Johns Hopkins University

NIH Research Projects · FY 2026 · 2024-08

Addressing the long-term care needs of a growing number of older individuals with Alzheimer's disease and related dementias (AD/ADRD) is one of the most daunting challenges facing the U.S. public health safety net. AD/ADRD is one of the most expensive categories of chronic conditions in the U.S. Older adults with AD/ADRDs have complex long-term care needs for medical, behavioral, and social supports. Medicaid is the public program that is chiefly responsible for paying the costs of long-term care supports and services (LTSS) for older adults with AD/ADRD who have exhausted their resources and ability to pay for needed long-term care. A growing trend in Medicaid programs has been to support older individuals with AD/ADRD at home rather than in nursing homes by offering Medicaid enrollees greater access to Home and Community Based Services (HCBS) services, such as in-home personal care services and case management. The rapid rise of Medicaid HCBS and homebased AD/ADRD care has served to highlight a growing problem of lack of coordination of Medicaid HCBS and other needed chronic care management services by duals’ primary health insurance carrier, which is Medicare. The long-term goal of this project is to provide an evidence base for viable solutions to this Medicare-Medicaid coordination problem. Medicare Advantage (MA) Dual Eligible Special Needs Plans (D-SNPs) are private managed care plans that only enroll dual eligible individuals. A special type of integrated D-SNP that combines Medicare Advantage and Medicaid benefits under one managed care provider may result in better care coordination, longer community tenure, less nursing home use, and improved health outcomes among older disadvantaged individuals with AD/ADRD. This project uses nationwide linked Medicare-Medicaid administrative data to compare the effectiveness of integrated D-SNPs to non-integrated D-SNPs among duals with AD/ADRD based on the results of three analyses. The first analysis compares HBCS use among duals with AD/ADRD in integrated and non-integrated D-SNPs; the second analysis compares in-home service and prescription drug process quality indicators among duals with AD/ADRD in integrated and non-integrated D-SNPs; and the third analysis compares nursing home use, community tenure, fall risk, and plan disenrollment among duals with AD/ADRD in integrated and non-integrated D-SNPs. This project uses linked Medicare and Medicaid managed care encounter data from the years 2021-2023. The final project dataset will contain over 150,000 year-quarter observations on D-SNP enrollees from over 250 unique D-SNPs. This project will be the first to test whether integration of Medicare and Medicaid benefits results in better coordination of Medicaid home-and-communitybased services among duals and, if so, whether these improvements result in improvements in measured health outcomes, including fall risk and days in institutional care.

NIH Research Projects · FY 2026 · 2024-08

PROJECT SUMMARY Sudden cardiac death due to ventricular arrhythmias (VAs) is a leading cause of mortality world-wide. Despite advancements in anti-arrhythmia therapies, VA rates remain high in part due to an incomplete understanding of the underlying disease-induced arrhythmigenic substrate. In patients with prior myocardial infarction, traditional dogma has maintained that heterogeneous scarring in the ventricles forms the arrhythmia substrate. While clinical studies have utilized the visualization of ventricular scar in localizing VA ablation targets, these efforts have failed to significantly improve VA recurrence rates, suggesting that scar characterization alone may be insufficient for identifying and eliminating VA. Infiltrating adipose tissue (inFAT) is a newly recognized aspect of post-infarct remodeling. However, because inFAT is intermingled with scar, the specific role of lnFAT In VA propensity In patients with ischemic cardiomyopathy has never been explored. The overall obJectlve of this appllcatlon Is to use a novel combination of mechanistic personallzed computatlonal modellng ("dlgltal twin" of the heart), Imaging, electroanatomlcal mapping, ex-vivo human heart experiments, and artificial intelligence (Al) to comprehensively characterize the role of inFAT vs. scar in post-infarct VAs, and to develop a new digital-twin approach for guidance of VA ablation in patients with ischemic cardiomyopathy. Leveraging our advancements in the acquisition of high-quality ventricular images of scar and inFAT distribution, our expertise in personalized computational modeling and Al, and our clinical and experimental expertise, we propose to develop personalized heart digital twins of ICM patinets that incorporate scar and inFAT distributions and are parameterized with experimental data. Using the digital twins and intra-procedure data, we will explore the mechanistic role of inFAT in arrhythmogenic propensity and in the components of the VA circuit. We will also utilize the digital twinning technology to develop a comprehensive VA ablation guidance strategy that accounts for the roles of inFAT and scar in VA circuits. The project will culminate in a clinical translation feasibility study to demonstrate that the novel digital twins offer accurate prediction of VA ablation sites, and can be used for pre-procedure guidance and optimal targeting, eliminating extensive electroanatomical mapping. Successful execution of the proposed studies will provide new mechanistic understanding of the role of inFAT in promoting and sustaining VAs, and will lead to significant improvements in the clinical procedure of VA ablation. Completion of this project will also be a major leap forward in the integration of imaging, computational modeling, intracardiac mapping, and Al in the treatment of heart rhythm disorders.

NIH Research Projects · FY 2025 · 2024-08

Immune checkpoint inhibitors (ICIs) have transformed cancer immunotherapy. ICIs optimize T cell activation and recognition to kill tumor cells. However, ICI treatments may also activate self- reactive immune cells. Cancer patients may then experience immune-related adverse events (irAEs), which can target the heart. Cardiac irAEs, like ICI-myocarditis, have low incidence but the highest mortality rate of all irAEs. Considering that ICI-treatments are suitable for 40% of cancer patients, ICI-myocarditis presents a significant public health risk. In our preliminary studies, we found that 1) PD-1 blockade caused myocarditis in 20% of mice, 2) PD-1 KO mice with myocarditis show high expression of T-cell immunoreceptor with Ig & ITIM domains (TIGIT) on T cells, 3) Other types of myocarditis like experimental autoimmune myocarditis (EAM) and Coxsackievirus B3 (CVB3) induced myocarditis also had high TIGIT+ T cells, 4) Regulatory T cells (Tregs) are the main expressors of TIGIT in myocarditis, and 5) Stimulation of TIGIT shielded the heart from myocarditis. In this project, we propose the PD-1/PD-L1 pathway together with TIGIT are essential for peripheral tolerance in protecting the heart from myocarditis. In Aim 1, we will study the role of TIGIT in ICI-myocarditis. We theorize that the loss of TIGIT signaling combined with PD-1 blockade will break the peripheral tolerance that protects the heart and worsen ICI- myocarditis severity. We will administrate a co-blockade of a blocking αTIGIT mAb with a blocking αPD-1 mAb (Subaim 1.1). We will examine TIGIT-expressing Tregs as the main protectors against ICI-myocarditis by treating TIGITfl/fl FoxP3cre mice with an αPD-1 blockade mAb (Subaim 1.2). In Aim 2, we will inspect the therapeutic potential of TIGIT for ICI-myocarditis. We hypothesize that upregulating TIGIT signaling will prevent and treat ICI-myocarditis. First, we will use an agonistic αTIGIT mAb and see its effect in treating and improving ICI-myocarditis disease (Subaim 2.1). Then we will test the overexpression of TIGIT in Tregs in preventing ICI-myocarditis by using viral vector delivery of TIGITfl-stop-fl plamid into FoxP3cre mice (Subaim 2.2). Our results may help elucidate a novel therapeutic target for ICI-induced myocarditis by using the TIGIT pathway. This would greatly help cancer patients who suffer from this devastating adverse effect because of their cancer treatment. Since TIGIT is expressed in other kinds of myocarditis, we can also explore this therapy in other inflammatory cardiovascular conditions.

