University Of California, San Francisco

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY / ABSTRACT The central autonomic network (CAN) is a putative collection of cortical and subcortical areas in the human brain that control autonomic outflow to regulate physiology in the body. A critical gap in knowledge is our lack of clarity on the functional organization of the central autonomic network. This gap has immediate implications for epilepsy and several neurologic and psychiatric diseases with autonomic dysfunction. Although many neuroimaging studies (fMRI and PET) have identified twelve candidate nodes that could be part of the central autonomic network, current central autonomic network m odels differ drastically in which subset of nodes are included and how sympathetic and parasympathetic function is organized across these nodes. In our study, we propose a unique approach of using stereo-EEG (sEEG) implanted in epilepsy patients for clinical purposes to determine which of the twelve candidate nodes are part of the central autonomic network and how sympathetic and parasympathetic functions are organized across this network. with full candidate node coverage, this approach suggests a Based on preliminary data of nine participants medial-sympathetic, lateral-parasympathetic functional organization. We will test this hypothesis by enrolling 32 total participants and leveraging the largest emotion video clip library to date to efficiently elicit a full range of autonomic states while recording neural activity, continuous measurements of skin conductance (sympathetic), and continuous respiratory sinus arrhythmia (parasympathetic). We will model network control of autonomic outflow from these direct intracranial recordings with millisecond-level resolution and directly stimulate candidate nodes to test their autonomic function. With this unique window into human neurophysiology, we will generate new data to map the organization of the central autonomic network in the human brain.

NIH Research Projects · FY 2025 · 2025-08

Abstract Patients with sickle cell disease (SCD) experience early onset bone morbidity; 60% of young adults with SCD live with low bone mass and are at increased risk for fracture. Zinc, an essential trace mineral, is crucial for red cell stability, growth, and bone metabolism. Zinc deficiency is reported in approximately 40% of young patients with SCD and has been related to poor growth, increased vaso-occlusive episodes, and decreased bone density. The etiology of zinc deficiency in SCD is multifactorial, including inadequate dietary intake, increased requirements due to escalations in red cell turnover, and elevated urinary losses from renal insufficiency. Our underlying hypothesis is that that zinc supplementation can ameliorate the steady deterioration of bone mass and structure in individuals with SCD. Though vitamin D has received much attention, zinc is perhaps more important for bone health, particularly for patients with SCD. In a previous interventional trial, we demonstrated that zinc supplementation increased bone density in patients with thalassemia, a hemoglobinopathy with similar bone deficits. Meta-analyses reported that zinc supplementation has the potential to improve growth and reduce the number and severity of sickle cell-related pain episodes. Yet, most of the reviewed studies are small, short-term, and single-center and none of the prior trials focused on bone outcomes. A Cochrane Review concluded that large, multi-center, long-term zinc supplementation trials focused on disease outcomes in sickle cell disease are needed. Although much attention has been paid recently to curative therapies for patients with SCD, very few patients will have access to these new therapeutics. Currently, no therapies in SCD focus on bone morbidity. The findings of this proposed research could lead to a new, low-cost adjunctive therapeutic paradigm that will improve the lives of individuals with SCD. Our investigative team demonstrates expertise to conduct a randomized multicenter nutritional study in SCD. The ASH Research Collaborative Clinical Trials Network is poised to facilitate such an interventional trial, and the patients with SCD and their families have expressed enthusiasm for participation in nutritional studies. This R34 phase is crucial for the follow-up UG3/UH3 funded study by obtaining data to: (1) clarify optimal skeletal sites to be studied by DXA imaging, (2) calculate more definitive sample size for the subsequent larger study, (3) establish an effective yet tolerable zinc dose, and (4) develop quality control imaging and blood collection protocols. The information gathered from this R34 study is indispensable for designing a robust, multi-center randomized clinical trial within the ASH Research Collaborative Clinical Trials Network. By determining these critical parameters, we will significantly enhance the likelihood of conducting a successful and scientifically rigorous larger ASH Research Collaborative Network UG3/UH3 funded study focused on bone response to zinc supplementation.

NIH Research Projects · FY 2026 · 2025-08

PROJECT SUMMARY The link between intervertebral disc degeneration and chronic low back pain (cLBP) is widely acknowledged but poorly understood. Emerging evidence suggests that early deficits in disc health increase cLBP risk, but this potentially important association is difficult to study because conventional imaging methods for quantifying disc health are qualitative, subjective, and insensitive to early deficits in disc health. Spin-lock T1ρ MRI, which is sensitive to disc biochemical composition, overcomes this limitation. Indeed, we recently found that T1ρ biomarkers of disc health in cLBP patients were distinct from the normal age-course of disc degeneration in asymptomatic controls. This led to the discovery of a new cLBP phenotype that’s not apparent with conventional MRI: young adult patients (20–40-year-olds) who have abnormal disc biochemical composition for their age. What’s more, this T1ρ biomarker of poor age-relative biochemical disc health — what we term a low T1ρ “Z-score” — predicts the development of new disc pathologies and associates with earlier onset of symptoms. A critical unknown is the etiology of low T1ρ Z-scores and whether poor age-relative disc health reflects lower peak disc health before skeletal maturity or a faster decline in disc health after. It’s also unknown if this T1ρ biomarker predicts clinical outcomes and stratifies future cLBP risk better than conventional MRI. Three complementary aims are proposed. In Aim 1 we’ll perform T1ρ MRI in 10–25-year-old subjects to discover the age-course of biochemical disc composition. Specifically, we’ll determine population variability in peak disc health and clarify whether early deficits in disc health reflect a lower peak before skeletal maturity or a faster decline after. In Aim 2 we’ll discover risk factors for early deficits in biochemical disc health using an innovative two-stage approach. In the first stage, we’ll conduct a meta-GWAS of adults with standardized measures of structural disc degeneration. The result will be a multi-ethnic, genome-wide polygenic risk score (PRS) for genetic propensity to disc degeneration. In the second stage, we’ll genotype the young subjects in Aim 1 and test if the genetic propensity to structural disc degeneration in adulthood associates with early deficits in biochemical disc health. Specifically, we’ll test if PRS associates with age-adjusted T1ρ values and how the association depends on sex and anatomic risk factors, e.g., lumbar lordosis. In Aim 3, we’ll leverage access to previously acquired spine MRIs (T1ρ and conventional), brain fMRIs, functional measurements, psychosocial profiles, and 24-month clinical outcomes in an ongoing surveillance study of 300 adult cLBP patients and 75 controls. This will enable us to test for associations between T1ρ Z-scores and cLBP status and to discover how changes in pain and disability from baseline depend on a variety of patient characteristics, including metrics from T1ρ and conventional MRI. Through these studies, we will establish a quantitative diagnostic framework for contextualizing disc degeneration in relation to cLBP risk that could eventually improve clinical management of cLBP and help shift clinical paradigms from reactive to preventative.

