University Of California, San Francisco

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY/ABSTRACT Background. Malignant effusions (ME) are frequent complications of metastatic breast cancer (MBC) associated with severe symptoms and dire prognosis. Treating MEs involves palliation through the serial removal of excess fluids, which are then typically discarded. Instead, these fluids could be used as substrates for liquid biopsy (LB) to guide the treatment of MEs and advanced MBCs. Problem. Drug targets and predictors of response for MBC are tremendous unmet clinical needs. Procuring solid metastatic tissue can be challenging due to the inaccessibility of disease sites and the risks associated with tissue collection. A major impetus for this proposed research is the opportunity for LB to circumvent these limitations. ME circulating tumor cells (ME-CTCs) can serve as surrogates for metastatic tissue for molecular characterization. However, the low proportion of METCs relative to immune cells in many MEs complicates profiling efforts. Solution. We have collaborated with Deepcell (DC), a company that developed an artificial intelligence (AI)- assisted, morphology-based approach to isolate ME-CTCs. DC’s biomarker-agnostic platform provides an advantage over traditional biomarker-based tumor enrichment methods by creating morphological atlases of ME- CTCs for mining novel biomarkers of treatment response and resistance. Our pilot studies demonstrate the feasibility of molecular characterization of ME-CTCs isolated using the DC platform. Hypothesis. We hypothesize that isolating ME-CTCs using the DC platform and downstream profiling can facilitate the development of LB tools for evaluating known actionable breast cancer (BCa) biomarkers (e.g., ER/PR/HER2, PIK3CA & ESR1 mutations) and discovering new predictive molecular and morphology-based biomarkers and drug targets. Specific Aims. In Aim 1, we will first validate the DC platform using primary cells from MEs and ME-derived organoids. Next, we will use the validated platform to isolate ME-CTCs, generate copy number and mutation profiles of these cells and matched archival tumors, compare the status of genes frequently mutated in BCa (e.g., PIK3CA and ESR1), and detect ME-CTC-specific aberrations. In Aim 2, we will perform single-cell RNA sequencing and immunocytochemistry of isolated ME-CTCs and ME-derived organoids to discover expression- based biomarkers and assess the status of known BCa biomarkers (e.g., ER/PR/HER2). In Aim 3, we will perform correlative analyses between treatment response vs. ME-CTC morphology and molecular signatures (Aims 1 & 2) and use ME-derived organoids for validation studies. Translational impact. Developing a platform for isolating tumor cells from MEs and liquid biopsy tools to discover novel response biomarkers and drug targets can transform the treatment of MEs from a palliative setting to a therapeutic opportunity to improve the outcomes of patients who develop these devastating complications.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY Diffuse midline gliomas (DMGs) are devastating primary brain tumors in children. Patient prognosis is abysmal with median survival of ~9 months after initial diagnosis. DMGs are driven by recurrent lysine to methionine mutations in histone H3 (H3K27M) that lead to widespread epigenetic dysregulation and oncogenic gene expression. Pinpointing vulnerabilities induced by the H3K27M mutation has the potential to lead to precision therapies for DMG patients. Tumors reprogram metabolism to generate biosynthetic precursors for uncontrolled proliferation and to maintain defense mechanisms. Glucose-6-phosphate dehydrogenase (G6PD) generates ribose-5-phosphate, which is a precursor for nucleotide biosynthesis. It also generates NADPH, which maintains glutathione (GSH) in the reduced state. GSH, in turn, is essential for glyoxalase 1 (GLO1) to detoxify methylglyoxal (MGO), a waste product of glycolysis. Our studies with isogenic and patient-derived models indicate that the H3K27M mutation transcriptionally upregulates G6PD and GLO1 expression in DMGs. Combined inhibition of G6PD and GLO1 using doxycycline-inducible shRNA or novel brain penetrant inhibitors is synergistically lethal in vitro and causes tumor regression in vivo. Mechanistically, G6PD and GLO1 inhibition depletes nucleotides and causes accumulation of MGO, leading to macromolecular glycation and apoptosis in DMGs. Deuterium metabolic imaging is a novel, clinically translatable method of visualizing glucose metabolism in vivo. Our studies indicate that MGO downregulates glycolysis by glycating phosphoglycerate kinase 1 (PGK1). Importantly, lactate production from [6,6’-2H]-glucose is altered at early timepoints following G6PD and GLO1 inhibition when changes cannot be observed on anatomical imaging in DMG-bearing mice. Based on these results, we will determine whether combined inhibition of G6PD and GLO1 abrogates DMG proliferation (Aim 1) and [6,6’-2H]-glucose provides an early readout of response to therapy at 3T (Aim 2). Our application is innovative because we identify, to the best of our knowledge for the first time, G6PD and GLO1 as oncogene-induced metabolic vulnerabilities in DMGs. Our proposal is significant because we have identified G6PD and GLO1 inhibitors that are synthetically lethal and have the potential for clinical translation. Furthermore, we will validate [6,6’-2H]-glucose as an agent that can provide a biologically meaningful readout of treatment response in vivo. We anticipate that our studies will provide the preclinical foundation needed to initiate imaging-driven clinical trials of our G6PD and GLO1 inhibitors in DMG patients. In summary, our proposal will develop metabolic therapy and imaging that can improve outcomes and quality of life for DMG patients.

NIH Research Projects · FY 2026 · 2024-08

PROJECT SUMMARY / ABSTRACT. In the era of precision medicine, molecular diagnostics (MDx) can deliver unprecedented opportunities for individualized approaches to care and improve clinical outcomes. Yet, the pace of precision medicine discovery has far exceeded the rate of implementation; consequently, MDx implementation across populations, diseases, and clinical settings is uneven, and disparities persist. Disparities stem from complex and multilevel barriers, but research indicates that patient-facing cost barriers are the biggest challenge for emerging MDx, where clinical guidelines are evolving and payer coverage is uneven. For many conditions, prompt MDx results are essential for personalized treatment approaches to improve outcomes, but barriers that prevent or delay payment for MDx testing can result in either mistreatment or delayed treatment. Institution-level interventions that facilitate access to MDx payment pathways and work towards increasing coverage for MDx will improve patient outcomes and guide effective, ethical, and equitable precision medicine implementation. However, developing strategies to increase MDx access requires new approaches to (1) empirically examine payment pathways to MDx access and (2) identify and characterize the range of institutional resources that best promote access to MDx payment pathways. The proposed research achieves this objective by using a case study of circulating tumor DNA (ctDNA) testing for lung cancer patients; the specific aims are: Aim 1: Analyze differences in patient-level factors associated with different payment pathways for MDx. Aim 2: Define institution-level resources associated with promoting access to MDx payment pathways. Aim 3: Identify and prioritize institution-level interventions that are promising candidates to promote equitable access to MDx payment pathways. The project will provide a knowledge base to understand and improve disparities in access to MDx payment and generate timely evidence to guide more equitable PM implementation. The training plan for the project builds on my expertise in conducting interdisciplinary research to identify PM disparities. It expands my range of qualitative (advanced skills in narrative elicitation) and qualitative data (advanced machine learning and natural language processing [NLP] skills to analyze electronic health record [EHR] data) to conduct rigorous mixed methods research. Comprehensive training and mentoring in health services research, health policy, clinical genetics, health disparities, and implementation science will enable me to effectively translate study findings into effective strategies to promote precision medicine access. The skills and knowledge gained from the training will inform my R01 and lay the foundation for developing practices and policies that can have a significant impact on reducing disparities in precision medicine.

