University Of California, San Francisco

NIH Research Projects · FY 2024 · 2023-09

Abstract The overall goal of this project is to collect pilot data to determine if treatment with a novel form of closed-loop digital meditation (MediTrain), which we have previously shown improves cognition and reduces stress in older adults (OA), also leads to sleep benefits in both cognitively normal OA and in those with mild cognitive impairment (MCI). MCI is a transitional stage between normal aging and dementia and is associated with increased risk of progressing to Alzheimer’s disease and related dementias (ADRD). We have demonstrated that a digital meditation intervention (MediTrain) improves regulation of focused attention in healthy OA. Variability in attention is a preclinical marker of incipient neuropathology and is elevated in MCI patients. In addition to exhibiting decreased stress reactivity and a lengthening of telomeres, there were several anecdotal reports from OA that they felt their sleep had improved. Because sleep disturbances are common in AD and significantly increase the risk of conversion from MCI to dementia, understanding if this intervention led to improved sleep is critical. The goal of this proposed research is to collect pilot data to evaluate the efficacy of MediTrain on improving quantitative metrics of sleep and stress in patients with MCI at levels beyond those seen in cognitively normal OA. To accomplish these aims, we will conduct a randomized controlled trial on 90 OA (45 cognitively normal and 45 with MCI) who will complete 6 weeks of our MediTrain intervention. Outcome measures will consist of cognitive/attention tasks coupled with neuroimaging (EEG and MRI), quantitative physiological indices of sleep and stress, and blood biomarkers of aging (telomere length). Objective measures of insomnia (latency to sleep onset and wake after sleep onset) and amount of NREM3 will be assessed using sleep profilers in participants’ homes throughout the intervention period. This research will provide an important contribution toward understanding the utility of using meditation as a therapeutic tool for bolstering cognitive reserve and increasing overall wellbeing in OA with MCI, by showing transfer to real-world metrics of improved sleep quality and reduced stress.

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY There is a critical clinical and commercial unmet need for novel pediatric devices that are designed specifically for the unique needs of children. The UCSF-Stanford Pediatric Device Consortium (PDC) has been a key player in this space since its inception in 2009, with a successful history in supporting over 250 pediatric device innovations in many clinical specialties and in all device classes on their path to commercialization and patient access. In the previous 5-year grant cycle, the UCSF-Stanford PDC supported 128 projects in research, development, and engineering, 67 projects in bench and animal testing, 21 projects in intellectual property, 55 projects in regulation, 71 projects in business and commercialization, and 30 projects in payment and reimbursement. This has led to over $100M in collective follow-on funding, 9 commercially available products, and over 20,000 children positively impacted by these technologies. The UCSF-Stanford PDC is also proud to be the first PDC to effectively use real-world clinical data and real-world evidence for successful regulatory clearance of a device and label expansion for pediatric use. UCSF-Stanford PDC combines the outstanding resources and unique innovation ecosystems available in two world-class universities and two leading children’s hospitals with the unsurpassed entrepreneurial network in the heart of the Bay Area, to equip pediatric innovators at all stages of development to translate their innovations into high-value, commercially viable, and equitable products that are accessible to all populations. The PDC is now further expanding its scope and impact through 1) a partnership with world-class device incubator Fogarty Innovation, 2) the diversification of leadership with actionable plans to promote diversity, equity and inclusion (DEI) in device development, and 3) the expansion of real-world evidence (RWE) consulting and education through a collaborative PDC Service Center as well as a new partnership with a leading RWE firm, Aetion. Two seasoned device innovators, Hanmin Lee, MD (Pediatric Surgeon and Surgeon in Chief at UCSF Benioff Children’s Hospitals) and James Wall, MD (Pediatric Surgeon and Biodesign Lead, Stanford University) will lead the PDC team consisting of device experts with clinical, technical, regulatory, and other relevant expertise. They will be supported by senior medtech industry professionals, multidisciplinary advisory committees, and multiple institutional stakeholders (UCSF-Stanford Center of Excellence in Regulatory Science and Innovation, clinical trials offices, and DEI Council),to catalyze promising pediatric device innovations to viable commercial products. Through committed leadership, collective efforts, great resources, and the unique expertise gained from previous grant cycles, the UCSF-Stanford PDC will be able to achieve the objectives detailed in the proposal to accelerate many high-impact, value-based pediatric device solutions to commercialization and patient impact. The UCSF- Stanford PDC will continue to play a leadership role, along with other PDCs, in creating a national network and ecosystem to foster pediatric device innovations.

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY/ABSTRACT Transgender and gender diverse (TGD) youth initiate gender-affirming medical therapy as early as Tanner Stage 2 with gonadotropin-releasing hormone agonists (GnRHa) for puberty suppression, with variable timing of gender-affirming sex hormones (GAH). Peak bone mass, achieved during puberty and young adulthood, largely determines age-related fractures in later life. There is compelling evidence that pre-treatment bone mineral density (BMD) is low in TGD youth, and that peak bone mass attainment may be attenuated in transfeminine youth. TGD youth who initiate GnRHa in early puberty develop bone geometry distinct from those who start in late puberty. All published longitudinal studies on bone measures in TGD youth have initiated GAH around 16 years (Dutch Model), and no studies have described skeletal trajectories of TGD youth who initiate GnRHa in early puberty and follow a peer-concordant puberty-timing model with GAH by 14 years. The objective of this proposal is to evaluate the trajectory of bone mass, architecture, and strength in TGD youth who follow the peer-concordant puberty-timing model, and to assess the determinants of skeletal health in this population. Dr. Lee will enroll 30 participants from her existing cohort of early pubertal TGD youth who have had detailed bone measures prior to and during the first year of GnRHa. She will determine the skeletal measures during 3 years of GAH by utilizing dual-energy X-ray absorptiometry (DXA) to quantify BMD accrual and BMD Z-score changes (Aim 1). Dr. Lee will correlate DXA measures to high-resolution peripheral quantitative computed tomography (HR-pQCT) for bone architecture and strength estimate changes at weight-bearing and non-weight-bearing sites, and at diaphyseal sites to examine muscle mass and density (Aim 2). She found that low pre-treatment BMD in early pubertal TGD youth was associated with low physical activity and that grip strength was a positive predictor of failure load. Dr. Lee will utilize thigh- mounted tri-axial accelerometers to measure intensity/duration of physical activity/sedentary time and hand- grip and knee extension dynamometry to measure isometric strength to develop threshold targets for future intervention studies (Aim 3). Dr. Lee has assembled a cross-disciplinary mentor team with the necessary expertise to achieve these aims and receive training in the endocrinology of bone and transgender medicine, adolescent DXA and HR-pQCT interpretation, biomechanical load evaluation and muscle strength testing, cohort study implementation, and complex longitudinal data analysis. The proposed research will generate data for Dr. Lee to develop a larger R01 prospective study to follow skeletal trajectories until peak bone mass attainment in order to optimize treatment protocols to mitigate potential impairment in peak bone mass accrual, which could impact future fracture risk. Dr. Lee is committed to rigorous investigation of skeletal development in TGD youth receiving gender-affirming medical therapies and is confident that this K23 proposal will prepare her for her long-term goal of being an independent physician-scientist focused on bone health in TGD youth.