NIH Research Projects · FY 2025 · 2025-08

This is a clinically grounded, patient-focused proposal aimed to improve the understanding of how pain is assessed, treated, and experienced by older adults during and after hospitalization. Despite the high prevalence of pain in this population, clinicians face challenges in balancing effective treatment with concerns about adverse effects, communication complexity, and functional outcomes. This award will support the scientific program and career development plan of Dr. Aksharananda Rambachan, to enable him to become an independently funded physician-investigator. In Aim 1, we will describe how pain is assessed and treated for older hospitalized adults. We will retrospectively analyze data from ~30,000 older adults hospitalized on a general medicine service using linear mixed models. In Aim 2, we will conduct a qualitative study using interviews and focus groups to understand the experiences and perspectives of patients, caregivers, and clinicians regarding pain during hospitalization. In Aim 3, we will prospectively examine the relationship between patient reported pain, inpatient pain treatment, and post-discharge functional measures and outcomes, in older hospitalized patients by integrating patient-reported data with clinical data. Dr. Rambachan’s career development plan consists of capacity building in three distinct training areas: (1) Core Principles of Geriatrics and Outcomes Assessments, (2) Specialized Advanced Quantitative Research Methods, and (3) Qualitative Research Methods. Dr. Rambachan will undertake coursework, seminars, structured tutorials, and experiential learning. His mentorship team includes Dr. Margaret Fang (primary mentor), Professor of Medicine and a nationally recognized NIA researcher, who will oversee Dr. Rambachan’s overall progress. Co-mentors include Dr. Andrew Auerbach, Professor of Medicine, who leads the multiinstitutional “Hospital Medicine ReEnginnering Network”; Dr. Kenneth Covinsky, Professor in Geriatrics, who is a nationally recognized geriatrics researcher; and Dr. Elizabeth Dzeng, Associate Professor of Medicine, and qualitative research expert. Dr. Rambachan will also collaborate with a team of advisors in pain management, communication, and statistics. The successful completion of this program will enable Dr. Rambachan to develop as an independent physician-investigator to improve treatment and outcomes for older, hospitalized adults.

NIH Research Projects · FY 2025 · 2025-08

Project Summary/Abstract: The goal of this application is to train Dr. Sasha Gupta, a physician scientist, with the skills necessary to become an independently funded investigator studying cellular therapeutics for the treatment of autoimmune and infectious neurologic conditions. In this research proposal, she proposes to identify, isolate and sequence clonally restricted T cell receptors from patients with diverse genetic backgrounds that are highly specific for JC virus VP1 antigens and have anti-viral activity in vitro and in vivo. These findings can advance the development of anti-JC virus T cell therapies that could revolutionize the treatment of progressive multifocal leukoencephalopathy. This research is accompanied by a career development and training plan that will build on Dr. Gupta’s clinical training in neuroimmunology and her postdoctoral training in in vivo testing of experimental cellular therapies. Her training will focus on 1) virology, 2) immunology, 3) bioinformatics, and 4) clinical implementation of cellular therapies. This career development and training plan will include a combination of formal coursework; mentored practical training; conference, meeting, and workshop attendance; and guidance from an exceptional team of mentors and advisors/collaborators. Altogether, this award will help prepare Dr. Gupta for an independent research career focused on developing cellular therapies for treatment of autoimmune and infectious neurologic conditions.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY/ABSTRACT Great progress was made in reducing the burden of malaria in sub-Saharan Africa from 2000 to 2015, with a majority of the cases averted attributed to the scale up of vector control with tools like insecticide-treated bednets. More recently, however, progress has stalled, and even reversed course in some high burden countries. The World Health Organization now recommends local tailoring of malaria control interventions to enhance their effectiveness. Few national malaria control programs have on hand malaria surveillance systems capable of producing the high-quality data necessary to tailor control interventions at the sub-national level. This creates an urgent public health need for enhanced malaria surveillance that can guide planning of control strategies by linking clinical outcomes to control interventions. Long-lasting insecticide-treated bednets (LLINs), the most widely used tool for malaria prevention, no longer seem as effective as they once were, likely as a result of resistance to pyrethroid-class insecticides and changes in the vector behaviors and species composition. Fur- thermore, human behaviors, such as lower rates of LLIN use and more time spent outdoors, may also be reduc- ing the effectiveness of vector control tools. Ultimately, it is the interactions between humans and vectors that determine the effectiveness of vector control. As a result, this proposal focuses on biological and behavioral factors that modulate interactions between humans and malaria vectors in the context of vector control interven- tions. Our central hypothesis is that there are gaps in protection despite the use of existing vector control tools (e.g. LLINs) which can only be elucidated by integrating human and vector monitoring data. Our proposed ap- proach will be to add rigorous human behavioral and entomological monitoring to our existing malaria surveil- lance network in 38 sites across Uganda. This network provides longitudinal estimates of clinical outcomes in- cluding malaria incidence and parasite prevalence from communities in target areas around government-run health facilities. Working in the context of “real-life” implementation of vector control interventions (e.g. LLIN distribution campaigns), our primary goal will be to link measures of human-vector interaction to epidemiological outcomes across geographic and transmission settings. Achieving this goal will enable us to answer fundamental questions about why malaria persists in the face of current control strategies and provide practical options for policy makers seeking evidence-based, targeted, interventions. In addition, this surveillance system will be ide- ally positioned to evaluate the impact of new vector-oriented interventions as they are implemented in the future. This proposal represents a unique opportunity to provide both actionable data for policymakers and also gener- ate fundamental insights for the many other countries throughout the world that rely on vector control to fight malaria. Our long term goal is to provide insights into how vector control tools affect clinical outcomes through reducing human-vector interaction and make progress in finding better ways to prevent malaria in the future.

