University Of California, San Francisco

NIH Research Projects · FY 2026 · 2024-07

PROJECT SUMMARY Using a combination of genetics and experimental evolution, our team seeks to understand complex epistasis with respect to genetic background in the human pathogen Cryptococcus neoformans. This yeast is an ideal platform for such investigations due to 1) its facile genetics, 2) the availability of hundreds of phylogenetically well-separated genomes, and 3) mouse infection models that recapitulate key aspects of human disease. Most studies have been performed with a reference strain, the clinical isolate H99, or in congenic derivatives (KN99a and KN99). In unpublished work, our lab has generated a gene deletion strain collection in the KN99 background and profiled it in mice and in over 100 diverse in vitro conditions. A reference strain is important for the field to be able to compare findings, but it has a major weakness: across genetic backgrounds, it is unknown whether the same genes are 1) essential for viability, 2) mediate the responses to small molecule challenges, and 3) are required for fitness in the mammalian host. In addition to being of fundamental scientific importance, answering these questions, which all relate to the larger question of complex epistasis, is important for developing effective therapies across genetic backgrounds and understanding drug resistance. Population genomic analyses have revealed that C. neoformans exists in roughly four major clades that diverged ~5 million years ago and show evidence of speciation. Over a million SNPs have been identified in a set of nearly 400 strains. Members of each clade have been identified in human infections, and there is evidence for clade- specific traits. Anecdotal studies have provided examples of strain-specific phenotypes, raising the question of what genotype-phenotype relationships are general vs. dependent on genetic background and the underlying mechanisms. Powerful new CRISPR/Cas9-based tools that we have recently developed and other technological advances now make it feasible to address this fundamental question. In this work, we will determine how Cryptococcus neoformans genetic background impacts the fundamental traits of gene essentiality (Aim 1), the role of genes in fitness in the mammalian host (Aim 2), and the fitness roles of genes under diverse environments (Aim 3). We will pursue mechanisms of the latter through experimental evolution (Aim 3).

NIH Research Projects · FY 2026 · 2024-07

PROJECT SUMMARY/ABSTRACT Fibroblasts are stromal cells that are critical to both wound repair and the support and regulation of tissue- resident immune cells; when dysregulated, they drive pathologic scarring and maladaptive immunity. While the Central Nervous System (CNS) is an immunoprivileged site, brain and spinal cord inflammation, injury, and pathologic aging all disrupt this delicate balance, leading to increased immune cell activation and infiltration, and contributing to a range of neuropsychiatric diseases. Although fibroblasts are essentially absent from CNS parenchyma, they are abundant at CNS borders, and perturbations drive the expansion and infiltration of fibroblasts, potentially regulating both acute brain injury and the long-term generation of de novo immune niches, which themselves can alter CNS function. However, the regulatory mechanisms and impacts of CNS fibroblast- immune crosstalk are poorly understood. Our preliminary data show that lesional CNS fibroblasts expand in mouse models of brain injury, transiently adopting a myofibroblast-like state that requires fibroblast-intrinsic TGF? signaling and is spatially correlated with macrophages. Mice with inducible myofibroblast loss have enlarged CNS lesions and sub-acute CNS functional deficits. The myofibroblast program subsides, yet fibroblasts persist for months, intimately associate with late lesional CNS lymphocytes, and are necessary and sufficient to support lymphocytes. Spatial transcriptomics indicate a lesional transition from an early myofibroblast to a late immunoregulatory state. We hypothesize that CNS damage promotes early myofibroblast expansion, requiring macrophages and TGF? activation, to drive wound contraction and limit CNS functional loss, followed by a transition to an immunoregulatory fibroblast state that persists and creates de novo CNS lymphocyte niches. The specific goals of this proposal are to understand how CNS fibroblast-macrophage interactions govern responses to brain damage and establishment of lymphoid niches. Here we will focus on three related questions: (1) How do early injury-associated myofibroblasts regulate CNS damage and functional impairment? (2) What are the cells and signals that regulate CNS fibroblast state transition? (3) How do late CNS immunofibroblasts regulate T-cell accumulation and function? Successful completion of the proposed work will illuminate how brain fibroblasts regulate early CNS damage responses and late immune cell accumulation, laying the foundation for future work in humans and driving therapeutic approaches that target stromal cells to modulate CNS immunity and function.

NIH Research Projects · FY 2026 · 2024-07

PROJECT SUMMARY The immune system plays key roles in brain development, but immune challenges in early life can also increase the risk for neurodevelopmental disorders including autism and schizophrenia. Microglia, the dominant immune cells of the brain parenchyma, mediate this brain-immune axis by regulating neural circuit development in response to immune cues. A relatively unexplored function of microglia in early brain development is the engulfment of whole neurons, which may engage distinct phagocytic mechanisms from those used, for example, to remodel synapses. In preliminary experiments, we have identified a molecularly distinct subset of microglia in the early postnatal mouse somatosensory cortex (P5) that is actively engulfing whole neurons. These microglia express a Type I Interferon (IFN-I) responsive molecular signature and have a unique phagocytic morphology in situ, frequently engulfing several neurons at a time. While these cells are rare in the typically developing cortex, they expand 20-fold in somatosensory cortex in a partial whisker deprivation model that accelerates developmental circuit remodeling. We find that both global and microglial-specific deletion of the IFN-I receptor (Ifnar1) leads to dysmorphic microglial with enlarged phagolysosomes and an accumulation of neurons with double strand DNA breaks, a damage/hyperexcitability marker. Our central hypothesis is that Type I Interferon- responsive microglia promote somatosensory circuit maturation by eliminating specific neurons in early postnatal development. We will test this hypothesis in three specific aims. In Aim 1, we will follow up on preliminary data showing that Ifnar1-deficient juvenile animals have altered numbers of deep layer cortical neuronal subtypes, with an increase in excitatory neuronal density, as well as hyperreactive sensory responses to whisker stimulation. We will further examine these phenotypes in global and microglial-specific Ifnar1 deletion by electrophysiology, behavior, and immunohistochemistry. Aim 2 will expand on our preliminary data showing that exogenous IFN-I (IFN-) is sufficient to expand IRMs and reduce the number of neurons with dsDNA breaks. Using our whisker deprivation and pharmacologic gain of function models, we will probe the sources and targets of IFN-I in the developing brain, and the circuit impact of excess IFN-I signaling. Aim 3 follows up on our data that identifies dsRNA sensing via MAVS as the potential molecular pattern that amplifies IFN-I responses in these microglia. We will use in vivo conditional deletion and in vitro cocultures to define the sources and cellular targets of dsRNA in developing cortex. Our long-term goal is fully define the unexpected implications of microglial engulfment of neurons in cortical development, and more broadly, to define the novel homeostatic role of this innate immune pathway in the developing nervous system. 