NIH Research Projects · FY 2025 · 2023-08

PROJECT SUMMARY Alzheimer's disease (AD) and frontotemporal dementia (FTD) are highly prevalent in Latinos, the largest and fastest-growing minority in the United States (US). Yet, due to financial and cultural inequities, this group is challenged to afford standard diagnostic and monitoring procedures. Also, research on Latinos lacks scalable, culturally valid tests and it rarely examines whether potential markers are robust across socio-biological profiles. Such issues can be tackled with low-cost automated speech and language analyses (ASLA). Participants are asked to produce natural speech, generating multiple acoustic (sound wave) and linguistic (e.g., semantic) data that can be digitally extracted and analyzed to identify diseases or predict neurocognitive disruptions. Yet, ASLA findings are minimal in Latinos. Also, most ASLA studies are small and very few ha differentiated between AD and FTD variants, compared ASLA with standard measures, accounted for socio-biological factors (e.g., sex, race, brain profile, bilingualism) or tested for validity across languages and dialects. This project will develop a novel ASLA framework to jointly address such challenges. To capture socio-biological diversity and meet requisites for robust machine and deep learning analyses, we will leverage 2740 participants. These encompass Spanish speakers from five Latin American countries (700 AD, 700 FTD, 800 controls), English speakers from the US (140 AD, 140 FTD, 160 controls), and US-based Latinos (30 AD, 30 FTD, 40 controls), including the main variants of each disease. This is possible due to a strategic partnership between UCSF and the Consortium to Expand Dementia Research in Latin America, a multi-funded network bringing a fully harmonized environment and a large, growing cohort. The Global Brain Health Institute, a dementia training hub at UCSF, hosts expert clinicians in all sites. Speech and language data will be gleaned through our new Toolkit to Examine Lifelike Language, a HIPPA-compliant app for speech collection, storage, and visualization, supported by a language battery and survey. Enrollees are characterized with demographic, clinical, cognitive, and social determinants of health measures, alongside MRI and fMRI. Our ASLA approach comprises top predicted markers for each syndrome, added fine-grained features, and embedding features. Novel machine and deep learning algorithms for high-dimensional settings will be used to pursue three aims. In Aim 1, we will employ machine and deep learning to reveal the ASLA markers that best identify AD and FTD syndromes; compare them with cognitive and imaging measures; and test them for generalizability from Spanish onto English (a typologically different language). In Aim 2, via linear regressions, we will use optimal ASLA markers to capture syndrome-specific patterns of cognitive dysfunction, brain atrophy, and connectivity. In Aim 3, using high-dimensional machine learning, we will test such markers for validity across diverse socio-biological profiles, dialects, and bilingual skills (null, low, high). We will forge an affordable, scalable approach to assist AD and FTD diagnosis in Latinos, at a time when disease-modifying therapies may emerge.

NIH Research Projects · FY 2026 · 2023-08

PROJECT SUMMARY The smoke-free home intervention study aims to reduce racial/ethnic disparities in tobacco use and exposure by increasing access to smoke-free homes and cessation resources among racially/ethnically- and linguistically-diverse populations in federally subsidized housing (“subsidized housing”). Black/African American, Hispanic/Latino, and Asian populations with limited English proficiency are over-represented in subsidized housing; these populations have higher rates of tobacco use and exposure than the general population. Tobacco-related cancer and cardiovascular disease contribute disproportionately to the excess morbidity and mortality in these populations. Comprehensive smoke-free policies have the potential to substantially reduce tobacco-related disparities among populations in subsidized housing. In 2018, the Department of Housing and Urban Development implemented a smoke-free policy in a minority of public housing, presenting a unique opportunity to expand the reach of such policies to all types of subsidized housing. This study fills this gap by identifying approaches to increase the implementation of smoke-free policies in all types of subsidized housing by increasing the voluntary adoption of smoke-free homes and promoting access to smoking cessation services. We will build on our pilot work, where we developed and evaluated the feasibility of a smoke-free home intervention to increase voluntary adoption of smoke-free homes in permanent supportive housing for formerly homeless adults. We adapted our previously-developed smoke-free home intervention to federally subsidized housing by incorporating new intervention components that align with racially-ethnically and linguistically-diverse populations in three geographically-diverse California Counties. The multi-faceted intervention, delivered by bilingual study staff in Chinese (Mandarin and Cantonese), English, or Spanish includes: 1) one-on-one counseling to residents who are smokers on how to adopt a smoke-free home, and 2) training housing staff as lay health workers to deliver monthly brief cessation coaching to residents. We propose to conduct a wait-list cluster randomized controlled trial of the adapted smoke-free home intervention compared to usual care among N=544 residents from 24 subsidized housing sites in Contra Costa, Oakland and San Francisco. Our specific aims are: Aim 1: To estimate the effect of our adapted smoke-free home intervention on the primary outcome of residents' voluntary adoption of smoke-free homes and the secondary outcome of biochemically-verified tobacco abstinence at 6-months follow-up. Aim 2: To determine the cost of our adapted smoke-free home intervention and determine whether it is a cost- effective use of health care resources. Aim 3: To evaluate variation in stakeholders’ perspectives on the adapted smoke-free home intervention’s adaptability, scalability and sustainability. The proposed intervention can expand access to smoke-free policies and smoking cessation services in subsidized housing, thereby reducing racial/ethnic disparities in tobacco use, tobacco exposure and chronic disease in these populations.

NIH Research Projects · FY 2026 · 2023-08

Project Summary/Abstract This proposal presents a five-year research career development program on the study of lysosomal pH and function in aging and disease to expand our understanding of the mechanisms by which aging contributes to neurodegenerative diseases, like Alzheimer’s disease (AD). The candidate, Dr. Courtney Lane-Donovan, is currently a Clinical Fellow in Neurology at the University of California, San Francisco, in the division of Memory and Aging. The outlined proposal builds on Dr. Lane-Donovan’s previous research experience in mouse models of AD to gain new domains of expertise represented by her mentor team of primary mentor Dr. Aimee Kao and co-mentor Dr. Anna Molofsky of the departments of neurology and psychiatry, respectively, at UCSF. The proposed experiments, didactic work, and training in academic skills will provide Dr. Lane-Donovan with a unique skillset that will enable her transition to independence as a physician scientist leader in the field of aging and neurodegenerative diseases. As our nation ages, the burden of the aging-related neurodegenerative diseases has increased substantially. How aging promotes protein aggregation in certain brain regions – and more importantly, how to reverse the effect – remains unknown. Protein aggregates can accumulate when protein degradation by proteases in the lysosome is impaired, and several genetic risk factors for AD encode proteins involved in endolysosomal function and autophagy. Lysosomal proteases function optimally at an acidic pH, and data from invertebrate models suggest that age and stress cause lysosomes to lose their acidity, resulting in impaired function; however, the relevance of these findings to human aging and disease is unclear. Regional variation in lysosomal protease activity may contribute to the selective vulnerability of certain brain regions to the accumulation of protein aggregates; however, regional lysosomal function is not fully characterized and thereby poorly understood. Together, this suggests a tantalizing hypothesis - regional variability of lysosomal protease expression leaves certain neurons more vulnerable to the lysosomal dysfunction caused by lysosomal alkalinization with age. To test this hypothesis, Aim 1 utilizes the novel lysosomal pH reporter, FIRE-pHLy (Fluorescent Indicator Reporting pH of the Lysosome) to delineate the effect of aging and amyloid beta accumulation on lysosomal pH. Aim 2 will determine regional changes in lysosomal protease activity and expression in the aging brain by combining lysosome isolations, immunohistochemistry, and spatial transcriptomics. The data generated by this study can be used to propose new models of lysosomal dysfunction in aging and disease and identify new therapeutic targets for neuroprotection in neurodegenerative disease.

