University Of California, San Francisco

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY/ABSTRACT Patients with advanced cancers often develop malignant pleural effusions (MPEs), a collection of fluid that develops between the surface of the lung and the chest wall that contains malignant tumor cells and benign inflammatory cells. In many cases, percutaneous or transbronchial tissue biopsies may be pauci-cellular or difficult to obtain, thus MPEs may be the only specimen available for pathologic evaluation and molecular testing. Thoracentesis removes this fluid, alleviating symptoms and also providing diagnostic material that can be used for downstream molecular analysis. In current clinical practice, the thoracentesis fluid is typically centrifuged and the cell-rich pellet is used to generate a formalin fixed paraffin embedded (FFPE) cell pellet that is subsequently used to make a hematoxylin & eosin (H&E) stained slide for diagnosis along with additional unstained slides for ancillary studies. Recent studies have highlighted the fact that pleural fluid samples often contain abundant cell- free DNA (cfDNA) within the supernatant fraction and this may represent an alternative source of DNA for molecular testing. Similar to cfDNA isolated from plasma, cfDNA isolated from MPEs could in theory circumvent the problem of intra-tumoral heterogeneity and tissue accessibility while at the same time obviate the time needed to create a cell block and reduce/eliminate the labor-intensive steps of scraping and extracting DNA from unstained slides. Despite its promise, there are no established guidelines for the collection, storage, processing, and molecular testing of cfDNA isolated from MPEs. Our proposal systematically tests several preanalytical variables as well as directly compares three different cfDNA isolation techniques to identify the best practices for processing cfDNA from MPEs. We predict that optimization and harmonization of the these preanalytical steps will lead to reduced false negative results, increased reproducibility, improved efficiency, and reduced turn- around-time in the testing of MPEs. We will leverage our collective expertise in cytopathology, molecular pathology, and test validation to develop standard operating procedures that can be easily adapted into existing clinical workflows. Finally, we will validate these pre-analytical protocols using a CLIA/CAP certified multi-gene sequencing assay.

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY Uterine fibroids are smooth muscle tumors that occur in >80% of Black women and 70% of white women by age 50 years. Fibroids cause heavy menstrual bleeding, pelvic pain or pressure, urinary and bowel dysfunction, infertility, and adverse pregnancy outcomes. Major surgery with hysterectomy and myomectomy is the most common fibroid treatment, but surgery generally requires 2-6 weeks of recovery with substantial time off work and the inability to perform usual activities. To avoid surgery, many women prefer medical therapy for fibroids, but few options are available. There are only two FDA approved oral medications to treat fibroids, GnRH antagonists that block gonadotropins and diminish ovarian estrogen production akin to menopause. These medications require concomitant use of estrogen and progestin “add-back” therapy to mitigate hot flashes and other side effects and risks of low serum estrogen. Many women aim to avoid this long-term hormone therapy or have contraindications to hormone use. New medications that alleviate fibroid symptoms but avoid low serum estrogen are needed to improve care for women with fibroids. Fibroids are hormonally responsive tumors that decrease in volume when deprived of estrogen. The ovary is the primary source of estrogen in premenopausal women, but fibroid cells also produce local estrogen through activity of the aromatase enzyme. Through both autocrine and paracrine action, estrogen produced by fibroids demonstrates local control over fibroid growth. Letrozole is an aromatase inhibitor (AI) that blocks estrogen synthesis within fibroid cells. Therefore, letrozole may decrease fibroid volume and improve symptoms. Low doses of letrozole will inhibit the modest aromatase activity within fibroids, but not significantly block the robust aromatase activity in the ovaries of premenopausal women. Letrozole may serve as a novel therapy that improves fibroid symptoms without adverse effects of low serum estrogen. Despite a biologic mechanism to support AIs as a fibroid treatment, clinical data is very limited. In a few small uncontrolled studies, fibroid volume decreased 35-55% during 8-12 weeks of treatment. We recently completed a pilot, randomized, placebo-controlled trial of letrozole. The letrozole group had greater improvement in fibroid symptoms and quality of life compared with the placebo during 2 months of treatment and reported few side effects. Building on this preliminary data, we propose a full scale randomized, blinded, placebo-controlled trial that is powered to detect clinically meaningful changes in fibroid symptoms and fibroid volume. We will enroll 140 racially and ethnically diverse premenopausal women randomly assigned to oral letrozole 2.5mg/day or an identical placebo for 3 months and assess clinical outcomes and the development of adverse events. We will also evaluate long-term letrozole use with an open-label follow-up phase for up to 6 months of letrozole therapy. This trial will provide gold standard evidence to evaluate the efficacy of a novel treatment for uterine fibroids that has significant advantages over existing medication.

NIH Research Projects · FY 2024 · 2023-09

PROJECT SUMMARY/ABSTRACT Head and Neck Cancer is a public health concern in the United States and a major challenge in oncology. Chemoradiotherapy has been mainly adopted to improve survival for patients with head and neck cancers. However, the benefit remains limited to patients with a high risk of complications, and the burden of toxicity in surviving patients with head and neck cancers is severe. Hyperthermia combined with other treatments, such as radiation, chemotherapy, and immunotherapy, has been shown in clinical trials to increase response for head and neck cancers, but success is highly dependent upon the delivered thermal dose distributions. Hence, this technology requires spatially controllable heat delivery and adequate temperature monitoring. MR-guided focused ultrasound (MRgFUS) can potentially be used to deliver hyperthermia. The focused ultrasound technique has been received much interest due to its completely non-invasive heat delivery with a high degree of spatial selectivity and dynamic control. With these inherent advantages, clinical MRgFUS systems have been developed and approved for thermal ablation treatments of various sites, such as the brain, uterine fibroids, prostate, pancreas, and bone metastases. However, the major technical challenges remain for MRgFUS hyperthermia delivery to head and neck cancers: There is a need for 1) optimizing sonication strategies for enhancing temperature distributions and delivering conformal hyperthermia to HNC, and 2) advanced MR imaging methods for accurate temperature imaging with significantly reduced artifacts and rapid MR imaging to evaluate tissue response. The proposed project will develop methods for more effective hyperthermia delivery under magnetic resonance imaging control to increase response rate and survival for patients with superficial and deep tumors in the head and neck, such as squamous cell carcinoma, melanoma, and soft tissue sarcoma. In this project, the specific aims are 1) to develop practical and optimal sonication strategies for conformal delivery of hyperthermia to target head and neck cancer, 2) develop robust real-time MR thermometry methods for temperature imaging with a minimal artifact in the complex anatomy of the head and neck, and 3) develop real-time simultaneous MR imaging of temperature and tissue response during hyperthermia (R00 Phase). These technical developments will advance MRgFUS-mediated hyperthermia delivery to head and neck cancers and the training plan includes opportunities to apply the new knowledge. I have assembled an outstanding team of renowned mentors (Drs. Diederich, Larson, and Payne) and specialized advisors (Drs. Ozhinsky, Bucknor, and Chan) with expertise in MR-guided Focused Ultrasound therapy, clinical head and neck cancer treatment, quantitative MRI, and MR thermometry. The proposed award will provide me with the necessary experiences to become an independent, transdisciplinary, and translational scientist dedicated to image-guided thermal therapy and therapeutic ultrasound.

