Johns Hopkins University

NIH Research Projects · FY 2025 · 2024-08

Project Summary: The post-translational modification (PTM) of core histones is integral to the regulation of transcription. The SAGA (Spt-ADA-GCN5-acetyltransferase) complex, capable of H3 acetylation and H2B deubiquitination, is a transcriptional co-activator involved in nearly all Pol II mediated transcription. This 1.8mDa complex, composed of 19 subunits in yeast, contains a core complex and two enzymatic complexes: the histone acetyltransferase (HAT) module and deubiquitinating (DUB) module. The heterotetrameric HAT module, composed of the acetyltransferase GCN5, ada2, ada3, and sgf29, contains multiple reader domains that bind chromatin to acetylate histone tails. Increasingly, the SAGA HAT module is being recognized as a therapeutic target in a multitude of c-myc driven cancers. While recent cryo-EM structures of yeast and human SAGA have been reported, neither the DUB nor HAT modules could be resolved, presumably due to their high mobility. In addition, none of these studies explored the structural engagement of these modules to chromatin. Interestingly, the distance between the DUB and HAT modules strongly suggests that these modules could act in concert on neighboring nucleosomes, thereby acetylating one while deubiquitinating the other. Despite this, the vast majority of research on SAGA has been done on peptides and, in a more limited way, on single nucleosomes. In Aim 1 of my studies, I plan to study the acetylation activity of SAGA complex on a library of mono- and di-nucleosomes with biologically relevant PTMs to probe how these modules act in concert to exert their enzymatic activities. More broadly, this will inform our understanding of how SAGA utilizes its reader, writer, and eraser functions to regulate transcription. Additionally, no structure exists to date of the SAGA HAT module, limiting our mechanistic understanding of how SAGA acts to promote active transcription. In Aim 2 of my studies, I plan to solve the cryo-EM structure of the SAGA HAT module bound to both unmodified and H3K4me3 modified nucleosomes. From biochemical data and other chromatin modifying enzymes, I hypothesize that the PTM H3K4me3, recognized by sgf29, limits the conformational landscape of the HAT module on a nucleosome for the processive acetylation of H3 histone tails. Altogether, our studies will provide insight into SAGA complex regulation in the context of histone crosstalk and establish a new paradigm for studying chromatin modifying enzymes. Furthermore, our research will provide the field with a mechanistic understanding of how the SAGA HAT promotes active transcription and, feasibly, will provide new therapeutic targets in c-myc driven cancers.

NIH Research Projects · FY 2025 · 2024-08

Project Summary/Abstract Alzheimer's disease (AD) is a global issue that must be solved urgently because of its significant impact on public health and economics, as well as the quality of life of individuals in the United States and other aging societies. Once cognitive impairment occurs in the AD continuum, there are great difficulties in modifying the devastating disease process. Pathological changes inside the brain begin silently many years before the onset of cognitive impairment. This long “preclinical” stage provides us with an opportunity for timely therapeutic and preventive interventions. Therefore, the development of tools that can predict future cognitive decline during the preclinical stage of AD is crucial. There is a consensus that neurodegeneration has a stronger correlation with cognition in the disease progression along the AD continuum, compared to the diagnostic AD biomarkers such as amyloid and tau proteins. In contrast, neuroimaging modalities currently used to detect biomarkers for neurodegeneration are not sensitive enough to detect minute changes during the preclinical stage of AD. Here, Dr. Yuto Uchida hypothesized that myeloarchitectonic features observed in the entorhinal-hippocampus pathway could serve as sensitive neurodegenerative biomarkers given that AD pathogenesis occurs in the entorhinal cortices. In this project, he will conduct a proof-of-concept study to examine microstructural neurodegeneration of the entorhinal- hippocampus pathway in a combined framework: ex vivo ultra-high-field quantitative MRI followed by histological verification in Aim 1, and in vivo ultra-high-field quantitative MRI in clinical settings for healthy controls in Aim 2 and for preclinical and prodromal AD individuals in Aim 3. In Aim 1, postmortem hemibrains will be scanned on a human 7T MRI scanner and compared with the corresponding histology in the entorhinal-hippocampus pathway to fill the gap between the MRI findings and microscopic observations. In Aim 2 and Aim 3, cutting-edge, deep learning-based susceptibility tensor imaging (DeepSTI) and DeepSTI-based tractography will be applied to an ongoing cohort study (RF1AG071515), which comprises healthy, preclinical, and prodromal AD individuals. In Aim 2, reference ranges for quantitative MRI measures in the entorhinal layer II and the perforant path fibers will be established. In Aim 3, comparative analyses of these quantitative MRI measures among the groups will be done cross-sectionally, which will be followed by a longitudinal study to examine these associations with cognitive decline along the AD continuum. In summary, the long-term objective of this K99/R00 application is to support Dr. Yuto Uchida’s ability to conduct studies aimed at developing biomarkers for neurodegeneration that can visualize and quantify microstructural brain alterations during the preclinical stage of AD using ultra-high- field quantitative MRI. Dr. Uchida will be co-mentored by Drs. Kenichi Oishi, Xu Li, Jeremias Sulam, Hanzhang Lu, and Juan C. Troncoso, who are experts in neuroanatomy, MRI physics, deep learning-based algorithms, neurofunction, and histopathology, respectively. Having multiple mentors with different areas of expertise can broaden Dr. Uchida’s technical and scientific skills and further his goal of becoming an independent investigator.

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.

