University Of California, San Francisco

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY: An estimated 800 pregnancy-related deaths occur daily. Most of these deaths occur in low- and middle-income countries (LMICs), with about two-thirds in sub-Saharan Africa (SSA) alone. Skilled care in health facilities is critical to improving maternal and neonatal outcomes. Yet, only about two-thirds of births in SSA occur in health facilities—with wide disparities, especially by socioeconomic status (SES). Poor person-centered maternal care (PCMC) is a key driver of both the low rates of facility-based deliveries and disparities. Further, where facility-based childbirth rates have increased, poor PCMC leads to morbidity and mortality due to delayed, inadequate, unnecessary, or harmful care. Yet, there is limited research on interventions to improve PCMC in LMICs; and existing interventions do not explicitly address inequities in PCMC experiences. To address this gap, we designed the “Caring for Providers to Improve Patient Experience” (CPIPE) intervention to address drivers of poor PCMC and center the unique needs of vulnerable women in LMICs. CPIPE is a theory and evidence-based intervention with 5 components: provider training, peer support, mentorship, embedded champions, and leadership engagement. The training is a simulation-based curriculum that integrates content on PCMC, stress, burnout, and bias into emergency obstetric and neonatal care drills. We target provider stress and bias because they are mutually reenforcing factors driving poor and inequitable PCMC. The other intervention components create an enabling environment for behavior change. Our pilot studies show high feasibility, acceptability, and preliminary effectiveness. We therefore propose a cluster randomized-controlled trial, in 40 high-volume delivery health facilities in Kenya and Ghana, to assess the impact of CPIPE on PCMC and intermediate and distal outcomes in our conceptual model. We will accomplish this through 3 aims. Aim 1: to assess the effectiveness of the CPIPE intervention on PCMC in Kenya and Ghana. We hypothesize that CPIPE will improve PCMC for all women, and especially for low SES women. Our primary outcome is PCMC measured with the PCMC scale through multiple cross-sectional surveys of mothers who gave birth in the preceding 9 weeks in study facilities at baseline (prior to intervention), midline (6 months post-baseline), and endline (12 months post-baseline) (N=2000 at each time point). A sub-aim 1 will assess the cost-effectiveness of CPIPE. Aim 2: to examine the mechanisms of impact of CPIPE on PCMC. We will assess the effect of CPIPE on intermediate outcomes such as provider knowledge, self-efficacy, stress, burnout, and bias levels; and conduct mediation analysis to assess if changes in these outcomes account for the effect of CPIPE on PCMC. Aim 3: to assess impact of the CPIPE intervention on distal outcomes including maternal health seeking behavior and maternal and neonatal health; and examine if changes in PCMC account for these effects.

NIH Research Projects · FY 2024 · 2023-07

PROJECT ABSTRACT The current proposal seeks to study implementation of integrated substance use and mental health services for justice-involved young (JIY) women in Brazil. Despite a significant rise in rates of substance use disorders among JIY women (age 18-24) globally the past decade, implementation of evidence-based substance use services remains critically low in low- and middle-income countries (LMIC), and the global health field has made minimal progress in rigorously examining factors governing their implementation. Co-occurrence of substance use and psychiatric disorders among JIY women is the norm worldwide, with exposure to trauma theorized as a mechanism underlying the onset and mutual maintenance of co-occurring symptoms. In LMIC like Brazil, substance use services are delivered in isolated and minimally funded healthcare systems by providers with low capacity to address simultaneous psychiatric symptoms and exposure to trauma that may generate and maintain substance use. Contextually appropriate integration of substance use and mental health services (i.e., concurrent provision of substance use and mental health services by one or a set of providers) may be a viable means of increasing implementation of substance use services for JIY women in LMIC settings. The proposed study leverages advances in substance use services research, implementation science, juvenile justice, and global health to guide integration of Contingency Management (CM), a gold standard substance use intervention, with brief cognitive behavioral therapy (CBT) services for JIY women re- entering community from juvenile detention in Brazil. JIY women released from detention (age 18-22 years) are a high-risk population with elevated rates of substance use relapse and high rates of co-occurring psychiatric disorders and trauma exposure. Mixed-methods data will be used to explore individual- and provider-level barriers and facilitators to integration of CM/CBT services for this population. An understanding of multi-level implementation factors will inform development of a provider implementation plan in integrated CM/CBT services delivery. A mixed-method open trial will examine preliminary feasibility and acceptability of integrated services. The provider implementation plan will include trauma-informed considerations to enhance implementation of substance use services. Study findings can be used to inform best practices for delivering integrated substance use and mental health services for JIY adult populations in LMIC, as well as high-income countries where implementation of integrated interventions significantly lags. Findings may also serve as an important demonstration project in LMIC settings as they tackle the significant burden of young adult substance use. The study benefits from well-established community collaborations in Brazil, a strong mentorship team, and the F32 applicant’s prior global mental health research training to fulfill its aims.

NIH Research Projects · FY 2024 · 2023-07

Project Summary/Abstract The human brain function relies on the formation and maintenance of precise neural circuits among more than 100 subtypes of neurons. These circuits are mediated by synapses, the characteristics of which vary depending on neuronal subtype. Synaptic dysfunction plays a critical role in most, if not all, human brain disorders. Thus, understanding synaptic diversity and its developmental origin are crucial for us to understand how the brain functions and how it goes awry in mental disorders. During brain development, synapses undergo profound changes to become mature and fully functional. Maturation of glutamatergic synapses involves changes in the postsynaptic density (PSD), a highly sophisticated protein complex composed of >1,000 proteins. However, the compositional changes of the PSD in development were not well characterized. My preliminary data revealed the temporal dynamics of >1,000 PSD proteins during cerebral cortex development, providing initial insight into mechanisms of synapse maturation. Moreover, integrative analysis of the developing PSD proteome and single- cell RNA-seq data suggested that different neuronal subtypes undergo divergent synapse maturation processes. However, we know little about the compositional diversity of neuronal subtype-specific synapses or the different maturation processes they go through. In addition, synapse maturation, diversity, and specificity can be controlled by transcription, but the underlying gene regulatory programs remain elusive. This information is particularly relevant to mental disorders like autism spectrum disorder, in which genetic mutations converge on transcription regulation and synaptic transmission. Thus, the specific aims of this project first seek to uncover the compositional diversity of neuronal subtype-specific synapses in the developing cerebral cortex using a novel chemogenetic method (Aim 1, K99 phase). The second aim is to decode the disease-relevant gene regulatory mechanisms that generate this diversity by applying single-cell genomics and machine learning approaches (Aim 2, K99 phase). Finally, using the training, tools, and preliminary data from the K99 phase of my proposal, I will launch an independent research project that focuses on investigating the effects of neuronal activity on synapse maturation and plasticity at neuronal subtype resolution (R00 phase). Results from these studies will provide insights into synapse diversity, its regulatory mechanisms, and its dysregulation in autism. My long-term goal is to study the functional importance of synapse diversity on neural circuits and behaviors and develop targeted therapies to alleviate synaptic dysfunction in mental disorders in patients. Additional training obtained during this award in developmental neurobiology (with Dr. Arnold Kriegstein), synaptic biology (with Dr. Robert Edwards), chemogenetics (with Dr. Alice Ting), and advanced machine learning (with Dr. Jingjing Li), combined with my previous experience in rodent models, proteomics, and single-cell genomics will provide me with a solid foundation for an independent research career to achieve my goal.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY/ABSTRACT Background: Mutations in receptor tyrosine kinase (RTK) signaling genes such as Fms-Like Tyrosine Kinase 3 (FLT3) and the KIT proto-oncogene occur in two-thirds of acute myeloid leukemia (AML) and are associated with high relapse rates. FLT3 tyrosine kinase inhibitors (TKIs) are clinically active in FLT3-mutant AML but duration of response is limited by the development of resistance due to re-activation of RAS signaling. No specific proven therapy exists for these relapsed patients or patients with other signaling mutations. Rationale: The protein tyrosine phosphatase SHP2 is a central node in RAS activation and propagation of growth factor signals. SHP2 modulates MAPK pathway activation downstream of RTKs but the full molecular mechanisms of SHP2 activity are not clear. Small molecule allosteric inhibitors of SHP2 such as RMC-4630 stabilize the closed, autoinhibited conformation of SHP2 and are in clinical development. The goal of this application is to leverage new allosteric SHP2 inhibitors (SHP2i) to elucidate the molecular role of SHP2 in RTK-mediated survival in AML and test the efficacy of SHP2i in combination with the BCL2 inhibitor (BCL2i) venetoclax. Methods: We will test the therapeutic efficacy of SHP2i in combination with BCL2i in FLT3 and KIT mutant AML. We will use single cell multiomic sequencing to discover biomarkers of response and resistance. Using biochemical and proteomic approaches, we will assess the effect of SHP2i on RTK signaling in FLT3 and KIT mutant AML cells and associated effects on apoptosis. We will isolate the role of RAS/MAPK transcriptional activation in SHP2-mediated survival and determine the role of SHP2 in adhesion-mediated survival signaling in RTK-driven AML. Expected Results: We anticipate that these studies will uncover new knowledge about the role of SHP2 in leukemic cell survival and facilitate rational development of SHP2i combination therapies, particularly in combination with BCL2i. The overall goal of this work is to develop SHP2 inhibitor therapy as a novel treatment strategy in RTK-driven AML.