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY Uveitis is an inflammatory eye disease that confers severe ocular morbidity and can cause long term blindness if not diagnosed and treated promptly. Current challenges exist in the diagnosis of infectious cases due to inadequate clinical laboratory methods to establish the exact cause and the current sample volume requirement for multiple analysis. Technological advancements with high-throughput sequencing have improved diagnostic strategies in medicine and are enabling the detection of several types of infectious organisms. Additionally, biomarker discovery is lacking in uveitis. Herein we propose a collaboration with stakeholders both local and international to enhance the understanding of the pathogenesis of uveitis to improve upon uveitis classification, diagnosis, biomarker identification, and deepen our understanding of the host response with the following aims. In the first aim we will perform worldwide surveillance of pathogens causing uveitis, identify geographic trends, and assess the effect of pathogen class and antimicrobial resistance on visual outcomes. We expect we will identify known and unknown causes of infectious uveitis using metagenomic sequencing and that the organisms will vary by geographic locale and seasonality. Visual outcomes will vary by pathogen class. In the second aim we will characterize the host gene expression profiles in infectious uveitis and determine what profiles predict clinical outcomes. We will identify host transcriptome signatures that will vary by pathogen class and determine the profiles implicated in clinical outcomes. In the last aim we will interrogate the tears for noninvasive biomarker discovery using the proteome and metabolomic signatures. These aims combine the characterization of pathogens, host transcriptomes, and the tear proteome and metabolite signatures to provide a comprehensive molecular approach to improve the diagnosis of uveitis. We will leverage international collaborators to use newer laboratory techniques with unbiased RNA deep sequencing and mass spectrometry. This will contribute to further our understanding of the eye as a surveillance site for infectious diseases and is paramount for establishing disease causality and will impart knowledge and data into public health priorities, programs, and policy.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY/ABSTRACT Loss of synapses is the strongest neuropathological correlate for clinical cognitive decline in Alzheimer’s Disease (AD) patients. In AD mouse models, synapse loss is dependent on neuroinflammatory glial cells and their phagocytic cell surface receptors, many of have been found to interact with extracellularly exposed phosphatidylserine (PS). PS is a plasma membrane phospholipid that is maintained on the cytosolic leaflet but can be flipped to the extracellular leaflet following cellular stress. These interactions led to the hypothesis that glial synapse removal in AD may require synaptic PS exposure. Recent studies have shown that disruption of glial receptor-PS interactions ameliorate synapse loss, electrophysiological deficits, and behavioral phenotypes across several models. While there have been numerous investigations into the mechanisms regulating glial phagocytic receptors, there has yet to be a systematic investigation into mechanisms regulating synaptic PS exposure. I have developed a novel pooled CRISPRi screening platform to systematically elucidate mechanisms of synaptic PS exposure. This initial screen has revealed potential roles for IL-6 and IL-11 signaling in regulating synaptic PS exposure. In my first aim, I propose to determine how the IL-6 and IL-11 signaling pathways differentially affect synaptic PS exposure, glial synaptic engulfment, and in vivo synaptic function both at baseline and within AD model systems using a combination of pharmacological, genetic, and electrophysiological approaches. In my second aim, I propose to identify other novel genetic regulatory mechanisms of synaptic PS exposure in AD. To do this, I will expand my initial functional genomics screen to cover the entire protein-coding genome and conduct differential phosphoproteomic analysis on synapses exposing high and low levels of PS both at baseline and within the context of an in vitro AD model. Finally, I will validate these newly discovered regulators using similar pharmacological, genetic, and electrophysiological approaches as I propose to use in my first aim. Finally, I will study how these validated pathways are differentially expressed within AD patient brains using immunohistochemical techniques. My sponsor, Dr. Martin Kampmann, who co-developed the CRISPRi screening technology, and my cosponsor, Dr. Robert Edwards, who is a physician-scientist and an expert in synaptic biology and neurotransmitter release, are ideally positioned to support my proposed research. In addition to my two sponsors, I will also receive clinical mentorship from Dr. Bruce Miller, a behavioral neurologist who specializes and the diagnosis and management of neurodegenerative diseases with a particular focus on AD and other tauopathies. Overall, the proposed work will uncover novel mechanisms regulating an understudied aspect of AD pathophysiology and identify new therapeutic targets for the treatment of AD. Furthermore, this work will provide me with essential expertise for my future as a physician-scientist studying the intersection of neurodegeneration and synaptic dysfunction.