NIH Research Projects · FY 2026 · 2024-08

ABSTRACT Asthma prevalence and morbidity is on the rise for recently migrated and multigenerational immigrant communities. It is well established that length of stay in the U.S. and acculturation to be associated with asthma in Latino/x/e communities. Yet, the mechanisms—in particular the environmental contributors— remain largely unknown. North Richmond, South Fresno, and Southwest Stockton, California are three environmental justice communities with large immigrant populations. As these immigrant-prominent communities reside near environmental hazards, including frequented truck routes, there is an imperative to increase our understanding of the short-term health effects of diesel exhaust pollution for individuals with asthma. In partnership with community-based organizations from these communities, this proposal seeks to: 1) estimate the short-term health effects of black carbon exposure on daily rescue medication use and symptom burden; 2) understand how acculturative stress and discrimination may modify or enhance this association; 3) identify multilevel protective factors that reduce the health effects of black carbon exposure in asthma; and 4) co-prioritize protective strategies at the individual, household, and community level. To accomplish these aims, we will enroll 300 Latine household with at least one residing child, 6–17 years old, with asthma (100 households/community), use a GPS-enabled cap for inhalers to collect information on time and place of rescue medication use, and set up a high-density black carbon sensor network and air quality model to derive an hourly 100-meter black carbon concentration grid. We will then examine for health effects of black carbon on rescue medication use and symptom burden using distributed lag models, examine for effect modification by acculturative stress and discrimination markers, and identify multi-level protective factors. These results will inform a community stakeholder engaged effort using a participatory action research approach. This will involve working with our established Youth Council in Richmond, CA (to be extended to Fresno and Stockton) to co-create and distribute a community-wide survey (n=600) and co-lead listening sessions to iteratively prioritize promising protective strategies for consideration of inclusion in local community emissions reduction plans. At the conclusion of the study, we will have a nuanced understanding of the short-term health effects of diesel exhaust pollution, measured as black carbon for this proposal, on daily asthma morbidity in Latine populations residing near roadways and other environmental hazards. Furthermore, we will examine how acculturative stress and discrimination may exacerbate this health disparity. Perhaps most impactful, we will not only identify promising multi-level protective factors but also co-prioritize these strategies with our community partners.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY Abnormal responses to inflammatory stimuli can lead to severe inflammation, acute tissue damage, and long- term scarring or fibrosis. One example is the rare disease fibrodysplasia ossificans progressiva (FOP), a congenital disease of progressive heterotopic ossification (HO) that leads to severe and irreversible loss of mobility. Patients with FOP show inflamed swellings (“flares”) that are associated with HO formation. Patients with FOP have evidence of increased immune system activity, including elevated levels of pro-inflammatory cytokines like IL1. Preliminary data from four FOP patients treated with anti-IL1 therapy showed a 60–90% decrease in flare activity. We hypothesize that blockade of IL1 signaling reduces the flare activity and subsequent new HO formation in patients with FOP. However, before we can perform a larger interventional study, several key knowledge gaps and tools need to be addressed. We address these needs via a clinical observational pre-post study on patients with severe FOP who are being recommended for rescue therapy with anti-IL1 medications. Eleven subjects, aged 6–18 years old with at least six flares/year (3 times higher than the reported average flare rate) will be enrolled when their primary medical team recommends initiating anti-IL1 therapy. Subjects will be monitored remotely to obtain pre-treatment flare rates and patient reported outcome assessments. Once anti-IL1 therapy is initiated, subjects will begin their post-treatment observational phase and have the first onsite visit for detailed assessments. Low-dose whole-body CT (WBCT) imaging, bloodwork, patient-reported outcomes, pain, and flare activity will be assessed during the subsequent year. Primary assessments: Determine if patients with FOP have decreased flare activity while on anti- IL1 therapy. We will use flare diaries and pain scale assessments to systematically determine if flare frequency and pain improve with anti-IL1 therapy. Aim 2: Secondary assessments: Determine the amount of new HO formation in FOP patients treated with anti-IL1 therapy. We will develop a “ground truth” HO segmentation that will serve as a basis for developing an automated artificial-intelligence analyses system. We will also quantitate the new HO bone formation that develops in patients with FOP who are treated with anti-IL1 therapy. Aim 3: Exploratory assessments: Determine if inflammatory cytokine measurements can be used as biomarkers for monitoring flare activity and inflammation in FOP patients treated with anti-IL-1 therapy. No effective biomarkers are available for FOP disease activity. We will determine if a commercial serum cytokine panel and thermal imaging are useful tools for assessing flare activity. These studies address urgent needs. No therapeutic options are available for FOP patients, particularly in children where intervention would have the greatest clinical benefit. The proposed studies provide critical clinical information potentially relevant to the immediate care of FOP patients and will generate key tools, such as methods for quantitative HO formation from CT scans, that will be useful for a future U01-level study and patient care. 1