NIH Research Projects · FY 2024 · 2023-07

Project Summary/Abstract Interleukin-1B (IL-1B) is a pro-inflammatory cytokine with conflicting roles in mouse and human cancers. The cytokine enhances tumor growth by promoting angiogenesis, and chronic inflammation mediated by IL-1B can induce carcinogenesis. At the same time, IL-1 signaling bolsters the adaptive immune system, polarizing CD4+ T cells toward T helper type 1 and 17 lineages and enhancing the effector function of CD8+ T cells to improve tumor cell killing. A large clinical trial found that anti-IL-1B treatment significantly reduced tumor incidence in humans, highlighting the effect of IL-1 signaling on human health. IL-1 signaling is well-regulated by both a receptor antagonist (IL-1RA) and a non-signaling decoy receptor (IL-1R2). IL-1RA acts at the organism level to suppress systemic inflammation, while IL-1R2 is thought to attenuate local inflammation in tissues. Using RNA sequencing, we have identified a population of highly activated IL-1R2+ regulatory T cells (Tregs) in healthy skin and tumor samples from mice and humans. Tregs are critical suppressors of inflammation in tissues, but tumor infiltrating Tregs can dampen adaptive immunity to promote cancer growth. However, the function of IL-1R2 in cancer and Treg biology is not well understood. In our hands, deleting IL-1R2 on Tregs led to increased tumor growth in mice, suggesting that IL-1 signaling enhances Treg activation. This proposal will test whether Treg expression of IL-1R2 attenuates their activation in a cell intrinsic fashion by neutralizing local IL-1B. First, we will define the factors that induce IL-1R2 expression on Tregs in mice and humans (Aim 1). We will then investigate the functional role of IL-1R2 on tumor infiltrating Tregs (Aim 2). Lastly, we will determine whether IL-1R2 can be used as a target to selectively deplete Tregs in tumors and bolster anti-tumor immunity (Aim 3). The proposal will not only broaden our understanding of IL-1 signaling in Tregs but may also establish a new approach for cancer immunotherapy. This research strategy will be conducted alongside a comprehensive training plan to develop the applicant’s career as an academic physician-scientist. Training will include structured and rigorous mentorship in technical skills and experimental design from a highly qualified physician-scientist sponsor, carried out through regular one-on-one and lab meetings, courses, seminars, journal clubs, and immunology department events. The research and training will take place at the University of California, San Francisco, which provides an excellent research environment for immunology alongside an outstanding graduate education in biomedical sciences.

NIH Research Projects · FY 2026 · 2023-07

PROJECT SUMMARY/ ABSTRACT Given the overlapping syndemics of HIV and HIV risk with substance use and the contribution of both HIV and substance use to chronic inflammation, robust, objective metrics to quantitate the type, amount, and patterns of substance use are needed. Self‐reported metrics are limited by social desirability bias, where individuals report behavior desired by the provider or researcher, and recall bias, especially with the use of memory‐altering substances. The UCSF Hair Analytical Laboratory (HAL) has been involved in developing objective adherence metrics in the field of HIV for 20 years, showing the utility of analyzing antiretroviral treatment (ART) levels in hair samples to assess ART and pre‐exposure prophylaxis (PrEP) adherence and exposure. The UCSF HAL has also developed hair measures of anti‐tuberculosis (TB) drugs. Given the critical importance of assessing substance use accurately, and the impact of substances on HIV outcomes, including inflammation, this proposal aims to direct our laboratory's technical expertise to the field of substance use monitoring. Although available for forensics as qualitative (yes/no) metrics, hair levels assessing quantitative use of multiple substances have not been widely available for substance use‐HIV studies. Polysubstance use is common and quantitative multi‐analyte metrics allow impacts on adherence and systemic inflammation to be assessed. Harnessing an important NIDA‐funded cohort study investigating substance use in those with or at risk of HIV (the mSTUDY cohort), this proposal aims to develop a suite of hair assays for substances in the UCSF HAL for NIH‐funded research studies investigating substance use, HIV, and inflammation A single muti‐analyte panel to simultaneously measure substances (e.g. methamphetamines, different opiates, cocaine, cannabis, tobacco, and others) will allow intentional or unintentional polysubstance use to be quantitated. The mSTUDY has enrolled a biobehavioral cohort since 2013 of over 500 young men who have sex with men (MSM) of color, half as active substance users (279 with and 278 without HIV) in Los Angeles. The robust specimen biorepository of mSTUDY contains 76,000 biological samples, with 1115 hair samples from 319 mSTUDY participants who report use of methamphetamine, ecstasy, cocaine, heroin, fentanyl, and/or cannabis. Hair sample collection was initiated in August 2014 and is ongoing. These hair samples will serve as the basis of developing and validating the methods for a multi‐analyte panel of substances in hair in the UCSF HAL (Aim 1); analyzing the relationship between hair levels and self‐reported adherence measures, urine toxicology screens, and clinical outcomes (Aim 2); and assessing the relationship between hair levels (of single or multiple substances) and biomarkers of inflammation (Aim 3). Via this proposal, the UCSF HAL aims to become the reference laboratory to provide quantitative, objective metrics of substance use exposure in hair samples for multiple studies examining the interaction between substance use and HIV.