NIH Research Projects · FY 2025 · 2024-07

ABSTRACT Please find attached our application entitled “Broadening the scale and impact of a comprehensive Long COVID clinic to serve diverse patient groups with multidisciplinary care and research access” being submitted to RFA-HS-23-012: Implementing and Evaluating New Models for Delivering Comprehensive, Coordinated, Person-Centered Care to People with Long COVID (U18). This application is responsive to SEN NOT-HS-23-013. While several models of dedicated outpatient Long COVID clinics have emerged across the U.S., features essential to implementing and providing equitable, comprehensive, coordinated, and person-centered Long COVID care have yet to be fully identified and evaluated. In April 2020, our team founded the multidisciplinary UCSF OPTIMAL Long COVID clinic, a dedicated center for individuals in the post- acute phase of COVID-19 modeled after the multidisciplinary structure of post- ICU clinics. The clinic currently serves a diverse population and the clinic has already had a major impact, resulting in lower odds of hospitalization or emergency department visits. The central goal of this proposal is to improve capacity, access, and equity for underserved, vulnerable, and minority populations being served by the OPTIMAL Long COVID Clinic. Specifically, we will scale up multidisciplinary care operations in the current UCSF OPTIMAL Clinic and expand the program to patients at San Francisco General Hospital, a safety net hospital serving a diverse and vulnerable patient population experiencing long COVID. We will increase coordination and communication between our clinical operations, established federally-funded Long COVID research programs, and community- based organizations (CBOs) and clinics serving populations affected by Long COVID. Using an implementation science approach and leveraging the existing OPTIMAL Long COVID care model and established relationships with community organizations and research studies, we will: Aim 1: Scale up Long COVID care in the San Francisco Bay Area to increase access for underserved, vulnerable, and minority populations. Aim 2: Enhance Long COVID care coordination and communication across clinical, research, and community settings. Aim 3: Identify key barriers and facilitators to implementation success and sustainability of the expanded and enhanced Long COVID care model. Results from this project will significantly inform Long COVID care delivery models and have a major impact on unmet Long COVID care needs among underserved populations.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY PAX3-FOXO1 and related fusions create oncogenic transcription factors that remodel chromatin to drive a subset of childhood rhabdomyosarcoma (RMS) with dismal cure rates. Therapies to target PAX3-FOXO1 are lacking. Recently, we established mTORC1 as a PAX3-FOXO1 genetic dependency that is exploitable with third generation bi-steric mTORC1 inhibitors, now in phase 1 testing. Unlike rapamycin, RMC-6272 prevents mTORC1-driven assembly of eIF4F and ensuing cap-dependent translation. This corresponds to striking efficacy in patient-derived xenografts (PDX): RMC-6272 induces prolonged remissions, while rapamycin analogs only stabilize disease, mirroring their modest effects in patients. However, PDX eventually regrow and show resistance to RMC-6272 re-treatment, making it clear that a knowledge gap prevents us from effectively targeting PAX3-FOXO1 via mTORC1. What is the molecular basis for PAX3-FOXO1 “addiction” to cap-dependent translation, and how can we rationally combine this agent to overcome resistance and enable curative therapy? This proposal addresses these questions with the goal of providing a molecularly informed strategy to aid ongoing clinical development of bi-steric mTORC1 inhibitors in childhood cancer. Aim 1 will define the molecular basis for RMC-6272 efficacy in fusion positive RMS. Excitingly, informatic and proteomic data lead us to the anchoring hypothesis that PAX3-FOXO1 requires cap-dependent translation for its own expression. We will use precise biochemical assays of mRNA translation and protein synthesis to test this. Building on the observation that patient-derived xenografts (PDX) driven by less frequent PAX7-FOXO1 fusions show reduced response to RMC-6272, we will define molecular features in the untranslated regions (UTRs) of PAX3 and PAX7 fusions that require mTORC1 and eIF4F for their translation, and test whether UTR sequence determines RMC-6272 efficacy. Aim 2 will define the best means to augment RMC-6272 efficacy in PDX. Single agents are rarely successful in curing even genetically simple cancers like fusion positive RMS, and indeed we observe the emergence of resistance to RMC-6272 monotherapy. We find that BET inhibitors (which decrease PAX3-FOXO1 expression) and RAS inhibitors (which blunt feedback activation of MAPK) each are synergistic with RMC-6272. We hypothesize that such mechanism-based combinations will offer curative treatment and will compare them to combinations with chemotherapy that are the mainstay of relapsed RMS studies. Using pharmacodynamic modeling in PDX, we will identify safe and optimal biologic dosing to combine agents, then find the strategy that best prolongs survival and prevents resistance to translate into clinical trials. Completion of these aims will detail how eIF4F orchestrates oncogene output in a frequently lethal pediatric cancer and define strategies to further enhance these effects to offer curative treatment. Beyond guiding bi-steric mTORC1 inhibitor use in RMS, the knowledge gained will enable study of translational control as a therapeutic target in other transcription factor-driven malignancies based on determinants of response we define here.

NIH Research Projects · FY 2024 · 2024-07

PROJECT SUMMARY Cocaine and methamphetamine-related deaths have risen steeply in the United States, the majority associated with fentanyl. Stimulant use is prevalent among people living with or at risk for HIV, and in this population, it is unknown what proportion of mixed stimulant-opioid overdose deaths are due to unintentional fentanyl exposure. As overdose deaths threaten gains in life expectancy among PWH in recent years, we need to use all available tools at our disposal to prevent unintentional opioid exposure and overdose. We propose a novel concept of opioid overdose pre-exposure prophylaxis (PrEP) for individuals using stimulants and living with or at risk for HIV. We will perform a randomized controlled trial of a long-acting injectable opioid antagonist (intramuscular naltrexone) vs. a conventional in-clinic harm reduction bundle, with stratified randomization based on baseline antiretroviral therapy delivery strategy (i.e., injectable vs. oral HIV prevention/treatment). Our three key objectives are: 1) investigate the feasibility, acceptability, and preliminary effectiveness of intramuscular naltrexone as a preventive measure for opioid overdose in individuals using stimulants, 2) capture the experiences of patients receiving concurrent long-acting injectable medicines for HIV and substance use, 3) employ short and long-term biomarkers of substance use, supplemented by participant interviews, to craft an epidemiological profile detailing intentional and unintentional opioid exposure among individuals living with or at risk of HIV. Our creative approach repurposes intramuscular naltrexone, conventionally used for opioid and/or alcohol use disorders, as an innovative method for opioid overdose prevention. This trial will be performed at University of California San Francisco (UCSF) at San Francisco General Hospital’s Ward 86 clinic, home to the largest known cohort of people who use drugs receiving long- acting injectable HIV treatment/prevention. San Francisco county's high per capita overdose death rate underscores the urgent need for our research, and our study promises to provide valuable insights into the interplay of HIV prevention/treatment, stimulant use, and opioid overdose prevention. .

NIH Research Projects · FY 2024 · 2024-07

Project Summary / Abstract Water insecurity (WI) is a major challenge in sub-Sharan Africa (SSA), where the number of people living with HIV (PLWH) is disproportionately higher, and where populations are most likely to bear the impact of climate change. The effects of water insecurity on health are well-documented in SSA: emotional distress is associated with lack of safe water, including fear of contamination, worry over safety, and anxiety, increased migration and thus HIV risk, as well as disruptions to health, care engagement, livelihoods, and relationships. Further, the prevalence of WI among PLWH is high, and household WI and food insecurity (FI) lead to poor mental and physical health. WI is also an important determinant of FI, suggesting multiple causal pathways to poor health outcomes. While SSA least contributes to global warming, especially as compared to more industrialized nations, it is expected to be amongst the hardest by climate change. Water is required for food production and preparation8, and WI may directly and indirectly influence health outcomes by impacting FI and health. Among PLWH, WI can lead to dehydration and undermine PLWH’s ability to manage unpleasant side effects associated with ART, including diarrhea, nausea, and vomiting. In Ghana, one of the most vulnerable countries to climate change in SSA, flooding affects around 45,000 Ghanaians annually while nearly half of Ghana’s coastline is vulnerable to erosion and flooding as a result of sea-level rise and atypical rainfall. Further, an estimated 70% of all disease burden in Ghana is attributed to WI. To effectively intervene, a deeper understanding of the drivers of and sequelae of WI is critical. Therefore, we propose the first longitudinal convergent mixed-methods study to quantify and elucidate the impact of WI on HIV, related to climate-related drivers, infrastructure challenges, water accessibility, and heightened risk of water-borne diseases, to inform interventions to address WI among PLWH. In Aim 1, we will utilize innovative remote sensing technologies to investigate the role of climate-sensitive patterns (droughts, precipitation anomalies, and floods, capitalizing on state-of-the-art satellite technologies) and seasonality on WI in Ghana. In Aim 2, we will determine the impact of WI on HIV treatment outcomes (ART adherence/viral suppression) and opportunistic infections and comorbidities, and the mechanisms through which WI may influence these outcomes (nutritional, mental health, water, hygiene and sanitation, and empowerment pathways). In aim 3, using intervention mapping framework, we will develop intervention options to mitigate WI and improve health for PLWH, synthesized from theory and literature. Findings from this R01 will a) provide initial data on the drivers of and sequelae of WI and it impact on HIV treatment outcome; b) guide the integration of HIV and water access programs; and c) help identify and prioritize intervention development to address WI among PLWH.