NIH Research Projects · FY 2025 · 2024-08

Project Abstract People living with HIV (PLWH) have poor clinical outcomes when they are excluded from care due to intersectional stigma related to HIV, mental health (MH), and other dimensions. Recent studies and reviews have highlighted three major challenges in identifying and addressing intersectional stigma: a lack of stigma assessment strategies that are multi-dimensional and can be incorporated into routine clinical care, a lack of tailored stigma-reduction activities, and a lack of implementation of multi-level interventions. These gaps make it difficult to recognize and address intersectional stigma, leading to poor HIV care outcomes globally. Digital health tools, co-designed with PLWH and healthcare workers (HCWs), have the potential to assist ART centers in addressing these challenges. Guided by the principles of human-centered design, which our team has utilized in a recent R34 study to improve adherence to HIV care in Nepal, we now propose to develop and pilot test a digital tool with three components that can address the challenges in assessing, prioritizing, and addressing intersectional stigma in ART centers. The components include: 1) a dynamic assessment strategy that can be used during a clinic visit to collect both quantitative (i.e., ratings) and qualitative data (i.e., free text of client’s perspectives) on stigma reported by PLWH; 2) a dashboard that incorporates this stigma assessment data alongside routine clinical data (i.e., existing registry of clients in the ART center) so that ART centers can directly link stigma with care engagement, and also identify relevant stigma-reduction activities; and 3) a repository of evidence-based, culturally appropriate activities that can reduce stigma at the intrapersonal-, interpersonal-, and clinic-levels. The three components of the digital intervention are theoretically grounded and are based on prior studies and consultations with local partners. The study’s Aim 1 is: To iteratively develop the digital health tool INterseCtional stigma assessment and reduction at multiple Levels and mUltiple DimEnsions (INCLUDE) for routine use in ART centers. We will achieve this by developing INCLUDE through a co-design process involving PLWH, HCWs, researchers. We will then pre-pilot INCLUDE at a single ART center to prepare it for Aim 2: To assess the acceptability and feasibility of INCLUDE among clients, HCWs, and ART center leads in four ART centers. For this aim, we will conduct a pilot trial at four ART centers to assess the acceptability and feasibility of INCLUDE. The human-centered co-design process ensures that INCLUDE meets the needs of stakeholders and can be integrated into routine care. This project brings together our team’s longstanding expertise and experience in HIV, stigma, MH, digital health, and in working closely with the local government. If successful, this study will provide an intervention that can be incorporated into routine clinical practice to systematically identify and address intersectional stigma to improve HIV care, and can be tested in a cluster randomized trial with ART centers in Nepal and other regions that face similar challenges.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY As the prevalence of obesity and associated disorders rises, manipulation of adipocyte energy expenditure has gained attention as a potential means to treat metabolic disease. This strategy leverages the physiology of thermogenic adipocytes, a cell type that relies on oxidative phosphorylation metabolism to drive futile chemical cycles that release energy as heat. Recent work has suggested the potential for ribosomal control of thermogenic gene expression. Elucidating the responsible mechanisms may reveal novel means to manipulate adipocyte metabolism for the treatment of obesity and diabetes. This proposal tests the hypothesis that the distinct metabolism of thermogenic fat is enabled by specialized mRNA translation preferences inherent in this cell type. A first set of studies focuses on a single mRNA, PPARGC1A, and aims to purify the proteins that confer its cell-type-specific translational output. This mRNA encodes PGC1α, a dominant regulator of mitochondrial biogenesis. A second set of studies develops an in vivo mouse model to test the hypothesis that the helicase DDX3X, a regulator of mRNA translation and cytoplasmic stress granules, is a thermogenic-fat- selective translational regulator that supports expression of genes critical for oxidative metabolism. A third set of studies uses ribosome profiling technology to define the global mRNA translation dynamics associated with thermogenic activation. Together, these studies expand the scope of my work while generating foundational datasets and mouse models for my scientific independence. They will be carried out in the lab of a recognized leader in the field of molecular metabolism, Dr. Bruce Spiegelman, at the Dana-Farber Cancer Institute and Harvard Medical School. In this rich environment, I will benefit from a mentorship team committed to instruct me in: adipocyte biology, including in vivo genetic manipulation; mouse metabolic phenotyping; mass spectrometry; and bioinformatics. The technical training is complemented by formal instruction in human metabolic pathophysiology, as well as activities for honing my leadership, speaking, and writing skills. In this way the NIH Pathway to Independence Award supports my transition from mentored work to an independent stage in which I intend to use cutting-edge methods to broadly define the translational dynamics of thermogenic fat, identify the responsible regulators, and test how post-transcriptional dynamics such as stress granule assembly may contribute. My ultimate goal is to lead an academic research group that investigates how the gene expression programs that define cellular identity and metabolism are established, how they are perturbed in metabolic disease, and how they may be therapeutically manipulated to prevent or treat metabolic disease.

NIH Research Projects · FY 2025 · 2024-08

ABSTRACT The long-term goal of this project is to develop and validate an injectable, biodegradable nanowire delivery platform for local and sustained release of a “painless” nerve growth factor (NGF) isoform to accelerate fracture healing in clinical scenarios of delayed healing. Approximately 15 million fracture injuries occur each year in the United States (US).6 An estimated 10-15% of fractures within a healthy population result in delayed- or non-union.7,8 However, delayed healing rates increase to almost 50% in patients with vascular damage or high co-morbidity burdens such as diabetes, increased age, smoking, and obesity.9,10 The current standard of care for delayed healing or non-union is surgical intervention to increase stability or to promote healing through application of bone grafts. Bone morphogenetic protein (BMP) is the only biologic with FDA approval for use in fracture repair, with “on-label” use only within a narrow indication window. However, BMP requires surgical implantation and is typically limited to only the most at-risk fractures due to the high cost, limited evidence of clinical efficacy, and risk of severe off-target effects.11-14 As such, there exists an unmet clinical need for biologics that could stimulate bone regeneration in a non-surgical delivery platform. This application builds on strong preliminary data demonstrating that NGF accelerates fracture repair when injected into the cartilaginous phase of long bone healing. Importantly, our preliminary data is the first to show that NGF acts on chondrocytes to promote programs associated with endochondral ossification (EO). The goal of this grant is to build upon these preliminary data to develop NGF into a platform suitable for clinical translation. In the first Aim, we optimize the dose and timing of a mutant form of NGF (NGFR100W) to stimulate endochondral fracture repair. NGFR100W is a novel “painless” NGF that efficiently binds to the TrkA receptor to provide the same trophic effect as wild type NGF, but fails to bind to the p75NTR receptor to significantly reduce risk of nociception.15,16 In the second Aim, we probe the mechanism by which NGF/NGFR100W stimulates fracture repair by conditionally deleting the TrkA receptor. To date the molecular pathways stimulated by therapeutic delivery of NGF have not been rigorously studied in long bone fracture healing. Lastly, in the third Aim, we modify our previously developed injectable heparin coated polycaprolactone (PCL) nanowires17 for encapsulation and sustained delivery of painless NGF. Here we also incorporate a pre-clinical model of diabetes (Lepob) established to demonstrate delayed healing to challenge our therapy in a clinically relevant scenario of malunion. These aims allow us to test the central hypothesis that a painless NGF therapy can improve fracture healing by acting through TrkA signaling to stimulate chondrocyte-to-osteoblast transformation. Our interdisciplinary team of experts in fracture healing, biomaterials, and NGF/TrkA signaling uniquely positions us to successfully accomplish the proposed study. Importantly, our approach is grounded in creating a translationally relevant therapeutic platform that has the potential to significantly improve patient outcomes following a fracture.

NIH Research Projects · FY 2026 · 2024-08

Despite remarkable progress in HIV testing and treatment, HIV incidence remains unacceptably high among women and girls in eastern and southern Africa. In Uganda, HIV infections are concentrated among women at elevated HIV risk due to factors such as working in venues. Although oral pre-exposure prophylaxis is being scaled up, many women at elevated HIV risk face barriers to accessing oral pre-exposure prophylaxis at health facilities and to storing and adhering to pills. A new era of choice in biomedical HIV prevention, including the dapivirine vaginal ring and long-acting cabotegravir, presents an opportunity to reduce new infections. Post-exposure prophylaxis could fill gaps in coverage. As new choices in HIV prevention are rolled out, strategies are needed to empower women to choose among prevention products and support sustained use. Our study team developed and tested the Sustainable East Africa Research in Community Health Dynamic Choice HIV Prevention intervention (including product choice, with option to switch over time, choice of facility or community-based visits, and provider training). In three randomized trials, Dynamic Choice HIV Prevention increased time covered by a biomedical prevention product over two-fold compared to standard of care prevention services. However, there were gaps in engaging women at elevated HIV risk. We have conducted formative work, in collaboration with our Community Advisory Board, to tailor the effective Dynamic Choice HIV Prevention intervention to further reach and engage women at elevated HIV risk. Key recommendations from this work included increasing access to long-acting product choices, expanding outreach beyond facilities, and extending existing peer services. Peer approaches are recommended in national guidelines and are being successfully implemented to reach women at elevated risk for HIV testing and prevention services – but peer models have not yet been deployed to deliver biomedical prevention choices. We propose to optimize and test a Peer-led Dynamic Choice HIV Prevention intervention to catalyze choice and use of biomedical prevention products. We will test the hypothesis that Peer-led Dynamic Choice HIV Prevention (with choice of pre-exposure prophylaxis product will increase biomedical HIV prevention coverage compared to standard of care among women at elevated HIV risk in southwestern Uganda. The proposed aims are: 1) To refine and optimize the Peer-led Dynamic Choice HIV Prevention intervention; 2) To determine the effect of the Peer-led Dynamic Choice HIV Prevention intervention on biomedical prevention coverage in a Hybrid Type 1 effectiveness-implementation cluster randomized trial; 3) To assess costs, efficiency, and cost-effectiveness of Peer-led Dynamic Choice HIV Prevention. Collectively, these aims will provide evidence for peer-led models to deliver choice of HIV prevention products for women at elevated HIV risk to enhance HIV prevention coverage using current and next-generation prevention modalities.