NSF Awards · FY 2024 · 2024-08

This project aims to advance the state of the art in analyzing data generated through high-throughput RNA sequencing experiments by developing cutting-edge software that addresses the current challenges in transcriptome assembly and gene annotation. RNA sequencing has become a vital method for understanding gene expression across various cell types and conditions, leading to discoveries of new genes and splice variants in a wide range of species. However, the increasing volume of data from large-scale sequencing experiments demands more efficient and precise computational methods. This project seeks to create innovative algorithms to improve the accuracy and scalability of computational methods for assembling the data from these experiments, thereby producing more accurate measurements of the genes and transcripts present in any tissue sample. By tackling these challenges, the project promises significant advancements in the understanding of gene expression and transcriptional activity, benefiting a wide range of scientific research. Additionally, by leveraging data from previous experiments in a new way, it will provide a cost-saving opportunity by reducing the number of samples required for sequencing. The project will focus on three key areas to overcome the limitations of current RNA-seq analysis methods. First, a scalable approach for assembling transcripts from large RNA-seq datasets will be developed by constructing a "universal splice graph" that captures all valid alignments and ensures consistent transcript structures across samples. Second, a new model of transcriptional noise will be introduced, which aggregates data from multiple experiments to distinguish genuine transcripts from background noise, enhancing the precision of transcript quantification. Third, collections of universal splicing graphs will be generated to represent transcriptional activity across different species, cell types, and tissues. These methodologies leverage the extensive RNA-seq data available today and provide essential tools for identifying structural variations in transcripts and performing differential expression analyses. The proposed software will be open-source, facilitating widespread adoption and furthering research capabilities in computational biology. All software will be freely available from https://ccb.jhu.edu/software/stringtie and on a public github archive. 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 Cells first interact with their environment through the plasma membrane where diverse interactions between lipids and proteins organize membrane complexes in response to external stimuli. One cellular behavior in which membrane organization plays a critical role is cell migration, wherein cells traverse complex three-dimensional landscapes to hone to new destinations. Cell migration events are at the root of many processes including embryonic tissue morphogenesis, immune cell surveillance, and cancer cell metastasis. Thus, a mechanistic understanding of how the plasma membrane is organized to orient cell migration is necessary for our appreciation of the basic principles of cell migration and for the identification and treatment of aberrant cell migration during human development and disease. While significant work has deciphered the adhesion, signaling, and mechanical proteins underlying migratory behaviors, we know far less about how individual lipids, and the biophysical properties they contribute to the membrane, regulate migratory behaviors. Research in our laboratory interrogates the role of lipid metabolism in regulating cell signaling, in vivo migration, and membrane fluidity with the ultimate goal of identifying new strategies to modulate aberrant cell migration during development and disease. We use the avian neural crest cell population as an ideal in vivo model to address these previously inaccessible questions due to their robust and synchronous migratory behavior, the ease by which they can be manipulated and visualized in vivo and measured for biophysical properties. Under this award we will answer the questions 1) how does membrane fluidity orient in vivo cell migration, and 2) how do cells regulate local membrane fluidity? We hypothesize that migrating cells undergo active lipid metabolism at the plasma membrane to tune local membrane fluidity, and that the organization of relative fluidity orients cell migration by positioning receptor proteins necessary for chemotaxis. We will test these hypotheses using in vivo and ex vivo live cell imaging, optogenetic approaches to locally alter membrane fluidity and protein localization, measuring transmembrane receptor protein diffusion rates, and performing targeted gene knockdown and mis-localization experiments. These projects will yield high-impact discoveries that shed new light on how to prevent cancer metastasis, improve wound healing and inflammation responses, and correct for atypical tissue morphogenesis. In addition, these experiments will reveal new directions for our lab as we continue to decipher how plasma membrane organization regulates cell signaling and migration.

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.

NIH Research Projects · FY 2024 · 2024-08

Project Abstract 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 diverse users of new treatments, who differ in clinical responsiveness, side effects tolerance, risk acceptance, spending preferences, and use of therapies driven by healthcare access inequities and cultural differences. In the planning phase (R61), we will conduct focus groups with diverse individuals 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, including racial and ethnic subgroups that have experienced inequities in management of ADRD. 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 and health equity impacts of new existing and hypothetical ADRD drugs, 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 2024 · 2024-08

PROJECT SUMMARY/ABSTRACT With an emphasis on the integration of basic, translational, and clinical approaches, the Americas Association of Sarcoidosis and Other Granulomatous Disorders (AASOG) 2024 Scientific Conference, entitled “The Art of Working Together for Progress,” will focus on a central question: how can multi-disciplinary care, research, and education in sarcoidosis improve patient outcomes, reduce health disparities, and advance disease understanding? To address this central question, the program is organized into a series of thematic sessions focusing on (i) the development of multi-disciplinary teams and training multi-disciplinary experts, (ii) health disparities in sarcoidosis (iii) clinical trials and outcome selection, (iv) precision medicine in sarcoidosis and (v) advanced disease management. The conference aims to accomplish the following objectives: 1) To establish the only large forum in the western hemisphere to present ongoing research and multidisciplinary collaboration of investigators specifically focused on the pathogenesis and treatment of sarcoidosis. 2) To stimulate interactions between the scientific fields of immunology, molecular biology, epigenetics, genetics, genomics, and public health to identify emerging, shared interests that may lead to the performance of more efficient and productive research. 3). To inspire interactions between the disciplines and multidisciplinary team members within sarcoidosis, including pulmonary, cardiology, rheumatology, ophthalmology, and neurology, to improve patient outcomes, develop management strategies, and reduce health disparities. 4) To challenge and stimulate the scientific interests of trainees, attracting a new generation of junior investigators into the field of sarcoidosis. The AASOG 2024 Planning Committee has identified outstanding thought leaders in sarcoidosis as well as selected experts from outside the field to achieve the mission of improving the collective clinical and scientific approach to sarcoidosis. Each session will consist of several presentations followed by dedicated time for discussion to stimulate collaboration and innovation. A major thematic focus of the conference is addressing health disparities in sarcoidosis through a multidisciplinary, collaborative approach. The program aims to achieve this by continuing AASOG’s commitment to diversity and inclusivity with conference faculty including approximately 50% women, 20% from underrepresented racial/ethnic groups, 17% early career faculty, 17% non-physician team members, including 4 patients. Participation of trainees and junior faculty is facilitated by an oral abstract session, poster sessions, and a clinical case discussion session. Networking and collaboration opportunities will include meal and coffee breaks, a structured speed mentoring event, a dinner reception and a breakout group session. The conference will conclude with a high-level summary and review of the impact and common themes from the conference to identify key future directions for basic, translational, and clinical research in sarcoidosis. Attendees will receive Continuing Medical Education credit and can attend in person or virtually to facilitate participation and dissemination of knowledge in the field.