NIH Research Projects · FY 2025 · 2023-09

ABSTRACT Alzheimer’s Disease and Alzheimer’s Disease Related Dementias (AD/ADRD) represent the most common causes of dementia (cognition decline that leads to a loss of independent function) among adults. Approximately 1 in 9 Americans age 65 and over (11%) lives with dementia from AD, representing approximately 6.5 million people; prevalence rates increase when including related dementias. There are currently no treatments that prevent or halt the progression of dementia, although the 6 FDA-approved medications can help slow symptoms. Living with AD/ADRD is associated with loss of independence, disability, poor health and well-being (morbidity), and increased mortality. The care needs for people living with dementia (PLWD) are complex. Providing care is associated with high costs and considerable caregiver burden. There are also considerable health disparities for PLWD from diverse racial/ethnic backgrounds. Thus, there is an immediate need to identify novel, accessible, culturally relevant, and cost-effective approaches to reduce the burden and improve quality of life for older adults living with these common neurodegenerative diseases without a cure. We have known for over 35 years that people living with AD can meaningfully engage with music, even into the late stages. An increasing number of studies conclude that PLWD who participate in music therapy or music-based interventions (MBIs) experience improvements in quality of life, and emotional well-being as well as decreases in behavior issues, anxiety, and depression. Despite these promising findings, the number of studies is small, many are low quality, samples lack diversity, and the underlying mechanisms are not yet well understood. In addition, little is known about potential benefits of MBIs for people living with related dementias (ADRD). Studies using the NIH Stage Model and Science of Behavior Change methods can help improve study quality and provide a framework for developing and testing MBIs in the context of AD/ADRD. Moreover, use of novel mobile body-brain imaging (MoBI) technologies could help elucidate how MBIs affect various functions of the brain (including neuromodulation) and body in real-world settings. To accelerate rigorous research about the mechanisms by which MBIs impact health and well-being for adults with AD/ADRD, we will create the multi-disciplinary Research Network to Accelerate Mechanistic Studies of Music for Dementia (RN-MusD). The Network, representing experts from cognitive neuroscience, music therapy, biomedical and neural engineering, geriatrics, and statistics will create three core nodes at the University of California San Francisco, University of Houston, and Arizona State University. The Network will accelerate rigorous, multi-disciplinary, and mechanistic studies of MBIs in the context of AD/ADRD by accomplishing the following aims: (1) build a collaborative Network that will grow over time; (2) promote multidisciplinary collaborations through a pilot project program, leveraging MoBI and research mentoring, and (3) disseminate resources generated by our Network to sustain impact.

NIH Research Projects · FY 2025 · 2023-09

Neurodegenerative diseases are one of the greatest threats to modern health, and there are few treatments available for these complex and progressive diseases. This proposal investigates the basic biology underlying progranulin (PGRN), a lysosomal protein whose haploinsufficiency causes the Alzheimer’s Disease-Related Dementia (ADRD) frontotemporal dementia (FTD) [1]. While PGRN deficiency is one of the leading genetic causes of FTD, its function is not completely understood. To further our understanding of the causes and pathophysiology of FTD, it’s imperative to determine the endogenous functions of PGRN in the lysosome. PGRN is inextricably linked with another lysosomal pro-protein, prosaposin (PSAP), which is also implicated in progranulin-FTD [2]. PSAP is cleaved into sphingolipidase activator proteins called saposins, which catalyze sphingolipid metabolism in the lysosome. Loss of saposins perturbs lysosomal lipase activity, resulting in accumulation of sphingolipids and lysosomal dysfunction. Interestingly, perturbed sphingolipid metabolism has recently emerged as a critical risk factor for the onset and progression of ADRDs, including FTD [3-11]. Moreover, PGRN has been implicated in ADRD-related dysregulation in lipid homeostasis [12, 13], however, the underlying molecular mechanisms are unknown. Together, this suggests a pathway where the FTD-risk factor PGRN regulates lipid homeostasis via PSAP, which in turn contributes to ADRD pathophysiology. Despite the clear role for saposins in sphingolipid metabolism, the mechanism by which saposins are released from PSAP, and thus available to modulate sphingolipidases, sphingolipid homeostasis, and downstream lysosomal function, is not well understood. I hypothesize that PSAP cleavage into saposins is subject to regulation by lysosomal enzymes, the FTD-risk factor PGRN, and age, and that regulation of PSAP cleavage plays a crucial role in lipid homeostasis and lysosome function. To test this hypothesis, I propose a several innovative experiments with recombinant human proteins in vitro, human cell lines, and in in vivo behavioral and imaging techniques in Caenorhabditis elegans. I will utilize well-established protocols for both in vitro protease function and C. elegans phenotypes alongside newly developed techniques to measure lysosomal pH and lipid content in vivo. I will determine how PGRN regulates the cleavage of PSAP into saposins, if PGRN influences lipid homeostasis via its regulation of PSAP, and how altered lipid homeostasis impacts lysosomal function. Successful completion of this proposal will fill a gap in knowledge about the basic biology underlying the relationship and function of the FTD-risk factors PGRN and PSAP in the lysosome and elucidate a critical link between PGRN and altered lipid homeostasis in ADRD via the lysosomal function of PSAP. Successful completion of this proposal will expand our understanding of FTD by generating fundamental knowledge on the endogenous function of the endolysosomal system in protein and lipid homeostasis, which could be the key to the generation of novel diagnostic techniques, prevention strategies, and treatments for FTD, AD, and other ADRDs. Key Words: FTD, progranulin, neurodegeneration, aging, lysosome, sphingolipid, prosaposin, C. elegans

NIH Research Projects · FY 2025 · 2023-09

Despite increased awareness and provision of resources, there remain challenges in developing a workforce in science, engineering, technology, and mathematics, medicine (STEMM) that broadly represents the US population. There is a “leaky pipeline” in which there is attrition at each stage of training and career advancement. Prior studies showed that diversity within teams has many benefits, including innovation and strong information processing. Several conceptual frameworks have identified social supports that are mediated by enhanced self-efficacy and scientific identity to improve persistence to pursue a career in a STEMM field. Career development programs that offer evidence-based interventions that are rooted in these empirical models may be an individual-level approach to ensure the success of the pipeline of researchers in biomedical sciences. The purpose of this project, in partnership with NIDDK, is to offer a career development program to early career trainees who are funded by NIDDK grants. We hypothesize that, over five years, program scholars will report a strong sense of belonging and self-efficacy in the field; sustain and advance in their current career trajectory; and obtain the next appropriate level of funding to establish their independent program of research. The potential impact of this project is to ensure the success of early- and mid-career researchers who represent all US population groups who conducting research relevant to the priority areas of NIDDK. Specifically, this project targets individuals who are at the transition from culmination of training or early career investigators to established researcher. The long-term potential implications include the potential to realize both direct benefits for program scholars as well as broader indirect effects for future researchers