NSF Awards · FY 2024 · 2024-08

Various plasma waves are excited in near-Earth space during geomagnetic storms, and the waves affect the behavior of particles carrying the ring current and the strength of the flux of energetic electrons in the radiation belts. Ultra-low-frequency (ULF) waves with frequencies below 100 mHz play an essential role in this regard, and understanding the spatial and temporal occurrence patterns and the excitation mechanism of the waves is a crucial element in magnetospheric research. The investigation focuses on a recently reported new type of compressional ULF waves in the inner magnetosphere with a symmetric (fundamental) mode structure about the magnetic equator. Antisymmetric (second harmonic) waves are commonly detected and well-documented in the literature. The team aims to determine the relevance of drift compressional instability (DCI) to stormtime magnetospheric ULF waves. The investigation has broader impacts regarding wave-particle interactions occurring on other planets and in laboratory plasmas. In addition, the investigation will contribute to building improved space weather models that are valuable beyond the context of basic research. The goal of the investigation is to observationally determine whether the physical properties of symmetric ULF waves and the particle environment associated with the symmetric waves are consistent with DCI. To this end, we will use data from the Van Allen Probes (RBSP), which include electric and magnetic fields, plasma, and energetic particles. With the RBSP mission providing measurements in the inner magnetosphere ( < 6) over a 7-year period (2012–2019), the data are ideal for determining the mode structure of ULF waves, their spatial and temporal distributions, and the properties of the background particles. We will determine the mode structure by paying attention to the relation between the spacecraft latitude and the location of the equatorial node/antinode of ULF waves. The relevance of DCI to observed symmetric waves will be discussed by evaluating the theoretical instability condition using observationally determined energy and radial distance dependence of the phase space density of ions in the ring current energy range (1-300 keV). We will discuss the statistically determined spatial occurrence pattern of the waves in relation to the drift of ions injected from a nightside source region. 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.

NSF Awards · FY 2024 · 2024-08

This award supports research in relativity and relativistic astrophysics and it addresses the priority areas of NSF's "Windows on the Universe" Big Idea. The era of gravitational-wave multi-messenger astronomy started on 2017 August 17, when LIGO (the Laser Interferometer Gravitational Wave Observatory) discovered an event dubbed GW170817. This was the very first direct observation of gravitational waves from a binary neutron star in-spiral, which was accompanied by the detection of light at all wavelengths. The multi-messenger observations of GW170817 have crucially informed a large variety of fields including gravitational physics, nuclear physics, cosmology, and relativistic astrophysics. In spite of the spectacular progress, several questions remain open. A key one is whether the stellar object leftover from the merger is a short-lived neutron star, a long-lived neutron star, or a promptly formed black hole. This award supports searches of LIGO data for signatures aimed at uncovering the nature of the merger remnant. Studying how the nature of the remnant depends on the properties of the merging objects can unlock the fundamental physics of matter at densities much larger than those that can be probed in Earth-based laboratories and clarify the physics of some of the most exotic objects in the stellar graveyard. This project also supports the training of graduate and undergraduate students who will constitute the next generation of scientists, and several outreach activities aimed at presenting LIGO results to the general public and K12 students. Specific intellectual goals are: (i) Unmasking the remnants of compact object mergers accompanied by gamma-ray bursts by carrying out searches for gravitational waves from newly formed neutron stars; (ii) Assessing the efficiency of the newly-developed Cross-Correlation Algorithm (CoCoA) in detecting the full zoo of possible gravitational wave signals from merger remnants, and its efficacy in post-detection parameter estimation; (iii) Quantifying the potential for discovery of gravitational waves from neutron stars formed in long gamma-ray bursts by future upgraded gravitational wave detectors. Broader impact goals are: (i) Bringing age-appropriate presentations and LIGO-related outreach activities to under-represented groups by leveraging the TTU Honors College-Bayless Elementary School mentoring program; (ii) Presenting a LIGO prize to the South Plains Regional Science Fair; (iii) Presenting LIGO results to the general public during the Astronight at TTU. 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.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY/ABSTRACT: Venous thromboembolism (VTE) is a major cause of morbidity and mortality. VTE is caused by acquired and genetic factors, but the genetic factors that modify the risk for VTE are not fully understood. Coagulation factors play a major role in VTE, but the regulation of coagulation factor expression in the liver is not well characterized. Our long-term goal is to dissect the transcriptional and epigenetic mechanisms that regulate hepatocyte expression of coagulation factors. Our strategy is to use genome wide association studies (GWAS) to identify novel candidate genes that are linked to VTE risk. A recent GWAS identified the BCL6 co-repressor (BCOR) locus as a risk for VTE in humans. The objective of this grant is to characterize the role of BCOR in epigenetic regulation of Factor VII and thrombosis. Our Preliminary Data show that (1) BCOR controls Factor VII expression in cells and mice, and (2) BCOR associates with two epigenetic modules: the Polycomb Repressor Complex (PRC1.1), and the Ada2a-containing complex (ATAC). Our central hypothesis is that BCOR suppresses Factor VII expression through the epigenetic regulators PRC1.1 and ATAC. Our rationale is that identification of epigenetic pathways that control coagulation may lead to new specific therapies to prevent or treat VTE. Our specific aims will test the following hypotheses: (1) BCOR suppresses Factor VII expression in hepatocytes by controlling the epigenetic modules PRC1.1 and ATAC. (2) The genetic variant in the BCOR locus linked to VTE risk decreases BCOR expression by controlling TEAD1 binding to the BCOR enhancer (where TEAD1 Is a TEA domain family member suppressor protein). (3) Inhibition of hepatic BCOR expression increases Factor VII levels and increases coagulation and thrombosis in vivo. Upon conclusion of this project, we will understand how human genetic variants in the BOCR locus contributes to risk of VTE. The significance of our studies is that we will establish epigenetic regulation as a pathway to control Factor VII levels, possibly leading to novel therapies for VTE by targeting specific epigenetic pathways. The innovation of our studies is: (A) BCOR has not been previously linked to VTE; (B) BCOR has not been shown to interact with the ATAC epigenetic complex; (C) epigenetic regulation of liver production of coagulation factors is not well characterized. In summary: human genetics suggests BCOR modulates the risk of VTE, our animal model shows that BCOR in the liver affects plasma Factor VII levels and coagulation in vivo, our cell studies show that BCOR associates with epigenetic regulators and modulates expression of Factor VII in vitro. We now propose to study the epigenetic mechanisms by which BCOR in the liver regulates coagulation.

