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Active and passive humoral immunity to enteric adenovirus infection in Bangladeshi children

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National Institute of Allergy and Infectious Diseases (NIAID)

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Candidate: I am an Assistant Professor at the University of Virginia (UVA) in the Division of Infectious Disease and International Health and a KL2- Funded Scholar in the Integrated Translational Health Research Institute of Virginia (iTHRIV) Scholars Program. I have pursued research in host pathogen immune interactions with Dr. William Petri for the past 6 years. Beginning initially with enteric pathogens and shifting to SARS-CoV-2 during the pandemic, I will now return to my work in diarrheal disease utilizing my background in viral immunology through study of adenovirus (AdV) 40/41 infection, a major cause of childhood diarrheal illness in low- and middle- income countries (LMIC). Career Development Plan/Career Goals & Objectives: My goal is to become an independent translational investigator. I will do so by furthering my knowledge base in the design of clinical trials, host pathogen immune interactions, viral immunology and data analysis. I will utilize my advisory committee who are not only successfully funded researchers but have a proven track record for mentoring young physician scientists. Research Plan: Characterize the systemic and mucosal immune response to AdV 40/41 infection in children in Bangladesh and determine the efficacy breast milk antibodies in providing passive immunity. Aim 1 (PASSIVE IMMUNITY): (1A) Describe the antibody repertoire to AdV 40/41 in the breast milk of mothers of Bangladeshi children using a novel protein microarray and (1B) determine their association with infection in the first 2 years of life. Plan: Determine maternal breast milk antibody breadth and magnitude, and test for its association to infant infection. Aim 2 (ACTIVE IMMUNITY): Characterize the antibody responses to AdV 40/41 infection in Bangladeshi children and test for their association with subsequent infection utilizing longitudinal (2A) serum and (2B) stool samples. Plan: Describe mucosal and systemic antibody scope and magnitude and test for association with protection from subsequent infection. Mentor/Co-Mentor(s), and Collaborator(s): The primary mentor of this K23, Dr. Petri, has a 30-year record of NIH Funding and has mentored 10 prior K awardees, 6 of whom have already made the K to R transition. My mentors include experts in immunology, virology, childhood diarrheal disease and statistics. Environment and Institutional Commitment to the Candidate: The intellectual environment at UVA is robust. I have a strong commitment from my Department and Division assuring 90% protected research time regardless of the outcome of this K23 proposal, and support of my continued mentorship under Dr. Petri at UVA.

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United States National Institutes of Health

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2025 Patrica Levy Zusman International Workshop on Neuroregeneration

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National Institute of Neurological Disorders and Stroke (NINDS)

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This R13 resulted from discussions between investigators in the fields of neurostimulation and neuroplasticity at the Houston Methodist Research Institute (HMRI). In 2017, we held an R13-funded pilot workshop that combined research in neural stimulation with new insight into the molecular understanding of neural plasticity and regeneration. The workshop received a strong, positive response by participants and interest in further catalysts for working collaboration. Thus, in 2019, we fostered relationship development and crossover opportunities among attendees via a blitz session wherein newly formed (i.e., established at the 2019 Workshop) collaborative teams competed for two $5K mini grants that supported travel to and from each other’s institutions. In 2021, we went 100% virtual due to COVID-19, however, this did not diminish the R13-funded Workshop’s impact. In 2023, our R13-funded workshop returned to an in-person event, bringing with it many of the successful virtual tools from 2021. On March 4th – 6th, 2025, we will host the 5th Patricia Levy Zusman International Workshop on Neuroregeneration (Zusman Workshop), which will focus on the intersection of electrical activity, brain connectomics, and molecular neural plasticity. Our specific aims are to: 1) formulate new ideas to fill the gap between physiology and functional-based brain stimulation technologies and the molecular and cellular understanding of innate neuronal plasticity; 2) provide promising trainees with various avenues to present their work; and 3) ensure trainees participate in substantial discussions and interactions with faculty members. The 2025 Workshop will be held at HMRI, which is part of the Texas Medical Center (TMC; a one-of-a-kind medical and research hub that fosters cross-institutional collaboration, creativity, and innovation) and is in Houston, Texas (one of the United States’ most diverse cities). A key aspect of the Zusman Workshop is the active inclusion and participation of trainees, particularly women and under-represented minorities. We will encourage their participation via travel scholarships and active promotion and recruitment throughout the TMC. The Workshop promotes the voices of graduate and postdoctoral trainees by including a trainee poster session as well as a session dedicated to trainee oral presentations (given by travel awardees). Further, goal-oriented breakout sessions, led by senior/early-stage investigators and selected trainees, will foster discussion and promote cross-training and collaboration among participants. Overall, this workshop distinguishes itself from established physiology conferences and dedicated neural regeneration conferences by being 1) highly focused on the gap between molecular regeneration and electrophysiology/stimulation, 2) concept driven by clinicians and experimentalists currently problem solving in human therapy, and 3) focused on the establishment of cross training and expertise development in graduate, post-graduate, and clinical fellows. The 2025 Zusman Workshop will ignite nascent collaborations and spur novel multidisciplinary teams to develop innovative, transdisciplinary methods, technologies, and treatments to modulate performance in the damaged nervous system.