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY/ABSTRACT This is a Beeson K76 career development award for Dr. Lindsay Hampson, a clinician investigator with a background in ethics, health services research, and stress urinary incontinence (SUI). Dr. Hampson is pivoting her career towards aging, with a goal of becoming a national leader in geriatric urology research focused on achieving goal-concordant care for older adults with urologic issues that affect quality of life (QOL) through reducing treatment disparities and improving treatment decision-making. This proposal seeks to improve goal-concordant management for post-prostatectomy SUI among older adults by: 1) identifying drivers of disparities in the care of older post-prostatectomy men, 2) determining treatment preferences and priorities of this patient population, and 3) promoting individualized evaluation and treatment decision-making in the context of geriatric-informed health and values. Significance: Post-prostatectomy SUI significantly impacts QOL, disproportionately impacting older men. Despite a focus on reducing treatment of prostate cancer, one quarter of men 65-75 years of age diagnosed with prostate cancer will still undergo prostatectomy. An estimated 25-30% of men are using pads, diapers, or complaining of bothersome incontinence beyond one year following prostatectomy, and these rates likely represent underestimation of continence rates in older men. SUI surgery has been shown to result in near-term QOL improvements with high satisfaction rates, yet is severely underutilized and delayed, and men facing treatment decisions have substantial decisional regret. In Aim 1’s national cohort study using Veterans Affairs and Medicare data, we aim to identify factors associated with post-prostatectomy SUI under-treatment and treatment delays among older men. In Aim 2’s discrete choice experiment survey of older post-prostatectomy men, we aim to identify patient-centered SUI treatment priorities and understand how these preferences vary based on characteristics associated with access to care. These data will be utilized to develop an Incontinence Post-Prostatectomy Assessment & Decision Support (I- PADS) tool which will be evaluated in Aim 3 through a mixed methods study and feasibility/acceptability trial. Mentoring team: Dr. Hampson’s exceptional multidisciplinary mentoring team is led by Dr. Louise Walter, an internationally recognized expert on individualized decision making for in older adults. This award will support Dr. Hampson’s transition to aging research through dedicated training in 1) conducting national cohort studies of older adults, 2) developing expertise in measuring treatment preferences, 3) implementation science theory and methods to implement interventions for older adults, and 4) leadership in geriatric urology to become a leader in goal-concordant urologic care among older adults by reducing treatment disparities and improving treatment decision-making. Next Steps: These results will serve as the foundation for a multicenter hybrid implementation-effectiveness study of the I-PADS tool to test its effect on addressing disparities in SUI surgery, decisional and treatment regret, and receipt of goal-concordant care for post-prostatectomy SUI.

NIH Research Projects · FY 2025 · 2023-09

PROJECT ABSTRACT Program Overview This is a single consolidated U2C/TL1 training program (the Learners to LeAders in benign Urology, benign Nephrology, and non-Cancer Hematology [LAUNCH] Program) that seeks to integrate, expand, and transform kidney, urologic, and hematologic (KUH) biomedical research training in Northern California. Based at four institutions with outstanding research resources and training accomplishments—University of California San Francisco (UCSF), University of California Berkeley (UC Berkeley), University of California Davis (UC Davis), and Stanford University—we propose an innovative approach to train 22 (4 pre- and 18 post-doctoral) trainees annually across adult and pediatric KUH disciplines. We will identify and recruit the most promising and diverse group of trainees to enable them to conduct KUH research and provide these LAUNCH Program trainees with outstanding basic, translational, or clinical research training. Our overall goal is to establish a unified training program that promotes interdisciplinary collaboration and training of the most promising junior investigators across our four institutions. Thus, we expect that the LAUNCH Program will graduate scientists who are well- trained, able to compete successfully for research funding, and able to think creatively and collaboratively to generate novel and impactful science. The LAUNCH Program will be led by the U2C multi-PI’s (Drs. Elaine Ku, Marshall Stoller, and Kathleen Sakamoto) as well as the TL1 multi-PI’s (Drs. Chi-yuan Hsu, Philip Beachy, and Mark Walters), each of whom possess complementary expertise in research and research training within the disciplines of nephrology, urology, and hematology. The world-class training faculty whom we have included in our program were selected not only based on their own scientific and scholarly achievements but also their track record of mentorship and commitment to training. The LAUNCH Program is modeled after several highly-successful training programs at our institutions that have trained numerous exceptional scientists from a wide range of disciplines using a team science approach.

NIH Research Projects · FY 2025 · 2023-09

Abstract The overall goal of this project, titled “De Confianza: Creating Medical Trust with Latinx Communities,” is to increase Medical Trust to lessen HIV prevention and treatment inequities experienced by Hispanic/Latino Gay, Bisexual and Other Men Who Have Sex with Men (HLMSM). The specific aims include: Aim 1. Identify main drivers of medical mistrust and trust among HLMSM. Aim 2. Adapt or develop an intervention plan by uncovering existing, effective, San Francisco Bay Area interventions aimed at building trust to improve access to, utilization of, and retention in HIV prevention and care services. Aim 3. Implement and evaluate a multilevel intervention to increase medical trust and improve access to, utilization of, and retention in HIV prevention and care services. The project will be based in the San Francisco Bay Area, in two priority jurisdictions of Phase I of the Ending the HIV Epidemic initiative: San Francisco and Alameda Counties. The San Francisco Bay Area has a substantial percentage of Hispanic/Latino population and the highest proportion of gender and sexual minority people in the country. Our team, including our community partner (AGUILAS), is fully bilingual (Spanish and English) and bi-cultural, with strong roots in the Bay Area and a solid record of HIV prevention work with HLMSM communities. While addressing medical mistrust in the context of HIV prevention and care is a multifactor and multisectoral effort, this project could have a significant impact given depth of the expertise in our team and the diversity of the population studied. The findings would inform multi-level interventions in settings with a significant proportion of Latinx and MSM population.

NIH Research Projects · FY 2025 · 2023-09

SUMMARY/ABSTRACT The overarching goal of this R25 Program is to leverage our rich institutional environment to iteratively develop the materials and curricula necessary to train the first generation of neurologists how to systematically advance both neurological care and research by prioritizing sex and gender considerations. From neurodevelopment to neurodegeneration, sex and gender influence the risk and course of neurological diseases. It is essential that neurologists provide care that is informed by a patient's reproductive goals and experiences, hormonal transitions and treatments, and their gendered societal roles. However, we identified a significant national training gap in these critical topics at all levels of neurology education and related key knowledge gaps in the scientific literature that hinder the growth of this field. The SAGE (Sex- and Gender-Enriched) Neurology Program at UCSF is designed to galvanize and integrate emerging clinical, educational and research efforts to fill these important gaps through three key aims. These curricula and educational materials will initially target UCSF neurology residency trainees (15 annually for a total class of 45) and UCSF medical students (165 annually) during core and/or selective neurology clerkships, as well as clinical fellows (20 annually). The approach to curriculum development will be guided by the UCSF Center for Faculty Educators, using evidence- based principles to optimize motivation, experiential learning, collaborative learning, and retention in adult mixed- level learners. Our first objective (Aim 1) is to develop and implement a core best practices clinical curriculum that accelerates the translation of SAGE principles into neurology clinical practice using both a core didactic for all trainees, and a week-long selective for any interested trainee. Trainee participants' core clinical competency and self-efficacy in providing neurological care informed by a patient's sex and gender will be systematically evaluated. Our second objective (Aim 2) is to develop and implement a core research curriculum to train the next generation of clinician-scientists to conduct and interpret neuroscience research by leveraging SAGE principles, whether bench or bedside. We will develop and pilot a tool to apply a sex/gender lens to analyzing the design and interpretation of basic, translational and clinical studies. We will evaluate learners' competency at using this tool. Our third objective (Aim 3) is to promote active generation of new knowledge by pairing interested trainees with a faculty mentor to develop and lead a quarterly interprofessional mentored inquiry workshops designed to identify new areas of inquiry and create interprofessional research teams. Teams will then distil key points from each session into publications and novel curricular materials that serve as evaluative benchmarks of success. SAGE Neurology will transform the training of clinicians and clinician-scientists through the continued sustainable long-term development, evaluation, and refinement of innovative, clinically-relevant curricular materials. Curricular products will then be disseminated widely across UCSF departments, national academic neurology programs, national neurological associations and the broader ORWH community.