NIH Research Projects · FY 2025 · 2024-08

Preventing Chronic Postsurgical Pain (CPSP) and reducing postsurgical opioid exposure is a public health imperative. Perioperative insomnia is an increasingly recognized modifiable risk factor for CPSP and opioid usage, but studies have yet to evaluate whether treating insomnia perioperatively reduces CPSP and opioid exposure. Insomnia has been linked to central nervous system alterations that contribute to the transition from acute to chronic pain and is prevalent in at least 50% of older adults with knee osteoarthritis (KOA), awaiting total knee arthroplasty (TKA). Currently, TKA for end stage KOA is the most common elective surgical procedure in the US. Rates of CPSP after TKA are high with ~ 20% of individuals reporting moderate to severe CPSP. Research determining whether optimizing sleep improves TKA outcomes is critical because TKAs are estimated to increase exponentially to 3.5 million per annum in the next decade. Benzodiazepine receptor agonists, the most commonly used therapies for insomnia are contraindicated in older adults and especially dangerous in the context of opioid pain management. Cognitive-behavioral therapy for insomnia (CBTi), is a safe, well-established treatment for insomnia that improves sleep in chronic pain and has demonstrated small, but significant effects on pain severity that require enhancement. Emerging data suggests that morning bright light treatment (MBLT) not only improves circadian rhythms and sleep, it has mood enhancing and analgesic properties. Although both CBTi and MBLT have distinct mechanisms of action, research on their combination is just emerging and neither has been used to prevent CPSP or reduce opioid use. We propose a randomized, controlled, parallel arm, clinical trial, to test the effects of CBTi and CBTi+MBLT on CPSP and opioid sparing following TKA. Five weeks prior to surgery, TKA patients with insomnia will be randomized to one of 3 conditions matched on timing and contact duration: 1) CBTi+placebo [four pre-surgical telehealth sessions + two post-TKA boosters (2-week and 3 mo. post TKA)] with 1-hour daily morning deactivated ion generator sham exposure (placebo) for 4-wks. pre and 4-wks. post-surgery; 2) CBTi+MBLT (1-hour daily morning bright light treatment for 4-wks. pre and 4-wks. post-surgery), and 3) Education (EDU)+placebo with 1-hour daily morning deactivated ion generator exposure (4-wks. pre and 4-wks. post-surgery). Outcomes will be assessed at baseline, post CBT-I (pre-surgery), 6-weeks, 3, and 6-months post-surgery. We have three aims: 1) To evaluate the effects of perioperative CBTi+placebo and CBTi+MBLT on CPSP [(3-6 mos.) primary] and opioid use [(6 weeks-6 mos.) 2ndry]; 2) To examine the effects of CBTi+placebo and CBTi+MBLT on pre-surgical, acute post-surgical (6-weeks), and chronic (3, 6 months) insomnia symptom severity, circadian rest activity rhythm (RAR), and depressed mood; 3) (exploratory) Evaluate whether the effects of treatment condition on CPSP and opioid use from 3 to 6 months post-TKA are partially mediated by improvements in insomnia severity, increases in circadian RAR strength and decreases in depressed mood at 6-weeks post-TKA.

NIH Research Projects · FY 2026 · 2024-08

The Nursing Science Incubator for Systemic Solutions (N-SISS) at the Johns Hopkins School of Nursing will support nurse scientists and scientists in aligned fields in developing innovative and rigorous programs of research focused on addressing health system gaps and the conditions of daily living. Because we intend to deliver N-SISS educational materials to two important but distinct audiences—that is, three annual cohorts of 10 core N-SISS Innovators as well as a national audience of nursing or aligned researchers and students (ancillary N-SISS network trainees)—we organized the N-SISS program into two tailored sets of activities and resources. At its core, the program will consist of a 10-month-long structured training curriculum of individualized research training, applied, hands-on, mentored research experiences, scientific mentoring, and career support, which will be offered to core N-SISS Innovators and which will culminate in the submission of an NIH (R, K, or F) grant proposal at the end of the program. Secondarily, the ancillary N-SISS network trainee program will provide a variety of training resources for self-directed learning via a dedicated web platform open to all researchers and students at no cost. The N-SISS program design is innovative in several respects: the curriculum draws upon the project team's integrated conceptual framework to provide the requisite theoretical and methodological skills to address health system gaps and the conditions for daily living; the program uses a three-pronged mentoring approach grounded in the literature of effective scientific and career mentoring for independent research; and the didactic and collaborative learning opportunities are additive, providing flexibility and enhancing the reach to national audiences. Program materials and events will be accessible to ancillary NSISS network trainees, who include members of the broader nursing and aligned scientific workforce (we estimate at least n=3,600 ancillary network trainees will use the program over the project period). N-SISS will leverage Johns Hopkins University's extensive research and training infrastructure and the program directors' national network of researchers committed to addressing health system gaps and the conditions of daily living to strengthen the scientific nursing workforce's capacity to conduct impactful, innovative research to redesign health.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY The overarching theme of the Johns Hopkins Autoimmunity Center of Excellence (ACE) is that distinct immune cell subsets are the major drivers of immunopathogenesis in different autoimmune diseases, and that targeted therapies at a critical juncture of disease trajectory will modify or halt the propagation of disease. The primary clinical project led by Pavan Bhargava, MBBS, MD, proposes to selectively target effector-memory T cells, class- switched memory B cells, and inflammatory microglia in secondary progressive multiple sclerosis (SPMS) by blocking the potassium channel Kv1.3 using dalazatide. Utilizing, cutting-edge immunological, imaging and biomarker assessments, this trial seeks to identify pathogenic immune cells driving disease in SPMS while testing a novel treatment strategy that could be applied to a range of other autoimmune disorders. The alternate clinical project led by Julie Paik, MD, MHS, proposes to target B-cells using a novel, third generation anti-CD 20 agent, ublituximab, early in the course of active, autoantibody positive myositis (excluding inclusion body myositis). The current challenge in the therapeutic landscape of myositis is that B-cell depleting agents are considered third line despite the wealth of literature supporting their efficacy. Therefore, this proposed Phase 2 randomized, double-blind trial of ublituximab in myositis can potentially lead to a paradigm shift in the utilization of B-cell depleting agents as first-add on therapy to background immunosuppression. And lastly, the collaborative project led by Elias Sotrichos, MD, seeks to perform deep phenotyping of single immune cells in the peripheral blood and cerebrospinal fluid in neuromyelitis optica spectrum disorder (NMOSD) and myelin oligodendrocyte glycoprotein antibody disease (MOGAD) to identify subsets that are involved in disease pathogenesis. All three projects highlight the extraordinary cross-discipline synergy that exists at Johns Hopkins through the collaborative resources of the Johns Hopkins Institutional Precision Medicine initiative. The establishment of the Johns Hopkins ACE will further leverage the Multiple Sclerosis and Myositis Precision Medicine Centers of Excellence to achieve the following aims: 1) Enable the implementation and execution of innovative, investigator initiated therapeutic trials, (2) Discover key cellular drivers of autoimmunity through modification of immune function with investigational therapeutic agents, and (3) Increase interdisciplinary collaborations within Johns Hopkins and the broader ACE network to advance the understanding and treatment of autoimmune diseases. These aims will be achieved through the resources of the Administrative coordination group which will be a conduit to integrate all scientific and administrative oversight of the Hopkins ACE. Additionally, the funds management core will provide support to studies throughout the ACE network, while the Biobanking core can handle a variety of samples and will be an indispensable resource to support the clinical research projects that are ongoing in the ACE network.