NIH Research Projects · FY 2026 · 2023-08

ABSTRACT Fibrosis is the final common pathway in chronic liver disease that leads to liver failure, and is characterized by an imbalance of extracellular matrix (ECM) deposition and remodeling. There are currently no FDA-approved therapies to target this endpoint of chronic liver disease. Moreover, there is a paucity of biomarkers that reflect disease-specific pathways in patients. Development of new therapeutics and biomarkers for patients with hepatic fibrosis is a critical unmet need. Our long-term goal is to develop antifibrotic therapies for the treatment of hepatic fibrosis and to develop biomarkers to define the patient populations that would benefit most from these therapies. Our prior studies discovered an antifibrotic target, the enzyme acid ceramidase (aCDase). Targeting aCDase ameliorates fibrosis by inhibiting YAP/TAZ, key effectors of the Hippo pathway, and promotes ECM remodeling. We developed a signature score of genes downregulated by ceramide, the Ceramide Responsiveness score (CRS), and demonstrated that the CRS is increased in patients with advanced fibrosis. Despite the fact that targeting aCDase in HSCs ameliorates activation in culture and ablating its expression prevents liver fibrosis in vivo, chronic ceramide accumulation may have untoward side effects. The overall objective of the proposal is to clarify the mechanisms by which ceramide regulates YAP/TAZ, ECM remodeling, and hepatic fibrosis. We also seek to validate the CRS as a pathway-specific biomarker in patients with hepatic fibrosis. The rationale for this project is that understanding the mechanisms of ceramide-mediated attenuation of HSC activation and hepatic fibrosis will offer a strong scientific framework to facilitate the development of antifibrotic therapeutics and biomarkers for patients. To achieve this objective, this proposal has three specific aims. In specific aim 1, we will determine the mechanism by which ceramide regulates Hippo signaling. In specific aim 2, we will characterize how ceramide regulates ECM remodeling. Specific aims 1 and 2 will be achieved by gain of function and loss of function techniques in vitro and testing HSC-specific knockout mice. In specific aim 3, we will analyze the correlation between the CRS, fibrosis stage, and fibrosis progression using deidentified human liver samples, and will identify clinical characteristics that correlate with the CRS. The mechanistic understanding to be gained from the successful completion of the proposed studies promises to reveal new targets for rational disease modification in hepatic fibrosis, a disease with limited treatment options available. Furthermore, by clarifying molecular mechanisms and defining a pathway-specific signature, our work will facilitate a personalized medicine approach for patients with hepatic fibrosis.

NIH Research Projects · FY 2024 · 2023-08

SUMMARY/ABSTRACT Due to challenges with available technology in regions of the world where schistosomiasis is endemic, the prevalence of schistosomiasis-associated pulmonary arterial hypertension (SchPAH) is unknown. SchPAH is an incurable and ultimately fatal disease for which early detection and treatment could extend the lives of those afflicted. New approaches to diagnose SchPAH are needed, as the current diagnostic criteria require invasive right heart catheterization leading to under and delayed diagnosis. An opportunity to develop noninvasive diagnostic risk scores for PAH is provided by the PVDomics dataset and a collaboration to conduct these analyses at UCSF using the PVDomics data has been established. The proposed studies will define diagnostic risk scores for PAH (i) using a broad range of clinical, echocardiographic (echo), and biomarker predictors and (ii) using predictors easily measured in low- and middle-income countries (LMIC). The risk scores would enable estimation of the probability of PAH in individuals, the PAH case-rate in clinic samples, and PAH prevalence in communities at risk. Regardless of LMIC, the scores will rely only on noninvasive predictors to support their repeated use in disease screening. After developing the risk score, its first application to will be to SchPAH disease, and will take place in the longitudinal prospective cohorts we are enrolling at 3 clinical sites in Ethiopia and Zambia, targeting 40 enrollees per site per year. We will estimate the case-rate of SchPAH by standard of care criteria and using the Aim-1 diagnostic risk score. Eligible patients will have a history of Schistosoma infection and be diagnosed with schistosomiasis-associated hepatosplenic disease (SchHSD), placing them at relatively high risk for SchPAH. At baseline and annual follow-up study visits each participant will undergo clinical and echocardiography assessments, and providing blood samples for biomarker assessments to ensure that the predictors on which the diagnostic score is based are on hand. Once it is defined, the risk score and probability of PAH will be calculated on each participants’ data, both at past and future visits, and the distribution the quantities will be summarized graphically. This study also will evaluate some biomarkers that reflect the pathobiology of SchPAH and may be particularly suitable for identifying PAH disease during its preclinical and early clinical periods, which could suggest a role as potential therapeutic targets. We believe these diagnostic tools will have enormous impact on all those worldwide who are at risk for developing PAH or living with undiagnosed PAH.

NIH Research Projects · FY 2026 · 2023-08

Abstract: White blood cell (WBC) counts and neutrophil counts are among the most commonly used medical tests. WBC counts and absolute neutrophil counts (ANC) are monitored closely in the setting of myelosuppressive therapy, and neutropenia is often the dose limiting toxicity when dosing chemotherapy. An elevated WBC count is also used in helping to diagnose and infection and risk stratifying patients with acute bacterial infections. Therefore, accurate interpretation of the WBC and neutrophil count is crucial in many branches of medicine. WBC and neutrophil counts vary substantially by race and ethnicity. African Americans, Latinos with African ancestry and some Middle Eastern populations have lower WBC and lower ANC. We have previously mapped the genetic variant underlying this difference. The variant maps to the promoter region of the Duffy Antigen Receptor Chemokine (DARC/ACKR1) locus and results in lack of expression of the DARC antigen on the surface of red blood cells. The allele which leads to loss of expression (Fya-/b- or Fy-) is the predominant allele in West Africa, but rare outside of Africa and the Middle East. Individuals with Fy-/- genotype have WBC and ANC that is > 1 standard deviation lower than individuals with the other genotype. Despite over a decade of knowledge about this effect, there has been little progress on incorporating this into clinical care. As a result, patients with this genotype who are predominantly African American in the U.S. may receive lower doses of myelosuppressive therapies and may be more likely to have reduced relative dose intensity of chemotherapy which may lead to disparities in outcomes. Since WBC and ANC are used to diagnose and make prognostic inferences among patients with infection, their care in the setting of severe infections may suffer. Therefore, large studies with outcomes are needed to help guide clinicians on how to treat these patients. We propose to leverage large biobanks tied to electronic health records to determine outcomes of patients on myelosuppressive therapies with this genotype and to determine how to use WBC and ANC in the setting of infection. (1) We will examine outcomes of patients on chronic myelosuppressive therapies by genotype. We will determine whether Fy-/- genotype is associated with high incidence of neutropenia on myelosuppressive therapies and whether this leads to dose reductions. We will examine the risk of infectious complications among patients with Fy-/- on myelosuppressive therapies. (2) We will examine outcomes of patients on chemotherapy according to genotype. We will determine if genotype is associated with relative dose intensity of chemotherapy and whether this is associated with differences in overall survival among these patients. We will determine if infectious complications are associated with genotype among patients on chemotherapy. (3) We will examine how WBC and neutrophil to lymphocyte count ratios vary in the setting of acute infections and how this affects diagnostic and prognostic use of these parameters. Our project will help clinicians optimize myelosuppressive therapy and diagnosis of infection among the large number of individuals with this genotype.