NIH Research Projects · FY 2025 · 2023-09

Project Summary Dr. Gabriel Chamie is an infectious diseases physician and Associate Professor of Medicine in the Division of HIV, Infectious Diseases and Global Medicine at the University of California, San Francisco (UCSF). His research has focused on developing effective approaches to promote community-based diagnosis of HIV, TB and SARS-CoV-2, and engagement in HIV and TB prevention and treatment, with a more recent focus on persons with unhealthy alcohol use in East Africa. He has over a decade of experience mentoring numerous early-stage investigators (ESI), including pre- and post-doctoral investigators and junior faculty, and now seeks the protected time of a K24 award to focus greater attention and time on mentoring, mentorship training and expanding his research program at the intersection of HIV and alcohol use. In this application, Dr. Chamie proposes a comprehensive mentorship, mid-career development, and research plan to address the challenge of reaching and engaging populations at increased risk of HIV in biomedical HIV prevention from alcohol drinking venues in East Africa. Despite a growing number of efficacious biomedical HIV prevention options, a major challenge remains reaching persons at highest risk of HIV – such as adults at alcohol drinking venues – who do not routinely engage in medical care, to overcome barriers to HIV prevention initiation and retention, including alcohol use. To further develop and expand his patient-oriented research (POR) program and mentoring, he proposes mid-career training in methods that support the application of quantitative preference elicitation and human-centered design for intervention development, and additional training in mentorship. Leveraging the infrastructure of his recently awarded R01 (the OPAL trial) and the ongoing SEARCH- SAPPHIRE trial, Dr. Chamie proposes research in this application to: a) elicit preferences for biomedical HIV prevention service delivery among adults at high risk of HIV who attend drinking venues in rural Kenya and Uganda, b) to adapt the SAPPHIRE trial’s clinic-based “dynamic PrEP/PEP choice” intervention for community- based delivery to this population at or near drinking venues, and c) to assess uptake, retention, and adherence to biomedical prevention in a pilot trial of community-based biomedical prevention delivery among adults who attend or work at drinking venues in rural Kenya and Uganda. With the guidance of an experienced senior mentorship team, Dr. Chamie will utilize multiple ongoing research projects, and long-standing research collaborations between UCSF and Makerere University in Uganda and the Kenya Medical Research Institute in Kenya, to provide mentees with a robust infrastructure on which to develop their research interests and support US-East African ESI partnerships in POR. The K24 award is instrumental to supporting him in achieving his long-term goals of becoming a global leader in HIV and alcohol use research and mentoring future leaders in patient-oriented research from the US and East Africa.

NIH Research Projects · FY 2024 · 2023-09

Project Summary G protein-coupled receptors (GPCRs) comprise the largest family of signaling receptors in animals, and as such, they represent an important class of therapeutic targets. Following ligand binding and G protein activation at the plasma membrane, GPCRs undergo regulated endocytosis and sorting for recycling or degradation. Traditionally, studies of ligand-dependent GPCR signaling have focused on receptor-G protein coupling at the plasma membrane (PM). However, it is now clear that GPCRs can continue to signal from internal membrane locations and that the downstream responses elicited from intracellular signaling are distinct from those elicited from PM signaling. While the biochemistry of GPCR activation has been studied in detail, the organization and regulation of GPCR signaling in living cells remains an underexplored frontier. The proposed studies will investigate fundamental mechanisms underpinning spatiotemporal regulation of GPCR signaling and will provide key training to enable Dr. Blythe to become an independent leader in this emerging area of molecular and cellular physiology. The mentored phase of this project will be carried out at the University of California, San Francisco under the primary mentorship of Dr. Mark von Zastrow, a leader in the field of GPCR trafficking and signaling. The long-term goals of this work are to understand (1) how the subcellular localization of GPCRs and their associated proteins change in response to signaling and (2) how this cellular reorganization regulates their distinct downstream responses. The first two Aims will focus on receptor trafficking and signaling, defining the mechanisms by which unique endocytic (Aim 1) and recycling (Aim 2) pathways sculpt signaling by endogenously expressed GPCRs in a HEK293 cell model. In carrying out these experiments, Dr. Blythe will gain new experience in advanced imaging techniques, as well as in integral membrane protein biochemistry with the help of Dr. Aashish Manglik (collaborator). Aim 3 frames the biology in a broader perspective by asking how the dynamic subcellular localization of other proteins contributes to the spatiotemporal regulation of GPCR signaling. Using a novel proximity labeling approach under the mentorship of Dr. Nevan Krogan (co-Mentor) and Dr. Ruth Hüttenhain (collaborator), Dr. Blythe will map the changes in the proteomes of specific cellular compartments during the activation of the same model GPCRs and explore how these changes dictate signaling. The proposed work will enable a systems-level analysis of GPCR signaling that was not feasible with current approaches and provide an invaluable training opportunity for Dr. Blythe in mass spectrometry-based proteomics. In summary, this project will take advantage of the expertise of a diverse mentorship team and the world-class resources and facilities at UCSF to tackle fundamental questions in GPCR biology.

NIH Research Projects · FY 2025 · 2023-09

Project Summary/Abstract As a trauma surgeon-scientist and early stage investigator in the 5th year of an NIGMS mentored career development award for the translational study of post-injury platelet function, I have developed expertise, infrastructure, and made significant contributions to demonstrating that early platelet dysfunction after injury is common, driven by changing physiology, and associated with later development of organ failure. This is important because injury remains a leading cause of death worldwide, but advances in initial care have shifted the burden of injury-related morbidity and mortality from early after injury to later, leaving two important challenges:1) identifying injured survivors at highest risk of developing initial and sustained organ failure leading to long-term morbidity and late mortality, and 2) discovering novel targets for early therapies to prevent development of organ failure after injury. Platelets contribute to organ failure through pathobiology in thromboinflammation. In similar diseases, platelet transcriptomics has improved mechanistic understandings and driven exploration of platelet-based therapeutics. Platelet megakaryocyte derived ribonucleic acids (RNAs) are stable in health, but modified by physiological signals in disease. Importantly, platelets are anucleate and lack RNA synthesis, thus providing the cleanest transcriptomic view of RNA modification in human biology. As such, my proposal seeks to re- imagine how we understand, measure, and intervene on early alterations in platelets after injury by focusing on the platelet transcriptome to explore prediction and prevention of organ failure among patients who initially survive their injuries, and to identify RNA modification targets that can be tested in model systems by addressing these knowledge gaps: 1) Identify the early platelet transcriptional landscape of severe injury and its relationship to development and resolution of organ failure in longitudinal patient studies; 2) Define the effect of platelet RNA modifications on platelet function in samples from patients with severe injury and in ex vivo modified healthy platelets; 3) Develop ex vivo and in vitro model systems to manipulate clinically relevant platelet RNA modifications as ultimate conduits to in vivo models and clinical testing. I will use feasible (next generation sequencing, ribosome footprint profiling), and novel (sub-population sequencing, ex vivo transgenic platelet model systems) methods to identify novel molecular biomarkers and preventative targets of development of organ failure after injury, and innovate our understanding of physiologically driven RNA modification through the ideal anucleate biology of platelets under the optimal acute physiologic changes of injury. This K to R award transition proposal is NIGMS mission-focused by using basic research to increase understanding of biological processes and lay the foundation for advances in disease diagnosis, treatment, and prevention within the area of ‘Injury’ (Pharmacological and Physiological Sciences Branch).