NIH Research Projects · FY 2025 · 2024-07

ABSTRACT/PROJECT SUMMARY Maintaining physical activity (PA) is critical for older adults with cardiovascular disease (CVD) who complete cardiac rehabilitation (CR) because it prevents adverse secondary cardiac events, declining functional status, and poor quality of life. CR is an evidence-based, exercise-based program prescribed after cardiac events (e.g., myocardial infarction, revascularization) to improve overall physical, mental, and social functioning. However, the majority (50-85%) of individuals report no exercise 6 months after completing CR, leaving them vulnerable to rapid clinical, functional, and cognitive decline. The objective of this 6-month randomized controlled trial (n=143 per arm) is to test the efficacy of a virtual coaching and social support intervention to improve PA, psychosocial, social cognitive, and clinical outcomes as well as understand the mechanisms that affect change in outcomes for older adults (age ≥ 60) exiting CR and living in urban and rural areas. Virtual coaching includes: 1) education, 2) personalized feedback, and 3) motivation; social support includes social networking in groups of 4-6. The rationale for our approach is that CR is typically only 12 weeks or less but older adults desire and require extended support to reap the numerous benefits of sustained PA. The specific aims are: 1) Determine the effect of a virtual coaching and social support intervention on adherence to PA (measured by objective step counts) in the intervention vs. control groups; secondary measures will be sedentary time, functional fitness, and self-reported exercise. 2) Determine the effect of the virtual coaching and social support on psychosocial and social cognitive factors (self-efficacy, self-regulation, perceived social support) in the intervention vs. control groups; and 2a) Evaluate the extent to which psychosocial and social cognitive factors mediate the effect of the intervention on PA adherence. 3) Examine differences in clinical outcomes including CVD risk factors (hypertension, hyperlipidemia, diabetes, obesity) between groups. We will also record and explore group differences in cardiac events/rehospitalization. This study is innovative because we will: 1) provide a virtual social network to mimic the social support received in CR; 2) include an optional leader board/buddy system/badges to increase engagement; 3) intentionally recruit diverse, under-represented groups (rural, women, racial/ethnic minorities) and deliver the intervention in Spanish; and 4) be the first clinical trial to address loneliness in patients with CVD. Significance: We address key NIH priorities to improve adherence to healthy behaviors and reduce burden of chronic conditions as well as promote a program in older adults to maintain maximum PA/functional fitness. Impact: While leveraging digital health innovations, we will test a novel and pragmatic solution to maintain PA after CR completion that may lead to an efficacious evidence-based intervention that improves critical outcomes for older adults with CVD living in urban and rural communities at risk for functional decline, secondary events, depression, and cognitive decline. Our long-term goal is to disseminate a low-cost program that is easily scalable to other CR centers.

NIH Research Projects · FY 2026 · 2024-07

PROJECT SUMMARY Each year, there over 200,000 hospitalizations for cirrhosis in the United States. Over one-third of these patients are readmitted within 30 days, and up to 10% will die in the hospital. Despite national quality measures and care guidelines, cirrhosis care remains suboptimal and highly variable. Clinical Decision Support (CDS) systems present an attractive strategy to improve guideline-adherence due to low implementation costs. These systems, however, remain largely untested in cirrhosis care and it remains unknown whether they are effective at improving guideline-adherence and whether improving guideline-adherence changes clinical outcomes in cirrhosis care. This proposal will leverage my ongoing KL2 work in which I designed “CirrhosisRx,” a cirrhosis-specific CDS system, to address these evidence gaps by: Comparing the effect of CirrhosisRx versus “usual care” on adherence to quality measures and clinical outcomes through a pragmatic randomized controlled trial (pRCT, Aim 1); Assessing whether changes in guideline-adherence mediate changes in outcomes (Sub-Aim 1); Studying CirrhosisRx's reach, adoption, and maintenance in care workflows (Aim 2); and Identifying facilitators and barriers to adopting electronic interventions for cirrhosis care at other centers (Aim 3). These aims will generate the necessary data and knowledge for a future multicenter pRCT of CirrhosisRx and other electronic interventions in hepatology care. I am an Assistant Professor of Medicine at the University of California, San Francisco (UCSF). Building upon a strong foundation of research support, this K23 will allow me to transition from being a retrospective researcher to a pragmatic trialist of electronic interventions in hepatology. I need dedicated training to gain expertise in the conduct, analysis, and dissemination of pRCTs of electronic interventions. Under the supervision of a multidisciplinary team of leaders in hepatology (Lai), clinical informatics (Pletcher), biostatistics (Huang), and implementation sciences and qualitative methods (Ackerman), I will execute a detailed career development plan outlined in this proposal to develop the following skills: 1) pRCT design and conduct, 2) Advanced statistical methods in pRCT data analysis, 3) Intervention evaluation frameworks, and 4) Multicenter collaborations. As part of my 4-year plan, I will actively engage in coursework and structured tutorials in the topics above, and in interdisciplinary development and leadership programs. RELEVANCE: Conducting a pragmatic randomized controlled trial of a cirrhosis-specific clinical decision support system to improve guideline-adherence and clinical outcomes will help provide evidence regarding to the effectiveness of such interventions and allow for the design and execution of future trials of similar interventions to improve cirrhosis care.