NIH Research Projects · FY 2025 · 2024-08

Overdose deaths continue to surge in the United States, with more than 100,000 deaths in 2021, largely driven by fentanyl. Buprenorphine is a highly effective medication for opioid use disorder (OUD) that reduces overdose deaths and opioid-related harms. Yet fewer than 20% of individuals with OUD receive buprenorphine, and fear of withdrawal during initiation—particularly precipitated withdrawal among people using fentanyl—remains a major barrier. Traditional initiation requires opioid abstinence and the presence of withdrawal, a process that many patients find intolerable. In response, clinicians have developed alternative initiation strategies, including Low-Dose Initiation (LDI), which gradually introduces buprenorphine over several days, and Direct-to-Inject (DTI), which begins treatment with an extended-release injectable formulation. Both approaches reduce the risk of precipitated withdrawal, but completion and retention remain suboptimal, and strategies to enhance their effectiveness are lacking. The proposed training and research plan for this K23 application will allow Dr. Leslie Suen to acquire the skills necessary to become an NIH-funded independent clinician investigator with expertise in implementation science and intervention development to improve OUD treatment outcomes. Guided by a strong mentorship team, Dr. Suen will apply advanced methods in intervention development, mixed methods research, and randomized trial design to develop and pilot an Enhanced Buprenorphine Initiation (EBI) program. EBI will combine DTI-focused initiation strategies with implementation science–guided enhancements (e.g., targeted education, daily check-ins, contingent incentives). The project includes: (1) identifying barriers to LDI completion; (2) designing the EBI program using participatory methods; and (3) piloting EBI in a randomized controlled trial at the San Francisco Outpatient Buprenorphine Induction Clinic. This work will establish the foundation for a future R01 to evaluate EBI’s effectiveness and advance the ultimate goal of improving buprenorphine uptake and reducing overdose deaths.

NIH Research Projects · FY 2026 · 2024-08

PROJECT SUMMARY/ABSTRACT: In Kenya, HIV incidence among adolescent girls and young women (AGYW) ages 15-24 years is 1-2 per 100 person-years and approximately 30% of AGYW have had at least one sexually transmitted infection (STI). Kisumu, Homa Bay, and Migori counties in Western Kenya have the highest HIV/STI incidence in the country. Food insecurity (Fl) and poverty are also highly prevalent in Western Kenya. Fl and poverty are important drivers of vulnerability to HIV and STls among AGYW. Poverty alleviation interventions have the potential to reduce STls and HIV risk among AGYW but, to date, these interventions have reported mixed findings on HIV/STI outcomes, have been primarily targeted at the individual level, and none have focused on agriculture or Fl. Therefore, there remains a critical need to develop sustainable, multi-level, economic and Fl interventions that improve AGYW STI/HIV prevention outcomes. Our team has successfully developed a household-level agricultural intervention in Western Kenya called Shamba Maisha ("farm life" in Kiswahili; SM) to reduce household Fl. In our prior pilot study with AGYW, we found that SM was feasible, acceptable, and associated with less Fl and improved mental health. In this proposal, we will build upon our promising SM work by examining the effectiveness and implementation of our SM intervention, including provision of a water pump and agricultural implements for use at home, training in farming agriculture delivered at school-based demonstration farms, and adolescent-caregiver relationship strengthening training. We plan to conduct this school- and home-based cluster randomized trial with 800 AGYW and their primary caregivers recruited from schools in Kisumu, Homa Bay, and Migori counties. We will randomize 20 schools in Western Kenya to intervention or control conditions and follow AGYW-caregiver dyads for 18 months with surveys and STl/pregnancy testing to assess intervention impacts. In Aim 1, we will determine the impact of SM on adolescent HIV prevention and sexual and reproductive health outcomes (primary outcome is gonorrhea and/or chlamydia incidence). In Aim 2, we will assess the effect of SM on intermediate outcomes theorized from our published conceptual framework to be on the causal pathway, including household food security and wealth, and adolescent and caregiver factors including mental health and aspects of the caregiver-AGYW relationship dyad (e.g., communication). In Aim 3, we will identify critical implementation facilitators and barriers influencing SM effectiveness and delivery and conduct a programmatic cost assessment. We will also evaluate the extent to which SM can have "spillover'' nutritional benefits for a larger population of adolescents who had access to demonstration farms at intervention schools but did not receive other aspects of the intervention. Our ultimate goal is to provide an innovative household-level intervention to halt the cycle of Fl, and poor HIV-related outcomes among vulnerable populations including AGYW, consistent with the "Ending the HIV Epidemic" and Sustainable Development Goals.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY/ABSTRACT The Problem: Cellular immunotherapies targeting surface proteins are one the most exciting new modalities in cancer. However, most tumors lack surface targets with acceptable efficacy and toxicity profiles. Our Solution to the Problem: In work currently accepted at Nature Cancer, to address this unmet need we developed a new technology called “structural surfaceomics”. This approach is designed to systematically probe an entirely new class of tumor-selective immunotherapy targets: those based on the cancer-specific, 3- dimensional conformation of plasma membrane proteins. To develop this methodology, we used our joint expertise in cell surface proteomics (Wiita) and crosslinking mass spectrometry (Huang). We initially applied this strategy to acute myeloid leukemia (AML), a deadly blood cancer with no known optimal cellular therapy targets. Using structural surfaceomics on AML models followed by patient sample validation, we identified the active conformation of integrin-β2 (aITGB2) as a promising, previously unknown AML target. Via recombinant antibody selection, we developed an engineered T-cell therapy (CAR-T) targeting aITGB2. We found this CAR- T had a highly favorable efficacy vs. toxicity profile compared to other AML targets under clinical investigation. We are now pursuing further preclinical development of this CAR-T as a therapy for AML patients. Overall Hypothesis and Aims: We hypothesize that tumor-specific surface protein conformations are actually widespread, and the structural surfaceomics technology has the potential to uncover these antigens. The objective of our proposal is two-fold: 1) further advance the technical and analytical aspects of the structural surfaceomics technology, to improve our ability to identify cancer-specific surface protein conformations across a broader range of indications; and 2) identify how we can even further improve therapeutic targeting of this conformation-specific surface antigen aITGB2 in AML, even beyond our current approach. To achieve these goals, Aim 1 will define the landscape of surface protein conformations via enhanced structural surfaceomics across several different tumor models, with validation in primary patient samples. This work will ultimately develop a pipeline to move from target discovery to potential therapeutic. Aim 2 will focus on identifying the mechanistic basis for conformation-specific targeting of integrin-β2 in AML with our current cellular therapy. Impact: Findings in Aim 1 will be broadly impactful toward the adoption and dissemination of the structural surfaceomics technology. These results will ideally not only identify new immunotherapy targets in cancer, but open the door to probing surface protein conformations in any biological system. An Aim 2 will inform design of a further optimized cellular therapy for potential clinical translation, directly benefitting AML patients. The Team: The PIs have an uncommon combination of expertise in implemented proteomic methods as well as blood cancer and cellular therapy development. Co-Investigators at UCSF and IIT Bombay are leading experts in integrin biology, structural biology, computational structural biology, and computational proteomics.