NSF Awards · FY 2024 · 2024-08

The goal of this project is to develop models to predict and describe the behavior for groups of particles, called colloidal assemblies, on curved surfaces. The behavior of interest is how the colloidal assemblies form different groupings and configurations called microstructures. By understanding the dynamics of how particle scale microstructures emerge on curved and deformable surfaces, real-time control will be developed for assembling particle-based surface structures with important and novel multifunctional properties. Practically, the aim is to assemble different shaped particles on different surface topographies to create synthetic materials that mimic natural materials as well as unnatural metasurfaces. Improving the control of these assemblies and resulting properties is expected to lead to techniques for fabricating these materials at a larger scale. Particle microstructures on curved surfaces will be targeted that exhibit novel properties (e.g., optical, electromagnetic, mechanical, wetting, etc.) essential to emerging technologies (e.g., optical coatings, solar cells, biomaterials, soft robotics, flexible electronics, responsive composites, etc.). To achieve these goals, microscopy and computer experiments will be used to understand and control mechanisms of non-equilibrium assembly of liquid crystal and crystal structures on curved surfaces including the role of curvature mediated packing defects. Broader impact activities will include educating a diverse and inclusive multidisciplinary workforce as well as outreach to underrepresented groups in Baltimore through classroom and laboratory modules involving microscopy and computational research visuals. The research plan includes a systematic series of connected aims to both gain fundamental understanding of dynamic pathways for assembly of different shaped particles on curved surfaces, and to enable feedback control of rapid microstructure evolution toward target states. In addition, the project aims are designed to address a central scientific hypothesis that different shaped particles on curved surfaces have different interactions, states, defects, and stochastic assembly, relaxation, and reconfiguration dynamics compared to particles on flat surfaces. In brief, the project aims are to: (1) obtain accurate high-dimensional particle scale dynamic simulations by matching potentials and diffusivities to microscopy experiments in a model material system with tunable potentials, (2) develop coarse-grained reaction coordinate based dynamic models, with pathway and rate information, for stochastic microstructure evolution in transient assembly processes including topological defect relaxation, and (3) implement feedback control with optimal control policies to achieve in minimum time low-defect target microstructures of different shaped particles in liquid crystalline and crystalline states on varying surface topographies. Achieving these aims will enable us to develop generalizable first principles models to control dynamic reversible assembly of different shaped particles into technologically useful ordered microstructures on curved surfaces. 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.

NIH Research Projects · FY 2025 · 2024-08

The newer disease-modifying drugs for Alzheimer’s Disease (AD) target Aβ42 proteins and p-tau production and accumulation and include antibodies directed at Aβ epitopes. While these drugs offer hope for individuals affected by AD and related dementias (ADRD) and their families, best practices are unclear due to potential harms, substantial costs, and modest efficacy. Those affected by ADRD, along with their families, clinicians, and payers, dynamically make decisions about therapies in response to the evolving cognitive, physical, behavioral, financial, and emotional challenges as dementia progresses. Standard cost effectiveness analyses fall short in incorporating the perspectives of the users of new treatments from varied backgrounds, who differ in clinical responsiveness, side effects tolerance, risk acceptance, spending preferences, and use of therapies driven by differences in healthcare access and preferences. In the planning phase (R61), we will conduct focus groups with individuals from varied backgrounds affected by ADRD to understand their medication decision-making processes. With this information, we will design discrete choice experiments to learn how different attributes of a therapy are valued by affected individuals and what tradeoffs they would make between treatments with different attributes. In the implementation phase (R33), we will administer the survey, in a web-based format, to a large, nationally representative sample of older adults conversant in English or Spanish. Experiment results will inform a risk-adjusted cost-effectiveness (GRACE) model, incorporating relative preferences and health risk attitudes, overall, and by specific subpopulations of interest. Using these estimates, data from the National Health and Aging Trends Study cohort (2011-2024) with their Medicare claims, and other input data from the literature, we will develop, validate, and calibrate a health economic evaluation microsimulation model of ADRD progression and outcomes. We will apply the model to estimate the cost-effectiveness as well as financial risk protection and the impacts of new existing and hypothetical ADRD drugs on health differences, overall and for specific patient populations disproportionately impacted by ADRD. We will prepare the final models so that they are accessible for use as additional novel therapies become available.

NIH Research Projects · FY 2025 · 2024-08

Project Summary Dengue remains stubbornly endemic in many countries. Vaccine development efforts have been hampered by a poor understanding of the immune response. We do know that pre-existing immunity from vaccination or historic infections is key to driving disease risk, however, accurate markers of risk or protection are lacking, including how they change over multiple years. Less is known about the role of non-neutralizing antibody functions, such as antibody-dependent cell cytotoxicity, and antibody-dependent enhancement in driving disease risk. Neutralizing and non-neutralizing antibody responses have not been characterized alongside cellular immune responses that have been identified to be associated with risk of illness. Here, we will expand upon previous work on the diversity of neutralization responses to specifically add characterization of non-neutralizing antibody responses and cellular immune responses from natural infection and vaccination using samples taken from the same individuals over numerous time points. These samples come from cohorts that had regular collection of sera and PBMC and were followed for instances of infection and illness, many of which severe. This includes a cohort of individuals that were vaccinated by the only licensed dengue vaccine, a cohort followed for 13 years. We also have access to samples from individuals vaccinated with another candidate vaccine followed over five years. Finally, we will re-recruit cohort participants to provide samples 23 years after their participation to investigate long term responses after infections. We will measure multiple non-neutralizing and neutralizing responses to a diverse set of dengue viruses a wide range of antibody measures as well as a limited set of cellular immune responses, providing a multi-dimensional, systems characterization of humoral and cellular immune responses. We will use this multi-dimensional measure and mathematical models to reconstruct full infection histories and immune dynamics. These efforts will provide a set of correlates of protection/risk of illness and infection that can be used to assess risk in vaccine trials and epidemiological studies. These mechanistic models will be generally useful to infer dynamics of immune responses to antigenically variable pathogens and can be used to assist in the design and analysis of vaccine trials and epidemiological studies. Relevance to Public Health Multiple candidate dengue vaccines are currently in development, however, their likely effectiveness over short and long time periods remain unknown due to a lack of good markers of protection or risk. Identifying such markers, and how they change over time is critical to their optimal use, continued efficacy and population safety. More broadly, characterization of non-neutralizing antibody and cellular immune responses to a diverse set of dengue viruses alongside neutralizing responses in humans followed over many years who have experienced dengue infection and/or vaccination will increase our understanding of immune responses to dengue.

NIH Research Projects · FY 2025 · 2024-08

PROPOSAL SUMMARY-ABSTRACT Adolescent suicide is a growing public health problem and a leading cause of death in the US. Rates of adolescent suicide and suicidal behavior have been on the rise for the last two decades increasing disproportionally among Black adolescents. Increasing rates of suicidal behaviors have also led to a surge in adolescent ED visits. Parents play a central role in suicide prevention efforts by protecting their children from self-harm and promoting their mental health following discharge from the ED for suicidal behavior (SB) when a child’s risk for recurrent SB is greatest. Parents’ needs in caring for suicidal adolescents are often not considered yet they hold primary responsibility for ensuring their child’s safety after ED discharge. Parental self-efficacy (PSE) is a parent’s belief in their ability to fulfill their parenting role effectively and is a powerful predictor of parenting competence and child well-being. In the context of this study, PSE to prevent SB is conceptualized as a parent’s perceived ability to support their child in crisis, keep them safe, and prevent future SB. This convergent mixed-methods study seeks to understand the psychosocial factors associated with SB prevention self-efficacy among parents caring for adolescents following an ED visit for SB by addressing the following specific aims: 1) Examine associations between parent-level psychosocial factors, adolescent suicide-related characteristics, and parents’ SB prevention self-efficacy, 2) Based on individual parent interviews, understand how psychosocial and contextual factors influence parents’ SB prevention self-efficacy with an emphasis on understanding potential differences in the experiences of Black parents; and 3) Integrating results from Aims 1 and 2, identify potential strategies for building parents’ SB prevention self- efficacy in caring for an adolescent following an ED visit for SB. The study will be guided by a parent advisory group and leverage the research infrastructure of a larger PCORI-funded adolescent suicide prevention study in the Johns Hopkins Hospital Pediatric ED. Aim 1 (quantitative) will use cross-sectional data (n=125; 60% Black/African American); Aim 2 (qualitative) will include individual interviews (sub-sample of parents n=20; 50% Black/African American). Correlations and multiple linear regression models will be used to test the quantitative data; a content analysis approach will be used to analyze the qualitative data. Data from Aims 1 and 2 will be integrated to compare parents’ qualitative descriptions and quantitative scores and assess for potential differences in parents’ SB prevention self-efficacy based on parent-level psychosocial factors, adolescent suicide-related characteristics, and between Black/African American and White parents. Results of this study will fill a clinical research gap with the future goal of developing interventions to bolster the protective role of parents in preventing adolescent SB. The proposed study addresses the NIMH’s Strategic Plan, Strategic Framework for Addressing Youth Mental Health Disparities, and recent calls to identify risk and protective factors for youth suicide and prevention.