NIH Research Projects · FY 2025 · 2025-08

Aggregation of the protein tau is a hallmark of several neurodegenerative diseases, collectively called tauopathies, which include Alzheimer’s disease (AD) and frontotemporal dementia (FTD). The presence of tau aggregates is highly correlated with disease progression, and there are disease-causing mutations in the tau- encoding gene, MAPT, but the molecular mechanisms linking pathological tau to neuronal dysfunction are not well understood. Dysregulation of RNA processing and metabolism are well-established properties of some neurodegenerative diseases. Tau is a known RNA binding protein (RBP), but there is little known about RNA dysregulation in tauopathies, and there is no known function of tau-RNA interactions in neurons, the discovery of which could lead to breakthroughs in deciphering the molecular determinants of tauopathies. In a collaboration with another trainee in the Kampmann Lab, I have demonstrated that iPSC-derived neurons harboring the FTD-causing MAPT V337M mutation display an aberrant axonogenesis signature linked to decreased phosphorylation of tau and other microtubule-associated proteins. In unpublished work, I have uncovered dysregulated RNA processing and localization as another consequence of MAPT knockdown (KD) and to a greater extent V337M mutation, which may contribute to axon phenotypes as well as FTD-relevant changes to cellular function, including V337M-induced hyperexcitability. It is my hypothesis that tau associates with RBPs to facilitate mRNA stability and transport along microtubules and that disruptions in mRNA processing and localization in V337M neurons are a direct result of aberrant tau functionality in this context. The goal of this proposal is to (1) characterize tau function in the context of RNA processing and transport and (2) identity mechanisms of tau-induced RNA dysregulation in FTD. I have shown that tau KD neurons and to a greater extent MAPT V337M neurons display altered RBP levels and phosphorylation as well as abnormal mRNA localization and exon usage. In Aim 1, I will acquire training in molecular RNA biology and in vitro biochemistry to characterize tau-RNA interactions in mRNA transport. In Aim 2, I will obtain training in spatial transcriptomics and RNA visualization to identify mislocalized and/or misprocessed mRNAs in FTD brain tissue. I will also expand my expertise in CRISPRi screening to discover modifiers of V337M tau- induced mRNA misprocessing. I am ideally positioned to complete the proposed research as this proposal complements my training in epigenetics and functional genomics in iPSC-derived neurons with RNA-based techniques and patient brain sample research. Completion of this proposal will transition promising molecular data to an interdisciplinary characterization of a novel and sometimes toxic tau function, supported by patient- derived data and directly relevant to therapeutic testing. The enclosed training plan will provide me the necessary scientific expertise and executive training to launch my career as an independent scientist.

NIH Research Projects · FY 2025 · 2025-08

Neurodevelopmental mechanisms in the human brain have emerged to support its larger size, increased complexity, and higher cognitive functions. Despite these benefits, the human brain encounters a variety of risks during development that can lead to developmental disabilities such as autism spectrum disorder (ASD). This evolutionary paradox has prompted a deep investigation into the distinctive developmental mechanisms in the human brain, seeking a new approach to human-based pathologies. One notable process is the protracted maturation of human cortical inhibitory neurons (CIN) during the perinatal period, before and after birth. CINs, a key population for network balance, still migrate postnatally into specific areas important for cognition. Indeed, children with ASD show an abnormal distribution of CINs and alternations in neural oscillations mediated by CIN in several cortical regions. Due to several obstacles, including limited access to the perinatal human brains, we have yet to elucidate how the protracted CIN migration contributes to regional specification and their vulnerability during the perinatal period. This proposal builds on my recent postdoctoral work on comparative analyses. I found immature inhibitory populations along the lateral ventricle (LV) and their regional migrations into the cingulate cortex (CC) and temporal cortex (TC) in the neonatal human brain. Strikingly, these populations are preserved in the large, gyrencephalic human, chimpanzee, and piglet brains, but not small, lissencephalic brains. This work provides a strong justification for utilizing the chimpanzee and piglet brains to study the migration of human CIN in this proposal. Here, I will test the central hypothesis that immature CINs at the perinatal stage have distinct migratory dynamics that differentially contribute to the regional cortical specifications, using the time-laps live imaging on larger brains (Aim 1, K99). Additionally, our gene expression data revealed that late-migratory CIN preferentially expresses ASD-risk genes. I will perturb ASD-risk genes using the CRISPR strategy to test the role of these genes in migration, integration, and differentiation of immature CINs in larger brains (Aim 2, K99). In the independent phase of this proposal, I will further expand my studies based on my significant finding that an additional population of immature inhibitory neurons in the temporal horn of the LV extensively migrate into the middle temporal gyrus (MTG), a part of TC in the neonatal human brain. My approach with comparative histology, single-nucleus RNA transcriptomic, live-imaging, and genetic perturbation techniques will uncover unique properties of CIN development in MTG that drive the structural and functional specification of MTG (Aim 3, R00). This proposal will expand our comprehensive understanding of the contribution of the protracted development of CIN to the specialization of cognitive regions. In turn, exploring the connection between ASD-risk genes and late-maturing CINs may provide greater insight into a novel therapeutic approach for human-based interneuron pathologies during the perinatal period.

NIH Research Projects · FY 2026 · 2025-08

Project summary/Abstract Centrioles, the core of centrosomes, have multiple fundamental roles including generating cilia, organizing the microtubule cytoskeleton, and facilitating mitosis. Inherited defects in centrioles can cause important human congenital diseases, including congenital heart defects and ciliopathies. Despite their importance to development and disease, the molecular and cell biological mechanisms through which centrioles participate in mammalian development remain poorly understood. We have been investigating how centrioles function in mouse embryonic development. Remarkably, disruption of different parts of the centriole affect different development events. For example, the distal centriole component CEP97 is critical for cardiac septation, but dispensable for many other centriole- and cilia-dependent events. In contrast, the proximal centriole component ALMS1 is critical for maintaining brain cilia, but dispensable for heart development. Interestingly, we found that removing centrioles altogether affects different cell types differently. For example, removing centrioles from the intestinal epithelium does not affect its development, but removing centrioles from the lung epithelium blocks lung branching. Thus, not only do different parts of the centriole have different functions in development, but different cell types use centrioles in different ways. Our proposal builds on this work by investigating how centrioles direct mammalian development, with a focus on heart, lung and inner ear development. Using tools like centrosome affinity capture mass spectrometry (CAPture-MS) and pan-Expansion Microscopy of tissue (pan-ExM-t) to mitigate barriers in studying centrioles, we examine how centriole defects lead to human disorders such as congenital heart disease and Alström syndrome. In Aim 1, we focus on how CEP97 promotes ciliogenesis in the second heart field, essential for cardiac septation. We investigate how CEP97 controls centriole length to enable ciliogenesis. In Aim 2, we explore how removing centrioles activates the mitotic surveillance pathway (MSP) to disrupt lung branching. We seek to understand how some lung progenitors apoptose in response to MSP activation while others do not. In Aim 3, we study how a proximal centriolar protein, ALMS1, supports ciliogenesis and transition zone assembly on the other end of the centriole. Thus, in addition to illuminating how centrioles function in development and disease, this project investigates how centrioles are constructed, how centrioles mature to generate cilia, how centrioles promote cell survival, and how cells ensure that they have neither too few nor too many centrioles.