NIH Research Projects · FY 2025 · 2024-08

Project Summary Abdominal aortic aneurysms (AAA) are a leading cause of death worldwide, and no medical treatment is currently available. It is now accepted that aneurysm growth is related to chronic progressive tissue destruction secondary to vascular inflammation, resulting in the breakdown of extracellular matrix (ECM) proteins. We have shown that a tailored Photodynamic Therapy (PDT) protocol in a mouse model can halt aortic aneurysm growth 21 days after AAA induction. Photodynamic therapy has been shown to enhance cross-linking of collagen, a key component of aortic ECM. This cross-linking substantially increases the strength of ECM. Further, in oncologic studies, PDT appears to selective kill rapidly dividing cells with an affinity for proliferating immune cells. Therefore, we hypothesize that applying PDT to AAA will enhance ECM cross-linking and eradicate proliferating immune cells within the adventitia layer of the vascular wall. Our specific aims are designed to test these hypotheses and determine the mechanism of action behind PDT treatment of AAA. In Aim 1 we will compare the changes to ECM proteins after PDT to what occurs in control mice. We will also evaluate matrix metalloproteases (MMPs) and tissue inhibitors of MMPs (TIMPs), key enzymatic regulators of ECM degradation. In Aim 2 we will investigate the changes in immune cell subpopulations within aortic tissue after PDT. In addition, we will use unbiased analysis to identify changes to gene expression of inflammatory proteins within aortic tissue after delivery of PDT. As our preliminary findings show that PDT can have a powerful effect on AAA growth, analysis of the molecular changes that coincides with this deceleration in growth may lead to a better understanding of the mechanisms that drive AAA progression. In addition, understanding the therapeutic mechanism of PDT may allow PDT to adapted for use in human AAA disease.

NIH Research Projects · FY 2024 · 2024-08

PROJECT SUMMARY SPLIS is an ultra-rare, often lethal inborn error of metabolism recognized just five years ago. Most affected children exhibit a rapidly progressive form of nephrotic syndrome which leads to failure-to-thrive and kidney failure, the main cause of death. Affected children may exhibit adrenal insufficiency, hypothyroidism, skin and neurological defects, and immunodeficiency. Although kidney transplantation can be lifesaving, there is no cure for SPLIS. SPLIS is caused by recessive mutations in SGPL1, which encodes sphingosine-1-phosphate (S1P) lyase, a vitamin B6-dependent enzyme responsible for catabolism of the bioactive lipid S1P in the final step of sphingolipid metabolism. SPLIS-associated SGPL1 mutations impair S1P lyase activity, enzyme localization and/or stability, and cause sphingolipid accumulation leading to multi-organ dysfunction and failure. Unlike classical sphingolipid metabolic disorders involving lysosomal enzymes (such as Tay-Sachs disease), SPLIS is an atypical (non-lysosomal) sphingolipid disorder. The study of SPLIS biology is revealing shared features of atypical sphingolipid disorders and the potential for common diagnostic, monitoring and treatment strategies. As pioneers in the field —having identified the first S1P lyase gene from budding yeast and studied its function for decades—we are now directing our expertise to develop targeted therapies for SPLIS. To our knowledge, we are the only group working toward that goal. Some children with less severe forms of SPLIS may respond to supplementation with vitamin B6, the enzyme’s cofactor. Studies in a mouse model of SPLIS have provided proof-of-concept for the use of adeno-associated virus-mediated SGPL1 gene therapy as potentially curative treatment for SPLIS. Clinical trials testing these two therapeutic strategies are in the planning stages. Further, we have developed disease biomarkers and are preparing to launch the first prospective SPLIS natural history study. However, there are major challenges to existing interventions. Pyridoxine is only useful for a limited number of patients harboring B6-responsive variants. Kidney transplantation requires adequate weight gain, is costly, and has high morbidity. Gene therapy is irreversible, can have severe toxicities, and cannot be used prenatally. We hypothesize that enzyme replacement therapy (ERT) represents a lifesaving treatment for SPLIS that acts by preserving kidney function and offers many advantages over other treatment strategies. In this project we will use two powerful and complementary mouse models of SPLIS, a well-established knock-out mouse and a novel knock-in mouse, to test our hypothesis with two specific aims: 1) Establish proof-of-concept for ERT as a lifesaving treatment for SPLIS; 2) Establish proof-of-concept for the ability of ERT to prevent or reverse SPLIS nephrosis. Our results will provide the rationale for further developing ERT as a treatment for SPLIS. Our team, comprised of an expert in sphingolipid biochemistry, S1P lyase and SPLIS and an expert in protein synthesis and ERT for inborn errors of metabolism, along with our scientific staff, are highly capable of undertaking the project and have all the necessary tools to initiate the study immediately.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY/ABSTRACT Empirical neuroethics studies of patient/user perspectives have demonstrated profound effects that novel neurotechnological therapies, such as implanted devices, can have on people’s understandings of themselves and their illnesses. However, to date the incorporation of such perspectives in the design of neurotechnologies is not a standard practice, and this gap presents risk for ethical harms and may negatively impact the usability and feasibility of interventions based on BRAIN Initiative-supported research. The long-term goal of this proposal is to facilitate the BRAIN Initiative’s success in discovering effective and ethically sound therapies for disorders of the nervous system. The central hypothesis is that human-centered design, an interdisciplinary approach that prioritizes user perspectives and has been successfully applied to implementation problems in fields such as digital technology and health systems design, can be applied to related problems in neurotechnology. The work will be conducted by pursuing three specific aims: 1) Examine adverse user experiences with non-human-centered design, highlighting pitfalls and needs for improvement; 2) Assess prevailing attitudes regarding human- centered design and barriers to adoption among neurotechnology developers; and 3) Convene neurotechnologists to identify needs and to develop strategies for integrating user perspectives in neurotechnology. Under the first aim, in-depth qualitative interviews will be conducted with blind people implanted with the Argus II retinal implant, a commercially non-viable technology no longer supported by its manufacturer, which may illustrate how failures to incorporate user perspectives in design can lead to ethical harm and to technology abandonment. For the second aim, professionals engaged in neurotechnology (including neuroscientists, engineers, businesspeople, and officials/regulators) will be interviewed about incorporating user perspectives generally and about human-centered design specifically. These interviews will offer insight into the lack of adoption of human-centered design in neurotechnology to date. In the third aim, two convenings of neurotechnologists will be organized to co- create plans for making the incorporation of user perspectives a standard practice in neurotechnology. The approach is innovative, shifting research paradigms in neuroethics and neurotechnology through new conceptual and methodological linkages with human-centered design. The proposed research is significant, because the ethical and effective provision of novel treatments depends on incorporating the priorities of patients and prospective users more directly in their design. Ultimately, we envision a mutually reinforcing relationship between neuroethics and human-centered design, two interdisciplinary fields that can bring needed new outlooks and methods to the practice of neuroscience.