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United States National Institutes of Health

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Aerosolized Chemically Modified Tetracycline Nanoformulation for the Treatment of Acute Respiratory Distress Syndrome

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National Heart Lung and Blood Institute (NHLBI)

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CMTx Biotech is a drug development company working to rescue, develop and commercialize a proprietary clinical-stage drug candidate, incyclinide (CMT-3 / COL-3), for the treatment of sepsis patients at risk of acute respiratory distress syndrome (ARDS). According to the U.S. Centers for Disease Control (CDC), at least 1.7 million American adults develop sepsis annually, resulting in nearly 270,000 deaths. Sepsis accounts for more than 50% of hospital deaths, and mortality increases dramatically with greater disease severity: 10–20% for sepsis, 20–40% for severe sepsis, and 40–80% for septic shock. Sepsis is a medical emergency characterized by severe immune dysregulation with a very complex immunopathogenesis. ARDS is a devastating complication of severe sepsis, both with similar underlying mechanisms characterized by inflammation and endothelial dysfunction. Sepsis is the leading cause of ARDS and accounts for 32% of the etiology of the condition. Approximately 6-7% of sepsis patients rapidly progress to ARDS, which is associated with a significantly increased risk of in-hospital mortality. There is currently no specific treatment for sepsis-induced ARDS. Moreover, researchers have not yet elucidated the multifactorial mechanisms by which sepsis induces ARDS, or why the inflammatory cytokine storm eventually induces diffuse alveolar damage and severe hypoxia. Though advances in treatment modalities have improved the outcome over recent decades, including lung protective ventilation, prone positioning, use of neuromuscular blockade, and extracorporeal membrane oxygenation, the mortality rate still remains high. There remains a critical unmet need for the development of safe and efficacious therapeutics to prevent the onset of sepsis-induced ARDS, protect against lung injury and improve survival. CMTx Biotech is working to develop and commercialize a novel and proprietary nanoformulation of incyclinide (nCMT-3) that can be aerosolized, and which can be delivered to specifically target the lung and treat sepsis- induced ARDS while limiting systemic toxicity. Incyclinide is a clinical-stage, non-antibiotic, chemically-modified tetracycline that belongs to a class of pleiotropic matrix metalloproteinase (MMP) modulators which inhibit pathologically-excessive collagenolysis and resolve systemic inflammation. Importantly, the safety of incyclinide has already been demonstrated in Investigational New Drug (IND)-enabling studies, and incyclinide has been evaluated in a number of human clinical trials for the treatment of diseases as disparate as AIDS-related Kaposi’s sarcoma, recurrent high-grade gliomas, refractory metastatic cancer, acne, rosacea and periodontitis. Published pre-clinical efficacy studies have shown that systemic administration of incyclinide prevents the development of ARDS and septic shock, and improves survival in several chronic insidious onset animal models of ARDS across several species, including mice, rats, pigs, and sheep. Our long-term goal is to obtain regulatory approval from the FDA and comparable international regulatory authorities to market aerosolized nCMT-3 for the treatment and prevention of sepsis-induced ARDS. We strongly anticipate that nCMT-3 will inhibit disease progression, mitigate acute lung injury and respiratory distress, reduce the need for intensive care and intubation, and improve clinical outcomes for sepsis patients, including overall survival. Our specific aims are (a) to determine the pharmacokinetics, biodistribution, and safety of aerosolized nCMT-3 in mechanically ventilated pigs with healthy lungs, (b) to demonstrate the efficacy of aerosolized nCMT-3 in reducing the incidence and mortality of sepsis- mediated ARDS in a high-fidelity, clinically applicable porcine sepsis-induced ARDS model, and (c) to demonstrate the efficacy of aerosolized nCMT-3 at reducing local and systemic inflammation. Successful completion of these studies will allow CMTx Biotech to advance nCMT-3 towards human clinical trials for the treatment of ARDS patients.

