisions[]
National Institute of Allergy and Infectious Diseases (NIAID)

# data[].attributes.abstract
Bats harbor many zoonotic viruses, including both genera of coronaviruses (CoVs) pathogenic in humans (α- and β- CoVs). Limited evidence to-date suggests that periods of active infection in bats—and thus opportunities to transmit zoonotic viruses to humans—are driven by energetically demanding periods that modulate immune tolerance of infection and facilitate viral replication and shedding. However, such work has largely ignored immune mechanisms and has focused primarily on reproductive and nutritional stress. This project will combine field studies and in vitro analyses to test long-distance migration in bats as a driver of CoV infection and shedding. We will focus on Mexican free-tailed bats (Tadarida brasiliensis), a common and widespread migratory bat species in North America for which we and others have detected CoVs similar to HCoV-229E and that are susceptible to SARS-CoV-2. In Aim 1, we will sample T. brasiliensis at monthly intervals at our established study site in western Oklahoma, capturing energetically demanding periods of spring migration from Mexico, birth and lactation, and fall migration back to Mexico. We will characterize CoV diversity and infection status in saliva and fecal samples using RT-PCR followed by Sanger sequencing and will attempt to isolate naturally occuring bat CoVs. We will also quantify stress physiology through fecal cortisol and ratios of neutrophils to lymphocytes in blood, followed by generalized additive models to assess seasonality in physiological metrics and viral infection as well as to test how bat physiology relates to viral shedding. In Aim 2, we will collect lung and intestine from male and female T. brasiliensis bats and use our established protocols to develop new primary and immortalized cell lines, expanding the limited in vitro resources currently available for this bat species from an existing lung epithelial cell line. We will then test virus susceptibility and permissivity by infecting these new cell lines with HCoV 229E, SARS-CoV-2, and MERS-CoV; if isolation of natural bat CoVs is successful, we will also include infections with these viruses. Viral replication will be assessed by qRT-PCR, immunofluorescence microscopy, and TCID50 assays. In Aim 3, we will use our novel T. brasiliensis cell lines to run factorial viral and cortisol challenge experiments to mimic the stressors observed in the field and their impacts on virus replication (i.e., HCoV 229E, SARS-CoV-2, and MERS-CoV as well as any CoVs we isolate here). Viral and cortisol challenges will be followed by global gene expression analyses via RNA-Seq to discover the response of bat cells to field-relevant cortisol concentrations in the face of CoV infection. This project will thus characterize relationships between the physiological demands of migration and CoV infection in wild bats and in vitro systems, establishing a pipeline for studying how stressors affect bat-borne zoonoses.

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Dideoxy Chain Termination DNA Sequencing