NIH Research Projects · FY 2025 · 2025-08

Salivary gland adenoid cystic carcinoma (ACC) is a rare but deadly disease that is well controlled in the head and neck with surgery and radiation. However, in over 50% of patients, distant metastasis will develop, yet there are no approved chemotherapy or targeted agents suitable for treatment when this occurs. Up to 70% of ACCs have an alteration or gene fusion in the oncogene Myb, mostly combining with the transcription factor NFIB. This unique gene fusion event can have multiple different breakpoints, and therefore can produce several different protein products. Unfortunately, little is known about the oncogenic function of these gene fusions, and currently, there are no drugs targeting Myb or the fusion protein specifically. Broadly speaking, when these unusual fusion events occur in cancer, they often represent key molecular changes that are critical to the function of that cancer and can be exploited for drug targets. Few research models exist to help study this cancer and better understand why it is so aggressive. In order to advance the field and identify new drugs for treatment, it is imperative to analyze the function of these new fusion proteins. We have created cell line models with 5 different fusions and have discovered that we can inject these into the tail veins of mice to create lung metastases. Interestingly, in our early studies, the different fusions appear to have a range of aggressiveness. We would like to better characterize these different fusion types by also injecting these cells into mouse salivary glands to create situations where the cancer cells can behave more like they do in humans. We can then perform analyses on how these different fusions are behaving in these situations through RNA sequencing. This technique will provide deep insight into what pathways are changed and expose what vulnerabilities might exist within the cells with fusions. The main cause of mortality in ACC is distant metastasis, predominantly in the lung. Unfortunately, there are no proven drugs that help patients with ACC when this occurs. We have developed the first animal model for metastasis and intend to create a viable orthotopic PDX model. Additionally, little is known about the Myb-NFIB fusion proteins and how they contribute to carcinogenesis. Thus, this proposal seeks to combine our innovative animal models along with the Myb fusion to both provide model systems to understand the function of Myb- NFIB and create a platform for drug testing. These findings will greatly accelerate the rational identification of drug targets in ACC and help fast track them by testing in our model system. Rather than testing of borrowed drugs from other cancer models, we can focus our attention on ACC-specific compounds and help patients afflicted with this deadly cancer.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY This study investigates the ‘reactive’ immune system in tumors, namely the cellular and molecular allies that allow immunotherapies to work. The tumor microenvironment (TME) is a key biological structure that regulates the effectiveness of cancer immunotherapies. Understanding its (rare) valuable components and niches as compared to the inhibitory ones is critical to guiding next-generation immunotherapies. We hypothesize that discrete niches exist in tumors that are the building blocks for reactive immunity and that these can be found by co-labeling T cell activity (e.g. motility/synapse duration) and gene-expression signatures together with unique innovative tools. By directly illuminating functional effector CD8 T cell states, we will discover hidden features of their local microenvironment and define these in such a way to be widely applicable in new settings. This program is unique in applying and developing spatial transcriptomics together with genetic tools and conventional cellular immunoassay methods to understand the critical phenotype-biology relationship between critical T cell populations and their partners. The resultant discoveries will be formative for designing new ways to boost anti-tumor immunity.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY/ABSTRACT Scale up of proven control interventions resulted in marked reductions in the global malaria burden following the turn of the century. However, since 2015 progress has stalled and even reversed course in some high burden African countries. These trends highlight the urgent need for new interventions, especially those that have shown promise but have been underutilized. One such intervention is intermittent preventive treatment in school-aged children (IPTsc), defined as giving full therapeutic courses of antimalarial drugs at regular intervals to clear and prevent malaria infections in children who are old enough to attend school. IPTsc has been shown to be safe and to improve the health and educational attainment of school-aged children, can easily be scaled up if integrated into school-based programs such as deworming, and has recently been recommended by the World Health Organization (WHO). However, some uncertainties remain, including what impact IPTsc may have at the community level. We believe that IPTsc will not only reduce malaria burden in schoolchildren but could be an innovative and cost-effective tool for reducing malaria burden in surrounding communities, in particular because schoolchildren comprise a majority of the human infectious reservoir driving malaria transmission. The use of IPTsc to reduce malaria burden at the community level could play a major role in turning the tide on malaria in high burden countries. We hypothesize that IPTsc will reduce the burden of malaria both in schoolchildren who receive the intervention and in people of all ages in the surrounding communities. To test this hypothesis, we propose to deliver IPTsc with dihydroartemisinin- piperaquine (DP) approximately every two months for 24 months to children attending primary school in highly endemic areas across Uganda. DP has been shown to be highly effective and safe when used for chemoprevention in a wide range of populations, including school-aged children.3,9,10 The intervention will be evaluated using a rigorous cluster randomized trial design to assess effectiveness at both the community level and among schoolchildren. Outcomes will be assessed during the 24-month period when the intervention is delivered and for an additional 12 months after the intervention is completed to assess for “resurgent” or “delayed” malaria. Our specific aims will be (1) to estimate the effectiveness of IPTsc with DP in reducing community level malaria burden, (2) to estimate the effectiveness of IPTsc with DP in reducing malaria burden in schoolchildren, and (3) to estimate the cost-effectiveness of IPTsc with DP as a tool for reducing community level malaria burden. This study will leverage infrastructure, resources, and baseline data from an existing robust malaria surveillance network in Uganda. If IPTsc is found to be a cost-effective intervention for reducing the burden of malaria among people of all ages, this study will have clear and achievable policy implications.

NIH Research Projects · FY 2025 · 2025-08

Project Summary In patients with liver cirrhosis, infection is directly responsible for 30-50% of all deaths. The most common infection in patients with cirrhosis is spontaneous bacterial peritonitis (SBP), an infection that develops in excess abdominal fluid, known as ascites fluid. SBP accounts for ~25% of infections in hospitalized patients with cirrhosis, and results in a 4-fold increase in mortality. An improved understanding of the microbial and host features in cirrhotic ascites that drive the susceptibility to SBP is central to improving outcomes. The objective of this proposal is to apply a two-pronged, unbiased approach to develop a foundational metagenomic, meta- transcriptomic, and serological atlas of ascites, to test the hypothesis that patients with cirrhosis have a unique host and microbial signature that can identify those at greatest risk of SBP and mortality. These objectives will be addressed in Aim 1 through the application of metagenomic next generation sequencing (mNGS) and meta-transcriptomics to the study of ascites fluid, to determine whether these gene signatures can predict poor outcomes in cirrhosis, specifically SBP and mortality. These objectives will be further carried out in Aim 2 by employing a customized phage display library of peptides (representing a broad array of intestinal bacteria) to identify the ascites antimicrobial antibody repertoire. These experiments will establish a foundational dataset to determine the bacterial composition of ascites, parallel host response, and impact on outcomes in patients with cirrhosis. Accomplishing these specific aims will yield a comprehensive atlas of ascites microbial and serological composition, uncovering novel host and microbial attributes with the potential to predict outcomes and inform interventions. The candidate’s long-term career development goal is to be an independent physician scientist focused on uncovering the mechanisms of increased infection risk in patients with cirrhosis. The proposed career development plan will help the candidate master molecular and analytic approaches required to identify mechanisms of disease directly in patients with cirrhosis, and develop into an intendent scientist, generating results that can be used to develop tailored prevention strategies, improved diagnostics, and targeted therapeutics.