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Centers for Disease Control and Prevention (U.S.)

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Small Business Technology Transfer Research

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Investigating fibrinogen as a pathologic and targetable mediator of COVID-19-associated coagulopathy

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National Heart Lung and Blood Institute (NHLBI)

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Severe COVID-19 remains a top ten leading cause of death in the United States and is a major risk factor for the development of post-acute sequelae of SARS-CoV-2 infection (PASC, or long COVID). Despite tremendous strides in preventing and mitigating COVID-19 through vaccines and antivirals, strategies for managing critical illness in patients who nevertheless develop severe disease are insufficient. This is in large part due to an incomplete understanding in the mechanisms driving severe disease, of which COVID-19-associated coagulopathy is believed to be a major mediator. At the beginning of the pandemic, we reported elevated blood viscosity in critically ill COVID-19 patients related to hyperfibrinogenemia. More recently, our mechanistic studies uncovered a unique mechanism by which pathologically elevated fibrinogen causes the formation of red blood cell aggregates that mechanically injure the vascular endothelium. Fibrinogen is an essential clotting factor induced as part of the hepatic acute phase response during inflammation; yet, fibrinogen levels are not affected by currently available anticoagulant therapies. Thus, our findings help to explain the link between inflammation and clotting in COVID-19, including the increased risk of macrovascular thrombosis and the decreased microcirculatory perfusion of critical organs, even in patients receiving anticoagulation. Since therapeutic plasma exchange (TPE) is the recommended intervention for treating hyperviscosity in other conditions, we initiated a small randomized controlled trial to determine the safety and efficacy of TPE for COVID-19 patients with hyperfibrinogenemia, and banked biospecimens for future study. Here we propose a series of experiments testing the central hypothesis that fibrinogen is a pathologic and targetable mediator of COVID-19-associated coagulopathy. Specifically, in Aim 1 we propose to define the impact of TPE on blood rheology and vascular integrity by interrogating the molecular signatures of plasma samples from COVID-19 patients before and after the procedure. In addition, we have identified significant elevation in a variant fibrinogen isoform, g ¢ fibrinogen, in COVID-19 patients, which is most pronounced in those developing acute thrombosis. This usually minor fibrinogen isoform has unique biochemical properties, most notably its substantial negative charge, expected to exaggerate alterations in blood rheology. Thus, in Aim 2 we propose to define the impact of g¢ fibrinogen on biophysical properties of red blood cells and thrombosis in COVID-19. Together, these aims will not only advance our understanding of critical illness and acute coagulopathy in COVID-19, but also may have relevance for PASC and other non-COVID-related conditions involving thromboinflammation. Finally, as an extension of the K99 work, the R00 will afford a protected transition period critical to facilitating R01-readiness and to establishing an independent blood sciences research program.

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Post-Acute Sequelae of SARS-CoV-2 Infection

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Spectrometry  Mass  Matrix-Assisted Laser Desorption-Ionization

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Altered protein structures and neoepitopes in lupus neutrophils from dysregulated splicing of messenger RNA

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National Institute of Allergy and Infectious Diseases (NIAID)