NIH Research Projects · FY 2026 · 2024-07

Project Summary Genome maintenance is essential for accurate cell and tissue function. The underlying repair needs differ based on cell type and differentiation stage. Deciphering the mechanism that govern DNA repair is of significant interest to public health, as defects in genome maintenance can drive diseases from degenerative disorders to cancer. Although a multitude of DNA repair factors have been identified to date, there remains a profound lack of understanding regarding the mechanisms that ensure appropriate repair factor engagement. The repair of DNA damage is tightly coupled to the nuclear environment in which it occurs. We hypothesize that dynamic changes in two fundamental regulators of mammalian DNA transactions, chromatin and nuclear RNAs, are essential to control DNA repair outcomes across distinct physiological contexts. Our long-term vision is to understand, and manipulate, how cell state transitions, both during differentiation and in disease, exploit these mechanisms to adjust to altered genome maintenance needs. We will pursue this goal through two complementary projects, combining our expertise in state-of the art genomics approaches and mouse genetics with innovative cell-based tools to study DNA repair. In the first project, we will investigate how macroH2A1, the third-most common histone H2A variant, links chromatin plasticity to DNA repair pathway choice. MacroH2A1 is alternatively spliced during differentiation as well as in cancer, and we and others have identified distinct DNA repair functions associated with each splice isoform, affecting both double- and single-stranded DNA damage. We propose that, by changing macroH2A1 isoform expression, cells have the capacity to optimize repair outcomes in response to a variety of DNA lesions. We will use isoform-specific knockout mouse models and a screen for macroH2A1 splicing effectors to uncover how macroH2A1 isoform plasticity affects genome maintenance and dissect its physiological consequences. In the second project, we will investigate the contribution of nuclear RNA to DNA damage control. RNA is an integral chromatin component that has direct implications for genome integrity, both as a mediator of repair factor recruitment through RNA:protein interactions and via RNA-mediated structural DNA perturbations, such as RNA:DNA hybrids. We propose that, much like chromatin, RNA provides a tunable and dynamic means to control genome maintenance. Using focused screening approaches, we have identified repair-relevant modulators of RNA structure and function and will investigate their roles as effectors of DNA repair pathway choice. A better understanding of the molecular mechanisms that define DNA repair capacity will have implications for diseases driven by impaired genome maintenance.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY/ABSTRACT A comprehensive understanding of adverse childhood experiences (ACEs) and positive childhood experiences (PCEs) would facilitate recognition of, and response to, signs and symptoms of trauma. While pediatricians may suspect that youth have experienced trauma, this trauma is not being captured in settings best equipped to identify and intervene to address childhood trauma, such as primary care. The objective of this proposal is to build and test a primary care trauma-informed care questionnaire (TICQ) that screens for trauma and resilience experiences (ACEs and PCEs) of youth. This study, entitled MOSAIC: Modifying and Optimizing a Screener of Adversity and Resilience in Pediatric Care, seeks to adapt, implement, and validate a TICQ by following the Patient-Reported Outcome Measurement Information System (PROMIS) qualitative item development and review process. Aim 1 Step 1 generates items through thematic analysis of focus group data, participatory ideation, and a priori identification of trauma screeners. Aim 1 Step 2 classifies (“bins”) and selects (“winnows”, pile-sorts, and ranks) items with youth and parents. Aim 1 Step 3 revises and reviews items via cognitive interviews with youth. Aim 2 pilot implements this new trauma TICQ in a pediatric primary care practice in Baltimore City. Aim 3 calibrates screening items included in the TICQ with adapted and piloted items through latent class analysis (LCA) of a large sample of youth. These research aims and career development plan provide Keith Martin, DO, MS the skills to achieve his overall career goal of becoming an independent investigator focused on trauma-informed, pediatric primary care. Dr. Martin’s training plan includes experiential learning and didactic coursework to achieve the following short-term training goals: 1) Gain expertise and understanding in the theory and clinical application of the intersection between intergenerational trauma and resilience; 2) Study and optimize screening and intervention in primary care; 3) Apply practical implementation science and clinical informatic strategies; 4) Develop skills in screening item development and construct validation; and, 5) Continue skill building in the responsible conduct of research (RCR), manuscript writing, and grant writing. Dr. Martin will receive focused mentorship and consultation from a team of experts in primary care level intervention (Dr. Perrin), early life adversity (Dr. Johnson), implementation science (Dr. Bass), psychometric analysis (Dr. Musci), and stakeholder-engaged research (Dr. Polk).The rich research environment at Johns Hopkins University will allow Dr. Martin to fulfill his research and career development plans and begin to address his long-term goal of improving the health of youth by leveraging pediatric primary care to further child well-being.