NIH Research Projects · FY 2026 · 2024-08

PROJECT SUMMARY/ABSTRACT Oral diseases are among the most common chronic conditions of humankind; their origins can often be traced to socioeconomic and behavioral circumstances much earlier in life. Frequently overlooked are key life transitions when behaviors and circumstances are especially fluid and potentially malleable with appropriately tailored interventions. Emerging adulthood (the transitional period from adolescence to adulthood) is one such life stage that has garnered limited attention in oral health research. Emerging adulthood is a particularly sensitive period marked by changes in socioeconomic stressors, health risk factors, and potential protective opportunities as young people enter new social circumstances. This proposed project combines detailed measures of economic, social, and behavioral factors with quality assessments of oral and systemic health in a diverse, prospective emerging adult cohort. We will examine potential interactions by race/ethnicity and gender identities and the specific behavioral pathways connecting socioeconomic factors to disease risk, potentially revealing health promotion opportunities during this formative developmental period. Indeed, such insight informs a long-term objective to test how acquired access to socioeconomic opportunity afforded by higher education impacts the trajectory of oral diseases, especially among those from minoritized and/or disadvantaged backgrounds. This time-sensitive proposal leverages the now-launching NHLBI-supported Economic and Educational Contributions to Emerging Adults' Cardiometabolic Health (“3E”) cohort study of 4,000 diverse first-year college students from two public Hispanic-Serving Institutions of higher education (>50% first-generation college students, >40% Pell Grant recipients). This proposal augments rich prospective economic and behavioral data with oral health-specific risk factors and self-reported and objective measures oral health. Specifically, this project will: Aim 1. Examine the influences of early adulthood socioeconomic stressors on oral health over time, including as potentially modified by race/ethnicity and gender. Aim 2. Examine the contributions of education-related opportunities (e.g., academic engagement programming, basic needs supports, social capital) as protective factors against adverse oral health outcomes (e.g., service non-utilization, gingival inflammation). Aim 3. Assess the mechanistic role of health-related behaviors in linking socioeconomic stressors and education-related opportunities to oral health outcomes. Emerging adulthood, a transition period in health behaviors and socioeconomic opportunity, is a potential pivot point in the development of chronic diseases and health inequality. Understanding influences of oral diseases near their emergence will inform more effective oral disease prevention efforts.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY/ABSTRACT The aggregation of misfolded proteins is a prominent pathological feature in most age-related neurodegenerative diseases. This includes Huntington's disease (HD) and various spinocerebellar ataxias, inherited diseases caused by expanded, aggregation-prone polyglutamine (polyQ) stretches in specific proteins. Understanding how cells prevent the misfolding of these mutant polyQ proteins holds the potential to reveal therapeutic strategies not only for polyQ disorders but also for other neurodegenerative conditions. I conducted large-scale CRISPR screens for modifiers of polyQ protein aggregation in human cells that revealed DNAJC7, an Hsp40 co-chaperone, as a top hit. Molecular chaperones are a diverse group of proteins that assist in proper protein folding, but we lack knowledge about the specific endogenous chaperones most effective in preventing polyQ protein aggregation, along with their roles in neurons. Importantly, DNAJC7 is highly expressed in neurons and has connections to other neurodegenerative diseases, leading to the central hypothesis of this proposal: DNAJC7 is a key neuronal Hsp40 capable of selectively inhibiting aggregation of amyloidogenic proteins, including mutant polyQ proteins. Aim 1 of this proposal will investigate the impact of DNAJC7 expression on disease phenotypes in neuronal models of HD, while Aim 2 will delve into DNAJC7’s mechanism and range of selectivity for different amyloidogenic disease proteins. My long-term goal is to establish myself as an academic neuropathologist with a research program dedicated to studying neuronal protein homeostasis pathways in neurodegeneration. This proposal outlines a comprehensive 5-year mentored career development plan that will provide me the essential knowledge and scientific training necessary to successfully transition to this goal. The training plan includes acquiring various new skills in cutting-edge techniques spanning microscopy, CRISPR functional genomics in iPSC neurons, and proteomics, as well as enhancing skills in bioinformatics and statistics. Additionally, the training plan covers the development of professional skills needed to successfully launch and manage a laboratory, including scientific communication, grant writing, and lab management. To achieve these objectives, I have assembled a multidisciplinary mentorship team with complementary expertise, and includes Dr. Martin Kampmann (mentor), Dr. Eric Huang (co-mentor), and advisory members Dr. Jason Gestwicki, Dr. Steven Finkbeiner, Dr. Lea Grinberg, and Dr. Arun Wiita. UCSF provides an exceptional research environment, equipped with cutting-edge technologies and a range of leaders across multiple disciplines. This proposal will empower me with the necessary skills to establish a thriving and rigorous independent laboratory, merging with my neuropathology training to become a leader in neurodegenerative disease research.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY Multiple neurological diseases [e.g. spinal cord injury (SCI), amyotrophic lateral sclerosis (ALS), brain stem stroke] can all result in severe and devastating limb paralysis. A recent comprehensive assessment found that >200,000 patients suffer from tetraplegia or severe tetraparesis that prevents completion of basic activities of daily living that require arm and hand functions. Surveys of such patients have indicated that improvement of arm and hand function is a top priority. There are no current therapies or assistive devices that can aid patients with tetraplegia or severe tetraparesis to experience restoration of reaching and grasping functionality. Our proposal aims to test methods to enable such patients to directly control a complex robotic arm and hand with the capacity to perform a set of clinically relevant tasks. Our specific goals are to leverage the stability of ECoG to establish robust robotic control that is stable across a period of at least 8 weeks without need for recalibration. Our published data along with new preliminary data supports the notion that ECoG signals can allow a paralyzed individual to learn complex neuroprosthetic control that requires no additional training. We will compare two decoding methods and their ability to enable long-term stable ‘plug-and-play’ complex control. We then aim to further boost robustness of real-world control in two ways. First, we will track fluctuations in neural states to reduce decoding errors; this is key for long-term continuous accurate control. Second, we will test a system that can assist with pre-shaping the robot during neuroprosthetic control. Together, our aims will determine the feasibility of complex control of neuroprosthetic technology in a target population of paralyzed patients with severe disability. We will determine how well ECoG can enable stable and intuitive control of a robotic arm and hand that can enable reaching, grasping and flexible manipulation of objects. We strongly believe that demonstration of these outcomes will drive the field towards clinically viable neuroprosthetic control and thereby dramatically improve the quality of life for paralyzed patients.