NIH Research Projects · FY 2024 · 2023-09

ABSTRACT/SUMMARY Hazardous alcohol use and binge drinking, the deadliest form of excessive alcohol use1-3, are substantially more prevalent among sexual and gender minority adults compared to their cisgender straight counterparts4-11. Minority stress from structural stigma drives sexual and gender minority health disparities12-16, but its potential effect on binge drinking and hazardous alcohol use has yet to be rigorously examined. Structural stigma is potentially amenable to intervention by equality-promoting policies at the state level that explicitly name sexual and gender minority people as protected classes in employment, housing, public accommodations, and other essential services17. The extent to which changes in state equality-promoting policies relate to changes in binge drinking and hazardous alcohol use for sexual and gender minority adults compared to their cisgender straight counterparts is unknown and the focus of the proposed study. This study aims to evaluate differential effects of state equality-promoting policies (Aim 1) and key policy domains (Aim 2) on binge drinking and hazardous alcohol use among sexual and gender minority adults. Non- randomized variation in state equality-promoting policies necessitates the application of advanced econometrics methods. To rigorously estimate effects and make causal inferences, triple differences models and identifiability assumptions will be specified to analyze nationally representative data18 on over 72,000 sexual and gender minority adults linked with indices of state equality-promoting policies19 from 2014-2022. The landscape of equality-promoting policies for sexual and gender minority people is ever evolving. This study will offer a timely evidence base to inform needed structural interventions that reduce alcohol-related morbidity and mortality among sexual and gender minority populations. With support from a premier mentorship team, the applicant will build skills in (1) advanced econometrics methods for causal inference, (2) alcohol research and social determinants of harmful alcohol use, and (3) identification of relevant and actionable social policies that influence sexual and gender minority health. Achievement of these training goals will launch the applicant’s career as a successful, independent researcher.

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY/ABSTRACT Sacrococcygeal teratomas (SCTs) are the most common tumor in newborns, have significant perinatal morbidity and mortality, a 35% rate of recurrence, and lack good biomarkers to predict recurrence risk. SCTs are believed to originate from apoptosis-resistant embryonic gamete-precursors known as primordial germ cells (PGCs). In mice, PGCs can revert to pluripotent cells called embryonic germ cells (EGCs) when exposed to a specific cocktail of growth factors, however, establishing an in vitro model of human EGCs has been technically and ethically challenging. The proposed Research Training Plan will leverage human induced pluripotent stem cell derived PGC-like cells (PGC-LCs) and EGC-like cells (EGC-LCs), single cell multi-omic technologies, and an innovative mouse embryonic injection model to study the process by which PGCs lead to teratoma formation. The central hypothesis is that SCTs arise from apoptosis-resistant ectopic PGCs that have been reverted to a pluripotent state resembling PGC to EGC reversion, and the most aggressive SCTs have tumor environment interactions that maintain these pluripotent cells. In Aim 1, the trainee, MD PhD candidate Ernesto Rojas, will define the chromatin and transcriptional landscape of PGC-LC to EGC-LC reversion with and without apoptosis- resistance. Then, using the in utero injection model he developed, he will characterize the differences in tumorigenic potential between PGC-LC and EGC-LCs, with and without inhibition of apoptosis. In Aim 2, the candidate will identify and modulate pathways maintaining pluripotency in SCTs. He will use single-cell transcriptomics to identify pathways that may modulate the tumorigenicity of EGC-LCs, and will functionally validate these pathways using the PGC-LC to EGC-LC reversion model and the transplant model to find those pathways that improve maintenance of EGC-LCs. The results of Aim 1 will provide the first roadmap of the changes in chromatin and gene expression that occur during reversion from germline to pluripotency to teratoma. The results of Aim 2 will provide potential biomarkers and targetable pathways for future clinical use in SCTs. These studies will identify the important developmental trajectories that occur with reversion from PGC to pluripotency, improve insight to aid biomarker development for recurrences of PGC-derived tumors, and provide potential targetable pathways to treat the most aggressive tumors. To successfully complete this project, the candidate will work with Drs. Diana Laird (sponsor) and Tippi Mackenzie (co-sponsor). Dr. Laird is a germ cell expert and Dr. Mackenzie is a fetal surgeon. Together with the candidate, they have established a training plan for him to gain new knowledge and skills in developmental and stem cell biology techniques and bioinformatic analyses, as well as clinical training, and professional development. Through the collaborators named in this proposal, the collaborative environment and excellent infrastructure at UCSF, and with the support provided by this fellowship, the candidate will be well equipped to investigate the role of development on early peri-natal health and advance his career as a surgeon-scientist.

NIH Research Projects · FY 2024 · 2023-09

PROJECT SUMMARY/ABSTRACT Despite the prevalence of prostate cancer worldwide, we lack an understanding of the genetic events that drive tumor initiation or drug resistance. Only a few genetic models exist, leaving hundreds of recurrent mutations unaccounted for, and most studies interrogate gene function by overexpression or knockout rather than studying the mutational variants present in disease. Better understanding of the mutations driving tumor initiation and drug resistance could allow us to screen for precancerous lesions or prevent fatal disease progression, greatly relieving the global burden of disease. Therefore, there is an urgent need for a new functional genomic approach to enable the functional study of multiple genetic variants per cell to identify mechanisms of tumor initiation and drug resistance. We have developed such a system in mouse prostate organoids by knocking out the tumor suppressor Pten and the mismatch repair gene Msh2 to induce the accumulation of point mutations and indels. This system has allowed us to interrogate which mutations complement PTEN loss to drive tumor initiation and drug resistance in vivo. We have discovered that hotspot mutations in IRS4 and CDK4 are uniquely enriched during tumor initiation and drug resistance, respectively. Thus, I propose to determine the mechanisms by which IRS4 and CDK4 gain of function mutations complement PTEN loss to drive prostate cancer initiation and drug resistance, respectively. In my first aim, I will test the necessity and sufficiency of IRS4 gain of function to drive tumor initiation through MAPK activation and downstream transcriptional alterations. For my second aim, I will test the necessity and sufficiency of CDK4 gain of function to drive drug resistance through cell cycle dysregulation and investigate the reversibility of this phenotype in patient-derived organoids. My sponsor Rohit Bose, MD, PhD, has extensive experience in genetic and transcriptional network alterations underlying prostate tumor initiation. My co-sponsor Kevin Shannon, MD, has renowned experience studying MAPK circuitry and drug resistance in cancer. Additionally, I have secured scientific support and career mentorship from a respected and prolific cadre of investigators with complementary expertise, Dr. Felix Feng (prostate cancer genomics), Dr. Rahul Aggarwal (drug-resistant tumor samples), Dr. Catherine Smith (cell cycle dysregulation and tumor evolution), Dr. Franklin Huang (prostate cancer genomics and health disparities), and Dr. Hani Goodarzi (multi-omics and tumor evolution). Concurrently, I will continue bimonthly clinical preceptorships with Drs. Aggarwal, Bose, and Feng at the UCSF Helen Diller Family Comprehensive Cancer Center. Overall, the proposed work will further our understanding of tumor initiation and drug resistance in prostate cancer, laying the groundwork for improved detection and treatment. Moreover, this fellowship will foster my training in cancer biology and genetics, supporting me through combined MD/PhD training towards a career as an academic medical oncologist studying tumor evolution and drug resistance in prostate cancer.