NIH Research Projects · FY 2025 · 2023-08

PROJECT SUMMARY Immune system dysfunction has been implicated in the pathogenesis of several age-related lung diseases. Interestingly, multiple recent studies have identified the tissue microenvironment as playing a critical role in the pathogenesis of some of these age-related immune system changes. The lung mesenchyme provides a supportive niche for the resident immune system. Therefore, to identify aging-related changes in the lung mesenchyme that might contribute to immune system dysfunction, we performed single-cell RNA-sequencing of lung mesenchyme from aged versus young mice, identifying evidence of nuclear-factor kappa-B (NF-kB) activation in aged relative to young adventitial fibroblasts. NF-kB is an important regulator of inflammation and cellular senescence, a multifaceted cellular stress response characterized by several features including permanent cell cycle arrest, expression of the cell cycle inhibitor 16INK4a, and a complex secretory profile known as the senescence-associated secretory phenotype. Using a novel p16INK4a reporter mouse to identify cells with senescent features in vivo, we found that p16INK4a+ lung fibroblasts were enriched for NF-kB activation and accumulated in the parenchyma with age. Therefore, to study the effects of mesenchymal NF-kB activation in regulating the immune system, we used a genetic model to conditionally delete Tnfaip3, which encodes an important negative regulator of NF-kB signaling, from the mesenchyme. Preliminary data in this proposal demonstrates that mesenchymal deletion of Tnfaip3 leads to the accumulation of CD8+ T cells within the lung adventitial mesenchyme of young mice, and that these T cells transcriptionally resemble an aging-associated CD8+ T cell population (Taa). Therefore, the central hypothesis of this proposal is that NF-kB activation within senescent fibroblasts plays a direct role in driving lung Taa accumulation. Aim 1 is to identify the contribution of lung fibroblast senescence to Taa formation using our novel p16INK4a+ reporter mouse. Aim 2 focuses on identifying the mechanism by which mesenchymal NF-kB drives Taa formation, and Aim 3 will determine the functional consequences of Taa formation in the setting of viral pneumonia. The training plan for this proposal has been developed to achieve Dr. Allen’s goal of becoming an independent physician-scientist studying the interactions between the lung mesenchyme and immune system in health and disease. The plan involves formal didactics, conferences, mentorship, and hands-on experience though which Dr. Allen will develop expertise in cellular senescence, adaptive immunity, mouse models of pulmonary infection, the lung mesenchyme and associated epithelial stem cell nice, as well as responsible and effective research practices. She will be supported by a strong mentorship team with expertise spanning lung biology, cellular senescence, tissue resident lymphocytes, and NF-kB signaling. With completion of this Career Development Award Dr. Allen will have made valuable contributions to the understanding of lung immune system aging, and will be well-prepared to launch her independent career.

NIH Research Projects · FY 2025 · 2023-08

SUMMARY Exosomes are nano-sized vesicles secreted into the extracellular milieu by all cells in physiological and pathological states. Exosomes can effectively mediate cell-cell communications, deliver macromolecules such as proteins and nucleic acids to cells, and induce functional changes in recipient cells. Recent studies have implicated that exosomes participate in a broad range of pathophysiological processes, including immune regulation, organogenesis, and carcinogenesis. Despite great interest in exosomes for both diagnostics and therapeutics applications, the basic understanding of the regulation of exosome secretion is not well established. Long noncoding RNAs (lncRNAs), defined as RNAs longer than 200nt without functional protein-coding capacity, are emerging as regulators of gene expression and cellular functions. Our preliminary data has shown that lncRNAs play regulatory roles in exosome biogenesis in both physiologic and cellular stress conditions, such as hypoxia and oxidative stress. How the biogenesis, intracellular trafficking, and cargo soring of the exosomes are regulated by lncRNAs is largely unknown. This project will investigate the role of cytoplasmic and nuclear lncRNAs in exosome biogenesis and identify how they function in the docking, cargo sorting, and fusion of late endosomes or multivesicular bodies to the plasma membrane. The role of lncRNA in the regulation of signaling pathways and genes that regulate different aspects of exosome biogenesis and exosome cargo selection will also be characterized. We will investigate how cellular stress pathways, such as the HIF1-alpha and MAPK pathways, through lncRNA or independent of the lncRNAs, influence exosome biogenesis and cargo selection. Research accomplishments from this project will deepen our understanding of the basic biology of regulation of exosome biogenesis and open new avenues for the therapeutic use of exosomes and lncRNAs in the treatment of various diseases. Exosomes play a vital role in many biological processes, including adaptive immune function, cancer metastasis, the development and differentiation of stem cells, tissue regeneration, and viral replication. They also exhibit profiles specific to the cell of origin and therefore represent novel biomarkers that show promise for improving disease diagnosis. Their central role in cell-to-cell communication presents opportunities for the development of improved therapeutics. Therefore, it is essential to understand the role of lncRNAs in regulating exosome production and release in order to realize these diagnostic and therapeutic opportunities.