NIH Research Projects · FY 2025 · 2024-08

Project Summary/Abstract Gene fusions between the transcriptional repressor Capicua (CIC) and several possible 3’ partner genes, including DUX4 and NUTM1, drive the progression of aggressive sarcomas with dismal prognoses and few treatment options. While CIC-fusions are increasingly recognized as a unique clinical entity, to date CIC-DUX4 is the only CIC fusion protein for which any mechanistic research has been published. Even for the limited available work, the suggested therapies are likely to be limited by a lack of specificity. A failure to understand the biology underpinning CIC-fused oncoproteins and their signaling pathways hampers the development of smarter and more effective treatment strategies. Due to the lack of existing research on CIC-fused oncoproteins, this proposal intends to leverage prior knowledge about the function of individual partner genes to inform hypotheses about how CIC-fusions function. Wild type CIC is known to be relocalized from the nucleus to the cytoplasm by FGF- or c-Src-mediated posttranslational mechanisms, and the WT CIC protein residues thought to be responsible for this shuttling are typically conserved in CIC-DUX4 proteins. Thus, Aim 1 of this proposal tests the hypothesis that FGF- or c-Src signaling can mediate CIC-DUX4 subcellular relocalization. This will be achieved using a novel EGFP-tagged CIC-DUX4 construct allowing for dynamic microscopic analysis of CIC-DUX4 localization, as well as using patient-derived cell lines for in vivo modeling. If this hypothesis is correct, then forced relocalization could be a novel therapeutic strategy. To move beyond the study of CIC-DUX4, Aim 2 will leverage structure-function studies to define the mechanistic underpinnings of the means by which CIC-NUTM1 drives tumorigenesis. CIC-NUTM1 is thought to recruit p300 via the NUTM1 moiety to activate CIC target genes, yet preliminary data suggests this is not the complete story. Thus, Aim 2 will test the hypothesis that NUTM1 possesses some yet unidentified p300-independent functional domain which contributes to the activity of the CIC-NUTM1 fusion. These experiments will leverage recently cloned synthetic, patient-based CIC-NUTM1 fusion plasmids that allow for the first modeling of CIC-NUTM1 tumors. Uncovering the mechanisms through which CIC-NUTM1 drives tumors will reveal targetable vulnerabilities that can shape future therapies. Together, the aims will provide foundations for improving treatments and outcomes in CIC-rearranged tumors. This proposal will be carried out in a world-class environment at UCSF, which specializes in translational cancer research. The fellowship will provide experimental training in advanced microscopy and mouse techniques as well as professional development opportunities in areas such as scientific writing and mentorship which will prepare the fellow for a career as an independent researcher.

NIH Research Projects · FY 2024 · 2024-08

Project Summary/Abstract Over the last decade, pancreatic islet transplantation has become a consistent and effective minimally invasive approach to restore normoglycemia in patients with type 1 diabetes1. Despite recent advances, widespread application has been limited by several barriers, including (1) poor survival and engraftment of islets following infusion into the portal vein of the liver, secondary to instant blood-mediated inflammatory reaction (IBMIR) and ischemia, (2) an inability to consistently achieve long-term insulin independence despite multiple infusions of islets from up to three donors, (3) a critical shortage of donor islets available for transplant, and (4) the inability to retrieve the graft in real time in case of adverse events. This proposal aims to address all four of these barriers utilizing genome-engineered stem-cell-derived beta cells. In contrast to cadaveric islets, human pluripotent stem cell-derived beta (SC-beta) cells represent a replenishable source of replacement beta cells2–7. Improving engraftment of SC-beta cells in an extra-hepatic site, together with engineering safety switches to delete any implanted SC-derived cells that display aberrant growth, will render this therapy safer and more effective, bringing benefit to more patients. Our prior work has shown that co-transplantation of parathyroid gland tissue with adult donor islets improves survival and engraftment at a retrievable intramuscular injection site in mice. We hypothesize that the secreted factors uniquely expressed by parathyroid gland may improve islet survival and vascularization. However, to overcome the limitations of parathyroid gland donor tissue availability and procurement, these effective factors will be introduced into stem-cell-derived beta cells using genome engineering strategies to improve engraftment and angiogenesis. Moreover, because the potential for outgrowth or oncogenesis is a major safety concern with any stem-cell-derived therapy, we will dually incorporate inducible safety switches that will allow for small molecule-driven clearance of residual pluripotent cells following beta cell differentiation, as well as clearance of the entire graft in the instance of an adverse event. These approaches will be vetted by transplanting engineered stem-cell-derived beta cells into immunodeficient mice that have induced diabetes, to directly assess the disease-modifying activity of these implanted cells in a physiological context. Ultimately, this work will advance the therapeutic potential of beta cell transplantation and address the major current clinical bottlenecks that prevent stem-cell-derived beta cell therapy from becoming a universal treatment strategy for diabetes.

NIH Research Projects · FY 2025 · 2024-08

ABSTRACT: Immunotherapy has led to remarkable improvements in patient survival for many tumor types. In particular, immune checkpoint inhibitors have shown efficacy in many cancer types. These drugs act by turning off pathways that inactivate T-cells and allow patients’ adaptive immune response to attack tumors,. However, very little is known about how immunotherapy affects different racial and ethnic populations. Breast cancer is a disease with substantial disparities in outcomes. Black women have particularly high risk of mortality from breast cancer and also have higher risk of “triple negative” (estrogen receptor, progesterone receptor and Her2 negative) breast cancer (TNBC) which is more responsive to immunotherapy. The tumor immune microenvironment is a strong prognostic factor among women with breast cancer and a strong predictor of benefit from immunotherapy. In preliminary data, we have found that breast tumors from women of African ancestry have higher rates of lymphocytic infiltration which is generally associated with better response to immunotherapy. However, there is no clear data on how well Black women, Hispanic/Latina or Asian women do on checkpoint inhibitors. In this application, we will focus on breast cancer disparities and immuno-oncology in the Research Project. First, we will population based (cancer registry) data to determine how frequently women of different racial, ethnic and ancestry groups with TNBC are treated with immunotherapy. We will also leverage an existing trial of locally advanced breast cancer, ISPY2, which includes an immune checkpoint inhibitor. The trial will allow us to examine genetic ancestry in addition to race and ethnicity. Second, we will examine the tumor immune microenvironment among women with breast cancer in relation to genetic ancestry and in relation to genetic variants that we have identified as associated with the tumor immune microenvironment. We will perform deep characterization using single nuclear RNA-sequencing of a subset of the trial women, comparing responders to non-responders selected by stratification on race and ethnicity. We will integrate all of these data and leverage the organizational structure of the accompanying Administrative Core to interpret these data within the context of what is already known about cancer immunology, immunotherapy and health disparities. We will build on these results and other projects and datasets to plan larger projects to address more ambitious questions of how different populations respond to immunotherapy, how their rates of adverse events compare.

NIH Research Projects · FY 2026 · 2024-08

PROJECT SUMMARY Periodontitis is a common, chronic, inflammatory disease, triggered by subgingival microbial agents, which can lead to tooth loss and contribute to systemic inflammation. Type 2 diabetes (T2DM) is an important systemic modifier of periodontitis, associated with increased severity and progression of periodontal destruction in affected individuals. Of note, there are large disparities in the prevalence of both periodontitis and T2DM, with minority and low socio-economic status individuals, especially Blacks, being disproportionately affected. Although pro-oxidative and pro-inflammatory signaling have been described as mechanisms underlying enhanced periodontal destruction, especially in the presence of T2DM, the specific, upstream events involving innate immunity and immune cell recruitment are still not fully understood. Recent studies at the single-cell level from our group revealed that: 1) there is heterogeneity in resident immune cells in gingival tissue and in circulating monocytes/macrophages in periodontitis and T2DM; 2) there is a systemic pre-programming of circulating monocytes towards a pro-inflammatory state in patients with periodontitis and T2DM; 3) there are race-specific cellular changes in gingival tissue in periodontitis, including a decrease in immune tolerant PD-L1+ monocyte/macrophages in Blacks, associated with reduced anti-inflammatory macrophage phenotype; and 4) the epigenetic regulator JMJD3 can control macrophage polarization and function in periodontitis. These preliminary findings strongly support the feasibility and significance of the three specific aims in the present application. The proposed work is original and innovative as it seeks to shift current thinking in the field. We plan to build upon our previous work and test our overarching hypothesis that periodontitis, on its own and especially when complicated by T2DM, significantly affects the cellular composition, transcriptomic profile, and monocyte/macrophage activation and function locally (gingival tissue) and systemically (circulation), and that race plays an important role in this setting. First, we propose to dissect the single-cell transcriptomic signature and functional network of myeloid-derived cells in periodontitis patients without or with T2DM. Using single-cell RNA-sequencing, we will identify the transcriptional networks associated with immune cells in gingival tissue and blood samples of periodontitis patients versus healthy controls, and the added burden conferred by T2DM. Then, we propose to identify the effects of race on monocyte/macrophage signaling and function in periodontitis patients without or with T2DM. We will explore the biological basis for the observed periodontal health disparities in Blacks, namely differences in immune cellular composition, function, and signaling locally and systemically. Lastly, we aim to identify the role of the epigenetic regulator JMJD3 in modulation of macrophage phenotype and function in periodontitis. Taken together, several notable conceptual and methodological innovations have been introduced in this application to move the field forward. The proposed studies, with a focus on health disparities, will assist in increasing our understanding of the pathogenesis of periodontitis and its link with T2DM.