NIH Research Projects · FY 2026 · 2023-07

PROJECT SUMMARY This is a clinical observational study that will fill an important gap in our understanding of how marijuana use, and secondhand exposure, impact cardiovascular health. A likely consequence of marijuana legalization is that intentional smoking of cannabis, and involuntary secondhand exposure, will greatly increase in coming years. While some retrospective human association studies have failed to find clear-cut associations between marijuana smoking and cardiovascular disease, other studies have indicated that marijuana use increases the risk of subsequent myocardial infarction (MI) and heart failure. It is unclear whether these adverse effects are caused by the cannabinoids or the smoke. Nonetheless, despite public awareness that tobacco smoke is harmful, many people still assume that marijuana smoke is benign. Moreover, cardiovascular effects of secondhand smoke (SHS) exposure have remained relatively unexplored in human studies. There is increasing evidence in rats that both active marijuana smoking and marijuana SHS exposure causes vascular endothelial dysfunction. While the endothelial dysfunction is transient, clinical studies have shown that not only do tobacco smokers have endothelial dysfunction, but repeated exposures to SHS lead to chronic dysfunction as well. Therefore, it is important to determine in humans if chronic active or passive marijuana smoking similarly causes endothelial dysfunction. The overall hypothesis of this proposal is that active use of marijuana, or secondhand exposure, causes adverse cardiovascular consequences in humans. The overarching goal is to test this hypothesis by measur- ing a panel of functional indicators and circulating biomarkers of cardiovascular risk, in otherwise healthy sub- jects who are actively or passively exposed on a regular basis in their daily lives to cannabis (this proposal does not involve exposing humans to cannabis). The impact is that an improved understanding of the adverse cardiovascular effects of intentional or involuntary exposure to cannabis will better inform personal health behavior, advice of physicians to their patients, public health policy decisions, legal doctrines, and potential regulation of the cannabis industry and its products. Aim 1 is to determine if vascular function is impaired by chronic active or passive marijuana smoking in otherwise healthy individuals (age ≤50), relative to tobacco smokers and to people who avoid exposure to tobacco and marijuana. Aim 2 is to determine if these chronic exposure conditions increase biomarkers of cardiovascular risk in the blood. Aim 3 is to determine if cultured endothelial cells incubated in sera from exposed individuals undergo adverse functional changes relative to non-users’ sera, indicating potential mechanisms by which vascular function is being impaired by exposure to these products.

NIH Research Projects · FY 2025 · 2023-07

Project Abstract: The size of a meal is carefully regulated to prevent over- or under-feeding. Direct control of meal size is attributed by brainstem areas, such as the caudal nucleus of the solitary tract (cNTS), that directly receive short-term sensory feedback from the GI tract during feeding. In contrast, the indirect controls, which include hypothalamic circuits and leptin, are hypothesized to encode long-term energy balance and regulate meal termination by modulating the potency of these short-term signals sensed in the brainstem. Interactions between these long-term and short-term systems are critical for the control of food intake, but how it is encoded in the dynamics of the underlying brainstem circuits remains unknown. The cNTS contains many cell types that are involved in controlling food intake. Among these cell types, prolactin releasing hormone (PRLH) and glucagon (GCG) neurons are particularly important for meal termination. In my recent studies, I performed the first neural recordings of these two cell types in awake behaving mice. I found unexpectedly that these cells were rapidly activated at the start of a meal by feedforward signals such as taste. These technical and conceptual advances create an opportunity for me to investigate the longstanding question of how signals of long-term energy balance modulate brainstem circuits to control meal termination. I propose here to address this question by investigating how two regulators of long-term energy balance – Agouti-related peptide (AgRP) neurons and leptin – modulate PRLH or GCG neuron dynamics or their control of feeding behavior. Together these results will reveal how long-term systems modulate brainstem circuits to regulate meal size, which is an important determinant of overall food intake and can be dysregulated in conditions like obesity.

NIH Research Projects · FY 2025 · 2023-07

Summary Implementation science (ImS) is a branch of research that focuses on the improving the uptake of evidence- based health interventions into real world settings. ImS holds promise for generating new knowledge to close the gap between what we know can optimize health and healthcare and what happens in everyday practice, which may be of particular importance for addressing health inequities that often result because of failure to deliver evidence-based practice to all populations. The goal of the Partnerships for Research in Implementation Science for Equity in Heart and Lung (PRISE-HL) diseases T32 program is to provide support to outstanding scientists equipped to build on their scholarship with interdisciplinary training in implementation science and health equity approaches to help transform the uptake and delivery of evidence-based interventions for heart and lung diseases in real-world settings. UCSF is one of the world’s leading health sciences campuses and this program will build on existing strengths in heart and lung diseases research as well as infrastructure established through the recently launched UCSF PRISE Center, an innovative research center bringing together ImS researchers with front-line implementers in local health systems and public health departments. A physician- scientist and public health trained epidemiologist, both with extensive experience in applying implementation science to health equity and who are leaders in ImS training, will direct the program. An exceptionally accomplished group of faculty with strong records of interdisciplinary collaboration will bring complementary expertise in clinical and translational research related to heart and lung diseases and key health equity and/or implementation science-relevant disciplines, including behavior change, community engagement, health economics, health policy, big data, and sociology. In addition, the program includes strong partnerships with community and tertiary care clinical sites that serve the diverse communities of the San Francisco Bay Area and with local (San Francisco) and regional (California) Departments of Public Health. An Advisory Committee will work with the program directors to select T32 trainees, monitor trainees’ progress, and identify opportunities for improving the program. The trainee recruitment process will benefit from access to a large and diverse pool of internal candidates from UCSF’s well-established training programs and provide additional opportunities for us to continue to recruit the most promising external trainees. Each trainee will work with mentors on their career development committee to establish goals and tailor didactic and hands-on training experiences to develop competencies in core areas of implementation science and health equity research. Trainees will also benefit from embedded healthcare delivery system or public health program rotations to develop experience with real-world practice change and a new PRISE-HL T32 Program Seminar that will integrate training in implementation science and health equity research.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY/ABSTRACT Pharmacogenomics has the potential to dramatically improve health care outcomes, but is currently failing on diversity among its research participants. As a consequence, we do not fully understand all of the factors influencing pharmacogical response in underrepresented populations, including those that contribute to racial/ethnic differences in drug efficacy and safety as reported by Food and Drug Administration (FDA) drug labels. For example, the clinical validity of genetic variants that are common in research participants from historically-excluded populations (e.g., lower proportions of European genetic ancestry), but rare in wellrepresented study populations remains unknown. In addition, gene expression studies have already provided insight into the underlying biology of disease susceptibility for numerous conditions beyond what genome wide association study (GWAS) results alone have discovered, but have not been fully applied to studies of pharmacogenomic discovery. Furthermore, social determinants of health may impact pharmacological drug response from a biological standpoint even after taking into account the effects of these factors on drug adherence, access, and utilization (e.g. social determinants of epigenetics). Addressing this gap in knowledge has the potential to prevent future healthcare disparities that may be exacerbated as the infrastructure to support clinical pharmacogenomics continues to gain traction across health institutions nationwide. Furthermore, elucidation of the genetic and nongenetic contributors to differences in drug response across race/ethnicity will obviate the use of this population descriptor as a proxy for these factors. Pharmacogenomic studies using large, diverse datasets are necessary to ensure that advances in this field benefit individuals equitably. Our primary goal in this project is to identify genetic and social determinants of pharmacological drug response among racial/ethnic minorities. To accomplish this goal, we will leverage data from the Kaiser Permanente Research Biobank (KPRB) and the National Institutes of Health (NIH) All Of Us research program, which are two of the largest electronic health record-linked biobanks in the United States. These cohorts are ideal for the proposed studies because they are large (>400,000 participants each), diverse (>25% racial/ethnic minorities), linked to genome-wide genetic data, and capture social determinants of health. In Aim 1, we will evaluate the relative contribution of genetic ancestry versus social factors on race/ethnicity- based differences in drug efficacy and safety. In Aim 2, we will identify genome-wide polymorphisms predictive of drug effects in historically-excluded populations from large pharmacogenetics studies. In Aim 3, we will use ancestry-specific gene expression results to identify genetic determinants of drug response. The aims will be carried out by an established multidisciplinary team of experts in clinical pharmacology, cardiovascular epidemiology, and molecular genetics. These findings from the current study will help to inform clinical decisions impacting communities historically-excluded from biomedical research.