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY Debilitating pain, a hallmark of tissue injury and neuropathy, is an unmet clinical challenge particularly in musculoskeletal diseases, such as heterotopic ossification (HO). HO can occur following orthopedic surgery and traumatic injuries, manifests with pathological bone formation in muscle and connective tissues. However, little progress has been made in developing effective treatments for either HO or its associated pain. Persistent neuropathic pain can arise from hyperexcitability of sensory neuron nociceptors in dorsal root ganglia (DRG), which release neuropeptides, interact with immune cells, and modulate the host response after injury to innervated tissues including bone and muscle. A critical link between bone homeostasis and neuropathic pain has been suggested by the impaired ossification and bone loss in mice lacking Trpv1+ nociceptors. Although the mechanisms that underlie HO formation or HO related pain are poorly understood, important insights derive from studies of an hereditary HO subset, namely Fibrodysplasia Ossificans Progressiva (FOP). FOP is commonly caused by an arginine206 to histidine gain-of-function point mutation in the BMP type I receptor (ACVR1, also known as ALK2) in 97% of patients. We recently found that adult patients with FOP have baseline heat and mechanical hypersensitivity, in the absence of an inflammatory flareup. Utilizing FOP patient induced pluripotent stem cell (iPSC)-derived nociceptive sensory neurons (iSNs), we demonstrated that ACVR1R206H is both necessary and sufficient for the hyperexcitability of nociceptors, a hallmark of neuropathic pain. To determine whether neuronal ACVR1 hyperactivity is also relevant to more common neuropathic pain conditions, we conditionally expressed activating Acvr1R206H in sensory neurons of non-FOP transgenic mice. This led to a remarkable recapitulation of the mechanical and heat hypersensitivity in patients with FOP. As Acvr1 expression is profoundly increased in axotomized DRG neurons in a traditional preclinical model of neuropathic pain produced by spared nerve injury (SNI), we found that inhibiting injury-induced active neuronal ACVR1 signaling in the DRG by intrathecal (IT) injections of a small-molecule ACVR1/ALK2 kinase inhibitor prevented injury-induced mechanical hypersensitivity and, most importantly, reversed persistent pain in the mouse SNI model. Based on our observation that trauma-induced HO triggered massive nociceptor sprouting at the injury site in a preclinical mouse model of FOP, we further hypothesize that active ACVR1 signaling in sensory neurons is a critical link between neuropathic pain and HO. Together, aiming to elucidate the mechanisms downstream of active ACVR1 signaling, mechanisms that may be shared by other chronic pain and musculoskeletal injury conditions; while developing new treatment strategies, we will define molecular targets of sensory neuron-specific ACVR1 that contribute to neuropathic pain (Aim 1); validate if inhibiting peripheral neuronal ACVR1 reduces hypersensitivity (Aim 2); and determine if sensory neuron-specific ACVR1 contributes to injury-induced HO (Aim 3).

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY Rigorous data from our lab and others indicate that the gut microbiome may an underappreciated contributor to inter-individual variations in cancer drug efficacy and side effect profiles; however, we currently lack the mechanistic insights and data from preclinical mouse models necessary to inform ongoing studies in cancer patients. We selected fluoropyrimidines, including 5-fluorouracil (5-FU) and its prodrug capecitabine (CAP), as an initial test case due to their critical role in colorectal cancer (CRC) therapy, increasing oral administration, highly variable pharmacokinetics, and unexplained differences in efficacy and toxicity. We propose a series of in vitro and mouse studies to dissect the human gut bacterial species, genes, and enzymes responsible for the metabolism of 5-FU (Aim 1) and CAP (Aim 2), including their downstream consequences for drug pharmacokinetics (PK) and pharmacodynamics (PD). Our overarching hypothesis is that the oral bioavailability and therapeutic effects of fluoropyrimidines are influenced by pathways for drug metabolism encoded by diverse human gut bacterial species. In Aim 1, we will identify and characterize the primary gut bacterial taxon responsible for 5-FU inactivation through a combination of biochemical and cell-based assays coupled to studies in gnotobiotic and xenograft mouse models. Based on our Preliminary Results, we hypothesize that Anaerostipes is the primary gut bacterial genus responsible for inter-individual variations in the metabolism of 5-FU. In Aim 2, we seek to discover the bacterial enzymes responsible for the activation of CAP to 5-FU, motivated by the surprising finding that E. coli can activate CAP leading to reduced bacterial growth at high concentrations. We hypothesize that E. coli catalyzes a 3-step metabolic pathway that mirrors the mammalian conversion of CAP to 5-FU. Our results in Aim 1 will provide a valuable proof-of-principle for dissecting the conservation and redundancies in clinically relevant microbial biotransformations, helping to move beyond studies of model gut bacteria to identify the most translationally relevant species. Aim 2 is potentially paradigm-shifting in that it would provide definitive evidence for CAP bioactivation outside of hepatocytes and cancer cells, creating new opportunities to improve treatment outcomes and study the physiological role and broader impacts of this metabolic pathway. Taken together, this research plan emphasizes the conservation of the pathways for metabolism of therapeutics across domains of life, highlighting the need to distinguish the relative contributions of human and microbial cells to drug disposition, efficacy, and side effect profiles. Due to our focus on drugs used as current standard of care and naturally occurring bacterial species prevalent in the human gut microbiome, this preclinical research program has clear translational relevance and is highly synergistic with ongoing clinical studies of cancer patients conducted by our team and the broader microbiome field.