# data[].attributes.keywords[]
Middle East Respiratory Syndrome Coronavirus

# data[].attributes.keywords[]
Reverse Transcriptase Polymerase Chain Reaction

# data[].attributes.title
Formation of a Novel SARS-CoV-2 Nucleocapsid Dimer: Impacts on Viral and Cellular Processes

# data[].attributes.funder_divisions[]
National Institute of Allergy and Infectious Diseases (NIAID)

# data[].attributes.principal_investigator.affiliations[].name
UNIVERSITY OF VERMONT & ST AGRIC COLLEGE

# data[].attributes.awardee_organization.name
UNIVERSITY OF VERMONT & ST AGRIC COLLEGE

# data[].attributes.abstract
While most SARS-CoV-2 research to date has focused on the biological consequences of mutations seen in the Spike (S) protein, the nucleocapsid protein (N) is also under selective pressure and an array of mutations within this protein have been documented in different Variants of Concern (VOCs). In this study, we identified three SARS-CoV-2 variants (Beta, Iota, and Delta) that encode different cysteine mutations, all introduced into the linker region of N. These mutations facilitate a highly stable N-N dimer mediated by the introduction of a cysteine and the formation of a di-sulfide bond. Beta, Iota, and Delta variants isolated and grown at BSL-3 all contained a novel cysteine residue in the linker region of N, which appear to be unique introductions amongst pandemic- causing Betacoronaviruses. Nucleoproteins encoding these cysteine mutations and transiently expressed in HEK-293T cells also form a dimer in the absence of other viral machinery. Removal of these cysteine mutations in the linker abolishes dimer formation. Notably, our biochemical studies also revealed this dimer is highly stable and can be visualized on standard non-reducing SDS-PAGE gels. Our proposal focuses on the G215C mutation, which quickly rose to dominance within the Delta lineages and mutations back to wildtype within transmission chains were quickly followed by a reversion to a cysteine at this position. Using reverse genetics, Drs Johnson and Menachery will construct a SARS-CoV-2 Delta virus that reverts the nucleocapsid cysteine back to the ancestral sequence to specifically evaluate N dimer impact on infection. This proposal aims to study the biological impact of stable N dimer formation during infection by characterizing viral growth kinetics (in vitro and in vivo) as well as the effect on viral fitness and transmission in the hamster model. Notably, a related virus (G215C in the WA1 background) showed substantially increased growth both in vitro and in vivo, suggesting that stable N dimer formation is important for viral replication. The stably dimerized form of N is highly enriched in virions (vs. the cellular environment) and we hypothesize it is increasing the efficiency of encapsidation and thus the stability of the viral RNA during transmission. As the cysteines we observe in the nucleocapsid linker lie near/on the N/NSP3 binding interface we will use proteomics to determine how the cellular and viral binding partners of the nucleoprotein change with/without this disulfide bond. Overall, the observation that mutations introducing a cysteine in the N linker have arisen multiple independent times and been maintained during human transmission, as well as our preliminary viral growth kinetics suggest that stable N dimer formation may drive positive selection and convey a growth advantage during SARS-CoV-2 infection and/or a selective benefit during animal-to-animal transmission.

# data[].attributes.title
Evaluating Veterans' Reproductive Healthcare Access, Quality and Outcomes in a Changing Landscape (EVOLVE)

# data[].attributes.abstract
Background: Recent years have witnessed unprecedented changes in the reproductive healthcare landscape in the US, including heightened awareness of reproductive health inequities following the 2020 nationwide racial justice reckoning, barriers to access resulting from the COVID-19 pandemic, and the proliferation of state abortion restrictions and bans following the 2022 Dobbs v Jackson Supreme Court decision. Today, access to high-quality, equitable contraceptive care has never been more vital for Veterans, who face elevated risks of poor outcomes from unintended pregnancy due to high rates of health comorbidities and psychosocial risks. The Examining Contraceptive Use and Unmet Need in Veterans (ECUUN) survey fielded in 2014-16 by study team members demonstrated high rates of unintended pregnancy and gaps in VA contraceptive access and quality, with significant disparities among Black and Latinx Veterans. While the ECUUN study helped inform VA’s reproductive health policies to date, updated data are urgently needed to capture VA’s progress in addressing disparities over time as well as its ability to meet Veterans’ needs in today’s shifted landscape. Significance: This study will generate timely quantitative and qualitative data necessary for VA as a learning health system to address gaps in access and quality and to adapt its policies and programming to meet Veterans’ changing needs. In addition, this study focuses on contraceptive counseling experiences in marginalized Veterans, for whom this care may be fraught due to the US history of reproductive oppression such as forced sterilization and policies to punish or limit reproduction in racial minority and low-income people. Findings will enable VA to respond to new White House and congressional directives related to women’s health that call for research to advance reproductive healthcare access and reduce disparities in care. Innovation & Impact: This proposal is innovative in its timeliness, use of prior data to draw novel comparisons over time, deployment of new state-of-the-art person-centered measures not yet fielded in VA such as the National Quality Forum (NQF)-endorsed Person-Centered Contraceptive Counseling (PCCC) measure, and collection of data to capture experiences of VA’s new policy to provide abortion care in select cases. Specific Aims: Aim 1: To use quantitative survey data to examine changes over time since ECUUN in contraceptive use, unintended pregnancy, and abortion, including differences by Veteran characteristics (e.g., race/ethnicity, geography). Aim 2: To use quantitative survey data to test for current disparities in novel person-centered measures (e.g., PCCC) by Veteran characteristics and characteristics of their health care. Aim 3: To contextualize Aim 1 & 2 findings, including disparities in experiences of contraceptive care and unintended pregnancy/abortion, by conducting qualitative interviews with Veterans. Methodology: This is a sequential explanatory mixed methods study beginning with a national survey of 3,600 pregnancy-capable reproductive-age Veterans who used VA primary or gynecology care in the past year. Qualitative interviews will then be conducted among Veteran survey respondents, purposively sampling at-risk subgroups (Black, Latinx, rural, residence in abortion-restrictive state) whose survey responses indicate gaps in care quality or equity. Quantitative data will inform qualitative sampling and data collection, and quantitative and qualitative data will be integrated using mixed methods analytic techniques including joint displays. Next Steps/Implementation: Next steps will include conducting a stakeholder engagement meeting with Veterans, women’s health providers, and operational partners from the Offices of Women’s Health, Health Equity, and Rural Health to share key research findings, develop strategic goals, and prioritize interventions to address disparities in contraceptive access and quality. Ultimately, this study has the potential to enhance VA’s ability to be a national leader in delivering high-quality and person-centered reproductive healthcare and to inform efforts to advance quality and equity in reproductive healthcare both within and beyond the VA.