NIH Research Projects · FY 2025 · 2023-07

ABSTRACT We have one specific aim: Train postdoctoral fellows who will be qualified and well-positioned to become leaders in the development and implementation of substance use research in tobacco control, public health, policy, and clinical practice. Specifically, we propose a postdoctoral fellowship program that will attract individuals with a strong commitment to transdisciplinary research from a variety of medical, biological, social, behavioral, and policy sciences to help build the next generation of scientific leaders in tobacco control and related substance use. Tobacco remains the leading preventable cause of death the U.S. and disproportionately burdens people with substance use disorders. The need for tobacco control expertise continues to grow with demand for research to inform FDA regulation of tobacco products, the implementation of the WHO Framework Convention on Tobacco Control, and state and local tobacco control efforts to address the rapidly evolving tobacco product environment. Considering the high rates of tobacco co-use with other substances, our program is expanding on points of synergy between tobacco, cannabis and opioid research. This includes training in: 1) Research on tobacco and cannabis co-use and cannabis health effects to inform policy and develop evidence-based interventions and 2) Research on industry behavior that has driven both the tobacco and opioid epidemics and is likely to become increasingly important with cannabis legalization. We provide this training through integrated transdisciplinary coursework in tobacco science, tobacco policy, addiction, and biostatistics, combined with mentored research with two faculty from different disciplines. Fellows complete a course in which they prepare, and submit grant proposals to funding agencies for their third year of fellowship funding. Research mentors include 31 faculty members from all four schools at UCSF (Dentistry, Medicine, Nursing, and Pharmacy) with active research programs in tobacco policy, marketing, addiction, health effects of smoking and secondhand smoke exposure, emerging tobacco, cannabis and vaping products, cessation, cannabis substitution for opioids, and analyses of tobacco and opioid industry documents. The diverse fellow backgrounds and interests in the Center for Tobacco Control Research and Education provides a cooperative environment that creates continuous opportunities to learn from and appreciate work in other disciplines. Each fellow creates an Individual Development Plan that is reviewed by both mentors and the Fellowship Committee. The Committee selects fellows from a competitive national pool: we average 29 applications per year for 3 slots. Between 2016-2021, our fellows produced 135 papers in 68 different journals. Since 2001, we have trained 92 fellows (62 funded by NIH training grants since 2006); 93% of our R25/T32 graduates have research careers in academic, government and nongovernmental institutions, and 54% are academic faculty.

NIH Research Projects · FY 2026 · 2023-07

Project Abstract Common mental health disorders (CMDs), like depression and anxiety, and non-communicable diseases (NCDs), like diabetes and hypertension, are highly prevalent and are the leading causes of death and disability worldwide, especially in low-resource settings like our research site in Nepal. Comorbidity among CMDs and NCDs is high and the relationship between these conditions is complex and multidirectional. Several common behavioral risk factors worsen both conditions: stress, isolation, tobacco use, low physical activity, low quality diet, and poor treatment adherence. Behavioral interventions can address these common risk factors, and improve CMDs and NCDs. The World Health Organization's (WHO) two clinical protocols for CMDs and NCDs recommend three behavioral interventions: a) evidence-based stress reduction (EBSR) for stress/anxiety; b) behavioral activation (BA) for depression; and c) motivational interviewing (MI) for healthy behaviors. Despite this potential, these interventions are rarely available in low-resource settings because of two important gaps: 1) behavioral interventions have often been studied for one or two CMDs and NCDs, rather than for the real-world need of an integrated intervention to simultaneously address multiple CMDs and NCDs; and 2) these interventions have not been studied using implementation strategies that can support easy access (i.e., making care available at or near the patient's home) and sustained implementation in real-world settings. Based on our extensive history and long-term commitment to working in Nepal, we now propose a hybrid implementation-effectiveness study of BECOME (BEhavioral Community-based COmbined Intervention for MEntal Health and Noncommunicable Diseases) delivered by community health workers (CHWs) in Nepal. Our team has a long-standing history of conducting implementation research, integrating evidence- based care for CMDs and NCDs into existing health-care systems in Nepal, training CHWs to deliver behavioral interventions at or near patient's homes, and conducting costing analysis. We have an extensive history of collaborating with the Government of Nepal and have a deep understanding of social norms and cultural factors that drive sustained healthcare delivery. The proposed study has three aims to address the gaps identified above: Aim 1) assess the effectiveness of BECOME on depression, anxiety, and two NCDs via a stepped-wedge cluster randomized trial (20 geographic clusters) and participants (n=600) with at least one CMD and one NCD; Aim 2) assess implementation outcomes of BECOME using the Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) framework at the patient, provider, and health system levels; and Aim 3) conduct a comprehensive costing analysis to provide strategic inputs to support long-term scale-up of BECOME. If successful, this study will provide evidence and a blueprint to the governments of Nepal and other low-resource settings with an integrated intervention and a set of implementation strategies to deliver behavioral interventions for CMDs and NCDs.