NIH Research Projects · FY 2025 · 2025-08

SUMMARY A robust heartbeat is essential for vertebrate life, as it is critical for sustained transport of nutrients and waste throughout large body plans. Given this fact, the emergence and maturation of cardiac activity during embryogenesis must be extremely reliable and must be bidirectionally coordinated with development of the heart’s form. The calcium physiology of the heart exemplifies this idea - it is the fundamental driver of cardiac contraction by sarcomeric protein assemblies in each individual beat, but simultaneously triggers many signal transduction pathways and induces gene expression. Here we will explore the changing patterns of cardiac calcium signaling during embryonic development and investigate their implications for the heart’s maturation. Calcium signaling contributes both to normal developmental processes and to disease in the adult heart, suggesting that its tuning serves an important instructive role but must occur within a set of appropriate bounds. Identifying these bounds requires definition of the precise rules that map cellular calcium to downstream outputs during development. These rules have remained elusive because cellular calcium shows dynamics on the timescale of hundreds of milliseconds, and spatial scales ranging from subcellular structures to entire tissues. These patterns will evolve due to slower developmental processes, and their features that define reciprocal flows of information can only be parsed in intact, live samples. I have established methods to image cardiac physiological dynamics in tens of intact zebrafish embryos simultaneously, while administering non-destructive, spatiotemporally programmable optogenetic control of these processes. My approaches open the door to an unprecedented exploration of the high-dimensional signal encoding space traversed by calcium signaling in cardiac development. First, we will develop all-optical approaches to measure calcineurin and calmodulin/calmodulin kinase signaling in developing zebrafish hearts, record the dynamics of their behaviors over normal development, and dissect response mechanisms with optogenetic reconstruction of cardiac calcium physiology. Second, we will manipulate the physiology of developing zebrafish hearts and perform single cell functional genomics to define a comprehensive list of calcium-sensitive developmental gene expression programs. Finally, we will investigate the roles of cell type-specific calcium signaling mechanisms in cardiac chamber specification. Together, these studies will define new rules by which the heart perceives its emerging calcium physiology to make developmental decisions, tracing the basic biophysics of the cardiac cycle through signal transduction, gene expression, and to organ-scale phenotype. In doing so, we will gain broader insight into what delineates physiological versus pathological adaptation during cardiac development, and into fundamental information-encoding mechanisms of calcium signaling which have been of longstanding interest in disciplines as diverse as neuroscience, immunology, and regeneration.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY/ABSTRACT Understanding transcription factors in human cells is essential for insights into development, health, and disease. However, our understanding of the protein-protein interactions driving transcriptional regulation remains incomplete. While high-throughput screens have identified hundreds of effector domains within transcription factors, their underlying molecular mechanisms remain largely unknown. We lack a comprehensive molecular understanding of which of the >1000 effector domains interact with which of the >700 cofactors, the specificity of these interactions, and how this specificity quantitatively influences gene regulation. This information is crucial for understanding basic principles of transcription and could also stimulate development of novel therapeutics capable of targeting these biologically essential but historically undruggable interactions. Current high-throughput interaction screens, capable of measuring many-by-many candidate interactors, employ transcription as a readout (e.g. two-hybrid approaches), making them ill-suited for studying transcription- associated networks. Furthermore, most methods for generating quantitative measurements of direct interactions (e.g. Kds, kons, koffs) are low-throughput and labor-intensive, involving extensive cloning, purification, and testing, which can take months if not years, severely limiting our ability to quantify the direct connections within these extensive protein-protein interaction networks. As a result, we have a very limited picture of how these interactions contribute to transcription. Here we will overcome these challenges by leveraging our expertise in development of high-throughput approaches, biophysics, and quantitative cell biology to first, develop a novel cell-based technology to generate a comprehensive matrix of 106 proximities between human transcriptional effector domains and the cofactors they recruit to regulate transcription (Aim 1). Next, we will determine the degree of specificity between these interactions using a high-throughput microfluidic technology we recently developed to quantitively measure the strength and timing of direct interactions (e.g. kon, koff, Kd) (Aim 2). Last, we will move beyond simple explanations of our observations towards predictive models to quantify how the specificity of interactions determines the strength and timing of gene regulation (Aim 3). The proposed research will generate a novel technology for large-scale mapping of many-by-many protein interactions with a wide dynamic range that will have immediate broad application to other biological systems beyond transcription (e.g. cell signaling networks). In addition to this technological innovation, by mapping the proximity network between effector domains and cofactors, quantifying their direct interactions, and linking these interaction specificities, strengths, and kinetics to gene regulatory dynamics, we will reveal new principles of transcription factor-mediated gene regulation.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY/ABSTRACT Long-acting antiretroviral therapy (LA-ART) has the potential to improve viral suppression and accelerate Ending the HIV Epidemic (EHE) goals in the U.S. Cabotegravir (an integrase strand transfer inhibitor, INSTI) and rilpivirine (a non-nucleoside reverse transcriptase inhibitor, NNRTI) (CAB/RPV), an every 4 or 8 week injection, is FDA-approved for maintenance of viral suppression among people with HIV (PWH). Based on data from clinics and the A5359 LATITUDE trial, U.S. HIV guidelines now also recommend CAB/RPV for select PWH with adherence challenges or persistent viremia on oral ART, ushering in an era of expanded use of LA- ART. Although CAB/RPV was highly effective in trials, rare, but significant, cases of virologic failure occurred among participants, resulting in emergence of 2-class (INSTI, NNRTI) resistance and limiting future ART options with preferred regimens, such as bictegravir or dolutegravir. Rare cases of virologic failure on CAB/RPV are being reported in routine clinical care, and early data suggest the risk of virologic failure may be higher among PWH starting CAB/RPV with initial viremia, compared to those switching in the setting of viral suppression on oral ART. With expanded CAB/RPV use in routine care in the U.S., investigation of virologic failure on LA-ART is needed to inform strategies to mitigate the risk of virologic failure and INSTI/NNRTI resistance. This application proposes a short-term, exploratory study investigating virologic failure on LA-ART, leveraging an ongoing study enrolling across the U.S. and established laboratory methods. The proposed aims are: 1) to assess CAB/RPV concentrations among persons with virologic failure on LA-ART and 2) to evaluate viral resistance mutations among PWH with virologic failure on LA-ART using standard and next-generation sequencing (NGS) methods. The proposed exploratory study, made feasible by existing infrastructure from a larger grant, will fill key knowledge gaps on PK and resistance outcomes after virologic failure on LA-ART in routine care across the U.S.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY Randomized controlled trials (RCTs) are the gold-standard in clinical research but are subject to many limitations including high costs, limited generalizability, and small sample sizes in patient subgroups. By contrast, electronic health records (EHRs) are widely available and contain information on large and representative patient cohorts. However, because they capture the uncontrolled observations of many clinicians, they are highly susceptible to bias. The recent availability of the raw data from RCTs has created a unique opportunity to integrate them with that from EHRs, and to innovate methods that exploit the distinct advantages of each dataset. We propose to identify the zone of overlap between these data and build bridges in data representations. These bridges could enable us to better emulate randomized trials using EHR data and measure the same effects seen in the trials. Consequently, it would allow us to study subgroups that were excluded from the pivotal trials associated with new drug approvals by the FDA. We will test these ideas out in the context of Ulcerative colitis (UC) and scale to others in future work. We have obtained access to the raw data from 12 RCTs in UC (N=6,226). These data contain timed and structured measurements of disease activity including the Mayo score, a composite score of patient symptoms and endoscopic severity. We have also obtained access to the EHR data of 3,270 UC patients treated at the University of California San Francisco. These data contain similar data as RCTs but largely in an unstructured form. In addition, these assessments tend to be incomplete relative to trials due to costs and invasiveness of some tests. We will address this problem of unharmonized and incomplete EHR data in three aims. In Aim 1, we will harmonize the RCT data into an analysis-ready format. We will also develop text classification tools to transform free-texted EHR data into Mayo subscores, and validate these tools against data from a second center. In Aim 2, we will integrate the RCT and EHR data, train algorithms to impute RCT- based representations of the patient state from partial measurements made in EHRs, and test them under conditions typifying real-world data capture. In Aim 3, we will use these algorithms to harmonize EHR data, validate them as a tool to recover the same effects as RCTs, and study new patient subgroups. The applicant will carry out these aims and train in biostatistics, natural language processing, machine learning, and overall career development. With the help of his mentors, he will launch a career dedicated to developing and disseminating methods for learning from complex clinical data, and in so doing, promote a future of better healthcare for all patients.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY Children with liver transplants who are maintained on low dose immunosuppression (IS) with ideal graft function according to clinical, biochemical, and histological criteria seemingly enjoy a harmonious equilibrium between the host immune system and the liver allograft. Reducing IS is a challenge that, for some but not all, precipitates alloimmune activation that can result in graft injury. Understanding the mechanisms of how allograft quiescence is sustained or lost when stressed is essential to walking the tightrope of too much versus too little IS. Achieving this balance is particularly critical for children and their families who typically face many decades of IS. Previously, we conducted prospective multicenter trials of IS withdrawal in children with liver transplants [WISP-R (NCT00320606) and iWITH (NCT01638559)]. We reported that, among allografts that appear normal by standard histological evaluation, objective quantification of inflammatory load using multiplex immunostaining accurately predicted the clinical outcome of success or failed IS withdrawal. The density of various inflammatory cell populations mapped allografts onto an alloreactivity spectrum that extended from quiescent to activated. Among inflammatory metrics, the density of immunologic synapses (iSYNs), defined as a lymphocyte interacting with an antigen-presenting cell based on positional, morphometric, and molecular metrics, was the best predictor of those who could withstand the perturbation of IS reduction and maintain allograft quiescence. These findings drive our primary hypothesis that the number and nature of interactions between intrahepatic immune cells constitutes the basis of liver allograft immunogenicity and determines whether quiescence is maintained or lost when challenged by reducing IS. iSYNAPSE proposes to conduct a multicenter, single-arm trial of 50% IS dose reduction for stable children on tacrolimus monotherapy with healthy liver allografts. Previous trials confirm that liver transplantation provides a unique context to safely study host and graft responses when their harmonious equilibrium is challenged by IS reduction. Utilizing allograft biopsies collected at the beginning and end of the trial, we will deeply characterize the liver microenvironment, precisely mapping the location, identity, state, and interactions of key immune cell subsets combining state-of-the-art technologies for tissue interrogation into a targeted and integrated multi- modal approach. These experiments will allow us to determine if the baseline phenotype and transcriptome of the lymphocytes and the antigen-presenting cells participating in iSYNs and their changes after IS is reduced differentiates participants who succeed versus fail IS reduction. Understanding the basic mechanisms of how allograft quiescence is maintained or lost in response to a discrete challenge addresses a fundamental knowledge gap in transplant immunobiology. The knowledge gained may accelerate the transition of IS management from empiricism to evidence-based with broad implications for all organ transplant recipients.