NIH Research Projects · FY 2024 · 2024-07

PROJECT SUMMARY As Parkinson’s disease (PD) progresses, patients develop slowness of movement (bradykinesia), tremor and rigidity. The first-line treatment for PD is the dopamine precursor levodopa. However, long-term use can lead to excessive movement (dyskinesia). To address levodopa-induced dyskinesia, medication dose is adjusted, and deep brain stimulation (DBS) of the basal ganglia is utilized. Without sufficiently lowering the medication dose, DBS can exacerbate dyskinesia. However, the mechanisms with which DBS causes dyskinesia, and how they are modulated by the dopaminergic cycle, are not fully understood. Excessive gamma band (65-90Hz) synchronization in the motor network correlates with dyskinesia in preliminary human studies. This signal has the potential to predict the onset of a dyskinetic episode when identified across a complete set of spectral features with continuous measures of motor fluctuations. During therapeutic DBS of either the subthalamic nucleus (STN) or globus pallidus (GP), the gamma oscillation is often entrained (amplified and modulated) to one-half the stimulation frequency. However, the clinical relevance of entrainment, and how it may interact with across stimulation settings, has not yet been investigated. We predict that stimulation-induced 1:2 entrainment of cortical oscillations (oscillations detected at one-half the stimulation frequency) will therapeutically increase movement, while simultaneously decreasing excessive/pathological movement, otherwise known as dyskinesia. The goals of this study are to use multisite, chronically implanted neurostimulators and continuous wrist-wearable sensors to identify correlates of dyskinesia across a complete set of spectral features and to assess the possible clinical benefit, as it relates to dyskinesia scores measured by the wearable sensors, of stimulation-induced entrainment of these spectral features. First, we will characterize correlates of dyskinesia using hundreds of hours of chronic neural recordings collected in a naturalistic environment across typical dopaminergic cycles with objective dyskinesia monitoring using wearables prior to the initialization of stimulation. The majority of these patients experience dyskinetic motor signs while taking their clinically recommended medications. Then, we will determine the most predictive features of dyskinesia using machine learning models to predict the continuous dyskinesia scores derived from validated wearable algorithms of the sensors worn on the wrist. We hypothesize that periodic gamma components will be most predictive of dyskinetic episodes prior to the onset of stimulation. Next, we will determine the relationship between gamma entrainment, dyskinesia severity, and deep brain stimulation amplitude. To do this, we will record neural data in a similar setting as before. However, during this process, patients will experience deep brain stimulation at the clinically recommended stimulation frequency, and patients will slowly increase their stimulation amplitude across a period of several weeks up to the clinically recommended setting. We hypothesize that gamma entrainment and dyskinesia severity will be inversely correlated at moderate levels of entrainment.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY / ABSTRACT Autism spectrum disorder (ASD) is a relatively commonneurodevelopmental disorder (NDD), for which hundreds of large-effect risk genes have been identified. However, the molecular mechanisms underlying ASD remain unknown. ASD is commonly comorbid with disorders caused by cilia defects, but the possibility that cilia defects underlie ASD pathogenesis has not been systematically investigated. My dissertation work addresses this gap in knowledge by investigating the role of large-effect ASD risk genes in cilia formation using complementary model systems. To date, I have demonstrated that six high-confidence ASD risk genes localize to the cilium and are required for their formation, using both in vivo Xenopus models and in vitro human cells and transcriptomics. Included in these genes is the leading ASD risk gene, SYNGAP1, which has a canonical role in synaptic plasticity. My results show that it also plays a role earlier in brain development at the cilium, reframing its potential molecular contributions to ASD risk. The work proposed here will dissect the domains of SYNGAP1 necessary for its localization and function at the cilium using the high-throughput Xenopus model (Aim 1A). Then these findings will be translated to rodent models to dissect SYNGAP1 localization and function in a neural context, both at cellular and organ-level resolution using Syngap1 mutant rats (Aim 1B). To model human haploinsufficiency, we will complement this work by analyzing cilia phenotypes in SYNGAP1 patient iPSC- derived neurons (Aim 1C). Results from these studies will shift our understanding of the molecular mechanisms underlying ASD pathogenesis, particularly for the leading ASD risk gene SYNGAP1, with implications for other ‘synaptic’ ASD risk genes. This proposed work and training plan will prepare me for success in the K00 phase by providing technical training in advanced microscopy, image analysis, tissue processing, bioinformatics, and iPSC culture, as well as professional skills and intellectual experience in dissecting molecular mechanisms of NDDs. In Aim 2 (the K00 phase), I will continue to pursue my interests in understanding the molecular mechanisms of NDDs by investigating the role of lipids in the pathogenesis of NDDs. I will identify a postdoctoral laboratory that studies NDDs and can support my training in cutting-edge techniques in lipid biology, lipidomics, and transcriptomics while I develop professional, communication, and inclusive leadership skills. With the tools, professional skills, and technical skills I develop in the K00 phase, I will be well-positioned to start my independent research laboratory studying NDDs and create an inclusive environment to lead a diverse team of trainees and scientists.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY The blood-brain barrier (BBB) plays a crucial role in brain health, but its role in brain development and the cellular interactions which govern its formation remain unknown. Recent studies have revealed specific time points during which microglia-like progenitors exit the prenatal liver and migrate into the brain, suggesting a complex development and function of the BBB throughout gestation. Furthermore, once in the brain, these progenitors differentiate into a population of cells similar to microglia, which are traditionally thought to arise from progenitors that exit the yolk sac and migrate directly into the brain. Understanding the developmental changes in BBB permeability is essential to unraveling the mechanisms by which it regulates cellular trafficking into the brain. Dr. MacKenzie's lab published these findings and is currently investigating the migration of these prenatal liver-derived (PL-derived) immune cells into the brain using an innovative in utero prenatal liver injection model. Additionally, Dr. Crouch's lab has developed a novel strategy to isolate endothelial and mural cells, key vascular cell types of the developing brain vasculature, for in vitro study and single-cell RNA sequencing analysis. With these techniques, this proposal aims to elucidate the cellular and molecular development of the BBB and its impact on cellular trafficking into the brain. Our overall hypothesis is that immature venous-like vasculature mediates the entry of PL-derived immune cells into the brain due to its heightened BBB permeability during development. To address this hypothesis, we will first characterize the spatiotemporal development of the BBB, identifying cell types and anatomical regions associated with increased vascular permeability. Second, we will trace the entry of PL-derived immune cells into the brain and track changes in their cell identity over time. The outcomes of this research will advance our understanding of brain vascular development and potentially inform the development of therapeutics targeting the unique selective permeability of the prenatal brain vasculature.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY/ABSTRACT A central question in reproductive immunology is how the fetus and placenta avoid being rejected by the maternal immune system. Despite the substantial progress made on this question in recent years, many key knowledge gaps remain. These gaps not only prevent us from leveraging underlying mechanisms to induce antigen-specific immune tolerance in the clinical arena, but also limit investigation into the pathogenesis of intrauterine growth restriction, spontaneous abortion, preeclampsia, and preterm labor, i.e., pregnancy complications that may all involve aberrant activation of the maternal immune system to placental antigens. Recently, our laboratory has described key roles for B cell-mediated antigen presentation and antigen glycosylation in suppressing immune responses to placental antigens in mice. Specifically, we found that a surrogate model antigen expressed by trophoblasts (t-mOVA) is presented to maternal CD4 T cells exclusively by antigen-specific B cells, and that these B cells are suppressed through the actions of t-mOVA’s heavily sialylated N-linked glycans, thus in turn suppressing the CD4 T cells. This major new line of investigation raises immediate questions that we address in this proposal. Specifically, Aim 1 will use both mouse (t-mOVA) and human models to evaluate the hypothesis that glycan-specific IgM natural antibodies bind to antigens shed from the placenta, activating complement and thus causing the antigens to accumulate on follicular dendritic cells in the spleen. This accumulation in turn allows the antigens’ glycans to suppress antigen-specific B cells. Substantiation of this pathway would suggest new ways to conceptualize the pathogenesis of human pregnancy complications such as preeclampsia that are linked to increased antibody and complement deposition on trophoblast membranes. Aim 2 then seeks to the determine the features of trophoblast glycans that impart them with immunosuppressive properties, which, together with Aim 1, would inform how best to harness trophoblast glycobiology for therapeutic purposes. It will employ a variety of techniques including mass spectrometry to define the structures of t-mOVA’s glycans, and will fingerprint the glycans that decorate human syncytiotrophoblast brush border membrane proteins bathed in maternal blood. Lastly, Aim 3 will address the behavior of the tissue resident memory T cells that populate the decidua. These cells are positioned to defend against congenital infection but also pose potential direct threats to fetal survival. Using mouse models, it will determine the responsiveness of the cells to trophoblast antigens, as well as whether they are suppressed by trophoblast antigen-associated glycans, like B and T cells are systemically. Together, we expect this work to have a major impact on the field as it begins to connect the discovery that glycans play a central role in fetomaternal tolerance with other critical questions in reproductive immunology and obstetrics. The work will also further a second long-term goal of the fetomaternal tolerance field, namely, to foster application of underlying mechanisms to immune tolerance induction in the clinical arena.