NIH Research Projects · FY 2025 · 2024-08

Project Summary Preserving and repairing injured neurons is the primary goal of treatments for brain injuries. Yet, delivering therapeutics specifically to neurons has been a challenge due many factor. Increased glucose uptake and its hypermetabolism, is a hallmark of injury or evolving injury in neurons in many pathological conditions (e.g. seizures, stroke, trauma). Delivering drugs specifically to injured neurons in the area of pathology, would address a significant gap in neuroprotective approaches, opening new treatment avenues for acute CNS disorders. We seek to address this gap by developing novel dendrimers that take advantage of altered glucose transport in injured neurons, without a need for a targeting ligand or antibody. Previously, our group developed hydroxyl polyamidoamine (PAMAM) dendrimers that specifically targeted reactive brain microglia/macrophages and attenuated neuroinflammation and injury in multiple models of brain injury, and now are in early Phase 2 clinical trials. This application aims to develop and validate a novel dendrimer made primarily from glucose that preferentially targets injured neurons. We have designed non- degradable dendrimers made primarily of glucose building blocks, that can facilitate enhanced uptake due to multivalent surface interactions with glucose transporters. We hypothesize that glucose dendrimers will localize primarily into injured neurons, enabling sustained delivery of drugs for neuroprotection and preventing neuronal loss. Importantly, our preliminary data, with a generation-2 glucose dendrimer (GD2) with 24 glucose molecules on the surface, suggests that they specifically localize in injured/active neurons in vitro and four clinically-relevant, diverse in vivo models of acute neuronal injury. Glucose dendrimer-ketamine conjugate (GD2-ket) is more effective than ketamine alone in suppressing clinical seizures in an established rodent epilepsy model. We will test our hypothesis by performing experiments in the following aims: Aim 1: Determine the extent and specific mechanisms of glucose-dendrimers (GD) uptake in neurons. Aim 2: Evaluate in vivo cellular biodistribution and pharmacokinetics (PK) of systemic glucose-dendrimers in a mouse model of acute neuronal injury induced by epilepsy; Aim 3: Determine efficacy of glucose-dendrimer-ketamine conjugates in rodent model of epilepsy. The proposed glucose dendrimer platform can impact treatments for multiple CNS disorders, especially in the acute phase, opening new avenues for nanomaterials. Our team has the combination of dendrimer nanomedicine, neuroscience, epilepsy, and brain injury expertise to carry out the proposed studies and enable translation from the bench to bedside.

NIH Research Projects · FY 2025 · 2024-08

Our LONG-TERM GOAL is to extend current biological and artificial vision research from a focus on 2D image recognition toward visual understanding of 3D structure in the real world. 3D object perception is the essence of real-world vision, underlying the “thousand words” of information the brain generates about precise object geometry on large and fine scales, structural design, mechanics, material composition, biological morphology and functionality, physical state, pose, mass distribution, balance/support against gravity, potential for movement from passive falling/rolling to self-generated motion and complex interactive behaviors, age, beauty, damage, value, etc. Our first AIM is to use artificial vision networks to decipher brain algorithms underlying biological 3D vision. We will train novel, analyzable network architectures developed for 3D vision by the Yuille lab, to replicate 3D shape tuning functions of individual neurons recorded in the Connor lab, from successive stages of object processing in macaque monkeys: area V4, posterior inferotemporal cortex (PIT) and anterior inferotemporal cortex (AIT). The Connor and Yuille labs will analyze the 3D shape processing algorithms learned by these neuron-trained networks (NTNs), tracing the pathways of information from V1- like 2D Gabor filters in layer 1 to the output neuron response, using a novel method for back-tracing the sources of excitatory and inhibitory signals through the network. Our second AIM is to develop artificial networks that implement biological algorithms to achieve human- level 3D visual performance. The Yuille lab will build on preliminary work proving the potential of novel network architectures performing analysis-by-synthesis with Neural Textured Deformable Meshes (NTDMs). These networks are designed for internal reconstruction of and high-level inference from 3D shape in natural scenes. The Connor lab will use components of these networks, in addition to more standard architectures like AlexNet, to train using neural responses (AIM 1). The trained network components and algorithms deciphered from them (AIM 1) will be incorporated by the Yuille lab into their evolving NTDM network designs to search for higher performance on larger 3D shape domains under a variety of real-world viewing conditions. Training and testing in larger 3D shape domains will depend on a unlimited photorealistic 3D ground truth-parameterized stimuli produced by genetic algorithms developed by the Connor lab (PRGAs). RELEVANCE (See instructions): This study aims to understand the neural algorithms that underlie visual understanding of 3D structure in the real world and apply those algorithms in artificial visual systems. Understanding these neural algorithms is relevant for future prosthetic approaches to restoring 3D visual experience through cortical implants. Using these algorithms to bring artificial vision closer to biological vision will be essential for intelligent driving of such prosthetics based on camera images.