# data[].attributes.keywords[]
United States Department of Veterans Affairs

# data[].attributes.title
Optimizing lipid RVn monophosphate prodrugs to maximize RVn-triphosphate delivery

# data[].attributes.funder_divisions[]
National Institute of Allergy and Infectious Diseases (NIAID)

# data[].attributes.abstract
Emerging RNA viruses, especially respiratory viruses, are among the leading threats to global health. With few treatments currently available, there is an urgent and ongoing need for the development of safe, effective oral antivirals. The objective of this application is to optimize an innovative lipid prodrug delivery strategy for remdesivir nucleoside monophosphate (RVn-MP), and additional broad-spectrum nucleoside antivirals, to achieve 1) excellent oral bioavailability, 2) efficient intracellular activation across tissue types, and 3) bypass of liver metabolism to enhance tissue delivery. The central hypothesis is that specific modifications to the lipid prodrug scaffold can improve in vivo antiviral efficacy by enhancing prodrug metabolism to the active metabolite and augmenting tissue delivery. The rationale for this project is that a better understanding of how lipid prodrug modifications increase antiviral activity will allow for the rational design and development of novel broad- spectrum oral antivirals for the treatment of clinically important RNA viruses. Strategy: Aim 1 will identify the mechanisms that determine prodrug antiviral potency in vitro to maximize antiviral activity. Quantitation of lipid RVn-MP prodrugs and their metabolites in cell culture using mass spectrometry will determine how scaffold modifications alter uptake, metabolism, and antiviral activity. Genetic knockout studies will identify the specific phospholipase C (PLC) enzyme/s that are necessary for lipid RVn-MP prodrug metabolism across cell types. Finally, PLC enzyme kinetic studies will identify scaffold modifications that maximize metabolism and antiviral activity in vitro. These data will inform lipid prodrug scaffold design that optimizes lipid RVn-MP potency. Aim 2 will determine how lipid prodrug modifications control distribution to maximize tissue delivery. First-pass removal of oral drugs by the liver is a common problem in drug development. We will evaluate how oral lipid nucleoside prodrugs can partition into chylomicrons, move through lymphatics to the thoracic duct, and thereby avoid first-pass liver metabolism while increasing lung delivery. Structure-activity relationship studies using a library of lipid RVn prodrugs will identify scaffold modifications that increase intestinal lymphatic trafficking and improve serum pharmacokinetics and tissue distribution. Scaffolds that maximize in vitro antiviral activity (Aim 1) and in vivo lung delivery (Aim 2) will be selected to rationally design new lipid RVn- MP prodrugs and novel lipid prodrugs containing nucleosides with broad spectrum activity against RNA viruses. New compounds will be evaluated for increased metabolism and antiviral activity in vitro, tissue delivery in vivo, and efficacy against pathogenic coronaviruses and dengue in mice. Collectively, this proposal will optimize the antiviral efficacy of oral lipid RVn-MP prodrugs for the treatment of many clinically important RNA viruses. Additionally, a better understanding of how to maximize the efficacy of lipid nucleoside prodrug design may be the key to unlocking a whole new generation of broad-spectrum antivirals.