NIH Research Projects · FY 2024 · 2024-07

PROJECT ABSTRACT There is an urgent need for new treatments capable of curing all forms of tuberculosis (TB) more rapidly. Limitations of the methods currently used to assess treatment effectiveness in human TB drug trials impede development of new shorter, more potent antibiotic regimens. The legacy pharmacodynamic (PD) marker (sputum culture) predicts clinical outcomes poorly, fails to detect residual M. tuberculosis (Mtb) that causes relapse, and requires 6-8 weeks to result. Because of the uncertain predictive value of existing culture-based outcomes, there is risk that PD signal in Phase 2 trials may not accurately translate to improved relapse outcomes in Phase 3 trials. Evidence from recent clinical trials suggest that several new non-culture assays performed at the time of treatment completion may predict subsequent microbiologic relapse. If validated, these assays could be developed as novel molecular end-of-treatment outcomes for Phase 2b/c TB trials, thereby assuring that the best new combination antibiotic regimens are advanced to Phase 3 testing. Embedded in the Rapid Research in Diagnostics Development for TB (R2D2) Network, the Candidate Clinical Condition as Prognostic Outcome for TB Study (C3PO) tests pathogen and host biomarkers at the end of treatment as predictors of microbiologic relapse among Vietnamese and Ugandan adolescents and adults completing the global standard 4-drug regimen for drug-susceptible pulmonary TB. C3PO will ascertain recurrent TB via intensive post-treatment microbiologic monitoring. The assays evaluated at the end of TB treatment include the RS ratio®, a novel non-culture sputum assay of bacterial ribosomal RNA synthesis developed by the Consortium for Applied Microbial Metrics (CAMM) and two human blood transcriptional signatures. C3PO hypothesizes that measurable residual disease detected by the RS ratio and a continuing TB-specific blood inflammatory signature at end of treatment will be associated with increased risk for microbiological recurrence. C3PO is designed to establish new molecular outcomes for use in TB clinical trials, thereby accelerating development of shorter, more effective TB treatments.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY/ABSTRACT Parkinson’s Disease (PD) is a debilitating neurodegenerative disease characterized by the progressive loss of substantia nigra pars compacta (SNc) dopamine neurons. The reasons for their selective vulnerability and the mechanisms that drive their degeneration remain unclear. There is mounting evidence that the activity of energetically-burdened SNc neurons is altered in PD, however the role of neural activity in the susceptibility of dopamine neurons is poorly understood. Additionally, while dopamine is known to be toxic to neurons that do not have a means of sequestering or metabolizing it, the role of dopamine itself in the degeneration of dopamine neurons in PD is not known. To investigate the role of activity in dopamine neuron selective vulnerability, we have developed novel mouse models in which we can chronically manipulate midbrain dopamine neuron activity using chemogenetics. With these models, we propose to determine how chronically manipulating activity and dopamine metabolism within dopamine neurons impacts their susceptibility to degeneration. These experiments will be the first to directly interrogate the role of neural activity in degeneration in a chronic, minimally-invasive manner. Furthermore, they will provide insight for future therapeutic strategies to protect dopamine neurons from degeneration in PD.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY/ABSTRACT Despite decades of HIV research, differences in rates of prevention and treatment engagement persist, particularly among populations facing significant barriers to care. Trauma, exposure to violence, and related mental health conditions such as post-traumatic stress disorder may impact individual’s ability to initiate and engage in HIV services. To help end the HIV epidemic, there is a need for interventions that improve PrEP uptake and viral suppression among populations with high-risk. The goal of the K23 award is to pilot a trauma-informed approach to increase HIV prevention and care engagement in a community clinic serving high-risk populations. This proposal includes three aims to achieve this goal. Aim 1 will examine how trauma and mental health influence HIV prevention and care engagement, using in-depth interview with 20 participants who face significant barriers to care. Aim 2 examines barriers and facilitators to implementing a trauma screener, brief intervention, and referral to treatment (T-SBIRT) in community clinics using in-depth interviews with 20 clinic stakeholders (e.g., leadership, health care providers, staff). Aim 3 will pilot test T-SBIRT with 50 participants in a community clinic to assess implementation outcomes. The intervention will be guided by an enhanced Consolidated Framework for Implementation Research. These specific aims will be achieved by the following training aims: 1) build content expertise on trauma stressors, mental health, and T-SBIRT, 2) develop methodological skills in clinical trials and intervention development, and 3) gain core competencies in implementation science. These objectives will be guided by a cross-disciplinary mentoring team with expertise in trauma, mental health, and implementation science. Findings from this research will generate data that will inform a future R01 proposal at scaling the T-SBIRT intervention across multiple clinics.

NIH Research Projects · FY 2025 · 2024-07

Project Summary/Abstract (from Parent R21NS138525) Patients diagnosed with genetic epilepsies suffer with severe seizures, neurobehavioral deficits and the uncertainty of a lifetime with diminished quality-of-life. Epilepsy in this population remains poorly controlled despite multiple antiseizure medications and is considered one of the greatest therapeutic challenges in the field. Despite tremendous effort, there remains a crucial need to study these epilepsy conditions at a preclinical level so we can identify new and safe drug treatments. Zebrafish mutants designed to represent these human genetic conditions would provide valuable tools for elucidating basic disease mechanisms and drug discovery. As such, we recently used CRISPR/Cas9 editing techniques to generate 37 different stable loss-of-function zebrafish mutants representing a broad spectrum of these epilepsies (Griffin et al. 2021). In this R21 proposal, would propose computational phenotyping of 12 different zebrafish mutants (arxa, cdkl5, chd2, depdc5, gabrb3, gabrg2, gnao1, pnpo, pcdh19, scn8a, stxbp1b, and syngap1b) and initiation of a program for large-scale drug screening. Using a recently developed high-resolution imaging system and machine learning based algorithms, this proposal offers an unbiased approach to behavioral phenotyping and drug discovery. This first-of-its-kind strategy could lead to a better understanding of a wide variety of currently intractable genetic epilepsies and new drug candidates for patients suffering with these conditions.