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The goal of our research is to better define the molecular mechanisms cause and perpetuate systemic lupus erythematosus (SLE). Based on our discovery that transcripts from a large number of genes are spliced differently in neutrophils from SLE patients compared to neutrophils from healthy donors or COVID-19 patients, we propose a novel hypothesis of SLE pathogenesis, namely that dysregulated mRNA splicing in SLE granulocytes can affect their function and generate (neo)autoantigens not seen by the immune system before. We propose to expand and substantiate the analysis of altered mRNA splicing and begin to search for its cause(s). We will define how specific it is to SLE, understand the relation of altered splicing to sex, age, disease activity, type I interferons, and patient heterogeneity. Our work will also embark on the quest to elucidate why mRNA slicing is dysregulated in SLE. Next, we propose to explore the consequences of altered mRNA splicing in SLE. Although we have high confidence in the alignment of RNAseq reads to support all the splicing events we detect, and the transcripts are present at good read counts, it needs to be demonstrated that at least some are translated into altered proteins. We will continue to use targeted LC-MS/MS to find evidence for those with novel amino acid sequences. The proteolytic processing into antigenic peptides presented on MHC seen by T cells will then be explored. We know the MHC haplotypes of all our donors from the RNAseq data, so can match putative neoepitopes with the right MHC. Our work will clarify whether the production of novel, and perhaps individual, neo-autoantigens are a feature of SLE. If so, the production of such antigenic peptides would drive an immune response against the specific cell type that produces them (rather than all cells expressing the gene), adding a new element of tissue or cell linage-targeting to the autoimmune response. This model also introduces a new avenue for the development of therapeutics: modulating mRNA splicing to eliminate the production of neo-autoantigens. This will only be possible once the mechanism(s) underpinning abnormal splicing have been elucidated.

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Sequence optimization for mRNA cancer therapy

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mRNA technology is in the public spotlight thanks to its role in fighting the COVID-19 pandemic, and it is also rapidly transforming cancer therapeutics development through application areas such as immunotherapy. This wave of mRNA therapeutics is the result of decades of work on many fronts including improved delivery using lipid nanoparticles and inclusion of modified nucleosides for modulating immunogenicity. However, optimization of primary sequences still remains a difficult yet coveted challenge due to its untapped potential in controlling protein expression or encoding complex pharmacokinetics. Currently, mRNA therapy design typically involves adding UTRs from highly expressed native genes such as globin genes to codon-optimized (choosing most frequent synonymous codons) or GC content-enriched coding sequences. However, there is growing evidence that these strategies may be conceptually questionable and empirically suboptimal. At present, there exists no systematically validated model for mRNA therapeutics that can accurately predict and/or generate an optimal sequence to express a given target gene at desired levels. There is a significant need for such an in silico platform to accelerate therapy development timelines. Finally, mRNA sequences are largely chosen to have high expression but future therapies will impose additional design specifications for controllable expression. For example, it might be desirable to target protein expression to specific locations such as the site of a tumor. Improved design algorithms are necessary to satisfy constraints such as cell type or tissue specificity. Here, we propose to combine machine learning with massively parallel reporter assays (MPRAs) to build predictive models that relate mRNA sequence to stability and translation. We will then combine these models with innovative design algorithms to generate synthetic UTR and CDS sequences that result in (1) high protein expression across cell types or (2) highly cell type-specific protein expression. We will take an iterative approach to sequence design wherein we will synthesize designed UTRs, experimentally test them in a panel of cell types and then use the data to retrain the predictors until we meet the design objective. We will validate our approach by engineering improved mRNAs for cancer immunotherapy. In Specific Aim 1, we will develop MPRAs that interrogate 5’UTRs and coding sequences as well as 3’UTRs. In Specific Aim 2, we will develop machine learning approaches that enable us to integrate results from multiple measurements and generalize predictive rules learned from such assays. In Specific Aim 3, we will validate models by engineering regulatory elements that target protein expression to specific cell types of interest or that result in a specific level of protein expression.

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Analyzing effectiveness of ongoing natural experiments in telehealth

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National Heart Lung and Blood Institute (NHLBI)