NIH Research Projects · FY 2024 · 2023-09

SUMMARY Non-alcoholic fatty liver disease (NAFLD) is a spectrum of disorders initiated by steatosis that can progress to nonalcoholic steatohepatitis (NASH) and cirrhosis. Although it is the leading cause of liver disease in the US, there are no targeted therapeutic interventions, highlighting the critical need for identifying molecular processes underlying its pathology. Transmembrane protein 55B (TMEM55B) is a PI(4,5)P2 phosphatase located on the lysosome that has been shown to impact lysosome levels and localization. In preliminary studies, we found that TMEM55B ASO treatment caused hepatic steatosis in C57BL/6J mice after 6 weeks on western diet, while TMEM55B knockout mice developed NASH after 12 weeks on a high-fat, cholesterol and fructose supplemented (GAN) diet. We have identified several effects of TMEM55B knockdown that can promote NAFLD: 1) accumulation of lipids within lysosomes, indicative of impaired fatty acid (FA) mobilization, 2) impaired mitochondrial FA oxidation together with reduced mitochondrial volume, mitochondrial fragmentation, and increased oxidative stress; and 3) in vivo inhibition of hepatic triglyceride secretion. The lysosome plays a critical role in sorting and processing lipids, where proper lysosome motility is essential for their ability to mobilize FA from lipid droplets and maintain mitochondrial homeostasis. TMEM55B plays a key role in regulating lysosomal positioning, thus our central hypothesis is that loss of TMEM55B promotes NAFLD onset and progression through lysosomal effects on hepatic FA mobilization and trafficking, mitochondrial FA oxidation, and triglyceride secretion. In Aim 1, we will determine whether TMEM55B impacts FA mobilization and mitochondrial function through its ability to impact lysosomal localization. We will also examine the impact of TMEM55B on mitochondrial morphology and dysfunction. Hepatic triglyceride (TG) is primary secreted within VLDL, which is generated through a multi-step process of lipidating nascent APOB with FA mobilized from lipid droplets. In Aim 2A we will test whether TMEM55B knockdown prevents lipidation of nascent VLDL and test the dependency of these effects on the lysosome. Men are well-known to have higher NAFLD risk than pre-menopausal women, however the basis for this sex difference is poorly understood. We found that TMEM55B knockdown caused steatosis in male, but not female, mice, and that loss of hepatic TMEM55B inhibited TG secretion to a much greater degree in male versus female mice. The sex-dependent differences in TG secretory defects were attributed to differences in sex hormones. In Aim 2B we will evaluate the interaction between TMEM55B and sex hormones on TG secretion in male and female mice, and in estrogen receptor knockout mice. Finally, in Aim 3 we will evaluate the effect pharmacologic and genetic inhibition of TMEM55B on the development and progression of NAFLD. Understanding the mechanism(s) by which loss of TMEM55B impacts multiple critical axes of FA metabolism through the lysosome can yield novel insight into factors contributing to NAFLD.

NIH Research Projects · FY 2025 · 2023-09

ABSTRACT Rates of cirrhosis from nonalcoholic steatohepatitis (NASH) are rapidly rising in young adults, and given limited therapies and the heterogeneity of affected individuals, there is an urgent and unmet need to identify tailored therapeutic targets for at-risk young populations. Androgens may reflect such target for the 10-15%, or nearly 10 million reproductive-aged women with Polycystic Ovary Syndrome (PCOS). PCOS is typically marked by elevated androgens, and over 50% of these women have NAFLD. We have shown PCOS to increase the risk of prevalent NASH and advanced NASH fibrosis, which occurs at a younger age than in non-PCOS controls. High androgens may explain their observed “head start” in disease severity, as our cross-sectional data from young women without PCOS found higher (though normal range) testosterone levels to be associated with NASH fibrosis. Whether elevated androgens underlie the risk of liver injury in PCOS, and the potential mechanistic pathways by which this occurs, are not known. Our findings would support androgen receptor antagonism as a potential therapeutic target for the large population of women with PCOS and liver disease. Our central hypothesis is that androgens promote liver injury and NASH progression in PCOS, which occurs through aberrant lipid activity (including lipotoxicity and dysregulated de novo lipogenesis), in part from androgenic effects on visceral fat. Exogenous androgen use in women does increase visceral fat, which in turn promotes NASH through several pathways, including production of lipotoxic lipid species. Androgens are also linked to dysregulated branched-chain amino acid metabolism in PCOS, which is relevant as co-investigators on our team have discovered an enzymatic imbalance that leads to dysregulated hepatic de novo lipogenesis and NASH, and is reflected by serum levels of branched-chain amino and ketoacids. Building upon these data, we propose a 2-center (UCSF and Duke) longitudinal study of 150 reproductive- aged women with NASH (125 PCOS and 25 non-PCOS controls) to determine the influence of androgens on liver injury and progression in PCOS and the mechanistic contributions of visceral adiposity (Aim 1) and aberrant lipid metabolism (Aim 2) to this process. Aim 3 is a mechanistic proof-of-concept trial of 50 PCOS participants to determine whether 24 weeks of androgen receptor blockade improves lipid metabolites that reflect hepatic lipotoxicity and dysregulated de novo lipogenesis, respectively, as well as imaging-quantified hepatic and visceral fat, and NASH histology. Leveraging our existing UCSF PCOS cohort and the established infrastructures and collaborations between UCSF and Duke in NAFLD, PCOS, obesity, and lipid metabolism, we are well positioned to accomplish the proposed aims. Impact of findings: Determining the contribution of androgens to liver injury in PCOS and the underlying mechanistic pathways will support efficacy studies evaluating androgen receptor antagonism for NASH, or the need to target lipid-specific pathways as a tailored approach to halt NASH progression in this hormonally-distinct and metabolically high-risk population.

NIH Research Projects · FY 2025 · 2023-09

Project Summary/Abstract Our current understanding of mechanisms underlying visceral hypersensitivity, such as that associated with irritable bowel syndrome (IBS), remains rudimentary. Importantly, treating this and other functional gut disorders is limited, with a clear need for alternative treatment options. For the growing population afflicted by IBS, GI hypersensitivity and pain persist long after signs of tissue injury have resolved. Unlike other intestinal disorders, patients with IBS are hypersensitive with a lower pain threshold following colonic rectal distention (CRD) testing. Identifying the molecular and cellular components that mediate both the acute and persistent phases of visceral pain is a critical first step in understanding how environmental and endogenous factors produce long-term changes in the nervous system or associated tissues to engender chronic pain syndromes. In this new multi-PI application, we have taken a team-science approach and a multifaceted strategy designed to maximize the relevance of our pre-clinical basic research discoveries. Enterochromaffin (EC) cells are key sensory cells in the intestinal epithelium that release serotonin onto primary sensory nerve fibers, thereby evoking a sensation of discomfort and pain in response to luminal irritants, such as bacterial metabolites, inflammatory agents, or ingested chemicals. Our group recently established that EC cell-mucosal afferent signaling is a major mediator of visceral pain. We also show that the strength of this signal differs in males versus females. We will leverage our new colitis-free chemogenetic model of visceral hypersensitivity to zero in on the contribution of EC cells to visceral pain and identify molecular mechanisms through which these cells modulate the activity of nearby sensory nerve fibers. We will also ask how estrogen signaling contributes to the strong female bias that is characteristic of human IBS. Our team brings expertise in neurophysiology, pharmacology, visceral tissue anatomy, sex differences, and hormone signaling in female physiology and an unusually wide-ranging set of innovative approaches to tackle a prevalent gut-brain disorder.

NIH Research Projects · FY 2025 · 2023-09

PROJECT ABSTRACT Training Core The LAUNCH Program Training Core will produce scientists who are well trained and able to compete successfully for research funding and who are also able to think creatively and collaboratively to generate impactful and innovative science. We have designed a comprehensive training program that includes didactic and experiential learning in scientific inquiry which will be paired with extensive mentoring, career development support and networking opportunities. Our Training Core will (1) provide a strong foundation in content and methodology of the trainee’s chosen research area (i.e. basic, translational, or clinical science); (2) generate highly interactive opportunities to learn from peers and faculty the language and culture of multidisciplinary team science; (3) support and nurture strong relationships between trainees and their mentoring committee to maximize the trainee’s research productivity as well as professional development; (4) facilitate access to the LAUNCH training faculty who represent a network of outstanding scientists, teachers, and mentors who are collectively tackling problems related to nephrology, urology, or hematology; and (5) expose trainees to career development skills that will help provide a springboard for scholars to advance from their training towards independent scientific careers. We aim to produce a cadre of outstanding junior investigators who are innovators and the future leaders in the fields of nephrology, nonmalignant urology, and non-malignant hematology. Following the completion of our LAUNCH Program, we expect that our alumni will be uniquely poised to develop new and creative approaches to the diagnosis, prevention, and treatment of diseases within KUH disciplines and to thrive in research careers. The LAUNCH Training Core will be led by Dr. Chi-yuan Hsu (nephrology), Dr. Mark Walters (pediatric hematology), and Dr. Philip Beachy (urology), all of whom have extensive mentorship experience and a successful track record in research training and scientific inquiry.