NIH Research Projects · FY 2026 · 2024-07

Abstract The goal of this study is to develop best practices for returning results to family child care home (FCCH) directors about pesticides present in their facilities. Best practices will be defined as activities that maximize comprehension of key knowledge and catalyze action to measurably reduce children’s exposure to agricultural and household-use pesticides, thus limiting potentially harmful exposures at an important stage of development. A mixed methods study will be conducted in four Central Valley counties in California in three phases. In Phase 1, multi-stakeholder working groups including local FCCH directors, child care, health and environmental organizations will meet with study staff to discuss ethical issues about reporting back results on pesticides detected in FCCHs using a bioethical environmental justice framework. Qualitative methods will identify common themes to inform the process of reporting back results with the Digital Exposure Report-Back Interface (DERBI) and understanding the barriers and facilitators. In Phase 2, a convenience sample of 30 FCCHs serving ethnically diverse young children in marginalized Central Valley communities will be recruited and participate in a 12-month integrated pest management (IPM) intervention, with carpet dust sampled and assessed for pesticides at baseline and 12 months later. FCCH directors will attend educational workshops, receive environmental assessments, and have regular consultations with study staff focused on IPM goals they have set. Three months post-baseline, FCCH directors will receive access to their pesticide results via the DERBI, including enhancements or modifications resulting from Phase 1 work. Immediately and over the next 9 months, FCCH directors will be interviewed to explore their reactions to and understanding of results, intention to change pest management strategies in response to their report, and plans to share results with families and their community. Throughout Phase 2, researchers will consider the impact of having returned results via DERBI, including barriers to or facilitators of impactful action and unintended consequences of returning results. Upon completion of post-intervention pesticide exposure assessment, Phase 3 of the study will begin. In Phase 3, the FCCH directors and local stakeholders will reconvene along with statewide stakeholders to discuss the quantitative and qualitative results of the IPM intervention, to identify best practices in reporting back pesticide results to FCCH directors, and to write a policy brief. The study aims are: (1) to develop a process for reporting back pesticides detected in FCCHs to program directors by collaborating with key local stakeholders, (2) to determine how an IPM intervention in FCCHs that includes reporting back pesticides using DERBI a) influences directors’ understanding of pesticides, IPM practices, intentions to act on and share their results, and b) whether the intervention subsequently, reduces pesticide exposures in FCCHs, and (3) To develop and disseminate best practices to report back pesticide exposure results for FCCHs and produce a policy brief by re-convening local stakeholders and meeting with statewide groups.

NIH Research Projects · FY 2024 · 2024-07

PROJECT SUMMARY The neural crest (NC) is a stem cell population that originates within the forming central nervous system. NC cells delaminate from the neuroepithelium by undergoing a spatiotemporally regulated epithelial-to- mesenchymal transition (EMT) that proceeds in a coordinated wave head-to-tail to exit from the neural tube. Cranial NC cells, which arise in the head region of the embryo and are the only NC population in vivo with the ability to differentiate into craniofacial skeleton and cartilage, are indispensable for the development of the face; mutations affecting NC development result in numerous diseases and malformations affecting the craniofacial structures (e.g. Treacher Collins syndrome, cleft palate, etc.). Thus, a thorough understanding of the regulation of cranial NC EMT is essential to identify the etiology of craniofacial abnormalities. To date, research has focused on unraveling early events governing cranial NC induction at the neural plate border and the mechanism of delamination from the neural tube. However, little is known about the regulatory changes governing the timing of NC EMT and exit from the neural tube. My preliminary studies demonstrate that a Wnt pathway antagonist, Draxin, plays an important role in controlling the timing of NC EMT, perturbations of which have negative consequences for cranial NC migration. This role for Draxin is particularly interesting in light of the fact that the Wnt signaling pathway has been shown to be a major driver of NC development. The goal of this Proposal is to investigate the molecular mechanism by which Draxin affects cranial NC EMT, with focus on its role in Wnt signaling. To this end, the Specific Aims of this Proposal seek to combine chick embryology with state-of-the-art imaging and biochemistry to: 1) Characterize the interaction of Draxin and Wnt signaling in cranial NC EMT; 2) Identify the role of Draxin in the regulation of cell adhesion proteins; 3) Characterize the post-transcriptional regulation of Draxin; and 4) Identify the role of Draxin in the regulation of extracellular matrix proteins. The results of this Proposal will significantly enhance our understanding of the regulation of cranial NC EMT and migration, providing new scientific avenues for translational research applications in the treatment of craniofacial defects.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY With the lack of disease-altering treatment in Alzheimer’s Disease and Alzheimer’s Disease and Related Dementias (AD/ADRD), timely identification of high-risk individuals and prevention targeting early stages of cognitive decline, has become a promising approach and a public health priority to reduce the care and cost burden of AD/ADRD. Over the lifecourse, midlife (age 40-65 years) is a critical and yet understudied period when cognitive function begins to decline, and the impact of modifiable risk factors (MRFs) becomes prominent. MRFs and AD/ADRD disproportionately impact race/ethnic minorities in the United States (US). However, race/ethnic minorities remain underrepresented in AD/ADRD research, and fundamental gaps exist in understanding the joint role of MRFs, which often co-occur, in race/ethnic disparities in cognitive aging, especially in midlife. Furthermore, whether the relationships between MRFs and midlife cognitive disparities in diverse populations are mediated by vascular, inflammatory, and neurodegenerative pathways needs to be elucidated. The overarching goal of this research program is to enhance our understanding of the roles and mechanisms of MRFs in race/ethnic disparities in cognition during midlife and explore underlying mechanistic pathways. Using a feasible and cost-effective approach, this project will leverage the strength of three NIH- funded longitudinal cohort studies in diverse populations, the Coronary Artery Risk Development in Young Adults study, the Health and Aging Brain Study: Health Disparities, and the Wisconsin Registry for Alzheimer’s Prevention. With more than 5,000 Black, Hispanic, and White middle-aged adults, all three cohorts also have state-of-the-art measurements of MRFs, cognitive function, and markers of vascular, inflammatory, and neurodegenerative pathways. Innovative and rigorous epidemiologic and statistical approaches will be applied to 1) create a diverse midlife cohort by harmonizing cognitive measures from the three cohorts, 2) determine the longitudinal association between MRFs and race/ethnic disparities in cognition during midlife, and 3) elucidate potential underlying mechanisms. The research program will be complemented by focused training in 1) etiology, epidemiology, and clinical assessment of cognitive aging and AD/ADRD, 2) psychometric methods, 3) machine learning, 4) advanced methods in health disparities. Together the candidate’s research aims, training activities, and mentorship from a multidisciplinary team led by Dr. Kristine Yaffe, will allow the candidate to develop a successful independent research program in MRFs and cognitive aging disparities. The current research plan seeks to provide critical insight into the joint effect of MRFs, cognitive disparities in midlife, and the underlying mechanisms. Our findings will have the potential to inform new prevention (on specific MRF clusters) and therapeutic targets (on prioritized mechanistic pathways) to lessen cognitive disparities among race/ethnic minorities in midlife, a critical time in life when the potential for risk modification may be the greatest.