NIH Research Projects · FY 2024 · 2024-08

PROJECT SUMMARY/ ABSTRACT The goal of HIV cure research is to induce “antiretroviral therapy (ART)-free” remission by eliminating persistent HIV to overcome the need for lifelong ART and improve clinical outcomes associated with persistent HIV (increased inflammation- and aging-associated diseases). However, HIV cure trials have thus far failed to demonstrate a clinically meaningful reduction in the HIV reservoir size or lead to sustained ART-free viral control. The goal of the proposed work is to address a critical need – to determine host in vivo mechanisms that drive HIV reservoir decay and sustain long-term viral control, identifying potential novel therapeutic candidates for HIV cure. We recently demonstrated that class II cytokines (specifically, IL-10 and type I and III interferons) exhibited ongoing fluctuations and predicted faster HIV reservoir decay during the first 24 weeks of ART. These data support prior work demonstrating a dynamic and temporal role of type I interferons in controlling HIV/SIV infection and two recent studies that showed a critical role for IL-10 in the maintenance of the HIV/SIV reservoir. However, these other studies did not specifically evaluate the role of host cellular drivers of class II cytokine-mediated viral control across HIV stages: acute HIV infection (AHI), ART initiation (ARTi), ART suppression (ART+), and ART interruption (ATI). Our central hypothesis is that class II cytokines dynamically control virus at different stages of HIV. We aim to identify the host cellular drivers of class II cytokine-mediated viral control across HIV stages from 50 participants from our UCSF Treat Acute HIV cohort (diagnosed and initiated ART <100 days from infection), which includes monthly biospecimen sampling as well as optional tissue sampling (gut, lymph node) and ATI sub-studies. Host viral control will be measured as (1) HIV reservoir decay and (2) post-ATI control (time-to-viral- rebound [TTVR]). Since there is no “gold standard” for measuring the HIV reservoir, we will leverage several HIV reservoir assays currently being performed in our cohort, using additional funded grants. We hypothesize that across longitudinal blood timepoints (Aim 1), class II cytokine-mediated cellular responses exert robust innate antiviral effects (e.g., after HIV transmission), enhance adaptive/cell survival responses during long-term ART+, and re-induce innate responses at ATI. We hypothesize that these cellular responses are more robust in tissues than in blood (Aim 2) since several class II cytokines (IL-10, IFN λ/IL 29) act as antiviral defenses specifically at mucosal barrier tissue sites. Finally, we hypothesize that plasma metabolic signatures will predict class II cytokine-driven viral control, priming their use in future HIV cure clinical monitoring (Aim 3). Targeting class II cytokines represents a promising interventional strategy, but given their complex host-viral temporal dynamics, a deeper understanding of the natural timing, cellular drivers, and tissue-specificity of these cytokines is needed to better inform future HIV cure trial design. By identifying the cellular drivers of class II cytokine-driven viral control across stages of HIV, we expect that findings form this study can be applied/compared to other acute HIV populations, as well as other class II cytokine-mediated diseases (e.g., cancer, autoimmune disorders).

NIH Research Projects · FY 2025 · 2024-08

Abstract Immunosuppressive and homeostatic mechanisms prevent immune cells and tissues from eliminating solid tumors, limiting the efficacy of anti-tumor immunity. Precise dissection of these homeostatic mechanisms can lead to better understanding of how tumors persist and grow within tissues. Our prior studies demonstrate that the A20 protein is a potent regulator of immune homeostasis, regulating both pro-inflammatory and cell death signals. Our recent preliminary data reveal that A20 is highly expressed in tumor microenvironments and that one specific biochemical motif of this protein restrains both acute and anamnestic antitumor immunity. This proposal will dissect the cellular and molecular pathways by which A20 regulates anti-tumor immunity.

NIH Research Projects · FY 2025 · 2024-08

This is a Beeson K76 Career Development Award for Dr. Sara LaHue, a fellowship-trained inpatient neurologist (neurohospitalist) clinician-investigator. Dr. LaHue requests 5 years of salary and research support to provide protected time and training to study delirium risk factors and associated longitudinal clinical trajectories in older adults with acute mild traumatic brain injury (mTBI). Delirium is a sudden change in mental status affecting over 7 million hospitalized adults in the United States annually and is a major risk factor for Alzheimer's Disease and Alzheimer's Disease Related Dementias (AD/ADRD), functional and cognitive decline, and death. Dr. LaHue’s long-term goal is to become a leading expert in geriatric inpatient neurology, applying an aging biology lens to advance delirium diagnostics and therapeutics to improve health outcomes for older hospitalized adults. This project will advance her career development through investigating post- traumatic delirium as a high-impact, patient-focused outcome with substantive importance to both geriatrics and neurology. While Dr. LaHue is uniquely qualified to pursue her career goals, additional advanced training in four areas is critical for her success: (1) aging biology research methods, (2) geriatric TBI research methods, (3) advanced biostatistical methods, and (4) leadership. Dr. LaHue developed a rigorous 5-year training program with her exceptional mentoring team to gain this foundation. This application will provide preliminary data and tangible skills to support Dr. LaHue’s future NIH R01 applications and launch her independent research career. As a neurohospitalist caring for patients with delirium, Dr. LaHue recognized that patients with neurological disorders are disproportionately excluded from delirium research, limiting generalizability of existing research to these populations. Delirium affects nearly half of adults with mild-moderate TBI, yet existing knowledge is largely limited to moderate-severe TBI (despite mTBI accounting for >75% of US TBI cases) or young populations. There is a critical need to identify how baseline vulnerabilities, such as advanced biological age, inform delirium risk in geriatric TBI, and how delirium impacts both cognitive and functional outcomes, to optimize recovery for older adults with mTBI. To address these critical knowledge gaps, Dr. LaHue will investigate the following specific aims in a prospective cohort of older adults with acute mTBI: (1) identify whether biological age metrics are associated with post-traumatic delirium, (2) identify whether post- traumatic delirium is associated with longitudinal cognitive and physical function, and (3) determine the association between biological age, delirium, and longitudinal clinical outcomes. The findings will illuminate vulnerable subgroups that may benefit from targeted acute delirium management, inform clinical guidance for patients at risk for impaired recovery, and lay the foundation for a multicenter study to uncover mechanistic links between TBI, specific biological aging pathways, and delirium to inform future therapeutics.