NIH Research Projects · FY 2025 · 2024-07

Project Summary Hepatitis B virus (HBV) is a leading cause of cirrhosis and liver cancer globally, resulting in over 800,000 deaths annually. Approximately 10% of people living with HIV (PLWH) worldwide are infected with HBV and prevention of HBV infection remains a critical goal in PLWH. Vaccination with ENGERIX-B and other alum adjuvanted hepatitis B surface antigen (HBsAg) vaccines has been the cornerstone of HBV prevention, but the response to current standard vaccination is suboptimal in PLWH. HEPLISAV-B vaccine is HBsAg combined with CpG 1018 adjuvant, a Toll-like receptor 9 (TLR9) agonist. A Phase III trial, A5379, randomized PLWH with a prior history of HBV vaccination who do not achieve protective HBsAb levels to receive three doses of HEPLISAV-B or ENGERIX-B. Preliminary analysis demonstrates significantly higher response rates with HEPLISAV-B. To explore the immunologic mechanisms associated with increased rates of response, we plan to compare innate and adaptive immune responses induced by HEPLISAV-B to those of ENGERIX-B vaccination. In Aim 1, we define the innate immune signatures of CpG 1018 and alum adjuvated HBsAg vaccination, including plasma chemokine and cytokine and transcriptomic profiles that are associated with response to vaccination and with adaptive cell phenotypes defined in Aim 2. In Aim 2, we compare HBsAg- specific B- and T-cell responses following three doses of HEPLISAV-B to those induced with a standard three- dose regimen of ENGERIX-B, using high dimensional flow cytometry and single cell RNAseq to define the immunologic and metabolic profiles of HBV-specific T and B cells associated with vaccine response. Previous studies have shown that TLR9 activation in HIV infection increases HIV-1 transcription and reduces proviral DNA, key outcomes in HIV-1 cure strategies. Thus, Aim 3 will assess the HIV reservoir and HIV-specific immune responses before and after vaccination with HEPLISAV-B. With these three complementary but independent aims, we will define innate and cellular characteristics associated with superior antibody production, with broad implications regarding the use of TLR9 agonist vaccine adjuvants in populations with suboptimal vaccine responses and improved understanding of dysregulation of immune responses in PLWH. Additionally, this research leverages a large and diverse participant group to explore the dynamics of HIV reservoir maintenance after TLR9 agonist exposure with the potential to inform development of HIV curative strategies.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY/ABSTRACT The HIV latent reservoir (LR) is the major barrier to cure of HIV. The persistence of the LR in blood and tissues in people living with HIV (PLWH) during ART is due to cellular proliferation of infected cells. Three mechanisms are postulated to drive infected cell proliferation: integration of the provirus in or near genes associated with cancer or cell proliferation; engagement of the infected CD4+ T cell receptor with its cognate antigen, leading to proliferative bursts; and cytokine-mediated homeostatic proliferation. Recent evidence suggests that oncogene- driven proliferation does not contribute significantly to infected cell proliferation. Meanwhile, antigen-driven proliferation of infected cells appears to account for many or most of the most-highly expanded, or dominant, infected cell clones. However, the degree to which homeostatic proliferation versus antigen-driven proliferation maintains the overall reservoir is difficult to discern. Because infected cells are so clonal, shallow sampling depths still reveal dominant clones (likely maintained by antigenic stimulation) while underestimating the extent of the non-dominant clones (the ‘tail’ of the clonality distribution, likely maintained by homeostatic proliferation). We will fill this knowledge gap by generating a near-full length HIV provirus sequencing dataset deep enough to accurately assess clonality richness and by developing models to more precisely quantify the fractional contribution of antigen-driven versus homeostatic proliferation to reservoir maintenance. In Aim 1, we will fully characterize the intact and defective provirus clonality distributions in PLWH on ART by generating near-full length HIV provirus sequencing datasets deep enough to approximate clonality richness saturation. We will test the hypothesis that provirus clonality distributions mirror those of uninfected memory CD4+ T cells, with a small number of dominant clones and a large number of non-dominant clones, and that they can be modeled with similar power-law exponents. In Aim 2, we will first generate longitudinal characterizations of in vivo antigen- driven and homeostatic CD4+ T cell proliferation of uninfected CD4s in PLWH on ART using T cell receptor repertoires. Then we will use this information to construct mathematical models to estimate the fractional contributions of antigen-driven and homeostatic proliferation to the persistence of the reservoir in PLWH on ART. We will test the hypothesis that both antigen-driven and homeostatic proliferation contributes significantly to the maintenance of the HIV LR. This work and the resulting models will help the HIV cure field design future therapeutic strategies and help the field predict more precisely outcomes when HIV cure strategies such as anti- proliferative therapies or personalized therapeutic vaccines are trialed.

NIH Research Projects · FY 2025 · 2024-07

Summary – This proposal takes crucial next steps towards illuminating the mechanistic impact of regulatory variation underlying common disease risk and progression, focusing on Parkinson's disease (PD) as a model. The majority of disease-associated variants identified by genome-wide association studies (GWAS) lie in noncoding DNA, likely influencing transcription of their cognate genes. Thus, improving our understanding of how regulatory variation can impact gene expression, and the downstream cellular mechanisms through which they modulate disease susceptibility, is crucial. The acquisition of biologically relevant genomic data, across the cellular contexts in which the variants may exert their effects, is imperative for the prioritization and functional assay of variants within associated loci, as well as the determination of their mechanistic impact. Towards this end, we have already made significant strides in studying the chromatin and transcriptional landscapes of gestational/early postnatal dopaminergic (DA) neurons and improved our understanding of how regulatory variation confers risk for PD. We have previously generated catalogs of open chromatin regions (OCRs) and similarly profiled gene expression of midbrain and forebrain DA neurons. We have developed and implemented computational classifiers to identify key transcription factors (TFs) that actively influence gene expression and have identified PD-associated functional variation falling within novel enhancers. Although they establish a powerful precedent, these studies query only a snapshot early in normal DA neuron biology. Here, we propose to link regulatory variants, the cell state(s) in which they act, the genes they influence, and the mechanisms through which they impact PD risk. We aim to define chromatin and transcriptional signatures derived from PD-vulnerable DA neurons over time and in response to PD-relevant insult of α-synuclein preformed fibrils (Aim 1). Further, we will develop novel tools to computationally “learn” the sequence-basis of the cell type/state dependent OCRs, via machine learning, undertaking massively parallel reporter assays (MPRA) to test thousands of OCRs, and predicted disease risk variation therein, using DA neurons derived from human induced pluripotent stem cells (hiPSC-DA) from unaffected individuals (Aim 2). In Aim 3, we will test the functional consequences of disrupting predicted key TFs and enhancers on a range of PD-relevant cellular phenotypes using hiPSC-DA neurons. We will similarly evaluate the molecular and cellular effects of risk and non-risk variation therein, using hiPSC-DA harboring established PD mutations, to provide a greater opportunity of observing functional effects. Our proposal will advance our understanding of regulatory encryption and how noncoding, functional variation perturbs molecular mechanisms in common disease risk and progression, particularly for PD. Additionally, our findings will inform mechanisms underpinning other PD-related disorders including diffuse Lewy Body Disease and Lewy Body Dementia and the increased risk of cognitive decline/dementia in Gaucher’s.

NIH Research Projects · FY 2026 · 2024-07

Hepatitis B virus (HBV) infects >300 million people chronically and is the leading cause of end-stage liver disease and hepatocellular carcinoma (HCC), resulting in ~1 million deaths annually. HIV is a common co- infection in people with chronic hepatitis B (CHB) and worsens HBV and liver disease outcomes. Liver disease is a leading cause of death among PWH in the era of antiretrovirals, mostly due to viral hepatitis. Antiviral treatment with nucleos(t)ide analogues (NUCs) suppresses plasma HBV DNA but does not eliminate the covalently closed circular DNA (cccDNA) HBV template that resides in every infected cell. NUC interruption leads to HBV DNA rebound and clinical hepatitis. Therefore, finding an HBV cure is of major importance for HBV mono- and HIV/HBV co-infection. Previously, we applied single-cell methods to HBV/HIV co-infected liver tissues and demonstrated that cccDNA is transcriptionally suppressed during NUCs, although the phenomenon is likely to be reversible. We now propose to uncover the mechanism underlying cccDNA transcriptional silencing since irreversible transcriptional silencing can lead to a functional cure. We propose an intensive study of NUC-associated cccDNA transcriptional suppression comparing people with HBV/HIV co- and HBV mono-infection. In aim one, we will quantify intrahepatic viral DNA and RNA quantities in hepatocytes from HBV mono- and HBV/HIV co- infected individuals during NUCs using single-cell laser capture microdissection and droplet digital PCR (scLCM/ddPCR) to quantify a cccDNA transcriptional index (cccDNA TI). We will compare the cccDNA TI between HBV mono- and HBV/HIV co-infection. In aim two we will characterize host genes that are differentially expressed with regards to HBV RNAs and compare these between HBV mono- and HBV/HIV co- infection. We will apply the 10X Visium spatial gene expression analysis (10x VSGEA) platform to liver tissues with high vs. low cccDNA TI, interrogating HBV transcription using the same platform. Genes of interest (GOI) identified by 10X VSGEA will be confirmed after enriching for cells with high vs. low cccDNA TI using scLCM/ddPCR. We will prove GOI are involved in regulating HBV transcription in vitro studies using CRISPR/cas9 knockout in HBV-infected NTCP-expressing HepG2 and primary human hepatocytes. We will perform co-immunoprecipitation of GOI with HBV proteins to confirm mechanisms. In aim three we will characterize epigenetic modifications of cccDNA in liver tissues already characterized with high vs low cccDNA TI, comparing findings in HBV mono- and HBV/HIV co-infection. We will quantify CpG methylation, histone modifications, and open chomatin in persons with high vs low cccDNA TI. In vitro, we will test the actions of methyltransferases, histone acetyl transferases, and histone deacetylase inhibitors on cccDNA transcription using an infection model of HBV. Our proposal fills knowledge gaps in understanding how to transform reversible cccDNA transcriptional suppression to a functional cure.