NIH Research Projects · FY 2026 · 2024-07

SUMMARY / ABSTRACT This proposal aims to reveal critical neural mechanisms for intelligent reward-driven learning and decision-making. It is well established that animals, including humans, use internal models of the world to guide their behavior. Model-based computations are especially vital in complex environments, where animals often need to plan a sequence of choices leading to later rewards. Furthermore, after receiving a reward animals update their reward predictions (“values”) – both for earlier choices they made, and for alternative ways of reaching that reward. These adaptive behaviors rely on combining simulations (of potential paths) with evaluations (of whether they are worthwhile). The hippocampus is believed to play a critical role in model-based decision-making, because it can generate coherent “non-local” representations of distant places. These take at least two distinct forms. First, as rats run through an environment hippocampal place cells generally represent current location, but during late phases of the theta rhythm this place code can sweep forward to potential future locations. It was previously found that these “theta sequences” can rapidly flicker between available choices, on alternating theta cycles – highly suggestive of a role in evaluating options. Second, during immobility the hippocampus can produce sharp-wave-ripple (SWR) events, that often encode highly-compressed sequences of places. These occur much more often shortly after rats receive rewards – highly suggestive of a role in updating values. However, whether hippocampal non-local activity patterns are actually used for these purposes is unknown, largely because whether they access values is unknown. There is intriguing evidence that SWRs evoke activity changes in the network of brain areas vital for value-guided decisions (including frontal cortex and ventral striatum). But whether hippocampal non-local activity is actually associated with value retrieval (during theta sequences) and/or value updating (during SWRs) is unknown. This proposal would rigorously assess the relationships between value-guided decision-making and hippocampal non-local representations. We will employ advanced recording techniques and an innovative foraging task, complemented by sophisticated decoding algorithms and precisely-timed manipulations. We will test two specific hypotheses: that post-reward SWRs are used to update values of distant locations (Aim 1), and that theta sequences are used for online, value-guided decisions (Aim 2). These Aims engage the full combined expertise of our team of experimentalists and theoreticians, including large-scale recordings across multiple regions, statistical methods to identify non-local representations, and reinforcement learning algorithms to estimate decision variables from behavior. These studies have the potential to transform our understanding of how our brains explore internal models to guide learning and decision-making.

NIH Research Projects · FY 2026 · 2024-06

ABSTRACT Despite advances in kidney transplantation (KT) with improved 1-year graft survival to >90%, KT attrition is unchanged due to persistent antibody mediated rejection (ABMR). Given limited ABMR treatment options, the outcome is persistent KT inflammation and accelerated KT loss. As subtypes of rejection are diverse in their pathogenesis and treatment response, the need for precise treatments based on molecular basis of rejection is well-founded. We propose to develop and apply a drug repurposing pipeline to ABMR expression profiles to query publicly available drug-gene expression databases, to identify single and combination drug repurposing candidates for ABMR (Aim 1). Our preliminary, published studies support the successful analyses for ABMR with identification of publically available histological and molecular stable (control) and ABMR renal allograft datasets, to be integrated with single-cell RNASeq analysis experiments that will be conducted on curated ABMR renal allograft biopsies. We will use transcriptomic-based computational drug-repurposing to identify potential new single agent and combination therapeutics for the treatment of ABMR, based on expression reversal, leveraging public and newly generated single cell data. We will further determine the kinetics and the mechanism of action of promising drugs or drug combinations in human cells and ABMR tissue, ex vivo (Aim 2). Promising single agent and combination agents will be further validated for efficacy for treatment or prevention of ABMR in vivo, in a pre-clinical, established, rodent renal allograft model of ABMR (Aim 3). Our approach is highly significant because we will investigate unique and novel cell-specific transcriptomic profiles, underlying biological processes and signaling pathways in ABMR and these data will be analyzed with a drug repurposing pipeline to discover novel single agents and combination therapies that can be used as a personalized approach to management of ABMR. The in vivo experiments will take these studies to validation of compound or combination of compound efficacy for reversing or preventing ABMR. The successful completion of these studies can propose new, FDA approved drugs, that could be repurposed for improving long term outcomes in kidney transplant recipients, by reducing ABMR injury, extend graft and patient survival.

NIH Research Projects · FY 2025 · 2024-06

ABSTRACT Genomic data can provide an invaluable source of information to understand pathogen evolution, identify patterns of transmission, and characterize phenotypes such as drug resistance and immune escape. For eukaryotic pathogens, larger genomes, sexual recombination, and complicated transmission dynamics including polyclonal infections have historically limited the use of genomic data for many of these applications. However, recent laboratory developments, including multiplexed targeted sequencing, have rapidly increased the pace of genomic data generation for eukaryotic pathogens. Fundamental differences in the biology and transmission of infections caused by these pathogens render many of the genomic data and analysis tools developed for other organisms (primarily humans, viruses, and bacteria) difficult or impossible to use. As a result, many research efforts have needed to rely on bespoke methods for processing and analysis, limiting the reusability of data, the accuracy and reproducibility of results, and more generally the productivity of scientists studying eukaryotic pathogens. There is a need to develop software and computational tools to process, store, share and analyze these data in a way which sets standards, encourages innovation, and facilities scientific discovery. We will develop a suite of data standards and robust software including a) bioinformatic pipelines including tools to facilitate the sharing and storage of these data, b) a modular software toolkit to conduct downstream statistical analyses relevant for epidemiologic and population genetic research, and c) work within a community of advisors and experts in the analysis of genomic data for eukaryotic pathogens to develop approaches that meet the needs of community and encourage broader uptake. The proposed work also includes harmonizing and developing standards for genomic, epidemiological, and clinical data. We will initially focus on Plasmodium falciparum, a species of parasite that causes malaria infections, as an organism of direct application which exhibits key complexities of eukaryotic pathogens (recombination, polyclonal infections). As such, standards and software developed during this proposal will have relevance beyond this single organism to other eukaryotic pathogens where similar biological and transmission complexities limit the use of existing tools to leverage genomic data to answer scientific and public health relevant questions. The expected outcome of the proposed research is computational software able to analyze targeted amplicon sequencing data for eukaryotic pathogens. By developing these approaches, with clear engagement within the broader research community, this work will help change the landscape of analyses possible with complex genomic data.