NIH Research Projects · FY 2025 · 2023-08

PROJECT ABSTRACT This K23 award will enable the candidate, Shih-Chuan Chou, MD, MPH, SM, to become an independent physician-scientist focused on the effect of out-of-pocket costs on care utilization and outcomes of acute chest pain and cardiovascular care. Chest pain is one of the most common reasons for emergency department (ED) evaluation, with over 7 million visits annually. ED visits ensure the timely identification and treatment of acute myocardial infarction (AMI) or acute coronary syndrome (ACS). However, the financial implications of care have escalated over the past two decades with the growth of high deductible health plans (HDHP). By 2020, nearly 6 in 10 US employees with employer-sponsored insurance will have deductibles of ≥$1,000. While research has begun to explore HDHP’s effect on cancer screening and chronic disease management, little research has examined how it affects acute cardiovascular care. In a preliminary study, Dr. Chou found that HDHP enrollment reduced ED visits for non-specific chest pain but increased AMI after chest pain admission among the lower-income population. In this K23, Dr. Chou will further extend this research with 3 proposed aims. Aim 1 will use segmented survival analysis in a large commercial claims database to examine whether employer-mandated HDHP enrollment negatively impacted AMI outcomes. Using the same database, aim 2 will utilize the natural randomization of patients to ED clinicians within each ED to determine whether HDHP reduces low-value chest pain admissions among clinicians with high admitting tendencies. Lastly, aim 3 will include patient surveys and interviews to elicit chest pain and AMI patients’ perspectives on how high out-of- pocket costs affected their decisions to seek care, perceived care quality, and subsequent financial impact. All aims will further focus on low-income patients that face disproportionate financial stress. Dr. Chou proposed a comprehensive career development curriculum to complement these aims, consisting of extensive didactic and experiential learning. Dr. Chou has assembled an interdisciplinary team of mentors with recognized expertise in quasi-experimental observational studies, insurance benefit design, cardiovascular emergencies, health care disparities, and emergency medicine, who will provide him with intensive mentorship in these topics. The proposed research and career development activities will allow Dr. Chou to establish his expertise in insurance-related policies, the financial burden of care, and their impact on the use and outcomes of patients with acute cardiovascular conditions. This award will enable Dr. Chou to transition into an independent clinician-scientist focusing on the short- and long-term impact of high out-of-pocket costs and the implications around the growing implementation of price transparency and cost discussions for acute unscheduled care visits. Completing the proposed research will generate robust evidence to advance the understanding of the clinical impact of patient financial burden, guide future regulations around insurance cost-sharing policies, and inform the implementation of price transparency initiatives in acute cardiovascular care.

NIH Research Projects · FY 2025 · 2023-08

PROJECT SUMMARY Many proteins function by forming macromolecular assemblies. Describing the structures of these assemblies in their cellular environment remains challenging. Traditional structural biology approaches may provide high- resolution atomic structures but usually require purified samples and might describe only a few conformers. We propose using data from in vivo genetic interaction and quantitative cross-linking mass-spectrometry (qXL-MS) experiments to build structural models of protein assemblies, empowering the scientific community to address structural questions that are currently out of reach of traditional structural biology methods. For example, genetic interaction mapping by point-mutant epistatic miniarray profile (pE-MAP) platform and deep mutational scanning (DMS) have emerged as powerful tools to interrogate proteins, at a residue resolution, in the context of their biologically relevant functions. Similarly, in vivo qXL-MS approaches are well-suited to dissect physical interactions between proteins, a full range of structural dynamics, and conformational changes at residue resolution. Notably, in vivo genetic interaction and cross-linking experiments can be performed under varying conditions to determine how protein functional states respond to changes in the cellular environment, a problem difficult to approach by other methods. However, in vivo genetic interaction and cross-linking datasets are usually noisy, sparse, and ambiguous, making structural interpretation challenging. To fully realize the potential of in vivo genetic and physical interaction data, we need new computational methods that maximize the structural information extracted from these datasets. Here, we propose a comprehensive research program to develop tools to build integrative/hybrid structure models of stable and transient protein assemblies. We will focus on (1) developing Bayesian scoring functions that objectively quantify the noise and ambiguity in the in vivo experimental data, therefore increasing the accuracy and precision of the models; (2) building Bayesian hierarchical models to represent the ensembles of protein assemblies, therefore allowing the application to conformational and compositionally heterogeneous systems; and (3) creating validation tools to assess the precision and accuracy of structural models obtained using in vivo data, therefore allowing judicious use of the models. Finally, in close collaboration with experimentalists, we will apply these methods to determine the structures of protein assemblies that have been refractive to traditional structural biology methods, including vaccinia virus protein assemblies, TRIM5α bound to the HIV-1 capsid, and Ddis shuttling factors associated with the proteasome. In conclusion, we will expand the scope of structural biology by increasing the variety of input information used for integrative/hybrid structure modeling and thus allow structural modeling of biological systems that are not amenable to traditional structural biology approaches. Our methods will be implemented in the open-source Integrative Modeling Platform (IMP) software and contribute to the worldwide Protein Data Bank (wwPDB) effort to validate, archive, and disseminate integrative structures.

NIH Research Projects · FY 2025 · 2023-08

Project Summary/Abstract Zimbabwe is a resource-constrained country with a high burden of HIV and cervical cancer (CXCA). Zimbabwean women with CXCA present with advanced disease and two-thirds die within a year of diagnosis. CXCA screening has low coverage (13%), and is conducted largely through visual inspection with acetic acid (VIA), with plans to migrate to human papillomavirus (HPV) deoxyribonucleic acid (DNA) testing. Precancer treatment is mostly cryotherapy or thermal ablation but is only accessed by 53% of women screen positive. To meet the WHO 2030 target of eliminating CXCA by 2120, Zimbabwe needs new interventions that are acceptable, affordable, point-of-care, scalable, and clinically proven. To optimize CXCA screening and the pre- cancer treatment cascade for women living with HIV (WLWH), University of California, San Francisco (UCSF) and the University of Zimbabwe–Clinical Trials Research Centre (CTRC), in collaboration with local PEPFAR- funded implementation partners Organization for Public Health Interventions and Development (OPHID) and the Zimbabwe Technical Assistance, Training and Education Center for Health (Zim-TTECH) (collectively, ZIM-CASCADE) propose to serve as a LMIC CASCADE UG1 Clinical Site. ZIM-CASCADE draws on extensive experience in conducting clinical research and CXCA screening and treatment among WLWH, with access to 95,000 WLWH, of whom >44,000 are currently receiving comprehensive CXCA screening and treatment through the OPHID and Zim-TTECH programs located in Zimbabwe’s high-density population centers of Harare and Chitungwiza. ZIM-CASCADE will be led by 2 gynecological oncologists with globally recognized expertise in CXCA screening and treatment and will utilize research personnel and infrastructure from dedicated clinical research sites and community-based primary care clinics, whose experience has been developed over nearly 3 decades of continuous research activities. ZIM-CASCADE will participate in all 4 scientific focus areas of the CASCADE Network, and will complete the following Specific Aims: (1) Provide insight as to clinical significance and feasibility of planned trials by drawing on extensive clinical expertise in CXCA prevention among WLWH; (2) Utilize the expansive pluripotent infrastructure and research management systems developed over 28 years to conduct high quality pragmatic clinical trials; (3) Accrue and retain eligible WLWH through effective and equitable engagement with community partners; and (4) Ensure compliance with all protocol procedures and applicable research regulations. Completion of the Aims will contribute critical evidence to inform optimization, implementation, and scale-up of effective cervical cancer prevention interventions for WLWH in resource-limited settings, and the multi-modal CASCADE data will inform public health policy in Zimbabwe and globally.