NIH Research Projects · FY 2025 · 2023-07

ABSTRACT Food insecurity among U.S. college students is alarmingly high. More than 30% of U.S. college students (over 6 million) experience food insecurity, and over 40% of California college students do so (~870,000). Current U.S. college students are unlike those of previous generations. Contemporary students are nontraditional—from low- income backgrounds, financially independent, and/or first in their families to attend college (first generation). These characteristics put students at risk for food insecurity, with disparities in Black and Latino students. Food insecurity in college students is associated with factors known to contribute to poor cardiovascular and metabolic health (CVMH). Heart disease is also the 5th leading cause of death among 12 to 24 year olds, calling attention to emerging adulthood (ages 18-26) as a critical period for modifying future risk of poor CVMH. The American Heart Association (AHA) recently defined that ideal CVMH is based on Life’s Essential 8, which includes CVMH behaviors (diet, physical activity, sleep, nicotine exposure) and factors (body mass index, blood glucose, blood pressure, blood lipids). It is biologically plausible that food insecurity influences CVMH among college students via several mechanisms, but there is limited knowledge in this area. Critical gaps include limited information regarding: 1) the chronicity of food insecurity in college students, 2) emerging adulthood in the context of food insecurity and CVMH, and 3) lack of objective assessment of CVMH. Longitudinal and objective information about this relationship would provide a more comprehensive understanding of food insecurity as a modifiable risk factor for CVMH in a vulnerable student population of emerging adults . The overall objective of the proposed work is to improve our understanding of the impact of food insecurity on risk for poor CVMH in emerging adults. We propose to recruit a randomly selected cohort of students (N = 563) from UC Santa Cruz, a campus that reflects the diversity of U.S. college students. We will assess food insecurity status monthly in Year 1 and CVMH annually over a 2-year period. CVMH will be determined by CVMH behaviors and factors, as described by the AHA. Factors that are salient during emerging adulthood (family obligation, parental and social support, stress) will also be assessed. We expect that more chronic food insecurity will predict poor CVMH among students over time (Aim 1); poorer CVMH behaviors will mediate the relationship between more chronic food insecurity and poorer CVMH factors (Aim 2); and the relation of SES and food insecurity will be moderated by family obligation and supports, and the relation of food insecurity and CVMH behaviors with CVMH factors will be mediated by stress (Aim 3). This project will address many concerns regarding food insecurity and the potential CVMH disparities that exist among young adults in higher education. Food insecurity as a modifiable target for CVMH prevention is biologically plausible and potentially high impact through new and existing policy interventions.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY / ABSTRACT Myelin oligodendrocyte glycoprotein (MOG) has been recognized as an autoantigen (autoAg) in EAE and as a putative T cell and antibody (Ab) target in MS. Recently, MOG has been identified as the target in several CNS autoimmune conditions, including acute disseminated encephalomyelitis (ADEM), optic neuritis (ON), and transverse myelitis (TM). Collectively, this spectrum is known as MOG Ab-associated disease (MOGAD). Currently, there are no FDA-approved treatments for MOGAD. Key aspects regarding MOGAD pathogenesis have not been elucidated. MOG-specific Abs in MOGAD are T cell-dependent and are not pathogenic in the absence of T cell-mediated CNS inflammation. Therefore, we hypothesize that MOG-specific T cells have a central role in MOGAD and cooperate with B cells, and possibly MOG-specific Abs, to promote CNS injury. MOG-induced EAE is an invaluable model to evaluate how MOG-specific T cells cooperate with MOG- specific B cells and Abs in MOGAD. Like MOGAD, MOG-induced EAE manifests as ON, TM and encephalomyelitis. Besides serving as a source of MOG-specific Abs, B cells are Ag presenting cells (APC). EAE induction by MOG protein is B cell MHC II-dependent. Whether B cell Ag presentation promotes development of a distinct pathogenic T cell repertoire is unknown. We hypothesize that B cell Ag presentation expands a unique TCRa/b repertoire of MOG-specific pathogenic T cells. Susceptibility to MOG protein-induced EAE is sensitive to certain human-specific amino acid (aa) sequence differences. Novel MOG T cell epitopes identified from studying MOGAD patients are located within the region where many aa sequence differences are clustered. To understand cellular and humoral responses to human MOG, and to better translate our findings, we created humanized MOG knock-in mice by replacing mouse MOG genomic sequence with human genomic MOG. In this program, we propose: (1) To identify and characterize MOG-specific T cells in patients with distinct MOGAD phenotypes. Peripheral blood mononuclear cells will be collected from patients enrolled at three collaborating institutions. MOG specificity will be determined by stimulation with overlapping MOG peptides and TCRa/b repertoire will be examined by single cell RNA sequencing (scRNA-Seq). (2) In subaim 2a we will determine how B cell Ag presentation in vivo may shape development of the pathogenic MOG-specific T cell repertoire. T cells from wild-type, B cell-deficient and MOG-specific B cell receptor (BCR) mice immunized with MOG protein (B cell-dependent) or MOG peptide (B cell-independent) will be subjected to TCRa/b repertoire analysis by scRNA-Seq. In subaim 2b, our humanized MOG mice will be characterized for MOG-specific T cell and humoral responses, and requirement for B cell-T cell cooperation in EAE. Serum MOG-specific Abs from MOGAD patients will also be tested for pathogenic potential in recipient humanized MOG mice. Our results should provide invaluable knowledge regarding MOGAD pathogenesis and insights regarding B- T cooperation in MOGAD and other organ-specific autoimmune diseases.

NIH Research Projects · FY 2026 · 2023-07

Project Summary The absence of effective therapies to slow or prevent progression have made Alzheimer’s Disease (AD) a global health crisis. Inflammation, neuronal dysfunction, and eventual neuronal loss are hallmarks of AD. Cholesterol metabolism is also implicated in AD and other neurodegenerative diseases. For example, accumulation of lipid droplets that store intracellular lipids are observed in AD brains. Cholesterol acts as a signaling molecules and is an essential component of biological membranes. Notably, cholesterol levels in the presynaptic and postsynaptic compartments influence synaptic transmission. Thus, changes to cholesterol metabolism could directly induce neuronal dysfunction and other AD-associated pathology. While most research focuses on neurons, non-neuronal glial cells are essential in regulating neuronal function and maintaining brain homeostasis. Astrocytes are a class of glial cell that interact with synapses, blood vessels, and other glial cells, playing essential roles in the regulation of synaptic connectivity and function throughout life. Recent studies suggest that changes to astrocytes are potential drivers of AD pathology. Astrocytes have decreased physiological functions and release inflammatory factors in disease states. As the main producers of cholesterol in the brain, cholesterol dysregulations in AD could also be primarily driven by changes in astrocyte metabolism. However, it is still unclear to what extent cholesterol metabolism is dysregulated in AD astrocytes and what specific genes could be targeted to reverse these changes. The overall goal of my dissertation and post-doctoral research is to characterize cholesterol metabolism in astrocytes in the context of AD. Preliminary data in Aim 1 demonstrates my ability to use human stem cell models to study intrinsic changes in astrocytes derived from individuals with AD using multi-omic and metabolomic approaches. In Aim 1, I propose taking a closer look at how cholesterol is dysregulated in AD astrocytes and how these dysregulations promote AD-related astrocyte dysfunctions, such as adoption of neurotoxic properties and loss of the ability to support neurons. During the K00 Phase, I propose expanding these analyses to in vivo models to probe system-wide contributions of astrocyte cholesterol metabolism. The Training Plan integrates scientific and professional development activities that will advance my long- term career goals of becoming an independent neuroscience researcher and principal investigator of an academic laboratory. The proposed research provides ample opportunities for developing technical expertise in astrocyte biology, metabolism, and analytical techniques. My Sponsors will be instrumental in helping me build skills in experimental design, scientific communication, and grantsmanship. They will also guide me in finding a postdoctoral training environment that aligns with my long-term research and career goals.

