University Of California, San Francisco

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY This is an application for a Mentored Patient-Oriented Research Career Development Award (K23) by Dr. Nijee Luthra, a neurologist specializing in movement disorders. As the number of people with Parkinson’s disease (PD) is expected to grow to pandemic proportions, cognitive deterioration associated with PD will prevail in a majority of this population. The integrated career development and research plan proposed for this K23 award is motivated by an increasing awareness of the urgent need to identify pathways that target cognitive impairment in PD. Exercise has potent anti-aging effects and can influence cognitive outcomes in PD but its underlying mechanisms remain unclear. Identifying biomarkers that respond to exercise, and how they associate with cognition and underlying disease pathology may elucidate key mechanisms for countering cognitive decline. This proposal focuses on longevity hormone klotho as a biomarker that may mediate exercise-induced benefits and contribute to cognitive resilience. Klotho has been shown to enhance cognition, synaptic plasticity, and brain volumes in mouse models of aging and neurodegeneration. Dr. Luthra and her team have also recently shown that klotho associates with better cognitive function in PD patients. While klotho levels decrease with aging and in PD, physical exercise robustly increases klotho levels in healthy adults. Whether exercise increases klotho in PD and protects against cognitive decline is not yet known. To this end, the aims of this research proposal are: 1) knowing its positive link with cognition, to now investigate whether klotho modifies underlying markers of PD pathology, and 2) in parallel, design a pilot study to determine if klotho increases in response to exercise in PD and correlates with improved cognitive abilities. Answers to these questions would highlight the potential of klotho as an exercise-related biomarker and as a new pathway for targeting cognitive dysfunction. The research plan is complemented by didactic and practical training in design and conduct of clinical trials, advanced biostatistical methods, and analysis and interpretation of multimodal biomarkers and cognitive assessments. To accomplish the goals of this research and training, the candidate has assembled a mentoring team with decades of experience in clinical trials and exercise interventions, along with expertise in biomarkers and cognitive impairment in PD. Completion of this research plan and training objectives will allow the candidate to advance her career in becoming an independent clinical investigator focused on investigating strategies such as exercise and multiple related biomarkers that mediate cognitive resilience in PD.

NIH Research Projects · FY 2025 · 2022-09

PROJECT ABSTRACT The Costello lab investigates cellular immortality and evolution in brain tumors with the goal of translating our discoveries into new therapies. I play an essential role in our studies to understand and overcome the genomic and epigenomic intra-tumor heterogeneity, driven by tumor evolution, that underlies therapeutic failures. One translational goal is to identify mutations that produce immunogenic neoantigens that are present throughout the whole tumor, to develop personalized immunotherapies in collaboration with Dr. Okada. Working with an interdisciplinary clinical team, we developed a unique, 3-dimensional whole tumor sampling approach in which we obtain 10 spatially mapped samples per tumor selected by the neurosurgeon to maximally represent the whole tumor. We have begun applying the genomic, transcriptomic and T cell receptor (TCR) sequencing data I produced from these spatially mapped samples to identify immunogenic neoantigens and their cognate TCR present throughout the tumor. I am also a significant contributor to our tumor immortality studies. To proliferate indefinitely, tumor cells must overcome the normal limits on lifespan dictated in large part by telomere shortening, a consequence of cell divisions in the absence of telomerase activity. Eighty percent of glioblastoma and many other cancers overcome this lifespan barrier to achieve cellular immortality by acquiring a mutation in the promoter of Telomerase Reverse Transcriptase (TERT). We discovered that the TERT promoter mutation activates the normally silent TERT gene and telomerase activity through selective recruitment of GABP, a transcription factor which does not normally regulate TERT. Using experimental targeting of GABP, we showed that TERT expression is reduced selectively in cells with the TERT promoter mutation, and when combined with chemotherapy, it dramatically reduces GBM growth in vivo. Currently, I am studying a newly discovered homeostatic control on GABP subunit expression and its relationship to TERT regulation. To translate these mechanistic studies into a new therapy, Dr. Costello co-founded a biotech startup which has discovered small molecules with drug-like properties that reduce TERT in a mutation dependent manner. In addition to performing bench research to address these translational goals, my responsibilities include: (1) management and oversight of the lab’s infrastructure and tumor sample collection; (2) technology and methods development for the group; (3) ensuring that all laboratory research is conducted safely in accordance with regulatory requirements; and (4) training new lab members and individuals throughout the Brain Tumor Center. This R50 application requests salary support for these ongoing activities to advance the scientific goals of the following NCI-funded projects: 3-D spatial approach to discover genomic effectors of immunosuppression during malignant transformation (R01 CA244838); The Brain Tumor SPORE P1 – A New Therapeutic Target for TERT Promoter Mutant Glioma (2P50CA097257).