NIH Research Projects · FY 2024 · 2023-08

PROJECT SUMMARY/ABSTRACT Malaria affects three billion people worldwide. Despite remarkable reductions in malaria incidence over the last 15 years, recent evidence shows that our traditional control tools are weakening. Long-lasting insecticide-treated bednets (LLINs) are the most widely used tool for malaria prevention and have contributed significantly to de- creases in malaria incidence, but recent studies suggest that LLINs are either less effective than before or people are not using them as reported. A rigorous assessment of the timing and circumstances of LLIN use could be vitally important to regain the initiative in malaria control, but we lack a reliable measure of LLIN use. Current measurement tools, like self-reported use, are subjective and unable to account for temporal variations in use. I previously invented an electronic monitor of LLIN use to address these limitations. In my NIAID-funded K23 work we use these tools to measure LLIN use related to malaria exposure. Most recently, I have pioneered a vastly improved approach using machine learning algorithms and accelerometer-based sensors to measure LLIN use. The central rationale for this project is that by leveraging this novel accelerometer LLIN use monitor we can be more ambitious with our goals for measuring malaria risk related to LLINs. When combined with a carefully trained machine learning algorithm, I believe that we can accurately classify a far wider range of behaviors than merely when an LLIN is used. In this study, we will additionally 1) measure if there is someone under the LLIN, 2) determine how many people are under the LLIN, 3) identify interruptions in LLIN use (such as entering or exiting an LLIN), and 4) characterize who is under the LLIN (e.g. adult versus child). Longitudinal surveillance of exactly this type of data is crucial to disentangle the role of LLINs in malaria prevention. The immediate goal of this R21 proposal is to train a comprehensive platform for highly accurate remote monitoring of LLIN use and other behaviors related to malaria risk. Our approach thus gathers data from the community, trains a machine learning algorithm and then tests the real-life accuracy of that system. We will pursue our research goal by with these three aims: 1) gather real-life data about how LLINs are hung and used in the community, 2) train the machine learning algorithms based off pre-defined protocols informed by actual practice and 3) test the accuracy of the machine learning algorithms in real-life settings. This high-risk, high-reward proposal represents an inno- vative approach to answer a pressing question that limits our understanding of how LLINs prevent malaria: when and how are LLINs used in practice? The long term goal for this novel surveillance platform is to develop a tool for measuring LLIN use and related behaviors to point the way towards identifying better interventions for malaria prevention. The single accelerometer and generality in the training of the machine were purposefully chosen to facilitate adoption of this approach for malaria surveillance in other settings. This proposal will establish a firm foundation upon which to pursue future research studies using this novel tool and prepare me for an independent research career using novel technologies and research methods to improve malaria control.

NIH Research Projects · FY 2024 · 2023-08

Project Summary/Abstract Metastasis is a feature of advanced disease whereby tumor cells spread to distant parts of the body, and is responsible for the vast majority of cancer-related deaths. Unfortunately, targeted therapies often aren’t effective in controlling metastatic disease, as tumors cells have been observed to employ a variety of mechanisms to metastasize. Therefore, many have begun to look to the surrounding microenvironment as a potential therapeutic avenue. Previous studies investigating the tumor immune microenvironment have identified monocytes as important mediators of metastatic progression. However, recent single cell transcriptomic studies have demonstrated that monocytes are a heterogeneous population of cells, and the role of specific subsets of monocytes in metastasis remains poorly understood. Preliminary work from the Goga lab has identified a novel subset of metastasis-associated monocytes with a discrete metabolic and phenotypic transcriptional profile. This proposal seeks to investigate the impact of metabolism on metastasis- associated monocytes and interrogate their role in the lung metastatic niche. We believe that a better understanding of the vulnerabilities of different subsets of immune cells will lead to new therapeutic targets for metastatic cancer. The proposed research training will take place at UCSF, a top-tier research institution and medical center at the cutting edge of cancer immunology research. The Biomedical Sciences program at UCSF provides a rigorous education in translational biology and science communication which prepares students to become future leaders in their fields. Under the mentorship of Dr. Andrei Goga, a practicing oncologist and expert in breast cancer metastasis, I am well poised to carry out the proposed research which will leave me with a broad experimental and computational skillset. Additionally, the training plan we have developed for the remainder of my thesis work places a strong emphasis on developing my teaching and mentoring skills, as well as my communication skills through various opportunities to present my work to the scientific community. This training, coupled with the experience I will gain in carrying out the proposed research, will leave me equipped for a future career in academia studying cancer metastasis as an independent investigator.

NIH Research Projects · FY 2024 · 2023-08

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 · 2023-08

PROJECT SUMMARY This K01 application seeks protected time for mentored research and career development training for Dr. Rosalyn Sayaman, PhD to successfully transition to tenure-track faculty with an independent research program in computational and systems biology, supported by the Chair of Department of Laboratory Medicine. Leveraging the advances in computational and Machine Learning methods and spearheading multi-omic technologies, Dr. Sayaman seeks to develop a highly integrative research program that can bridge the gap between in-silico research and translational medicine, with specific focus on advancing personalized medicine in breast cancer. As a computational biologist with broad training and methodological experience, and a solid experimental background, Dr. Sayaman is uniquely positioned to carry out this comprehensive study incorporating the parallel multi-omic dataset for ~2000 women from the I-SPY 2 Trial. The I-SPY 2 neoadjuvant breast cancer clinical trial is a personalized, adaptive trial designed to improve outcomes in high-risk breast cancer patients. Dr. Sayaman’s research proposal employs computational and Machine Learning approaches to dissect the complex interactions between intrinsic host germline and tumor somatic mutations, and extrinsic tumor microenvironment (TME) features that mediate the tumor immune response. In Aim 1, Dr. Sayaman elucidates the role of genomic and TME features in determining the topography of immune populations in the tumor bed. In Aim 2, she assesses the relative predictive value of these genomic and TME features in predicting subtype- specific response to neoadjuvant therapy, and 5-year survival in patients who do not respond to therapy. This work has the potential to generate response-predictive biomarkers that could inform optimal treatment decisions. To address the multi-disciplinary aspect of this study, Dr. Sayaman has assembled an exemplary team of mentors who have complementary domains of expertise. Dr. Sayaman’s primary mentor is Dr. Laura van ‘t Veer, the Co-Leader of the NCI-designated Breast Oncology Program (BOP) and Director of Applied Genomics at the University of California, San Francisco (UCSF), and Chair of the I-SPY 2 Biomarker Committee. Dr. van ‘t Veer is the inventor of the FDA-cleared MammaPrint® test included in many national and international breast cancer guidelines. Dr. Sayaman’s co-mentors include Dr. Laura Esserman, the Director of the UCSF Breast Care Center, the Clinical Co-Leader of the BOP, and the national Principal Investigator of the I-SPY 2 trial; Dr. Elad Ziv, a leading cancer geneticist with expertise in statistical genetics and computational approaches in cancer genomics; and Dr. Michael Campbell, an expert in cancer immunology, who leads the development of multiplex Immune-Fluorescence assays for immune profiling in breast cancer. Dr. Sayaman’s proposed work benefits from the world-class research and clinical expertise of the I-SPY 2 Trial Consortium and the rich institutional environment of UCSF and the Helen Diller Family Comprehensive Cancer Center, one of the premier cancer centers in the country.