# data[].attributes.keywords[]
National Institute of Allergy and Infectious Disease

# data[].attributes.title
Clinician cannabis use-related preconceptions perpetuating low quality of prenatal care for women who use cannabis during pregnancy

# data[].attributes.abstract
Cannabis is the most used illicit substance during pregnancy. Rates of self-medicating with cannabis escalated during the COVID-19 pandemic. The scientific objective of this proposal is to investigate the mechanisms contributing to preconceptions about those who use cannabis, especially during pregnancy. The central hypothesis is that preconceptions about those who use cannabis result in negative interactions between patients and clinicians that reduce the quality of healthcare and result in poor outcomes. This innovative project will be the first to: (a) leverage natural language processing/artificial intelligence (NLP/AI) techniques to investigate preconceptions about cannabis use in clinical notes, and (b) investigate associations between cannabis use and prenatal care quality. Research aims will: (Aim 1) Investigate preconceptions about those who use cannabis during pregnancy using a mixed methods approach that integrates NLP/AI and qualitative interviews; (Aim 2) Investigate associations between cannabis use and prenatal care quality among different population groups, such as differences in socioeconomic status and education levels; and (Aim 3) Develop, adapt, and test the feasibility and usability of a clinician training on quality health care practices for those who use cannabis during  pregnancy using a multistage modified Delphi process, survey, and qualitative focus groups. This research is complemented by a training plan that builds upon Dr. Rachel Carmen Ceasar’s background in mixed qualitative-quantitative methods and substance use research. The training plan includes using NLP/AI approaches, advanced survey methods in reproductive epidemiology, and implementation science. Together, this research and training will prepare Dr. Ceasar to advance as an independent investigator conducting research on health and substance use among those who are pregnant across the lifespan. The proposed project will improve clinicians’ care of those who use cannabis during pregnancy, providing evidence to inform the development of interventions designed to reduce cannabis-use-related notions in prenatal care.

# data[].attributes.keywords[]
American College of Obstetricians and Gynecologists

# data[].attributes.keywords[]
Mentored Research Scientist Development Award

# data[].attributes.title
Rational Design and Fundamental Understanding of Multimodal Amyloid Probes

# data[].attributes.abstract
The hallmark of many debilitating diseases, such as Alzeimer’s disease (AD) and type II diabetes (T2D), is the presence of abnormal masses/aggregates of proteins termed “amyloids”. These amyloids, in which composition is disease dependent, are generally considered to be ideal markers for disease diagnosis and therapeutic intervention. Unfortunately, existing probes are limited in that they are only able to detect the presence of a single targeted amyloid protein. This project will develop a new class of generic, multiple-mode, multi-target amyloid probes that will detect a wide variety of proteins associated with different amyloid diseases. Design principles for the multimodal probes can be transformed to numerous molecular-recognition applications for targeted drug therapy, biomarker detection, and disease diagnostics (e.g., cancers and COVID-19). The proposed multi-disciplinary research activities will provide diverse training for students at all levels, especially from underrepresented and low-income families. The students will develop knowledge and skills in data mining, molecular simulations, neuroscience, and lab-on-chip techniques in close relation to public health problems. Finally, the integrated educational and research activities will enrich the curriculum of the Corrosion Engineering program at the University of Akron.