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Uncontrolled blood pressure (BP) is the most prevalent modifiable risk for cardiovascular disease (CVD) and disorders directly influencing CVD (e.g., diabetes, chronic kidney disease, etc.). Along with many other aspects of U.S. healthcare, management of uncontrolled BP was severely disrupted during the COVID- 19 pandemic. In response, many health systems rapidly accelerated implementation of new technologies, including telehealth visits for BP control and support for self-monitoring with home-based measurement of BP. Anecdotally, new BP control technologies and strategies have been implemented differentially with wide variation in timing and degree of utilization, but systematic analyses showing the extent and variability of implementation across sites are lacking. Meanwhile, substantial and variable backsliding in BP control rates across health systems was documented at the onset of the pandemic, and it is unclear how much of the variability is driven by differential implementation of new BP-related technologies and strategies.  To learn from this unprecedented natural experiment and help guide the US healthcare enterprise towards more effective and equitable practices for management of BP control, we propose a mixed methods comparative effectiveness analysis. We will leverage our nationally scoped PCORnet Blood Pressure Control Laboratory (BPCL) – designed fundamentally for efficient surveillance of BP control and related process metrics using electronic health record (EHR) data – to develop and validate process metric queries that track implementation of new BP-related technologies & strategies, field these queries along with our previously developed metrics, extract trend results and individual patient-level data from participating sites, and conduct descriptive and causal inference analyses to decipher successful patterns of care for uncontrolled BP. And, we will conduct a positive deviance analysis with mixed methods approach to assess residual variability in BP control across clinics and learn from clinics with unexplained excellence. Our specific aims are to: 1) evaluate time trends and disparities in utilization of BP-related telehealth and home BP monitoring; 2) estimate causal effects of telehealth implementation on BP control and related metrics in hypertension management; and, 3) identify clinics with unexplained resilience in BP control and use mixed methods to analyze potential mechanisms and opportunities for dissemination of effective, scalable practices. As we have done in prior work, we will test for effect heterogeneity across important subgroups (sex, race, ethnicity) and place special emphasis on BP control in non-Hispanic Black patients, for whom disparities are historically largest. Findings from these aims will be discussed with stakeholders via webinar including a panel of frontline clinicians and leaders from positive deviant clinical sites, and disseminated via conference presentations and publications.

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Effects of Covid-19 Pandemic on Long-Term Care for High Need Older Adults with and without Alzheimer's Disease and Related Dementia.

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Nearly 20 million adults (38%) aged 65 and older have limitations with one or more self-care activities (e.g., dressing, getting out of bed) and one in ten older adults are living with Alzheimer’s Disease and Related Dementias (ADRD). Together these two overlapping groups of “high-need” older adults typically rely on a variety of long-term care (LTC) sources to assist with daily activities, including family and unpaid care, paid care in the home, residential care such as assisted living and nursing home care. Inadequate care may lead to adverse consequences in daily self-care and avoidable health care utilization. The sudden onset of the COVID- 19 pandemic may have profoundly affected access to and use of LTC and contributed to further adverse consequences for high-need older adults, particularly for those living with ADRD. This project will draw upon two complementary longitudinal, nationally representative surveys of older adults–the Health and Retirement Study (HRS) and the National Health and Aging Trends Study (NHATS)–linked to geographic data and Medicare claims. Using statistical approaches that strengthen our ability to draw causal inferences, we will: 1) Evaluate the short-term impact (2018-2020) of the COVID-19 pandemic on the type and amount of LTC use, comparing high-need older adults with and without ADRD and identify arrangements more likely to be “stable” with lower risks of change. 2) Determine whether care trajectories were disrupted after the start of the pandemic, comparing high-need older adults with and without ADRD from 2016 through 2024/2025. 3) Assess the impact of COVID-19 on adverse consequences related to care gaps among high-need older adults with and without ADRD. We will estimate the effect of the COVID-19 pandemic on self-reports of unmet need (using NHATS) and claims-based measures of avoidable hospitalizations and emergency department visits (using HRS) for those with and without ADRD. Detailed geographic data will allow us to take into account local conditions while identifying more “vulnerable” care arrangements with higher risks of adverse consequences. The results of this project will provide a comprehensive understanding of the COVID-19 pandemic’s impact on LTC outcomes in the short and longer term. This study aligns with NIA’s priority to understand community support for dementia care, in particular the determinants of availability LTC, LTC utilization and how the effects of community level factors including infrastructure and risk environment.