NIH Research Projects · FY 2025 · 2023-08

PROJECT SUMMARY/ABSTRACT A major frontier of genomic medicine is to convert annotations of disease-associated variants and gene expression states into actionable therapeutic targets. Genomic sequence editing by CRISPR/Cas has garnered heightened interest as potential therapeutics, but still carries risks of off-target mutagenicity, and is less effective at targeting cis-regulatory elements, where the majority of disease-associated variants reside. A conceptual alternative to DNA sequence editing is to deliver a brief pulse of a synthetic therapeutic that can trigger memorized silencing of target promoters and enhancers in a "hit-and-run" strategy, bypassing concerns of mutagenicity associated with DNA sequence editing, and immunogenicity associated with constitutive expression of CRISPR/Cas components. In practice, engineering sustained epigenetic transcriptional silencing has had mixed success, but recent efforts demonstrate that constructing specific combinations of chromatin signals -- broadly encompassing cis- regulatory elements, regulatory protein complexes, and covalent chromatin modifications -- can be critical for success. However, existing tools for manipulating chromatin signals at high throughput are limited in combinatorial capacity. This proposal builds the knowledge base and generalizable CRISPR/Cas tools to overcome such limitations to enable systematic engineering of epigenetic silencing memory across genomic loci in human cells. The results will pave the way for future epigenetic therapeutics that expand the directly targetable portion of the human genome, including cis-regulatory elements that can be highly specific with respect to cell types and disease pathophysiology. To achieve these objectives, I am proposing to train in CRISPR/Cas synthetic biology, functional genomics, single-cell methods and neurogenetics. This training will be mentored by a co-mentorhsip team consisting of Dr. Luke Gilbert (UCSF, Innovative Genomics Institute, and Arc Institute), Dr. Howard Chang (Stanford) and Dr. Thomas Montine (Stanford), each providing critical intellectual and physical resources for specific areas proposed in the training plan and my career development. My career goal is to conduct research at the forefront of genome regulation and genomic medicine as an academic principle investigator.

NIH Research Projects · FY 2025 · 2023-08

Project Summary Nearly 20 million older adults undergo major elective surgical procedures, yet very few receive advance care planning (ACP). This is a critical missed opportunity to ensure optimal and patient-aligned medical decisions and communications. Despite ACP being incorporated into national quality metrics and society guidelines for surgical care for older adults, there are few examples of effective integration into the pre-surgical phase. Efforts to date have mostly focused on improving surgeons’ use of ACP but barriers remain significant, including varying levels of familiarity and comfort to conduct ACP conversations, lack of dedicated time during the pre-surgical care episode for these often-delicate conversations, and lack of appropriate patient-facing ACP tools to help patients and caregivers make complex decisions about their surgical treatment. Our team has designed and tested a theory-based, interactive ACP patient-facing technology solution (PREPARE) based on the new ACP paradigm of preparing people for communication and medical decision-making. Despite consistent evidence that PREPARE increases ACP engagement and patient and clinician empowerment to discuss ACP, a gap remains in extending PREPARE’s use to pre-surgical populations. We hypothesize that by including PREPARE into the electronic health record (HER)-centric pre-surgery workflow for older adults and including automated reminders, we can empower patients and surgical teams to engage in ACP discussions. Given the limited time and resources in the surgical setting to conduct ACP, we will be testing 3 delivery strategies in increasing resource intensity (PREPARE alone, PREPARE with text/phone reminders, or the additional of a healthcare navigator). To ensure generalizability, we will conduct our work in 3 healthcare systems (HCS): Univ. of CA, San Francisco (UCSF), Univ. of CA, Irvine (UCI) and M Health Fairview (UMN, a collaboration among the Univ. of MN Medical School, Univ of MN Physicians, and Fairview Health Services). We will first establish trial infrastructure (UG3) to conduct (UH3) an NIH Stage Model III (efficacy-effectiveness) three arm RCT in 3 HCS. Patients aged 65 or older, or with serious illness, who are referred for major elective surgery will be randomized to Arms: (1) Letter about ACP, PREPARE advanced directive (AD), PREPARE website; (2) Letter, AD, PREPARE plus reminder text/phone messages; (3) Letter, AD, PREPARE plus reminders plus a healthcare navigator on ACP documentation (discussions and care plans, primary outcome) and patient-reported ACP engagement. Using mixed methods, we will assess patients’ and surgical care teams' experience with surgery ACP. ACP note content will be evaluated using natural language processing (NLP) and data mining to begin to identify assess thematic completeness of ACP notes. This work is innovative because we are coalescing existing collaborations between HCS into a transdisciplinary group of surgeons, geriatricians, and informaticians across three health systems that will develop infrastructure and rigorously test a novel patient-centered system-level approach to integrating ACP into the surgical care episode, the first step towards goal-concordant surgical care.

NIH Research Projects · FY 2025 · 2023-08

ABSTRACT Single-cell genomic, epigenomic, and transcriptomic technologies can identify unique cell subsets with important physiologic roles; however, RNA or DNA signatures cannot always be linked to unique surface markers, hampering the re-isolation of these cell subsets for in-depth analyses. Moreover, conventional single-cell methods require sequencing prohibitively large numbers of cells to characterize rare subsets. Here we will develop and apply SEARCH-seq, a high-throughput cytometry method that detects RNA or DNA markers with single molecule sensitivity that allows the rapid isolation of target cells for in-depth transcriptomic, genomic, or epigenomic analyses. We will use the method to study the regulatory mechanisms controlling an astrocyte subpopulation characterized by an alternatively spliced XBP1 transcript, which promotes disease pathology in multiple sclerosis (MS). This subpopulation also manifests in the pre-clinical mouse model of experimental autoimmune encephalomyelitis (EAE). Using SEARCH-seq in combination with conditional knock-out mice, in vivo CRISPR/Cas9-driven perturbation studies, and RNA-seq analyses of mouse EAE and human MS samples, we will characterize the role of these cells and their interaction with the nuclear receptor NR3C2 and its corepressor NCOR2 in limiting XBP1-driven pathogenic astrocyte responses. In summary, SEARCH-seq is a novel, sensitive, and high throughput method to capture rare brain cell subsets that are difficult to study with existing technology and may have therapeutically targetable mechanisms relevant to MS pathogenesis.

NIH Research Projects · FY 2025 · 2023-08

PROJECT SUMMARY Lung function measurements are routinely compared to racial/ethnic norms, biasing interpretation and perpetuating asthma disparities. The race/ethnicity-based lung function reference equations used to calculate these norms do not account for genetic ancestry—the genetic origin of one’s population, which can explain over 15% of lung function variation within a racial/ethnic group. Consequently, race/ethnicity-based equations misestimate lung function, often resulting in delayed disease detection and inadequate treatment, especially among populations disproportionately affected by asthma. Dr. Witonsky (candidate) derived equations that use genetic ancestry instead of race/ethnicity to more accurately predict lung function. While genetic ancestry- informed equations appear to remove racial/ethnic bias from lung function measurement, establishing their clinical utility and equity requires evidence that they better predict asthma-related outcomes. In addition, further research is needed to disentangle the social and genetic determinants of genetic ancestry differences in lung function. The proposed mentored research will address these knowledge gaps using data from existing and new cohorts of Black and Hispanic/Latino individuals with and without asthma via three specific aims: (1) to evaluate genetic ancestry-informed, race/ethnicity-based, and “one size fits all” lung function equations for predicting asthma-related outcomes, (2) to quantify the proportion of genetic ancestry differences in lung function that is explained by social exposures, and (3) to quantify the proportion of genetic ancestry differences in lung function that is explained by known lung function-associated genetic loci. In support of this research and Dr. Witonsky’s goal of becoming an independent clinical investigator, this K23 proposal includes formal training with experts in the areas of asthma translational and clinical research (Dr. Prescott Woodruff, primary mentor); advanced statistical and predictive analytic methods (Dr. Stephen Shiboski, co-mentor); social epidemiology and health disparities research (Dr. Luísa Borrell, co-mentor); genetic epidemiology (Dr. Elad Ziv, co-mentor); and statistical genetics (Dr. Noah Zaitlen, advisor). In addition, professional development planning will involve structured meetings with Dr. Woodruff and a leader within Dr. Witonsky’s Division of Pediatric Allergy, Immunology, and Bone Marrow Transplant (Dr. Morna Dorsey, advisor). As a faculty member in the Department of Pediatrics at the University of California, San Francisco, Dr. Witonsky will have access to world-class biomedical and research facilities, workshops and seminars, and an NCATS-funded K Scholars Program. Completion of the proposed research and career development activities in this application will inform the development of an R01 proposal and enable Dr. Witonsky to develop an innovative research program applying computational precision health methods that integrate clinical, social, and genomic data to reduce asthma disparities.