The overall objectives of this project are to (1) fully explore, identify, and engineer – with both data-driven simulations and experiments – a new family of AIE@βPs (an aggregation-induced emission (AIE) molecule conjugated with small β-sheet-forming peptides (βPs)) probes capable of early and enhanced detection of multiple pathological aggregates and co-aggregates formed by the same and different amyloid proteins, which co-exist in human body fluids across different amyloid diseases and (2) conduct fundamental sequence-structure-recognition studies on these multi-mode, multiple-target AIE@βPs probes. The AIE molecule targets the aggregated amyloids and avoids the aggregation-induced quenching, while βPs target the β-structures of amyloid aggregates via specific β-sheet interactions. The project’s objectives will be achieved via three tasks: (1) develop a machine-learning model, combined with molecular simulations and biophysical experiments, to screen, identify, and validate a library of βPs capable of self-assembling into β-sheet structures and cross-interacting with both Aβ (associated with AD) and hIAPP (associated with T2D); (2) design and synthesize a series of AIE@βPs probes to detect Aβ, hIAPP, and hybrid Aβ-hIAPP species at different aggregation states for demonstrating “conformational-specific, sequence-independent” mechanisms via synergetic AIE- and βPs-induced binding modes; and (3) transform AIE@βPs probes into different amyloid sensors via surface immobilization by controlling their packing structures, densities, and patterns of AIE@βPs. In parallel, multiscale molecular simulations will be conducted to study the structures, dynamics, and interactions of βPs and AIE@βPs with amyloid aggregates in solution and on surfaces, which will be correlated with amyloid recognition mechanisms of AIE@βPs by experiments. If successful, this work will provide new design principles and sensor systems for early amyloid detection beyond few available today.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

# data[].attributes.title
Enhancing the Reach and Contributions of Informal STEM Learning: A Consensus Study

# data[].attributes.abstract
Opportunities to learn about science, technology, engineering, and mathematics (STEM) are all around. Yet, people often assume that formal school settings are the only places to learn about the STEM disciplines. A consensus report from The National Academies, Learning Science in Informal Environments: People, Places and Pursuits (NRC, 2009), helped to upend this assumption and galvanized over a decade of expansion in programming and research focused on informal STEM learning. In the years since publication of the 2009 report, opportunities to learn science and STEM more broadly in informal environments have greatly expanded and they now serve as an essential component of STEM education and engagement across the country. In parallel with the expansion of programs, research on all aspects of STEM learning has continued to progress, offering new insights into how to improve people's STEM learning in all settings. Given this tremendous growth, the new insights generated by advances in research, and the considerable changes wrought by the COVID-19 pandemic the time is ripe for taking stock of the past 15 years of work. This new consensus study will update the 2009 report to codify what is currently known about how to best support learning across informal STEM environments, thus laying the groundwork for effective decision-making in practice, policy, and research in the field. The report will help to identify gaps for where additional programming in informal STEM education would be valuable and help decisionmakers to better understand the landscape in order to advocate for high-quality STEM learning opportunities.

The Board on Science Education at the National Academies of Sciences, Engineering, and Medicine will appoint an expert committee to conduct a consensus study on Enhancing the Reach and Contributions of Informal STEM Learning. The study will take stock of the evidence base on STEM learning in informal environments, and identify trends in research and practice across the range of informal STEM learning experiences and environments that compose the field of lifelong STEM learning. The consensus report will: (1) characterize the state of informal STEM learning by defining who participates and supports learning in informal environments, as well as describing the nature of programming and learning opportunities in the United States; (2) discuss how understandings of learning have evolved over time, describe where the field has seen the most growth over the past decade in research and practice, and identify infrastructures and organizational/institutional practices that have emerged in that time; (3) identify evidence-based strategies that can be used to expand the reach of informal STEM learning, and point to relevant challenges and opportunities; and (4) develop recommendations for policy, practice, and research for enhancing the reach and contributions of informal STEM learning experiences.

This consensus study project is funded by the Advancing Informal STEM Learning (AISL) program, which seeks to advance new approaches to, and evidence-based understanding of, the design and development of STEM learning in informal environments. This includes providing everyone multiple pathways for accessing and engaging in STEM learning experiences.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

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CAREER: Re-Thinking the Perception-Action Paradigm for Agile Autonomous Robots

# data[].attributes.abstract
Autonomous robots will become pervasive in our society and will solve complex tasks, actively collaborating with each other and with humans. As the recent COVID-19 outbreak has highlighted, autonomous robots can solve a range of time-sensitive problems including logistics, reconnaissance, and disinfection of critical areas. Beyond pandemic, small-scale robots can help humans in complex or dangerous tasks such as search and rescue, security, and surveillance, and, thanks to their lighter weight, they pose only a modest risk to human safety. These time-sensitive tasks require robots to make fast decisions and agile maneuvers in complex and dynamic environments. State-of-the-art autonomous navigation approaches, while mature, are slow and brittle and prevent robust and resilient agile navigation. This Faculty Early Career Development (CAREER) Program studies the fundamental perception-action problem for agile navigation of autonomous robots in complex environments by planning a novel, low-latency, robust, adaptive, safe, and resilient paradigm. This project aims also to educate students on the technical aspects, societal benefits, and ethical use of autonomous systems by establishing a unique multi-disciplinary, and integrated research and educational platform which includes a core curriculum on robot localization and navigation, and a series of online racing hackathons for a post-pandemic customized and integrated research and educational experience. These will contribute to lowering the barrier to participation in research and education for students.