NIH Research Projects · FY 2026 · 2024-08

Project Summary/Abstract In-vivo proton magnetic resonance spectroscopy (1H-MRS) can non-invasively measure levels of more than 20 biochemicals in the human brain. With its ability to detect surrogate markers of neuronal health and cell proliferation, neurotransmitters, antioxidants, tumor markers and others, 1H-MRS provides a unique window onto metabolic changes in health and disease. It therefore holds great potential for clinical research, diagnosis, and treatment response monitoring. Clinical translation of MRS has been curbed by the wide range of available technical methods for data acquisition and analysis. These have often produced inconsistent results. Recent research has particularly recognized that metabolite level estimates depend strongly on the way that the measured data are modeled. Traditional 1H-MRS analysis procedures do not capture this uncertainty, and there are currently no methods to determine whether one model is preferable over another. The core theme of this project is a paradigm shift: fitting the measured data with a set of multiple candidate models will replace traditional single-model analysis. A multiverse analysis framework will then capture and quantify the variability across the candidate models, particularly focusing on currently existing MRS software. Model selection tools, in contrast, will use statistical information criteria to actively discriminate which models are the most suitable for a given dataset. These twin strategies (simultaneous consideration of multiple candidate models and data-driven identification of the ‘best’ models) are complementary and provide practical tools to boost the accuracy and precision of metabolite measurement. Clinical and research utility of the new strategies are further amplified by interfacing them with stochastic Markov Chain Monte Carlo sampling. These methods allow model parameter distributions to be characterized more accurately, providing alternative means of uncertainty estimation that eliminate many weaknesses of traditional Cramer-Rao Lower Bounds (CRLB). The project will further demonstrate that these new methods improve the accuracy and precision of non-invasive measurement of 2-hydroxyglutarate (2-HG), a highly specific oncometabolite that plays a pivotal role in IDH- mutated low-grade glioma. In summary, this project proposes several novel data analysis strategies for in-vivo 1H-MRS that address the challenge of analytic variability associated with the choice of modeling approach. All developed software code will be made available to the community through our well-established open-source software ‘Osprey’.

NIH Research Projects · FY 2025 · 2024-08

Musculoskeletal (MSK) pain is a major burden on the US population, representing the leading cause of disability and non-cancer reason for opioids prescriptions, as well as the top health care spending category in the country. Physical therapy (PT) has been shown to be effective in reducing pain and disability among patients with MSK pain. PT has also been shown to help reduce health care spending related to MSK pain by reducing the utilization of major cost drivers, such as imaging and surgery. However, the effects of PT are closely tied to patients’ engagement with PT care, especially how often they complete prescribed home exercises. Unfortunately, these rates are often low, which means patients are not experiencing the full benefit of PT and are likely going on to receive more invasive procedures or use opioids following a “non-response” to PT. In 2021, new procedural codes were announced by the Centers for Medicare and Medicaid Services that facilitate the use of Remote Therapeutic Monitoring (RTM) by physical therapists. RTM is a point of care mobile health (mHealth) solution that includes the integration of a mobile application into the PT episode of care. Through the use of a digital RTM platform, RTM allows physical therapists to assign exercises to patients in a mobile application, track their adherence to home exercise programs, and to track patient progress through the use of patient-reported surveys administered through the mobile application. While RTM stands to improve patients’ experiences with PT and the effectiveness of PT, little to no research has been conducted on the effectiveness of RTM-enhanced PT nor has research been conducted examining the feasibility of implementing RTM in health care systems. As such, there is an urgent need for research examining the use of RTM among patients with MSK pain. To address this gap, we propose a phased project (R21/R33) that will examine the feasibility, effectiveness, and implementation of RTM at a large US academic health care system. During the R21 phase of the project, we will examine the feasibility of implementing RTM among a pilot group of physical therapists that provide care for patients with MSK pain (R21 Aim 1). We will also elicit feedback from these physical therapists and their patients receiving RTM to refine our approach to delivering RTM (R21 Aim 2). Informed by our experiences during the R21 project phase, the R33 project phase will include full-scale implementation of RTM among all MSK physical therapists at our institution. During this project phase we will utilize routinely collected patient-reported data (i.e., PROMIS) to examine the clinical effectiveness of RTM-enhanced PT compared to standard PT (R33 Aim 1), the influence of RTM-enhanced PT on cost and downstream health care utilization (e.g., imaging, opioids) (R33 Aim 2), and key implementation outcomes based on the RE-AIM framework. This study will represent one of the first studies of RTM-enhanced PT and is likely to have major implications for the use of RTM services in the US. Our team plans to leverage the experience and data we obtain during this project to inform the development of a multi- center clinical trial examining the clinical and cost-effectiveness of RTM outside of our institution.