NIH Research Projects · FY 2025 · 2022-08

Project Summary/Abstract: More than 40% of adult Americans are obese and obesity is common among patients with severe asthma. The mechanisms underlying the association between obesity and severe asthma are poorly understood, but a clue comes from the metabolic consequences of obesity, which include insulin resistance and systemic interleukin-6 inflammation. We recently showed that a subset of obese asthma patients have metabolic dysfunction (MD) and that obese patients with MD have more severe asthma than obese patients without MD. In addition, we found that lower lung function in obesity is more strongly related to measures of MD than measures of body mass index. Furthermore, we found that obese patients with MD respond poorly to inhaled and systemic corticosteroids. All of these findings lead us to hypothesize that obesity-related MD and insulin resistance causes airway pathology that leads to corticosteroid resistant airway dysfunction. Here, we propose to test this hypothesis by comprehensively characterizing airway physiology and pathology in obese asthma patients with MD and exploring mechanisms by which insulin mediates airway dysfunction. We have 3 aims: Aim 1 will characterize the radiographic and physiologic abnormalities in obese asthma patients with and without metabolic dysfunction (MD). Here we will analyze computed tomography lung scans and perform cardiopulmonary exercise testing in asthma patients with and without MD. We hypothesize that patients with MD have radiographic measures of bronchial wall thickness and air trapping and suffer dynamic hyperinflation during exercise leading to exercise intolerance. Aim 2 will characterize airway inflammation and airway remodeling in asthma patients with metabolic dysfunction; Here, we will map the cellular profile of asthma patients with MD using transcriptomic profiles from induced sputum samples and measure basement membrane zone thickness from endobronchial biopsy samples to test our hypothesis that airway inflammation in obese patients with MD is type-2 low and that these patients have airway remodeling characterized by subepithelial fibrosis. Aim 3 will develop gene signatures of insulin-related airway disease and determine if these signatures are upregulated in asthma patients with insulin resistance. Here we will utilize in vitro cell cultures and spatial transcriptomics to identify gene expression signatures of insulin-mediated airway disease in airway fibroblasts and epithelial cells. We will then determine if these gene signatures are upregulated in airway epithelial brushings or sputum cells from asthma patients with IR. Together these aims will help address an important gap in knowledge about disease mechanisms operating in obese patients with severe asthma and promises to provide data to inform novel treatment approaches for these patients.

NIH Research Projects · FY 2025 · 2022-08

Project Summary The overarching goal of this proposal is to define the interplay of epigenetics and developmental context in driving pediatric high-grade gliomas (pHGG), universally lethal tumors defined by histone mutations, so as to identify better targeted treatments. This work utilizes an innovative cerebral organoid-based model that allows side-by-side comparison of oncohistone mutants and dynamic modulation of oncogene expression in a three- dimensional human context. Leveraging this innovative model, Dr. Graham will use cutting-edge single cell profiling techniques and preclinical glioma modeling to address unanswered questions that currently hamper therapeutic development for these patients. In Aim 1, chromatin profiling and single cell RNA sequencing will be used to investigate the distinct effects of two different oncohistones (H3.3K27M and H3.3G34V) during neural development. In Aim 2, the timing and order of mutations will be manipulated to evaluate the impact of cellular and mutational context on tumor phenotype. Finally, in Aim 3, orthogonal genetic “rescue” and pharmacologic inhibition approaches will be used to interrogate the role of these mutations in tumor maintenance. This work, as well as Dr. Graham's career goal, is well-aligned with the NINDS mission to seek basic knowledge about the brain and to translate that knowledge into clinical impact. Through the proposed studies and the accompanying career development plan, Dr. Graham will gain essential training in epigenetics, bioinformatics and preclinical glioma studies, critical gaps in her current skillset. Dr. Graham is an Instructor of Neuro-Oncology under the mentorship of Dr. Ingo Mellinghoff at Memorial Sloan Kettering Cancer Center (MSK). Dr. Mellinghoff is a leader in translational glioma research with a strong track record of mentoring trainees to independence. He and Dr. Graham have assembled an exceptional Advisory Committee with expertise in chromatin biology, translational oncology, and bioinformatic analyses: Dr. Kristian Helin, Dr. Ross Levine and Dr. Nicholas Socci. MSK provides an outstanding environment for cultivating budding careers in biomedical research, with unparalleled resources, support, and opportunities for collaboration. Upon completion of the proposed work, Dr. Graham will be ideally positioned and uniquely qualified for a career as an independent investigator elucidating fundamental aspects of epigenetic regulation in neural lineage commitment and applying her findings to address the unmet needs in the treatment of malignant glioma.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY The orbitofrontal cortex (OFC) is a major hub in the brain that interacts with numerous other brain circuits to control many behaviors related to learning, memory and decision-making. OFC has also emerged as a significant node of dysfunction in alcohol use disorder (AUD). Nevertheless, how different OFC outputs contribute to AUD remains largely unknown. One major challenge in such an investigation is that AUD develops over long time- scales and is a chronic relapsing condition. Another challenge is that distinct projection outputs of OFC have different functions. Thus, investigation into the neuronal mechanisms underlying AUD will benefit from a longitu- dinal study of projection-specific neurons that spans the long timescale representative of AUD. Recent advances in two-photon microendoscopic calcium imaging allows the longitudinal tracking of the same projection-specific OFC neurons across months. In this proposal, we will use this cutting-edge technology to study the function of two OFC circuits—projections to dorsal striatum (targeting the densest projection near the border between dorsal and ventral striatum) and the ventral tegmental area (VTA) in alcohol related behaviors. These downstream targets are themselves critical regulators of natural reward or alcohol related behaviors, and these projections have been demonstrated to have at least some non-overlapping functions in natural reward learning. The central question of interest in this proposal is whether the encoding adaptations during initial alcohol use in neuronal ensembles within these OFC circuits predict their subsequent encoding and control of aversion-resistant operant alcohol seeking or cue-induced reinstatement. In aim 1, we will image alcohol related neuronal activity weekly in the above OFC outputs while C57/BL6 mice have intermittent access to 20% alcohol in a two-bottle choice paradigm (IA20%2BC) for 7-8 weeks. We will test the hypothesis that OFC→dorsal striatum, but not OFC→VTA, neurons strengthen their responses to alcohol, as animals begin preferring alcohol. In aim 2, we will longitudinally track the same neurons from initial alcohol consumption to subsequent tests of aversion-resistant seeking. Spe- cifically, we will investigate the role of the above circuits during operant self-administration of alcohol with or without quinine adulteration, and test the hypothesis that the same OFC→dorsal striatum neurons that encode initial escalation of alcohol preference also encode and mediate aversion-resistant seeking. In aim 3, we will longitudinally track neurons from initial alcohol use to subsequent extinction and cue-induced reinstatement of operant alcohol seeking. We will test the hypothesis that OFC→VTA neuronal activity predicts and mediates cue-induced reinstatement of operant alcohol seeking. Overall, these studies will yield insights on the extent of overlap of neuronal encoding of alcohol consumption/preference, aversion-resistant operant seeking, and cue- induced reinstatement.