NIH Research Projects · FY 2025 · 2025-08

Abstract Among the estimated 155 million TB survivors worldwide, a substantial proportion have post-tuberculosis lung disease (PTLD), characterized by persistent respiratory complaints, abnormal lung function, and/or chest X-ray abnormalities. Despite its prevalence, PTLD is poorly characterized and poorly understood. Our objectives are to establish a well-characterized PTLD cohort in a low-income and high-TB/HIV burden country and determine whether sex, HIV serostatus, and air pollution are associated with distinct lung function-chest CT PTLD phenotypes. This proposal builds upon a successful 17+ year collaboration in Kampala, Uganda. Our previous research found significant sex-based and HIV-specific differences in spirometry post-pneumonia, and preliminary data indicate similar trends in spirometry, total lung capacity (TLC), and diffusing capacity for carbon monoxide (DLco) post-TB. Specifically, post-TB women with HIV exhibited stronger trends towards abnormal spirometry, TLC, and DLco compared to post-TB men with HIV; this was not seen in post-TB persons without HIV or in persons without TB. Post-TB women with HIV also had significantly higher PM2.5 levels than their male counterparts. These findings support our central hypothesis that there are sex-based and HIV-specific differences in the lung function-chest CT presentations of PTLD and that women with HIV are at increased risk. We hypothesize that these sex and HIV differences are exacerbated by higher PM2.5 levels in women and an enhanced deleterious effect of PM2.5 exposure in HIV. To address this, we will enroll 650 post-TB and 165 non- TB adults. We will determine the impact of sex and HIV on lung function-CT findings and investigate whether sex or HIV modifies the associations between PM2.5 and PTLD. Aim 1: Determine the impact of sex and HIV on spirometry, TLC, and DLco in persons with and without TB at baseline (end of TB treatment for TB) and follow- up (2 years later). Hypothesis: Post-TB women with HIV will have higher odds of abnormal lung function than post-TB men with HIV; no such sex difference will be found in post-TB persons without HIV (primary hypothesis) or those without TB (secondary). Aim 2: Determine the impact of sex and HIV on CT findings using conventional chest radiologist interpretation and novel, automated AI algorithms in persons with and without TB at baseline and follow-up. Hypothesis: Post-TB women with HIV will have higher odds of emphysema, fibrosis, small airways disease, and vascular abnormalities on CT than post-TB men with HIV; no such sex difference will be found in post-TB persons without HIV or those without TB. Aim 3: Determine whether sex or HIV are effect modifiers of the relationship between PM2.5 and lung function-CT findings using short- and long-term PM2.5 measurements from personal samplers and residential satellite-based spatiotemporal models. Hypothesis: The relationships between PM2.5 and PTLD findings will be more pronounced among women compared to men and among persons with HIV compared to persons without HIV. This research will serve as a foundational study of PTLD, leading to advancements in its diagnosis and management, mechanistic studies, and targeted interventions in the future.