NIH Research Projects · FY 2025 · 2024-07

Rates of syphilis in the U.S. have increased each year for the past 20 years and are elevated in people living with HIV (PWH). PWH are at higher risk of syphilis complications including neurosyphilis. For decades, the mainstay of syphilis treatment monitoring has been the serum nontreponemal antibody (NTr) titer (usually RPR). Guidelines suggest NTr titers should decline by ≥4-fold at 12 months in adequately treated patients with primary or secondary and 24 months in PWH or those with latent syphilis. Yet, a significant percentage (~12%) of patients with syphilis will exhibit “serological non-response” (i.e. although asymptomatic, they have a <4-fold decline in NTr titer). Others (1.2-24%) will exhibit “serologic failure” (i.e. asymptomatic but exhibit a sustained >=4-fold increase in NTr titers in the absence of reinfection). Guidelines recommend those with serologic failure should undergo lumbar puncture (LP), while serologic non-responders should be retreated with 3 doses of benzathine penicillin G (BPG) and considered for LP, at least if follow up is uncertain or an initial high NTr titer (>1:32) in latent syphilis does not decline. The concern in these individuals is for undiagnosed central nervous system (CNS) infection, which could lead over time to relapse or progression to symptomatic neurosyphilis (SNS). However, LPs come with risks and logistical challenges, additional antibiotics may not be benign, and healthcare-related costs can be high. Currently, the best management approach (and whether LPs and additional antibiotics are necessary) for PWH who exhibit serological non-response and serological failure is uncertain, mainly because, in the antibiotic era, data on long term SNS outcomes in these patients are lacking. Longitudinal data on incident SNS in PWH comparing those with appropriate serologic response, serologic failure and serologic non-response following initial treatment are needed to inform often confusing treatment guidelines. Prospective trials would be ideal but are impractical given the decades of follow-up and large number of participants needed to identify this relatively uncommon outcome. We therefore propose to leverage the Johns Hopkins HIV Clinical Cohort-a dynamic and well characterized group followed from 1990- 2024 to 1. Determine SNS incidence over time in PWH with treated syphilis and compare the incidence in three groups: a. those who exhibit serologic non-response (i.e. <4 fold decline in NTr) b. serologic failure (i.e. sustained ≥4 fold increase in NTr after treatment) and c. those with appropriate serological response, and 2. Determine whether additional interventions (e.g. CSF examination and/or type and duration of antibiotic treatment) among persons with serologic non-response or failure, are associated with improved serological and clinical (i.e. development of SNS) outcomes. The results of this study have the potential to change national policy, reducing unnecessary lumbar punctures and potentially antibiotic treatment in PWH with serologic non- response or even serologic failure after initial syphilis treatment.

NIH Research Projects · FY 2025 · 2024-07

HIV-1 infection in infants persists at high rates despite efforts to prevent perinatal transmission. In 2022, an estimated 130,000 new perinatal HIV-1 infections were reported globally. Antiretroviral therapy (ART) is lifesaving for these infants. However, HIV-1 creates a hidden pool of proviruses that escape HIV-1 treatment and cause the virus to rebound. These proviruses make it necessary for children and adults to require lifelong ART. Novel therapeutic interventions such as very early antiretroviral treatment of newborns or combining ART with broadly neutralizing antibodies (bNAbs) are under study in the International Maternal Pediatric Adolescent AIDS Clinical Trials (IMPAACT) Network. These studies aim to restrict HIV-1 reservoir size to achieve ART-free remission in neonates and infants. The proposed project will characterize proviral pool composition in neonates and infants with HIV-1 initiating ART-free remission treatments. It will also investigate the proviral pool's contribution to viremic rebound during therapy and analytic treatment interruption (ATI). We hypothesize that achieving ART-free remission in infants depends on the proportion of intact proviruses and their integration sites at treatment initiation, along with their clearance susceptibility through very early and enhanced early treatment. We further hypothesize that clonal expansion contributes to a high proviral load before treatment and governs the time to rebound viremia on and off ART. The Specific Aims of this proposed project are to (1) Quantify and characterize the intact proviral pool in neonates and infants receiving very early and enhanced early therapies toward HIV-1 ART-free remission; (2) Evaluate HIV integration sites, clonal abundance of infected cells, infection dynamics in prenatal and early postnatal life, and viral clearance under ART interventions; (3) Assess the potential to improve bNAb susceptibility testing in neonates and infants to fully determine the selection and persistence of bNAb resistance during ART-free remission therapies. We plan to use cutting-edge approaches using near full-length single genome sequencing (nFLSGS) and integration site analyses on proviral DNA, along with a pan-subtype IPDA on genomic DNA from peripheral blood mononuclear cells (PBMCs) collected during therapy in two NIH-sponsored pediatric clinical trials involving very early treatment of neonates and infants in combination with broadly neutralizing antibodies, IMPAACT P1115 and 2008. We will also comprehensively assess the provirus susceptibility to a panel of bNAbs and their escape potential during bNAb therapy. The resulting data will fill a critical gap in understanding HIV-1 bNAb efficacy for neonates and infants globally.

NIH Research Projects · FY 2024 · 2024-07

PROJECT SUMMARY / ABSTRACT Atopic dermatitis, or eczema, affects up to 20% of children and is associated with significant physical, emotional, and social morbidity. Up to one-third of children with atopic dermatitis have moderate-to-severe disease and require systemic medications to achieve adequate disease control. While systemic therapies for pediatric atopic dermatitis were historically limited and consisted of broadly immunosuppressive medications such as methotrexate, highly efficacious and targeted systemic treatments, such as dupilumab and oral Janus kinase inhibitors, have recently emerged. However, the optimal treatment for any individual child remains uncertain, as real-world data on the long-term effectiveness and safety of both novel and traditional systemic medications for pediatric atopic dermatitis remain sparse. Thus, comparative effectiveness research (CER) is critically needed to fill these current knowledge gaps. Since new treatments for atopic dermatitis continue to rapidly emerge and traditional randomized trials are often lengthy and expensive, pragmatic trials and observational studies may be more efficient for CER in pediatric populations and nimbler in adapting to the expanding treatment landscape for atopic dermatitis. The growth of large clinical research networks, such as the national Patient-Centered Outcomes Research Network (PCORnet), also provides opportunities to leverage real-world data to conduct CER in pediatric atopic dermatitis. However, before such efforts can be undertaken, tools to easily and accurately identify children with atopic dermatitis within clinical research networks must be developed and methods to utilize observational data for CER in a way that ensures valid inferences must be employed. To meet these needs, this proposal has two specific aims: (1) develop and validate computable phenotypes for pediatric atopic dermatitis, and (2) apply a target trial emulation framework to compare the effectiveness and safety of dupilumab and methotrexate for atopic dermatitis treatment. Utilizing routinely-collected electronic health data held in the PCORnet common data model, this project will apply machine learning approaches to develop validated computable phenotypes for pediatric atopic dermatitis, including those distinguishing moderate-to-severe disease from mild disease, using structured data elements. In the target trial emulation comparing new pediatric users of dupilumab or methotrexate for atopic dermatitis, this project will test the hypothesis that dupilumab is associated with fewer topical medication prescriptions, lower rates of systemic treatment switching or intensification, and lower rates of adverse effects compared to methotrexate. This research will enable the efficient conduct of future pragmatic trials in pediatric atopic dermatitis and provide preliminary data for large, multi-center observational CER studies that will be the focus of future R01 applications. Ultimately, the findings from this proposal will help to meet the long-term goal of generating an evidence base to guide systemic treatment selection for children with atopic dermatitis.