NIH Research Projects · FY 2025 · 2023-07

Although CD4 T cells are essential for immunity to tuberculosis (TB), the features of CD4 T cells that provide protective immunity are not well understood. This knowledge gap is due in part to limited knowledge of the M. tuberculosis (Mtb) antigens that induce protective immune responses. In other pathogens, immune recognition of some antigens provides protection, while recognition of other antigens does not. Likewise in other pathogens, the antigenic targets of protective immunity undergo diversifying evolutionary selection to generate antigenic variation and escape immune recognition. We hypothesized that these principles apply to Mtb, and in earlier studies we made the unexpected discovery that the commonly-studied antigenic targets of human T cells (epitopes) in Mtb are hyperconserved; they are the most conserved elements of the Mtb genome. We then sought to find exceptions, and combined comparative genomics of phylogenetically diverse strains of Mtb with experimental immunology. This led to our discovery of seven novel Mtb antigens (that we term Mtb Rare Variable Antigens; RVA) that are recognized by human T cells and exhibit evidence of evolutionary diversifying selection. Together, these results suggest that human T cell recognition of RVA is detrimental to Mtb and that recognition of conserved 'classical' Mtb antigens is not detrimental to Mtb. We recently studied CD4 T cells from healthy Quantiferon-TB positive (QFT+) recent close contacts of infectious cases of TB, and discovered that RVA induce CD4 T cells characterized by dominant interleukin 17 responses and expression of the lineage-defining transcription factor RORγt, in contrast to CD4 T cells that recognize classical Mtb antigens and exhibit interferon gamma responses and expression of T-bet. These results indicate that human CD4 T cells that recognize RVA are functionally distinct from those that recognize conserved antigens, and we hypothesize that T cells that recognize RVA provide protection against active TB, as indicated by their evolutionary selection. In this project, we will use innovative assays to intensively characterize CD4 T cells from QFT+ adults by comparing the features of CD4 T cells that recognize RVA versus classical Mtb antigens. We will compare their functional responses, longitudinal memory phenotypes, and extent of differentiation. We will also employ an innovative new platform developed by our team, using DNA barcoded peptide epitopes and next generation sequencing to test the hypothesis that associations between CD4 T cell antigen specificity and certain functional responses are widespread in Mtb. To determine the significance of RVA in protective immunity to TB, we will compare CD4 T cells that recognize RVA vs classical Mtb antigens in adults with active TB and those with 'controlled' (or latent) TB. We will also test the hypothesis that defects in RVA-specific CD4 T cells are primary and do not reverse with treatment of active TB. The long term objective of this project is to inform development of TB vaccines that prevent progression to active TB disease, the form that causes human morbidity and mortality, and the form that is responsible for TB transmission.

NIH Research Projects · FY 2025 · 2023-07

In the United States, new HIV infections continue at a high level, with an estimated 37,515 Americans receiving an HIV diagnosis each year. In 2019, the “Ending the HIV Epidemic” (EHE) plan for the United States was developed with the goal of reducing new HIV infections by 75% by 2025, and by at least 90% by 2030, representing an effort to refocus national attention on ending the domestic HIV epidemic. The need for nurse scientists who can plan and conduct rigorous and innovative research in HIV prevention and care, including implementation science, is greater today than ever. To address this need, we propose to launch the “Next Generation Nurse Scientists Ending the HIV Epidemic” program in the University of California, San Francisco (UCSF) School of Nursing. The overarching goal of this T32 program is to train a qualified cadre of nurse scientists in research methods to lead efforts to End the HIV Epidemic. This program will (1) Increase the number of nurse scholars who are prepared with the knowledge and skills necessary: to design and conduct research that advances the science on HIV, HIV interventions, and HIV implementation strategies; and to employ implementation science methods for studying translation of HIV interventions into real-world clinical and community settings; (2) Mentor trainees to identify a specific area of HIV research that will allow them to establish a program of research that outlines their content and methods expertise; (3) Prepare trainees with grantsmanship and leadership skills to conceptualize, write, conduct, administer, and disseminate results for an extramural grant-funded study, and (4) Conduct an evaluation of the Program to determine process and outcome. This training program will be delivered within the research-intensive academic setting of UCSF, with extensive opportunities for cross-disciplinary collaboration with entities such as the AIDS Research Institute, the Center for AIDS Research, and the Center for AIDS Prevention Studies, along with clinical settings that include the original San Francisco Model clinic Ward 86 at Zuckerberg San Francisco General Hospital. With a focus on nursing approaches to prevention and care, this program will also build on over 20 years of the HIV/AIDS Nursing Care and Prevention Training Program (T32NR07081), which produced many nurse scientists who have gone on to be leaders in HIV nursing research in the United States and beyond. The “Next Generation Nurse Scientists Ending the HIV Epidemic” program will include training opportunities for 4 predoctoral and 2 postdoctoral nurse scholars each year. Our goal is to train the next generation of scientists in nursing research approaches to End the HIV Epidemic.

NIH Research Projects · FY 2026 · 2023-07

PROJECT SUMMARY / ABSTRACT During development, specific synaptic partners connect in order to ensure proper neural circuit function, but how these connections are disassembled during neurodegeneration is less well understood. In rodent experimental glaucoma (EG) models, synapse loss occurs early, preceding retinal ganglion cell (RGC) dendrite retraction and cell death. Converging evidence in rodents suggests that specific RGC types are more susceptible to elevated intraocular pressure, but little is known about retinal circuit disassembly in glaucomatous primate retina. Indeed, significant differences in mice, which lack a lamina cribrosa and macula and have dissimilar RGC types, limit the translation and generalizability of findings to humans. It is critically important to address this knowledge gap in order to advance successful development of clinically relevant diagnostics and novel treatment approaches, such as neuroprotection, gene therapy, and cell-based vision restoration strategies. Here we assemble a highly collaborative team of investigators with complementary expertise well-matched to our goal of systematically determining the connectivity, function, and transcriptomes of RGCs undergoing circuit and synapse disassembly in glaucomatous primate retina. Our approach builds on a well-established rhesus macaque non-human primate (NHP) model of experimental glaucoma that closely recapitulates structural and functional changes observed in human glaucoma, and permits detailed and precise staging of disease. Based on our studies in mice and preliminary data in NHP, we hypothesize that specific microcircuits in the injured adult NHP retina may exhibit susceptibility in connectivity and function, which is reflected in differential gene expression. To test this hypothesis, we apply rigorous quantitative electrophysiological, anatomical, and molecular assessments focusing on the four main RGC types in NHP retina: ON and OFF midget and parasol ganglion cells. Aim 1 will use high-density multielectrode arrays, single cell recordings, and Patch-seq to identify the functional RGC types that are vulnerable in NHP EG and probe their transcriptomes to reveal mechanistic insights and novel therapeutic targets. Aim 2 will determine the specificity and patterns of circuit and synapse disassembly in NHP EG from both lamina-specific and cell type-specific perspectives using detailed circuit and synapse mapping. The proposal is innovative because it brings together multi-modal function, morphologic, and molecular analyses, and is significant because it focuses on the four main RGC types in primate that account for the majority of human vision and are affected in glaucoma. We will generate significant resources for the scientific community and reveal insights into retinal circuit disassembly and the potential for circuit repair in a highly clinically relevant model of glaucoma.