NIH Research Projects · FY 2025 · 2024-08

The goal of CHIPP-PrEP: Cabotegravir-Hormone Interrogation of Pharmacokinetics/Pharmacodynamics for HIV Prevention is to characterize the relationship between endogenous and exogenous hormones and long-acting cabotegravir (CAB-LA) for HIV pre-exposure prophylaxis. A key strategy to improve the quality of life for all people at risk of HIV acquisition is to ensure that HIV prevention tools are efficacious for all populations; therefore, more nuanced understanding of drug-hormone interactions is required to understand HIV acquisition vulnerability in the female genital tract and the rectal compartment. The HIV Prevention Trials Network (HPTN) 077 clinical trial revealed sex-based differences in CAB-LA pharmacokinetic (PK) parameters, including trough concentrations (Ctau), maximum concentrations (Cmax), and the area under the concentration curve (AUC); further, the terminal apparent half-life (t1/2) of CAB-LA was longer in females than males. Via population pharmacokinetic (popPK) modeling, CAB-LA PK parameters, including the CAB-LA absorption rate constant (Ka), are influenced by sex, body mass index (BMI) and needle length (indicator of injection site fat distribution). Notably, CAB-LA maximal concentrations (Cmax-SS) are predicted to be lower and Ctau-SS are predicted to be higher in women as compared to men, which may result in protective pharmacologic advantages in women; these observations may be driven by estradiol-mediated changes in fat disposition. While the Phase 2B/3 HPTN 083 and Phase 3 HPTN 084 trials demonstrated superior HIV prevention efficacy of CAB-LA to daily oral emtricitabine/tenofovir disoproxil fumarate (F/TDF) in preventing HIV in males and females, respectively, there was a higher relative risk reduction of HIV acquisition in the HPTN 084 study, which enrolled women. Based on the complex interactions of estrogens on body composition and fat distribution, absence of CAB-LA pharmacologic correlates of protection, and the paucity of data detailing drug interactions between endogenous and exogenous hormones and CAB-LA, additional data are needed to understand the PK and PD of CAB-LA in males and females. The proposed work will address these gaps through the following: a) evaluation of the multi-compartment CAB-LA PK in males and females, including individuals on stable exogenous hormone regimens; b) development of a CAB-LA PK/PD model using ex vivo HIV susceptibility assays; and c) generation of a popPK model inclusive of PK and PD data and subsequent simulations to evaluate the contribution of endogenous and exogenous hormones, such as estradiol, on CAB-LA PK parameters. The proposed research provides a critical next step in our understanding of CAB-LA for HIV prevention and may provide rationale for sex-specific CAB-LA dosing with current and future CAB-LA formulations to optimize protection efficacy.

NIH Research Projects · FY 2025 · 2024-08

Sexually reproducing organisms depend on the precise segregation of chromosomes during meiosis to ensure the inheritance of the genome through the formation of haploid gametes. Defects in this process can lead to infertility and the production of gametes with an abnormal number of chromosomes, known as aneuploidy. To successfully segregate chromosomes during meiosis, homologous chromosomes must pair, synapse, and undergo crossover recombination during prophase I. Synapsis is defined by the formation of a highly conserved, zipper-like proteinaceous structure called the synaptonemal complex (SC) that links two homologs together and serves as a scaffold for crossover recombination. The SC is a tripartite structure comprised of two parallel stretches of chromatin-associated axial elements and a central region that connects the two. Despite its conserved role and appearance across most eukaryotes, little is known about its molecular architecture and the mechanisms that underlie the assembly of higher-order SC structures. The nematode Caenorhabditis elegans has been an excellent model organism for studying meiotic mechanisms. In C. elegans, the SC central region has been known to be composed of six interdependent coiled-coil proteins SYP-1, SYP-2, SYP-3 SYP- 4, and SYP-5/6. Recently, we have identified that two paralogous Skp1-related (SKR) proteins, SKR-1/2, which are adaptors of the Skp1-Cul1-F-box (SCF) ubiquitin ligase complex, play moonlighting functions as structural components of the SC. Their identification has enabled me to reconstitute the SC central region in vitro using a bacterial protein expression system. SKR-1 and all previously known SYP proteins are purified together throughout multiple purification steps at stoichiometric ratios, suggesting that the complete set of SC components has been identified in C. elegans. Here, I propose to use these purified components as a platform to address long-standing questions regarding the molecular architecture and assembly mechanisms of the SC. In Aim 1, I will determine the stoichiometry of the SC central region proteins using size-exclusion chromatography coupled with multi-angle light scattering (SEC-MALS) and Mass Photometry (MP). I will then construct a map of the SC by identifying areas of protein-protein interactions via cross-linking mass spectrometry. In Aim 2, I will investigate the necessary requirements that potentiate and regulate SC assembly. Recent evidence has suggested that the SC exhibits liquid-crystalline properties that allow for rapid diffusion and condensation of pro-crossover factors along chromosome lengths, which in turn controls the number and distribution of crossovers. I will induce the formation of phase-separated droplets using purified components and assess their behavior under conditions that are known to affect SC assembly in vivo. Ultimately, this work will provide crucial insights into the organization and assembly requirements of the SC and establish a foundation for understanding the SC structure in other eukaryotic organisms.