NIH Research Projects · FY 2025 · 2024-07

Project Summary Candidate: Mark K. Meiselbach is an early career health economist and health services researcher. His long- term career goal is to become a leading mental health services researcher whose research informs policies to improve access to mental and behavioral health treatment for underserved populations. Research Context: There is a growing mental health crisis among older adults, but most older adults with mental illness do not receive treatment. This may be exacerbated by the rapid growth of Medicare Advantage (MA), which now enrolls most Medicare beneficiaries, as Dr. Meiselbach’s recent work shows that few psychiatrists accept MA plans compared to traditional Medicare or other forms of insurance. There is a critical need to understand access to mental health specialists in MA and how networks for mental health specialists in MA impact mental health care and outcomes for older adults. Specific Aims: Using Medicare claims data with novel data linkages, we will 1) characterize variation in geographic access to mental health specialists for older adults; 2) evaluate the impact of access to in-network mental health specialists in MA on utilization of mental health care and clinical outcomes among older adults in MA; and 3) investigate patient- and provider-level factors that modify the impact of access to in-network mental health specialists on utilization of mental health care and clinical outcomes. Career Development Plan: Dr. Meiselbach has a strong foundation in health policy, economics, and econometrics and substantial experience working with administrative claims data and other large databases. To achieve his long-term career goals, however, he needs to bolster his skillset to better understand how the quantitative findings of his research relate to the experience of patients and clinicians and how to translate these findings to meaningful policy change. Through this K01 career development award, he will receive training to 1) enhance his clinical understanding of mental health treatment in older adults, 2) gain expertise in geospatial measurement and modeling, 3) become expert in causal inference in mental health research, and 4) develop independence and leadership skills to inform policies that improve access to mental health care. Dr. Meiselbach’s mentorship team includes experts in mental health services research, geriatrics and geriatric psychiatry, spatial statistics, causal inference, economics, and policy dissemination. Research Goals: The goal of this research is to evaluate the impact of access to mental health specialists on older adults and identify the geographic areas and factors associated with worse access. Provider networks in MA are a mutable policy target. These findings can directly inform policies, such as network adequacy regulation, to improve access to mental health care and outcomes for older adults. The proposed study is closely aligned with NIMH’s strategic goal 4 to: Advance Mental Health Services to Strengthen Public Health, Objective 4.1: Improve the efficiency, effectiveness, and reach of mental health services through research.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY Multiple lines of evidence point to the role of adaptive immunity as response to viral infections and/or as misdirected autoimmune response in subjects with COPD and emphysema. There is support for an association between adaptive immune responses and COPD progression, but a direct link has not been made. In this proposal, we will utilize blood samples from 3,000 well-characterized subjects from the COPDGene Study, which include longitudinal follow-up and extensive available omics datasets. We will employ state of the art Phage ImmunoPrecipitation Sequencing (PhIP-Seq) technology to efficiently and comprehensively assess samples for autoantibodies and antibodies indicative of prior viral infections. Our first hypothesis is that previous infections with respiratory viruses, or differential immune responses to viral infections, are associated with more rapid progression of COPD, specifically lung function decline. The second hypothesis is that autoantibodies are associated with COPD, emphysema, and more rapid lung function decline. Aim 1: Human Virome and Lung Function Decline. We will test for associations between baseline viral antibodies and longitudinal decline in lung function at the 5 and 10-year study visits. We will also measure antiviral antibodies at the 5-year visit and test for lung function decline over the subsequent 5 years in subjects who acquire new or higher levels of specific viral antibodies, signifying interval infections. We will test whether these effects are modified by host factors including sex and HLA genotypes. Aim 2: Autoimmunity and COPD Outcomes. We will use PhIP-Seq to identify the presence of autoantibodies, we and will test for association between autoantibodies and COPD status, lung function decline, and quantitative emphysema parameters from chest CT scans. We will measure autoantibodies at the 5-year visit and test for lung function decline over the subsequent 5 years in subjects who acquire new or higher levels of autoantibodies. We will again test whether these effects are modified by host factors including sex and HLA genotypes. Aim 3: Adaptive Immunity and Chronic Inflammation Using whole blood RNA- sequencing data from the year 5 visit, we will derive gene expression scores representing antiviral and inflammatory pathways. We will test the association of these gene expression scores with viral antibodies and autoantibodies to discover novel drivers of persistent inflammation. We will validate the association of inflammatory gene expression scores with lung function and CT emphysema in a larger sample of COPDGene subjects with RNA-sequencing data. This proposal will complement the existing clinical, genetic and transcriptomic data in COPDGene by incorporating viral exposures and autoantibodies into longitudinal models of COPD progression. To accomplish this research, we have assembled a multidisciplinary team with expertise in in PhIP-Seq, COPD phenotyping, molecular immunology, genetic epidemiology, biostatistics and bioinformatics.

NIH Research Projects · FY 2024 · 2024-07

PROJECT SUMMARY / ABSTRACT Ischemic heart disease, the leading cause of mortality worldwide and at $475 billion/year also the costliest disease in the US, is highly heritable. Ischemia initiates specific biological processes that are highly dependent on genetic, transcriptional, and translational variation. In particular, regulation by noncoding RNAs (ncRNA), crucial components in the human genome, play a significant role in the biology of myocytes undergoing ischemia. Extracellular vesicles (EV) are emerging as new regulators of cell-to-cell communication carrying biological information, including proteins, lipids, and ncRNAs. The ncRNAs contained in EV, namely extracellular RNAs (exRNA), include microRNAs and other types of small RNAs and lncRNAs, some of which have been shown to be regulated by stressors and mediate functional effects in their recipient cells. Thus, exRNA offer tremendous potential as therapeutic molecules and biomarkers of disease. We have built a unique human tissue sample bank of over 230 patients experiencing myocardial ischemia while undergoing cardiac surgery with cardiopulmonary bypass (CPB). CPB is an applied human model of ischemia, as it is associated with obligatory ischemic myocardial injury evidenced by cardiac biomarker release, and therefore shares commonality with ambulatory myocardial infarction. Using this resource and as part of our NHLBI award, in the past four years we examined mRNA differential expression, lncRNAs, and microRNAs in ischemic human left ventricular myocardium, putting us in an ideal position to study the significance of exRNA in myocardial ischemic injury. We now propose to further explore the role of various short- and long ncRNAs by examining acute dynamic changes in ncRNAs in response to ischemia. Therefore, we will characterize the ncRNA transcriptome in the human and mouse heart, examine exRNA at various non-ischemic and ischemic time points in humans and mice, test for expressed quantitative trait loci (eQTL), and validate in a large population of cardiac surgical patients. Furthermore, we will use an ischemic mouse model to determine if the dynamically regulated exRNAs are present specifically in cardiomyocyte-derived EVs which will provide the framework for future interventional genetic studies. The results of this study will define the link between genetic variation, altered ncRNA expression and myocardial injury in human myocardial tissue and its associated ncRNA peripheral biomarkers. These ncRNA biomarkers can have an immediate clinical impact and advance the biological understanding, diagnosis and therapy of myocardial injury in humans.