NIH Research Projects · FY 2026 · 2025-08

PROJECT SUMMARY Building a nationally interoperable health care delivery system remains a top priority in US health care, with early studies theorizing that robust data exchange could reduce health care costs by over $80 billion annually. Despite recent efforts to enhance interoperable health information exchange, there is mixed or insufficient evidence that increased connectivity between health care delivery organizations is improving outcomes or reducing costs. One potential reason for this is the “last mile” of interoperability; busy clinicians lack the time to search for, view, and process patient data delivered via interoperability, which is often not integrated into the local electronic health record (EHR). Delivering on the promise of interoperability requires a better understanding how clinicians use data generated outside their institution, and the value of that data for improving outcomes such as utilization, quality, and patient satisfaction. Finally, developing actionable guidelines for when and where outside records data (ORD) is valuable within the context of a given encounter is critical to building interoperability solutions that facilitate high-value use by clinicians. To address this, our study – The Last Mile of Interoperability: Integrating Outside Data Into Clinical Workflows to Improve Care – will leverage a natural experiment and detailed EHR metadata from two institutions to identify the causal impact of HIE use on a range of patient outcomes including costs and utilization, health, and patient satisfaction. We will use an innovative combination of robust econometric instrumental variables to identify the impact of ORD review and novel machine learning methods to reveal the clinical scenarios where HIE use is likely to be valuable within the context of a specific clinical encounter. We will use these results to generate public goods that will guide the development and evaluation of tools designed to streamline clinician information consumption and optimize the review of outside records data with a focus on new artificial intelligence and large language model applications. Our study will generate actionable evidence on the impact of outside record integration, the value of viewing outside records data by clinicians, and inform the development and evaluation of new technologies towards the goal of realizing the benefits of the national investment in interoperability.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY/ABSTRACT Background: Despite the success of T cell therapies in treating hematologic malignancies, solid tumors remain a significant challenge due to their dense fibrotic stroma, immunosuppressive microenvironments, and antigen heterogeneity. Current adaptive cell therapy approaches struggle to overcome these barriers, highlighting the need for novel strategies. Myeloid cells, including macrophages and dendritic cells, possess inherent abilities to infiltrate tumors, secrete cytokines, and cross-present antigens within the tumor microenvironment, making them ideal candidates for therapeutic engineering. However, engineering these cells is technically challenging, and tumors often co-opt myeloid cells to suppress adaptive immunity. We aim to overcome these obstacles by applying advanced genetic engineering tools to reprogram myeloid cells, enhancing their tumoricidal activities and resistance to polarization into immunosuppressive states. Toolbox: We have developed a toolbox of new techniques that will allow us to overcome key engineering challenges in human myeloid cells. Recognizing that nucleofection can lead to significant toxicity and dysfunction, we have found that using enveloped delivery vehicles (EDVs) to deliver Cas9 preserves myeloid cell viability and functionality. Additionally, through a collaboration with the Landau lab, we have shown that lentivirus incorporating the Vpx system leads to highly efficient transduction of human myeloid cells. We have further engineered these lentiviruses to express a mutant VSVG and scFvs targeting myeloid-specific surface proteins, enabling selective transduction of specific myeloid compartments. Approach: 1) CRISPR Gene Editing: These tools will enable us to perform CRISPR-based knockout and base editing screens in primary human macrophages and dendritic cells to identify and modify key genes that regulate myeloid cell polarization and effector functions. In addition, we will explore base editing of genes with known roles and mutations in autoinflammatory diseases driven by overactive myeloid cells. 2) Synthetic Receptor (Innate-CAR) Library: To complement these gene editing approaches, we will design and test a library of synthetic receptors, which we call Innate-CARs, to enhance myeloid cell immunogenicity. These Innate-CARs will combine a tumor- specific scFv with intracellular domains from a variety of diverse innate immune receptors and intracellular proximal signaling molecules to optimize myeloid cell responses to tumor antigens. After we screen and identify top-performing Innate-CARs and gene edits, we will use a variety of immunodeficient and immunocompetent preclinical models to assess these enhancements in CAR-myeloid cell antitumor immunity. 3) In Vivo Engineering: Using our novel myeloid-targeting lentiviruses, we will evaluate the efficiency and efficacy of in vivo manufactured Innate-CAR myeloid cells in tumor-bearing humanized mouse models. Impact: By exploring the synthetic space of myeloid cell biology, we aim to push the boundaries of current immunotherapy paradigms and pave the way for new, effective living medicines to treat refractory solid tumors.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY / ABSTRACT I am an MD/PhD-trained neurointensivist and physiologist navigating a critical career development transition towards becoming an independent investigator. My long-term goal is to improve clinical outcomes of patients with severe ischemic strokes admitted to the intensive care unit (ICU). In the ICU, we can change the levels of carbon dioxide (CO2) or hydrogen ion (H+) in the bloodstream of intubated, mechanically ventilated patients. However, we do not know the optimal ranges of H+ or CO2 to target to support brain recovery and limit secondary injury following stroke. Experimentally elevating systemic CO2 and H+ can reduce the size of strokes in rodents, by mechanisms that are incompletely understood. H+ and CO2 influence cerebral blood flow, and may also shift cellular energy phenotypes in neurons or other brain cells. In parallel, H+ and CO2 levels may also inhibit spreading depolarizations (SDs), waves of powerful neuronal activation that propagate through the vulnerable brain territories adjacent to infarcts, exert immense energetic stress on neurons, and kill neurons with insufficient metabolic supply. SDs play a key role in expanding the size of strokes for many days, corresponding to the time period when patients are in the ICU. In this project, my objective is to identify protective and harmful mechanisms of acid-base physiology relevant to stroke. My hypothesis is that augmenting H+ will improve metabolic supply and energy utilization, inhibit SDs, and reduce the size of strokes. I will test this hypothesis with two specific aims: 1) comparing the effects of systemic and cerebral H+ vs CO2 on cerebral blood flow, cellular energy metabolism, and stroke outcomes in mice, and 2) testing whether elevated extracellular H+ decreases the incidence of SD by inhibiting NMDA receptors. The significance of the proposed research is that completing these studies will provide high-quality physiologic evidence to inform clinical guidelines for the management of acid-base status in ICU patients with stroke and other acute brain injuries.