NIH Research Projects · FY 2025 · 2023-07

Summary/Abstract: TGF-b is a key driver of lung fibrosis. The long-term goal of our research is to acquire a deep understanding of the regulation of TGF-b activity to develop new strategies and treatments for fibrosing lung disease. Currently, there are no effective therapies to treat lung fibrosis. The multifunctional cytokine TGF- b is a potent mediator of fibrosis and is a potential therapeutic target in fibrosing lung disease. However, targeting TGF-b itself or its receptors is associated with demonstrated risks as evidenced by toxicities in rodents, primates and humans. More selective targeting of the fibroinflammatory effects of TGF-b, without perturbing its normal essential functions are highly desirable. One property of TGF-b that may allow more selective targeting is to target its “activation” since it is always produced in a latent form (L-TGF-b) that requires activation in order to function. Another feature of L-TGF-b that could facilitate more specific targeting is to that it is normally covalently bound to the extracellular matrix or to the surface of cells by association with TGF-b binding proteins such as latent-TGF-b binding protein (LTBP) or glycoprotein-A repetitions predominant (GARP). We and others have shown that L-TGF-b binding to two integrins, a 8 and a vb vb 6 is essential for TGF-b activation in vivo. For the integrin a 6 activation mechanism, it has long been assumed that TGF-b vb must be released from LAP so that free TGF-b can diffuse and bind its receptors on target cells. The structural mechanism for such release of TGF-b is incompletely understood since full-length a vb 6 has not been studied in complex with TGF-b bound to TGF-b binding proteins. Based on recent structural data obtained using single particle electron cryomicroscopy (cryo-EM), we have recently proposed a new model whereby a vb 8 can bind to L-TGF-b on cells presenting the L-TGF-b/GARP complex and induce signaling without release and diffusion of TGF-b. These two different models of TGF-b activation may be able to be separately targeted, which could help mitigate therapeutic risk. Here in four aims, we will employ a structure-based approach to address the mechanism of a vb 6-mediated TGF-b activation. We will use the technique of electron cryomicroscopy (cryo- EM), which is a technique that allows for high-resolution structures of proteins and protein complexes in physiologically relevant conditions. Cryo-EM will be used to examine the role of integrin a vb 6 conformation in the mechanism of TGF-b activation. These studies will improve mechanistic understanding of TGF-b activation and therapeutic targeting strategies to more selectively and safely inhibit it.

NIH Research Projects · FY 2024 · 2023-07

Project Summary/Abstract Here we develop a platform for protease-activated peptide prodrugs. We initially focus the effort on antimicrobial peptides (AMP), which have a broad spectrum of cell-penetrating, antimicrobial and cytotoxic activities. However, they have multiple limitations, including off-target cytotoxicity and proteolytic instability. To circumvent these unwanted effects, linear protease-activated prodrugs have been employed. Although effective at enhancing the activity of the active payload, it does not adequately address the side effects stated above. To mitigate the side effects of the traditional protease-activated prodrug approach, the proposed research strategy herein seeks to design a branched protease-activated prodrug by coupling a cleavable linker to the sidechains of amino acid residue that significantly impacts antimicrobial peptide activity. As a proof-of-concept, bombolitin (an AMP that is cytotoxic to mammalian cells) will be used as the payload, masked with caspase-3 and fibroblast activation protein (cancer biomarkers) substrate-specific linkers. By modifying the sidechains of Lys, Ser, Thr, and Tyr with these linkers, we hypothesize that the physicochemical properties of bombolitin will be significantly altered, thus reducing peptide-membrane interaction until activation. In this research, we propose to 1) design and synthesize single and double-branched protease-activated prodrugs cleaved in the presence of either caspase-3 and/or fibroblast activation protein to yield the active peptide, 2) confirm caspase-3 and fibroblast activation protein cleavage of linker from prodrugs by performing in vitro enzymatic assays and biophysical analysis, and 3) perform cell-based assays to validate prodrug cleavage, target specificity, activity enhancement, and reduction of off-target effects.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY / ABSTRACT The mission of the UCSF Graduate Program in Biophysics is to train students to tackle some of the most challenging problems in biology and biomedicine at the interfaces with physics, mathematics, chemistry, and engineering, while equipping our graduates with the knowledge, tools, and skills to become leaders in academic science, biotechnology, and affiliated sectors. With the extraordinarily rapid advances in technologies and the new biological data they generate, there is an increasing need to understand the molecular basis for complex biological behavior. Concurrently, advances in the ability to computationally model molecular behavior are transforming biomedical research. To train leaders who can address the most critical questions in their fields through integration of these disciplines, our program is designed to (i) provide our students with both a foundation in quantitative, physical approaches and a sophisticated understanding of biology; (ii) bridge computational and experimental biophysical methods; (iii) create an environment where all students are supported and succeed; and (iv) promote key skills for success in a wide range of careers. From the start, “Onboarding” and community circles emphasize our values of collaboration, a supportive community, and ethically responsible rigorous research. Our well-tested and new project- and team-based based core courses lay the foundation to conceptualize, design, and execute innovative thesis projects. These courses also build a foundation in the communication, leadership, management, and team skills we emphasize throughout the graduate training. Current and new “minicourses” and “State of the Field” discussions facilitate deep exploration of research topics in small groups with faculty experts, allow the curriculum to stay current with latest scientific developments, and allow the students to identify important research questions. Students can participate in career preparation workshops and internships, and many take on leadership roles in outreach and teaching. Our alumni include leaders in both academia and industry, including several who have started successful companies, and they actively participate in career development through our Biophysics Alumni Speaker Forum and the new Biophysics Alumni Mentorship Program. Our goal to support student success includes activities to promote mentorship and academic achievement, formalized through an actionable plan that includes required faculty training on effective mentoring practices and increased guidance and support of trainees throughout the PhD. The 54 Biophysics faculty participating in this training program have an outstanding record of interdisciplinary and collaborative research, and a strong commitment to mentorship and training. Chosen from a highly qualified pool of Biophysics applicants from a range of quantitative disciplines, we plan to appoint 6 trainees for a duration of 2 years (in their 1st and 2nd year), for a total of 12 annual slots on this training grant.

NIH Research Projects · FY 2025 · 2023-07

Abstract Various cell types establish polarity to generate complex morphology and exert function. Schwann cells (SCs) are polarized with an adaxonal membrane facing the axon and a basolateral membrane facing the extracellular matrix (ECM). Previous work established that known polarity proteins, Par-3 and LKB-1/Par-4, localize to the adaxonal membrane prior to myelination and are required within SCs for the timely progression of myelination and Remak bundle formation. Although SC polarity is critical for proper peripheral nerve development, the mechanism for establishing polarity within SCs remains unknown. The basal lamina, a specialized structure of the ECM that abuts the basolateral membrane, is believed to be important for regulating polarity; additionally, in other epithelial cells collagen-IV is necessary for the establishment of polarity. SCs secrete collagen-IV into the basal lamina and express integrin alpha2, a collagen-IV receptor also known for its role in polarity. Therefore, I hypothesize that collagen-IV initiates SC polarity by signaling through integrin alpha2 and is necessary for rSC polarity but dispensable for myelination. I test this possibility by analyzing the role of SC secreted collagen-IV on peripheral nerve development, determining whether collagen-IV within the SC basal lamina is necessary and sufficient for SC polarity, and identifying the SC binding partner for collagen-IV. Preliminary data suggests that SC-secreted collagen-IV is important for timely myelination and Remak bundle formation. These results phenocopy those observed when polarity is disrupted by knocking out LKB1 specifically from SCs. Upon completion, this study will have important implications on the integration of extrinsic signals from the ECM onto the internal cell state. Thereby regulating polarity, which is critical for peripheral nerve health. Additionally, understanding the results and mechanisms of polarity defects can inform the understanding of peripheral neuropathies. In order to perform these studies, I will learn various techniques including protein biochemistry, including Western blot and co-immunoprecipitation, primary cell culture techniques, CRISPR- based gene editing, mouse behavioral assays, and viral construction/purification/transduction under the guidance of my sponsor Dr. Jonah Chan. I will receive additional training of career development skills such as experimental design, presenting posters/presentations, manuscript writing, and manuscript reviewing through my sponsor, classes within the UCSF Neuroscience Program, and workshops through UCSF Office of Career and Professional Development. I am confident that the rigorous training I receive during my PhD at UCSF will enable me to pursue my long-term goal of becoming a tenure track principal investigator within academia.