NSF Awards · FY 2024 · 2024-08

The goal of this workshop is to bring communities together to create a new generation of biomedical and neuro-engineering technologies that operate with extreme energy and data efficiency, adaptability, and performance advantages compared to current approaches. The plan is to congregate biomedical engineers, neural engineers, neuroscientists (computational and physiologists), neuromorphic scientists and engineers, materials scientists, clinicians, and mainstream engineers (e.g., electrical engineers, optical engineers, computer engineers, device engineers) to introduce new brain- and biology-inspired design principles to engineers who are currently investigating non-von Neumann architectures. It is expected that these new principles will provide alternative methods to solve relevant problems in the biomedical field, and to do so with significant improvements in the various metrics of the field. The planned interactions will leverage the synergistic interests of the National Institutes of Health (NIH) [including the National Institute of Neurological Disorders and Stroke (NINDS) and the National Institute of Biomedical Imaging and Bioengineering (NIBIB)] and the National Science Foundation (NSF) to improve healthcare technologies, while also discovering fundamental concepts in engineering. An expected output of the workshop will be a neuromorphic biotechnology roadmap that articulates the benefits of the approach, highlights the challenges and proposes a potential pathway to achieve the benefits. We expect analysis of the needs of the field, presentation of emerging technologies and concepts, and their potential impact on the common interests of the NIH and NSF. This roadmap will clearly identify the near-term and longer-term opportunities and elucidate the potential partners – including the private sector – who should participate in driving these efforts. The 2-day workshop program will include 2 keynote addresses, 12 invited presentations, poster sessions for graduate student attendees, moderated discussion sessions and meetings with NIH and NSF program managers. It is also planned to invite the program committee, composed of 5 experts, to serve on discussion panels. A further group of 6 scholars/entrepreneur/innovator will be convened for this workshop. All of them will be encouraged to bring their students to participate in the discourse and present posters. In-person and virtual participants are expected. 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 The brain is nature’s most sophisticated signal-processing system. Unlike human-made integrated circuits, the brain circuits organize in a complex three-dimensional and intertwined manner, which makes it challenging to spatially resolve neuronal activities. Among all available neural recording technologies, penetrating neural probes hold great promise and are vital to neuroscience research. In common practice, neural probes are linearly inserted into the brain to map the local activity, which, however, can only probe a single spot in the targeted brain region. An entire circuit or structure can be mapped by deploying multiple probes, but the spatial resolution is modest. To date, how to spatially resolve single-unit activities from nonlinearly organized brain structures and circuits is still a challenge. Here, we propose to fill the technological gap via a nonlinear probe implantation modality. In contrast to the conventional linear implantation, we will conformally deploy high-density microelectrode arrays along designated curved brain circuits or structures with minimal surgical lesions. Ultraflexible neural probes with high electrode density will be designed accordingly to obtain the optimal nonlinear implantation outcome. The proposed technology will be fulfilled via three Aims: In Aim 1, we will develop the implantation apparatus and optimize the probe design using an in-vitro test platform; In Aim 2, we will evaluate and optimize the nonlinear implantation in vivo and characterize the surgical lesion and biocompatibility of the probes; in Aim 3, we will systematically examine the nonlinear probe in single-unit neuronal recording and demonstrate its usefulness in studying the place codes of the mouse hippocampus. In our preliminary study, we validated the feasibility of the proposed method by deploying nonlinear probes along the longitudinal axis of the mouse hippocampus, a well-known nonlinear structure in the brain. Precise targeting, low surgical lesion, and chronic single-unit tracking were shown. The technology, if successful, will significantly increase the spatial resolution of brain mapping along nonlinear circuits or brain structures, make the hard-to- access brain regions within reach, offer alternative routes toward designated brain regions, and offer a generalizable approach for other brain interventions. In all, we believe the nonlinear delivery of neural probes enabled by this project will be a valuable modality complementary to the conventional linear implantation for both basic and translational neurosciences.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY Copper (Cu) has a critical and multifaceted role in the development and function of mammalian brain. Cu misbalance is observed in many disorders affecting the central nervous system: Menkes disease, Wilson disease, Alzheimer’s and Parkinson’s diseases, multiple sclerosis, and others. With the exception of Menkes disease, for most of these disorders the origin of Cu misbalance in the brain is not well understood, and whether Cu fluxes in and out of the brain are compromised remains unknown. The information about Cu entry into the healthy brain is also very limited. The proposed program of studies will clarify the mechanism regulating Cu transfer through choroid plexus (ChPl), an important secretory tissue, which produces cerebrospinal fluid and forms the brain-cerebrospinal fluid barrier. Studies under Specific Aim 1 will determine the role of ChPl in Cu entry into the perinatal brain. The abundance, localization, and functional interactions between the Cu transporters Atp7a, Atp7b, and Slc31a1(Ctr1) as well as endogenous Cu chelators, metallothioneins, will be characterized at different time points of healthy brain maturation, and these characteristics will be compared for control and Atp7b-/- mice, an animal model of Wilson disease. Targeted deletion of Ctr1 and Atp7a in mouse ChPl epithelium will be used to measure contribution of ChPl to Cu transport into the perinatal brain. Specific Aim 2 will identify the mechanistic link between Cu homeostasis in ChPl, organization of ChPl cytoskeleton and the development of cilia; this will be achieved using transmission electron microscopy, immunocytochemistry, and proteomics. The impact of Cu misbalance in Atp7b-/- choroid plexus on expression and activity of peptidyl-a-amidating mono-oxygenase (PAM), a Cu-dependent enzyme associated with cilia development will be examined. How changes in Cu homeostasis in ChPl modify the ChPl secretome will be determined by employing iSLET methodology (in situ Secretory protein Labeling via ER- anchored TurboID) and mass-spectrometry.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY Transcription plays an oversized role in determining proper inflammatory response in immune cells such as macrophages (MF). Transcriptional master regulators of MFs are thought to be the main drivers of chromatin reprogramming during myeloid cell differentiation, polarization and activation. However, recent studies have expanded this “developmental TF-centric” model and suggest that signal-dependent TFs, in particular repressors, likely to have a pioneer role in the shaping the MF epigenome. Such an expanded model also predicts that active transcriptional repression and chromatin bookmarking by signal-dependent master regulators is a key mechanism for the safeguarding the enhancer repertoire and proper deployment and resolution of an inflammatory response. Recently, we identified such a signal-dependent TF, the heme- regulated repressor BACH1 (BTB Domain and CNC Homolog 1), with properties of a master regulator of the MF epigenome. Our preliminary data is contrary to current dogma about this TF and also challenging the current view of inflammatory gene regulation. The central hypothesis of this proposal is that BACH1 acts as a pioneering repressor, signal-dependent master regulator and an epigenomic safeguard that plays a key role during macrophage differentiation and polarization/specification by actively repressing enhancers, genome-wide, controlling inflammatory, metabolic and differentiation-specific genes with effects on the baseline, amplitude and proper kinetics of the inflammatory gene expression. We propose three interrelated and integrated but independent Specific Aims in which we will combine new genetic mouse models with cutting edge molecular biology approaches to establish BACH1 as a critical modulator of MF inflammatory gene expression and subtype specification. Our approaches aim to provide deep mechanistic insights on BACH1 function on active repression, pioneering, transcriptional activation, 3D chromatin structure and inflammatory gene expression and establish BACH1 as a novel signal-dependent master regulator and as part of the core hardwired transcriptional circuit of MFs. Moreover, results from the proposed work are expected to push the field forward by providing a mechanistic framework of how heme, a molecule vital for life and cell metabolism but cytotoxic when in excess, can affect the differentiation and inflammatory potential of MFs.