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Synthetic RNA Switch-Based Temporal and Dose Control of in Vivo Gene Therapies

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National Institute of Biomedical Imaging and Bioengineering (NIBIB)

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One-time in vivo gene therapies, based on adeno-associated viral (AAV) vector delivery of genes encoding therapeutic proteins, noncoding RNAs, or genome/epigenome editors, may provide long-lasting (years of, or even lifelong) treatments or cures for many rare and common diseases. However, we cannot currently tune or inactivate transgene expression to reflect disease progression or the emergence of adverse events or contraindications over time, limiting the utility of AAV gene therapies. The constrained packaging capacity of AAV vectors (~4.7 kb) has thwarted development of genetic switches that can regulate transgene expression timing or levels—the solution to these limitations. To date, just a few AAV-compatible switches function in animals. Typically, these switches are activated or repressed by ligands with undesirable side effect, including rapamycin, a potent immune suppressant; tetracycline, an antibiotic not suitable for chronic use; and branaplam, a compound that causes peripheral neurotoxicity. We previously engineered an efficient synthetic RNA ON switch based on our novel self-cleaving ribozyme T3H38, which is regulated by a complementary morpholino oligonucleotide. At 63 bp long, the tiny T3H38 ribozyme can be inserted into the 3′ UTR of a transgene. Its regulator, a 25 nt morpholino oligo is part of a class of chemically modified RNA drugs that have proven safe for chronic use in humans. The T3H38 ribozyme showed a ~200-fold regulation in AAV transgene expression in mice upon administration of the complementary morpholino oligo to the animals. Optimizing the T3H38 ribozyme switch towards a leak-free system with no detectable baseline transgene expression in the absence of the morpholino oligo could transform AAV-based gene therapy. For example, it can enable safe use of AAV to express a variety of transgenes with narrow therapeutic windows (e.g., cytokines, hormones, genome editors), where an overdose or prolonged exposure can cause severe adverse events, or to conditionally express therapeutics with major contraindications (e.g., cytokines), specific disease conditions where a drug should not be used or should be discontinued. In preliminary studies, we have developed an enhanced RNA ON switch (regulatory range: up to 35,000-fold in mice) based on the T3H38 ribozyme. Here, we will (i) optimize the enhanced RNA switch to engineer an ultra-efficient switch with negligible leakiness; (ii) use the optimized switch for precise dose control of an AAV expressing erythropoietin—a paradigmatic biologic with a short half-life, a narrow therapeutic window, and major contraindications—for the treatment of chronic Epo-deficient anemia in a mouse model; and (iii) further optimize the switch system in mouse airways for temporal control of an AAV expressing a broadly anti-coronavirus immunoadhesin—a prototype of a broadly effective prophylaxis for immunocompromised individuals against a panel of coronaviruses of pandemic potential. The completion of this project will provide a broadly useful and potentially transformative regulatable gene therapy technology and proofs of concept showcasing the utility of this technology.

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Comprehensive analysis of epistasis in drug resistance potential of Mpro from SARS-CoV-2

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National Institute of Allergy and Infectious Diseases (NIAID)

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This project aims to systematically investigate a critical, but poorly understood aspect of drug resistance evolution: the interdependence of mutations that disrupt drug binding (usually also decreasing enzyme activity) and compensatory mutations that increase enzyme activity. Combinations of these types of mutations are typically observed in pathogens that evolve clinically relevant resistance. The mechanisms that underlie these mutations have not been extensively investigated. Here, we plan to comprehensively analyze all combinations of mutations in Mpro from SARS-CoV-2 that disrupt binding to nirmatrelvir with those that increase enzyme activity. Nirmatrelvir is the active component in Paxlovid that is currently an effective treatment for COVID19. We developed a yeast screen for Mpro activity that is both safe because it does not create or use virus and biologically relevant because it uses a cut-site that is used by the virus. Mutations we identified with this screen have been observed in SARS-CoV-2 viruses selected for resistance, further indicating the screens biological relevance. In the first aim of this work, we will quantify how all combinations of drug-binding and increased activity mutations impact Mpro activity and drug disruption in our yeast screen. The resulting data will be analyzed to elucidate patterns and their structural underpinnings. As compensatory mutations can be specific, in the second aim, we will perform an unbiased analysis of all possible point mutations in the background of two mutations that strongly disrupt nirmatrelvir binding. Together these aims will provide a new view of how mutational interdependencies impact the evolution of drug resistance in a clinically important pathogen.