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY/ABSTRACT Life expectancy is increasing, and consequently, the burden of chronic age-related disease is also increasing. Interventions and treatments that target the fundamental biological process of human aging have the potential to mitigate risk of multiple diseases faced by our aging population. To develop interventions targeting the aging process, one must identify predictive factors and biomarkers associated with the aging clinical endpoints. By definition, the development of aging-based conditions and diseases takes time and requires a great deal of follow-up time. To accelerate research in human aging, biomarkers of human aging and prognostic biomarkers of healthy human aging are desperately needed. Without reliable biomarkers, early-stage drug development is severely limited. In this application, we propose a framework to identify biomarkers of healthy human aging using advanced Artificial Intelligence (AI) methods applied to a wide range of deeply phenotyped studies that collected data from humans and non-humans. We have assembled a team with deep expertise in clinical research of aging, genetic epidemiology, biology of aging, and AI. To identify biomarkers of aging through the integrative analysis of omic data with AI, we propose the following specific aims: Aim 1 (R21, first stage). Assemble datasets from the Framingham Heart Study (FHS) and the Longevity Consortium (LC) with multiple omics to test AI methods and to identify biomarkers associated with human aging. Aim 2 (R21, first stage). Test biologically informed AI Deep Neural Network (DNN) models with FHS and LC data to integrate omic data, predict outcomes, and identify predictive omic features. Aim 3 (R33, second stage). Apply models from public data onto exceptional longevity (EL) data. Aim 4 (R33, second stage). Establishing causal relationship between biomarkers and longevity phenotypes through Mendelian Randomization (MR) analysis and cell culture experiments.

NIH Research Projects · FY 2024 · 2023-09

Project Summary/Abstract The proposed F31 NRSA Predoctoral Fellowship to Promote Diversity in Health-Related Research project aims to develop new MR detector hardware and acquisition & analysis methods to enable a major improvement in the clinical management of prostate cancer. This is of relevance to all prostate cancer patients, but also especially for under-represented minorities. African-American men have the world's highest incidence of prostate cancer and a more than two-fold higher mortality rate compared with whites. Also, African-American men have twice the risk of non-Hispanic whites for presenting with advanced-stage prostate cancer. This means that it is important to identify and stage aggressive, advanced prostate cancer accurately in this under-represented population. Prior studies by our group have been focused on improved MR molecular imaging of primary, organ- confined prostate-cancer and detecting response to therapy in bone and liver (distant) metastases. The PI, an African-American graduate student, has designed the proposed research training in this diversity fellowship project to focus on developing novel 13C/1H RF detector hardware and methods for increased HP [1-13C]pyruvate & 1H mpMRI sensitivity and coverage to detect aggressive cancers within the prostate and local spread to the prostatic bed & adjacent lymph-nodes. This is important for newly diagnosed patients and of particular relevance for African-American patients who more often present with advanced stage disease that has extra-capsular spread beyond the prostate and to nearby lymph nodes. As shown in his attached biosketch and through his outstanding initial research, the candidate is a highly motivated, successful trainee who meets the eligibility criteria as an African-American graduate student and will benefit greatly from this fellowship in terms of his research, education, and efforts to promote diversity in biomedical research. This project was designed by the PI applicant (with sponsor input & guidance) to fit his career goal of becoming a professor leading advanced MRI technology development to improve the clinical care of prostate cancer patients specifically, and patients with other deadly diseases in general. This award will also enable the PI candidate to promote diversity within the joint Bioengineering program at UC Berkeley and UCSF and ultimately science nationally to expand the number and input of under-represented minority scientists especially in the field of Bioengineering. He has been highly active in promoting diversity currently as a UC BioE graduate student and a member of Black Graduate Engineering and Science Students (BGESS). The diversity fellowship career development plan is designed to expand the scientific knowledge and independent research capabilities of the candidate. The goals are to: 1) Improve knowledge and research skills in MR hardware and acquisition methods; 2) Learn research study design and conduct; 3) Statistical and clinical study considerations; and 4) the conduct of first-rate research designed to ultimately improve prostate cancer imaging of newly diagnosed patients presenting with advanced disease.

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY/ABSTRACT As critical mediators of immunity against intracellular pathogens and cancer, type 1 conventional dendritic cells (cDC1s) cross-present exogenous, cell-associated antigens to CD8+ T cells, facilitated by the colocalization of these two cell types in the T cell zone of secondary lymphoid tissues. This microanatomical organization is orchestrated by CCR7 and XCR1, two G protein-coupled receptors (GPCRs) on cDC1s that guide their migration towards gradients of chemoattractant ligand. Recent reports have established a crucial role for tumor-associated cDC1s in cancer immunity. However, the GPCRs mediating cDC1 recruitment and positioning at sites of inflammation and in tumors are incompletely understood. Preliminary work has revealed that GPR34, an understudied X-linked GPCR, is highly expressed by cDC1s, and in vitro studies have shown that this lysophosphatidylserine (lysoPS)-responsive receptor supports cell migration. Preliminary data presented herein indicate that GPR34 promotes the accumulation of cDC1s in the inflamed mouse peritoneal cavity (PerC) in a cell-intrinsic manner. The PerC is a clinically important site for colon and ovarian cancer metastasis. In a preliminary experiment inspired by the connection between cDC1 accumulation and cancer outcomes, GPR34-deficiency led to increased growth of a subcutaneous (SQ) tumor model. This proposal will test the hypothesis that GPR34 regulates cDC1 organization and function during inflammation and cancer. Aim 1 will mechanistically define how GPR34 controls the abundance, trafficking, and positioning of PerC cDC1s using a combination of techniques including in vivo kinetic immune phenotyping, in vitro migration assays, and immunofluorescence microscopy. Aim 2 will investigate the role of GPR34 and lysoPS in cancer immunity using ectopic SQ and PerC tumor models along with tools to study antigen-specific T cell responses and to manipulate ligand levels. Completion of these Aims will elucidate key mechanisms by which GPR34 on cDC1s influences the response to inflammation and malignancy, providing opportunities for the development of therapeutics that modulate the lysoPS-GPR34 chemoattractant system. These research goals will be conducted in conjunction with a comprehensive training plan to prepare the applicant for an independent career as an academic physician-scientist. Training includes rigorous mentorship in scientific skills from a highly qualified sponsor, Dr. Jason Cyster; technical education from postdoctoral fellows in the applicant’s lab and collaborating labs; seminars, journal clubs, workshops, and conferences; and clinically geared activities. Research and training will take place at the University of California, San Francisco, which offers a highly innovative and collaborative immunology research environment and an exceptional medical school for clinical training.