NIH Research Projects · FY 2025 · 2024-08

A preclinical therapeutic platform to develop GABAA α5 receptor positive allosteric modulators to improve cognitive function in schizophrenia. Cognitive dysfunction in neuropsychiatric disorders such as schizophrenia predicts long-term disability and poor patient outcome and is not effectively treated with existing standard-of-care medications. Converging evidence indicates that a primary source of this cognitive impairment is an imbalance in excitatory/inhibitory (E/I) neural responses in critical circuitry for episodic memory. In the medial temporal lobe, weakened inhibition induces an aberrant condition of increased excitation in the hippocampus of individuals with schizophrenia. The aim of this proposal is to develop novel therapeutics to remediate E/I imbalances to improve cognitive function. Using a preclinical platform for drug development, the proposed research is focused on GABAA α5 receptor positive allosteric modulation (PAM) for the treatment of neuropsychiatric conditions characterized by heightened excitation in the hippocampus. The high expression of α5-containing GABAA receptors in the hippocampus, which mediate tonic inhibition, could be ideal for controlling excitation in this circuitry. We will use a series of small molecules with high potency and selectivity for GABAA α5 receptors and PAM activity at the α5 subunit that have met preclinical in vitro and in vivo drug discovery criteria with potential for translational development as therapeutic agents. The current proposed studies will advance this drug development platform to test the efficacy of two GABAA α5 receptor PAMs to improve hippocampal-dependent cognition in a preparation of hippocampal overactivity in rodents. The studies will also assess efficacy by using fiber photometry to monitor neural hyperexcitation in the hippocampal formation during in vivo testing. Together, these studies establish a foundation for a preclinical small molecule drug development program to remediate E/I imbalances underlying cognitive dysfunction in neuropsychiatry.

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.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY/ABSTRACT The winged-helix DNA-binding FoxA transcription factors (TFs) play major roles in the development and homeostasis of many organs. Importantly, FoxA proteins are expressed early and continuously in many tissues and are essential both during development and postnatally for morphogenesis, glucose metabolism, and expression of multiple organ-specific genes. Mutations in FoxA proteins are linked to cancer in multiple tissue types (including the salivary gland), developmental defects that result in Parkinson-like phenotypes, and glucose dysregulation, causing hypoglycemia. However, the identity of the downstream effectors and the extent of coordination of FoxA proteins with other TFs to accomplish morphogenesis and regulate metabolic function are largely unknown. Identifying these downstream effectors and their mechanistic nuances becomes possible by studying the single Drosophila orthologue Fork head (Fkh) that represents all three FoxA members: FOXA1, FOXA2, and FOXA3. Like FoxA proteins in vertebrates, Fkh is required for morphogenesis and maintenance of organs in Drosophila, including the embryonic salivary gland (SG). In addition to its role in organ formation, Fkh is known to coordinate with two other TFs, Sage and Senseless (Sens), to maintain SG viability and to regulate the “secretome” – the collection of secreted products made by the SG. By performing ChIP-sequencing in parallel with scRNA-sequencing followed by computational analysis, we will uncover the mechanistic details of how Fkh coordinates with Sage and Sens to regulate the secretome (Aim 1). Furthermore, I will use our computational analysis to identify candidate partner TFs of Fkh to then perform a mutational screen and look for morphological phenotypes to characterize possible co-regulators of Fkh for morphogenesis (Aim 2). Through these proposed experiments in Aims 1 and 2, the mechanistic details of how Fkh coordinates with Sage and Sens to regulate the secretome can be elucidated while uncovering and characterizing co-regulators of Fkh for morphogenesis. In addition to controlling organ form and function, FoxA family proteins also play a role in metabolism. Currently, the SG is not known to have any metabolic roles but recent findings from our lab and others indicate that the SG secretome may have additional endocrine functions related to systemic growth. In Drosophila, salivary gland secreted factor (Sgsf) has been discovered as a SG secreted peptide that acts upon the AKT-MTOR pathway to ultimately affect systemic growth. By studying Fkhs role in regulating secreted factors from the SG, the novel function of the SG acting as endocrine organ can be further understood. To study this, I will utilize the biotinylating enzyme BirA*G3 in conjunction with mass spectrometry and confocal imagery to explore the potential secretion of metabolites from the SG. Candidate metabolites identified through these will then be tested for metabolic consequences within both the larval and adult stage (Aim 3). The outcomes from these experiments will provide new insights upon Fkh regulation of secretion and the SG acting as an endocrine organ.

NIH Research Projects · FY 2024 · 2024-08

PROJECT SUMMARY Lung cancer remains the most lethal cancer in the United States, with its diagnosis often hindered by delays. The complexity of these delays stems from a patient's diagnostic journey that spans across multiple care systems. In many instances, key decision-influencing factors are unrecorded, and medical records frequently miss essential elements of the patient's experience. Recognizing this, the focus of my career development and current research proposal is to undertake a multi-faceted analysis utilizing a mixed-methods approach to characterize the lung cancer diagnostic journey, incorporating both physicians' and patients' perspectives to construct a comprehensive narrative of the diagnostic process. The project will answer key questions: Q1: How does the diagnostic process begin? Q2: How do patients progress from presentation to diagnosis? Q3: How long does the diagnostic process take? Q4: Are there risks or harms associated with a prolonged diagnostic process? Q5: Are minority patients at a higher risk of experiencing extended diagnosis durations and/or associated harm? Q6: Do healthcare use patterns suggest earlier diagnosis could be possible? Q7: Could anything has been done differently to reach the correct diagnosis sooner? The proposed research project will develop novel measurement and intervention strategies to prevent lung cancer diagnostic delay and harm by generating novel insights about patients' journeys toward lung cancer diagnosis. We seek to apply the Theory of Constraints paradigm to identify the weakest links in the diagnostic process chain for lung cancer. Leveraging data from the Johns Hopkins Health System, we will (1) measure delays in patient, provider, and system time intervals for the lung cancer diagnostic journey; (2) estimate associated harms and health disparities, and identify if certain clinical presentations were more likely to be missed or lead to diagnostic delay; and (3) conduct in-depth mixed-methods case reviews, provider input, and patient interviews to identify obstacles that could impact diagnostic performance and patients' health outcomes. This study will yield novel insights that answer the seven key questions above related to lung cancer diagnosis. These answers will inform subsequent efforts to prevent avoidable harm due to lung cancer diagnostic delay more broadly in Maryland as well as nationally. The proposed study and training activities will uniquely position me to launch a career as an independent investigator developing and testing potential intervention strategies to improve lung cancer diagnostic safety. I anticipate a pilot intervention study during the follow-on R01 phase.