NIH Research Projects · FY 2025 · 2024-07

Project Summary Immunoglobulin E (IgE) binds with high affinity to its receptor, FCeR1, found on the surface of basophils and mast cells. When an antigen binds to receptor bound IgE, it can lead to IgE receptor cross-linking and activation of basophils and mast cells. In this case, the antigen is subcategorized as an allergen. Thus, IgE is a pivotal molecule in the initiation of allergic reaction in a wide range of tissue. The IgE-dependent activation of basophils leads to the release of granular mediators and, also, to the production of Th2 inflammatory cytokines, IL4/5/13. Recent work has revealed a novel, allergen independent mechanism by which IgE, bound to its receptor, can lead to basophil activation resulting in greater IL4/13 production compared to standard IgE- dependent activation. The mechanism of this allergen-independent activation involves the sugar-binding protein Galectin-3 (Gal-3), which has been shown to bind directly to IgE. The data reveal that when a Gal-3 bearing cell physically comes into contact with a basophil, it leads to strong basophil activation. However, the parameters of this interaction remain poorly defined. I hypothesize that Gal-3 interacts with IgE independently of allergen specificity due to IgE’s variable glycosylation patterns, and that such glycosylation patterns may differ between allergic and non-allergic subjects. IgE with more N-glycan sugars will interact better with Gal-3 while IgE with more sialic acid will not interact as well. My first aim is to compare Gal-3 with standard IgE- dependent activation of basophils sensitized by serum from either allergic or non-allergic patients. My second aim examines the hypothesis that the affinity of Gal-3 for IgE is based on the presence of N-glycan structures and that this binding can be masked by terminal sialic acid residues. I will treat both whole cells and purified IgE with glycan modifying enzymes and quantify the Gal-3-induced cytokine production in basophils. My preliminary data shows that neuraminidase treatment, to remove terminal sialic acid residues, of whole basophils primed with IL-3 and bearing IgE augments Th2 cytokine production when placed in co-culture with Gal-3 bearing cells. The results of the study are expected to provide insight into a novel mechanism of allergen independent IgE activation and should prompt investigation to correlate it with clinical relevance.

NIH Research Projects · FY 2026 · 2024-07

PROJECT SUMMARY/ABSTRACT Adolescents commonly develop delayed sleep schedules in normal development related to physiologic processes, turning into “night owls” (late chronotype). Youth-onset type 2 diabetes (YoT2D) is a disorder with fast progression and early complications. Delayed sleep timing has been identified as a possible modifiable risk factor for YoT2D. Although prior studies have linked shifted sleep timing to impaired glucose metabolism, these studies may not extrapolate to youth with late chronotype as they utilize standard morning testing with oral glucose tolerance tests (OGTTs), at a time mis-aligned to the typical schedule of an individual with late chronotype. As glucose tolerance worsens as the day progresses until the middle of the night in healthy individuals, testing at a time when youth with late chronotype are typically asleep may alter results and lead to potential mis-diagnoses. Under the expert mentorship of Drs. Sheela Magge and co-mentor, Jonathan Jun, Dr. Talia Hitt will investigate whether alignment of glucose metabolic testing with chronotype improves glycemic outcomes and whether alignment of first morning meal timing to chronotype improves post-prandial glycemic response in youth with late chronotype. The proposed study uses a novel and rigorous randomized cross-over study design in youth (17-23y) with late and non-late chronotype (n=35 per group) to assess the glycemic effect of “aligning” an OGTT or first-meal of day to a subject’s chronotype. Both groups will undergo 2 OGTTs (aligned and mis-aligned with chronotype) to compare glucose tolerance and insulin sensitivity within-subject (primary outcome) and between groups (Aim 1). Then, youth will also undergo two standardized meals (aligned and mis-aligned with chronotype) while wearing continuous glucose monitoring to compare post- prandial glucose excursions within-subject and between groups (Aim 2). A pilot Exploratory Aim 3 (n=12 per group) will investigate delayed melatonin patterns under dim-light as a potential pathophysiologic mechanism behind abnormal glucose tolerance in youth with late chronotype on morning OGTTs. This study has potential implications for both clinical and research practices, as well as meal timing recommendations. It will provide preliminary data for a future R01 study of the relationships between sleep and circadian rhythm with glucose metabolism and YoT2D risk. This Career Development Award will develop Dr. Hitt’s training in 4 areas of focus addressing gaps in her prior research background: (1) longitudinal data analysis, (2) glucose metabolism mathematical modeling, (3) sleep and circadian phenotyping, and (4) experimental study design. Training goals will be accomplished through didactic coursework, one-on-one meetings with expert mentors and a multi- disciplinary advisory team, the study’s research activities, and attendance at scientific and career development seminars, and conferences. Dr. Hitt will have all needed resources and a supportive environment at Johns Hopkins. By the end of this 5-year award, Dr. Hitt will have the necessary skills to reach her long-term career goal to become an independent researcher in the intersection of youth chronobiology and glucose metabolism.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY / ABSTRACT Indirect-detection x-ray Flat Panel Detectors (FPDs) use a scintillator to convert x-rays to light, which is then detected by photodiodes coupled to readout electronics. During the past two decades, the latter evolved from noisy amorphous Silicon arrays with coarse pixels (>130 µm) to low-noise CMOS sensors with very fine pixels (<100 µm). There has been comparatively little innovation in the scintillator, which is now the principal factor limiting FPD spatial resolution. The scintillator bur is caused by the lateral spread of light between the x-ray interaction site and the photodiodes. To overcome this challenge, we propose to use laser ablation to pixelate the scintillator film – here, a ~700 µm thick CsI:Tl commonly used in FPDs - at a pitch matching the readout array. We will develop Atomic Layer Deposition (ALD) techniques to coat the high-aspect ratio pixelation grooves with an optimized combination of absorptive and reflective layers to ensure that there is no inter-pixel cross-talk and that the majority of x-ray interaction light is directed towards the photodiodes. To mitigate signal losses due to the loss of film volume in pixelation grooves, we will use a novel crystalline form of micro-columnar CsI:Tl (CMS CsI:Tl) which enhances the sensor signal-to-noise ratio (SNR) by exploiting the higher density and increased transparency of the crystalline material. The proposed scintillator has the potential to substantially improve the performance of modern FPDs by enabling ultra- high spatial resolution imaging without sacrificing x-ray attenuation provided by using a relatively thick CsI:Tl. We have performed initial experimental studies of this approach and found ~20% better limiting spatial resolution than conventional detectors. This proposal will build on this early work by (i) refining the pixelation technique to obtain even thinner pixel grooves for better detection efficiency, and (ii) optimizing the CMS deposition process and the inter-pixel coatings for improved light output. Our technology will benefit applications where visualization of ~100 µm details is desired, but currently challenged by image noise due to body size and/or patient dose: 2D and 3D angiography, pulmonology, breast, otolaryngology imaging, and orthopedics. For an initial demonstration of potential clinical utility, we target quantitative in vivo assessment of bone microarchitecture in osteoporosis (OP) and osteoarthritis (OA). We will pursue the following specific aims: Aim 1: Optimize the pixelation process to maximize spatial resolution, detection efficiency, and brightness of the pixelated CsI:Tl films. Achieve light yield approaching that of a conventional scintillator and improved SNR for ~100 µm features. Aim 2: Validation in quantitative high-resolution Cone Beam CT of trabecular bone. Characterize of the pixelated detector in terms of fundamental metrics of CBCT imaging performance and in 3D trabecular measurements (bone volume, trabecular thickness and spacing) in a range of body sites pertinent to OA and OP. The results will inform future development of other possible applications of FPDs based on pixelated scintillators with high detective efficiency, e.g. in interventional radiology and pulmonary imaging.