NIH Research Projects · FY 2026 · 2023-08

Project Summary/Abstract Cells alter their gene expression landscape to change their cellular state. The ability of cells to quickly transit between cell states is essential for many processes in biology—from development to wound healing and regeneration, processes which often go awry in pathological conditions like cancer or fibrosis. Thus, there is a biomedical need to understand the basic mechanisms driving these rapid cellular transitions. The epithelial- mesenchymal transition (EMT) is one such cellular transition that has reiterative roles in human health and disease. While much is known about the transcriptional programs that promote EMT, there are additional levels of gene expression control that impact cell state transitions and by extension EMT. The role of post- transcriptional regulation, and how it drives and contributes to a spectrum of EMT states, is not well understood. Here, we examine the role of post-transcriptional regulation, with emphasis on transcript turnover, during EMT. Neural crest cells undergo a tightly regulated EMT and offer a tractable model system in which to investigate the basic mechanisms of RNA turnover during EMT. We hypothesize that, in addition to pro-EMT transcriptional activation, transcripts that inhibit EMT (anti- EMT) or serve to maintain a previous cellular state must be degraded to drive EMT and cell state transitions. Using neural crest EMT as a model system, we seek to test this hypothesis by answering the following questions: 1) How are anti-EMT and residual transcripts targeted for turnover; and 2) What are the targets of RNA turnover during EMT and how does specific RNA turnover contribute to hybrid EMT states? To answer these questions, we will: 1) Apply a combination of unbiased multi-omic and candidate gene approaches to identify the RNA-binding proteins that promote RNA turnover during EMT; and 2) Apply RNA-sequencing approaches to broadly identify the targets of RNA turnover, the mechanism of how they are turned over, and how this contributes to hybrid EMT states. This Proposal seeks to understand the mechanisms of RNA turnover during EMT. The results of these studies will greatly advance current understanding of the basic cellular mechanisms driving EMT, providing novel targets for modulating EMT in human health and disease.

NIH Research Projects · FY 2025 · 2023-08

Project Summary/Abstract of CARE 2.0 Despite being the fastest growing racial population in the United States, Asian American, Native Hawaiian, and Pacific Islander (AANHPI) persons remain severely underrepresented in research. For example, less than 3% of participants in the National Alzheimer's Coordinating Center database are AANHPI individuals and even fewer are enrolled in clinical trials of promising therapeutics. The Collaborative Approach for Research and Education (CARE) registry (R24 AG063718) is a US multi-lingual registry built to improve AANHPI representation in Alzheimer’s disease and related dementias (ADRD), aging, and caregiving research. Launched in October 2020, CARE has enrolled 9,405 AANHPI adults (as of 10/2/22) including 55.9% with limited English proficiency and 80.9% with no prior research participation experience. CARE has referred more than >5,500 participants to 27 studies that are in various stages of recruitment and study completion. As a critical next step and guided by the NIA health disparities framework, we propose CARE 2.0 to strategically expand the registry, advance the science of recruitment and retention of AANHPI participants, and examine the factors associated with research enrollment decisions among referred registry participants. Our specific aims include: 1) Examine attitudes toward health research in a diverse cohort of 10,000 newly recruited AANHPI adults in the US; 2) Elicit perspectives and recommendations from CARE participants about registry retention, and develop, implement, and evaluate recommended registry retention strategies. The Lightning Report Method will be used to conduct dynamic qualitative data analysis and rapid synthesis of the findings to allow rapid comparative analyses across groups and contexts to derive targeted strategies that are sensitive to the diverse needs of retaining AANHPI participants; and 3) Optimize CARE registry participants’ inclusion in NIA- funded and other aging studies and examine factors including study- and participant-level factors associated with participation in research. These innovative aims will increase and test the value of the CARE registry and inform the field more broadly on how best to increase representation of AANHPI groups in research. CARE is well-positioned to complete these aims and contribute to the growing science of recruitment and retention. This proposed application is responsive to PAR-22-093 (Research on Current Topics in ADRD) and NOT-AG-21-033 (Notice of Special Interest: Health Disparities and AD).

NIH Research Projects · FY 2025 · 2023-08

Project Summary As a member of the E. Alejandro Sweet-Cordero laboratory my efforts are directed at executing the computational aspects of the grants, manuscripts, and the general goals of the lab as well as mentoring other lab members. The goals of our projects are to study the mechanism of cancer progression and obtain clinically relevant insights for pediatric and adult solid tumors. The R50 NCI Research Specialist Award would provide me with the necessary funds to continue to further develop my computational tools and ongoing support for the following NCI-funded projects: (1) Development of Advanced Preclinical Models for Pediatric Solid Tumors (R01CA243555). There are three main goals to this project: a) verify that matched patient tissue and patient- derived xenografts (PDX) or PDX-derived cell lines are transcriptionally and molecularly similar; b) utilize high- throughput analyses to nominate drug targets for testing, and c) study drug resistance using single-cell RNAseq technologies. (2) Development of Novel Protein-based Therapeutics for Lung Cancer (R01CA225103). The main goals of this grant are to understand the biology of CLCF1-CNTFR as it relates to adult lung cancer and evaluate the synergistic outcomes of the engineered “decoy” CNTFR receptor (eCNTFR) with other compounds (e.g., eCNTFR+ PDL1 checkpoint inhibitor). (3) Investigate the Role of Long Non-coding RNAs (lncRNA) in Sarcoma Pathogenesis (R01CA211657). The goals of this grant are to elucidate the role of lncRNA EWSAT1/2 in chromatin remodeling at EWS-FLI repressed enhancer sites, utilizing ChIRP-Seq and ATACseq. Other lncRNAs revealed from a prior lncRNA CRISPR-mediated interference screen will also be investigated for their role in Ewing Sarcoma using both in vitro and in vivo models. My ongoing efforts to develop software and computational pipelines will not only go toward the goals of these NCI grants but also align with my long-term career goals and benefit the broader cancer research community.