NIH Research Projects · FY 2025 · 2025-08

ABSTRACT Transcranial low-intensity focused ultrasound (LIFU) is an emerging modality for noninvasive and targeted modulation of cortical and deep targets in the human brain. LIFU has enormous potential to realize a transformative treatment for myriad neurological and psychiatric disorders, but significant challenges exist for the clinical translation of LIFU neuromodulation protocols due to the unknown underlying neurophysiological mechanisms and the relatively large parameter space that remains poorly understood. Dissecting the mechanistic underpinnings of LIFU neuromodulation with systematic and carefully controlled experimental approaches is a critical step to facilitate the effective development of therapeutic protocols. Recent studies have established that LIFU elicits differential responses in diverse neuronal cell types depending on the pulsing parameters . However, dynamic circuit-level effects resulting from synaptic interactions between cell types have remained largely undisclosed. In this project, we will develop a systematic approach based on cutting-edge technologies to generate new fundamental knowledge on the underlying mechanisms of LIFU neuromodulation in specific cell types, focusing on circuit and network-level effects. In our analysis of the temporal dynamic responses, we will directly assess whether LIFU can enhance gamma-frequency (30-100 Hz) neural oscillations, which play a key role in information processing and cognition and are implicated in the pathophysiology of many neuropsychiatric disorders, including autism, schizophrenia, and neurodegenerative disorders. In all the proposed experiments, we will implement carefully designed control conditions to disentangle direct neuromodulatory outcomes from potential nonspecific auditory effects. In Aim 1, we will use cell-type specific fluorescent calcium indicators to map the LIFU neuromodulation parameter space in excitatory neurons and in parvalbumin (PV) and somatostatin (SST)-positive inhibitory interneurons. These cell types are particularly interesting due to their specialized role in the generation of gamma oscillations. In Aim 2, we will record cell- type-specific transmembrane voltage dynamics from cortical excitatory and inhibitory neurons to shed light on the circuit-level responses to LIFU neuromodulation. In Aim 3, we will use functional ultrasound imaging to map whole-brain network-level responses. Taken together, our Aims will yield new fundamental insights on the underlying mechanisms of LIFU neuromodulation. Excitingly, our Aims will lay the groundwork for a clinically translatable approach to systematically modulate neural oscillations in deep brain regions.

NIH Research Projects · FY 2026 · 2025-08

7. PROJECT SUMMARY The proposed work focuses on interorgan communication between the gut microbiome and the joint in the pathogenesis of osteoarthritis (OA). Although historically viewed as a disease caused by mechanical overload, recent studies indicate that systemic factors are a major contributor to OA. The gut microbiome is a critical regulator of systemic inflammation and is readily modified in individuals, making it an enticing therapeutic target. Studies by our group and others indicate that the gut microbiome is a potent regulator of OA capable of enhancing or blunting trauma-induced osteoarthritis in animal models. Aging is associated with alterations in the composition of the gut microbiota, increased systemic inflammation and increased susceptibility to OA. In several cases, age-related changes in the gut microbiome are major contributors to disease. However, it is not known if the gut microbiome influences spontaneous age-related osteoarthritis, nor is it clear if age-related changes in OA are due to age-related changes in host physiology or age-related changes in the gut microbiota. Clinical and preclinical studies have implicated microbially-derived molecules that transit from the gut into the systemic circulation as regulators of the relationship between the gut microbiome and the joint. However, the association between microbiome-induced changes in musculoskeletal tissues and microbially-derived metabolites is currently limited to examination of fecal samples. Supported by robust PRELIMINARY STUDIES suggesting an effect of the gut microbiome on age-related OA and implicating key microbiota-dependent metabolites with severity of OA, we propose the global hypothesis that the gut microbiota regulates the effects of aging on joint degeneration. Specifically, we ask: Does the microbiome influence spontaneous, age-related joint degeneration? To what degree do age-related changes in the gut microbiota v. age-related changes in host physiology promote joint degeneration? Which of the circulating microbiota-dependent molecules link the gut microbiome to joint degeneration? How do these effects differ by sex? The proposed work has three aims explored using mouse models: 1) Determine the effects of the gut microbiome on age-related spontaneous osteoarthritis; 2) Determine the contribution of age-related changes in the gut microbiota to osteoarthritis; and 3) Determine the role of circulating microbiome-derived metabolites on the severity of osteoarthritis. At the completion of the proposed work, we will have addressed key interactions between the gut microbiome and aging in the context of joint degeneration and determined the effects of microbiota-derived molecules as signaling factors linking the gut microbiome to OA.

NIH Research Projects · FY 2025 · 2025-08

Project Summary Our earlier work identified the neural stem cells (NSC) and intermediate progenitors that generate new neurons and glial cells in the adult mouse brain. These NSCs are regionally specified to produce unique sets of inhibitory interneurons that migrate along the rostral migratory stream (RMS) to the olfactory bulb. Unlike rodents, the adult human brain does not contain an RMS, but this and other migratory streams are present in infants. In young children, we recently found two major streams of migrating young neurons (the ARC and the EC stream) that supply inhibitory cortical interneurons (cIN) to the frontal and entorhinal cortices respectively. The neuronal progenitor cells that generate these postnatally recruited young neurons have not been identified. Our overall goal for the next 8 years is to investigate how NSC niches transition from embryonic to postnatal stages in the human forebrain. We aim to characterize the different NSCs and progenitor populations involved in the production of large numbers of cINs required for the greatly expanded human neocortex. We plan to focus on the ventral forebrain germinal regions, in particular, on the caudal ganglionic eminence (CGE), which is the source of half of all cINs in humans, including the majority of cells observed in the ARC and the EC stream. CGE-derived cINs are considered key to higher cognitive function, and dysregulation of their numbers has been linked to neurological disorders and tumor formation. We hypothesize that the human CGE has increased its output of cINs by (1) increasing the proliferation of intermediate progenitors at multiple stages in the cIN lineage, and (2) extending the period of neurogenesis into postnatal life. We propose to use multi-omics, spatial transcriptomics, and electron and light microscopy to investigate the cellular composition and organization of the human CGE. We aim to identify the different CGE progenitor populations and how this germinal niche is organized. Preliminary data suggests that epidermal growth factor receptor (EGFR) could be key to CGE intermediate progenitor amplification. Using CGE organoids and genetic approaches in mice, we will investigate the role of EGFR signaling in CGE neurogenesis and gliogenesis. We will then study what progenitor cells persist postnatally in the CGE and other ganglionic eminences and how their niches change from prenatal to postnatal stages. Finally, we propose to resolve the controversy of whether NSCs in the postnatal brain produce both neurons and glial cells in vivo. The proposed work will elucidate how cIN production is amplified to satisfy the needs for a greatly expanded human neocortex. This basic new knowledge of human brain development could lead to novel approaches for the treatment of neurological disorders and the identification of progenitor cells implicated in tumor formation.