This project will generate a new foundational theory, which includes models and algorithms resulting from a principled combination of perception, learning, and control to holistically design visual perception and action to create small-scale agile autonomous robots. The goal is to capture the strict cross–coupling effects between perception and action to jointly and concurrently resolve the perception-action problem to speed up the robots’ decision making process and increase their agility. The project is organized in three thrusts according to a series of objectives, culminating in innovations in robotics autonomy research and education. A compressed and unified representation of the perception and action spaces guarantees to reduce the robot's inference latency and naturally reveals the cross-coupling effects among them. Next, the robot will exploit using this representation its action-predictive information to enhance its inference capabilities and will employ an optimal control/planning approach to maximize its perception accuracy and quality.

This project is supported by the cross-directorate Foundational Research in Robotics program, jointly managed and funded by the Directorates for Engineering (ENG) and Computer and Information Science and Engineering (CISE).

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

# data[].attributes.title
Impact of Natural Infection on the Baseline Immune States in Humans

# data[].attributes.funder_divisions[]
National Institute of Allergy and Infectious Diseases (NIAID)

# data[].attributes.abstract
Influenza is a year-round public health burden, causing millions of severe illnesses and hundreds of thousands of respiratory deaths globally. A key challenge in developing more effective vaccines lies in the inherent variability of the human immune system, as vaccine responses are highly variable across individuals, with many failing to develop adequate protective immunity. Low vaccine responsiveness has been associated with specific pre- vaccination baseline immune states. The baseline immune state of an individual determines their immune function and response. We and others have linked inter-individual variations in vaccination outcomes to molecular and cellular immune components that encode the baseline state. Our group previously showed that high vaccine responsiveness is associated with a “naturally adjuvanted” baseline state characterized by enhanced innate immune response potential, a finding supported by corresponding differences in stimulation responses of immune cells from high and low vaccine responders in vitro. We also found that clinically healthy males recovered from mild COVID-19 exhibited a more “poised” baseline state and stronger immune responses to subsequent influenza vaccination. These studies suggest that variations in baseline immune states contribute to heterogenous responses to vaccination, and that prior exposures may establish new baseline states that impact future responses in an antigen-agnostic manner. It remains unclear how infection alters an individual's baseline state over time, how these changes vary across individuals, and if they have functional consequences. Using longitudinal samples from a household cohort that allows control for environmental confounders, and using influenza infection as a model, my proposal aims to address these gaps to better understand the functional impact of infection on baseline immune states. Given the antigen-nonspecific nature of innate immune cells, understanding how infection impacts their function is a key to revealing potential underlying mechanisms. I hypothesize that influenza infection induces durable antigen-agnostic transcriptional and epigenetic changes that give rise to enhanced innate immune response potential. Aim 1 will assess the impact of infection on baseline immune states and innate cell response capacity. Through single-cell multimodal immune profiling, I will assess infection-induced transcriptional and epigenetic changes in peripheral immune cells. Using the same samples, I will examine innate response capacity to in vitro stimulation. Aim 2 will elucidate how infection-induced durable changes mechanistically drive innate cell responses to stimulation. I will implement a causal network inference approach to infer immune determinants of response capacity, followed by experimental validation to establish causality. This work will advance our understanding of infection-induced antigen-agnostic immune reprogramming, potentially revealing key drivers of human immune variation and strategies to modulate baseline states for improving vaccination outcome. Rigorous scientific training will be guided by mentors with experimental and computational expertise, complemented by longitudinal clinical and professional skill development.

# data[].attributes.keywords[]
Cellular Indexing of Transcriptomes and Epitopes by Sequencing