NIH Research Projects · FY 2024 · 2023-06

Project Summary/Abstract Sex hormones and sex chromosome genes instruct development of sex-specific features during neurodevelopment, including differences in somatic gene expression and gray matter volume. Together, these developmental programs lead to fundamental differences at the molecular, cellular, and tissue level between males and females. While some neurological disorders have clear links to X chromosome genes, such as Rett Syndrome and Fragile X Syndrome, other disorders including Autism show sex-biased penetrance with no clear genetic mechanism. This proposal aims to address the mechanistic basis of sex-dimorphic transcriptional responses to retinoic acid signaling in the developing brain. Retinoic acid signaling is indispensable for modulating gene regulatory programs that orchestrate proper nervous system development, and recent work has shown that the Autism risk gene FOXP1 is upregulated in response to retinoic acid signaling. Preliminary studies have shown specific upregulation of FOXP1 in response to retinoic acid signaling in female cortical organoids, and not in males. This project will similarly leverage stem cell-derived cortical organoids to model neurodevelopment in vitro to better understand the molecular basis of sex-dimorphic phenotypes upon exposure to retinoic acid. Aim 1 will characterize sex-dimorphic genome wide expression changes in response to retinoic acid. Male and female organoids will be treated with vitamin A, the precursor to retinoic acid, and used for scRNA-seq. This dataset will uncover genes upregulated specifically in female organoids in response to retinoic acid. Additionally, I will identify cell types in both male and female organoids that exhibit the greatest gene expression changes in response to retinoic acid, lending insight into cell type-specific sensitives to retinoic acid during neurodevelopment. In Aim 2, the relationship between dosage of X-linked lysine demethylase KDM5C and retinoic acid-induced sex-specific gene regulatory programs will be characterized. Knockdown of KDM5C in female stem cell-derived organoids and subsequent genome-wide changes in H3K4 methylation, which is demethylated by KDM5C, will be determined by CUT&Tag. A putative enhancer at the FOXP1 locus coincides with H3K4me3 marks, and KDM5C-dependent methylation at this genomic site will be of particular importance. The impact of KDM5C knockdown on retinoic acid-induced FOXP1 expression will then be interrogated by immunohistochemistry. Together, these experiments will further our understanding of the intersection of epigenetics, gene expression, and cell signaling pathways during neurodevelopment, providing an an important mechanistic basis for sex-dimorphic developmental programs. This will further our understanding of the etiology of neurodevelopmental disorders with sex-biased penetrance, while uncovering potential candidates for therapeutic interventions.

NIH Research Projects · FY 2026 · 2023-06

PROJECT SUMMARY This study investigates the ‘reactive’ immune system in tumors, namely the cellular and molecular allies that allow immunotherapies to work. In the previous cycle of this funding, we discovered that one set of intratumoral dendritic cells type 1 (cDC1) present tumor antigens to T cells and that natural killer cells provide critical Flt3L to cDC1 cells within reactive tumor microenvironments. The overall hypothesis of this proposal is that reactive tumor immunity, based on CD8 T cells and those cDC1, has an archetype and a niche—a collection of cell types that organize and support it. By defining those cells, their associated genes and their relationships, we will be in a position to better create this niche and to thus engineer tumor clearance. This program is unique in applying spatial transcriptomics together with genetic tools and conventional cellular immunoassay methods to understand the critical phenotype-biology relationship between critical cDC populations and their partners. The resultant discoveries will be formative for designing new ways to boost anti- tumor immunity.

NIH Research Projects · FY 2026 · 2023-06

ABSTRACT Infections by different pathogens can manifest with similar symptoms, but appropriate treatment requires specific and accurate diagnosis. Clinicians often turn to multiplexed assays testing for many organisms (e.g. BioFire). While these approaches can test for 50-70 organisms, they do not provide concentration titers, which is necessary to identify the causative pathogen among the several false positives or clinically meaningless commensals. As a result, the clinician must perform additional tests to identify which of the positives is causative. Although these tests use quantitative PCR, in clinical labs the results are reported as presence/absence due to the finicky nature of PCR in this setting, which is sensitive to minor variations in reaction efficiency, operator variability. As a result, today, only a few widespread PCR tests are FDA approved to report quantitative result. In contrast to qPCR, digital PCR (dPCR) measures target titers by counting individual molecules. As a result, dPCR provides an absolute concentration measurement that doesn’t require a standard curve. In addition, the reaction is cycled to endpoint, then quantified; it does not require careful estimation of the amplification rate, which is a major source of variability in qPCR. Thus, dPCR is less sensitive to variations in reaction efficiency and provides superior consistency. However, current dPCR methods are limited in multiplexing, allowing just 5- 6 targets per assay, while qPCR can test up to 100. Moreover, dPCR requires complex microfluidic equipment that burdens testing lab personnel and increases cost. Until these issues can be addressed, qPCR will continue to dominate the clinical lab, and quantitative and absolute pathogen load reporting will remain beyond reach. Here, we propose a novel nucleic acid technology combining the quantitativeness and robustness of dPCR with the simplicity and multiplexing of qPCR. Our vision is to enable broad spectrum detection wherein each pathogen is associated with a high confidence, quantitative titer. Our approach – gigapixel PCR (gPCR) – is enabled by our recent discoveries of self-assembled partitioning, for microfluidic-free generation of monodispersed emulsions, and linearized target quantitation with capillary electrophoresis (CE). CE allows sensitive quantitation over 7 decades and provides amplicon length information with single nucleotide resolution. In gPCR, we use this to perform multiplexed detection of over 100 amplicons per reaction. In contrast to qPCR, which requires that the sample be split to test for different targets, thereby diluting it and reducing sensitivity, with gPCR the targets are tested without splitting, maintaining them at maximal concentration, and substantially increasing sensitivity. Moreover, based on robust dPCR, gPCR provides reproducible, quantitative results across testing conditions. It thus addresses the major limitations of current dPCR technologies and provides the first viable alternative to qPCR in the clinic. We will develop and validate the technology against accepted standards (SeraCare), and work with our longstanding collaborators (Drs. Melanie Ott and Charles Chiu) to apply it to respiratory and CNS infections from samples previously collected at UCSF hospitals.