NIH Research Projects · FY 2025 · 2022-08

ABSTRACT A sea-change in attitudes towards reproducible research in social science and epidemiology has occurred over the past 30 years. Reproducibility has moved from a footnote to center-stage and is now recognized as an essential component of scientific rigor. The concepts of reproducible science relate not only to the capacity to reproduce the work of a specific study when using the same data, but to the larger ecosystem in which research is planned, fielded, critiqued, and interpreted. Systemic biases and error-prone research pipelines both compromise reproducibility and are now recognized to hinder scientific progress. The nature of research has also evolved, with increasing emphasis on data analysis, growing access to extensive computational power, and large, complex data sets. Behavioral and social science research on healthy aging faces special concerns for reproducibility and these concepts should be integral to training on aging research. The University of California, San Francisco Training in Reproducible Research on Aging for Social Science and Epidemiology (UCSF-TRASE) program will develop (AIM 1) intensive short courses on reproducible research perspectives and skills. We propose four brief (3-day), intensive training modules. Each module combines didactics and experiential learning, with a substantive focus on health disparities and aging, and methodologic focus on causal inference. Module 1 introduces concepts of reproducibility for research on population health and aging. This module is appropriate for researchers and consumers of scientific research and will provide critical evaluation skills relevant for reviewing journal articles and grant applications, interpreting published findings, and leading research Module 1 assumes a basic scientific research background but will be accessible to, for example, practicing physicians, science journalists, administrators, as well as graduate and post-doctoral trainees. Module 2 provides skills for implementing reproducible analyses, such as pre-registration; statistical coding hygiene and evaluation; transparent reporting; and documentation, including for collaborative projects. Module 3 addresses fielding primary data collection to foster reproducibility, considering study design, statistical power, protocol documentation, data quality control. Module 4 provides training on integrating evidence to enhance reproducibility of scientific advances, e.g., meta-research, evidence triangulation approaches. Each training module can stand alone or be combined for a more comprehensive skill set. We emphasize hands-on skills building to learn best practices in the context of contemporary problems. The modules build on the outstanding foundation in the existing UCSF training programs, using many activities already demonstrated to succeed in our other training programs, and curating for the intensive short-course format to provide participants, across career stages, with both conceptual and technical skills to enhance reproducibility. We propose (AIM 2) to roll out the modules with ongoing evaluation and refinement and (AIM 3) use multiple dissemination strategies to maximize the impact of the curriculum.

NIH Research Projects · FY 2024 · 2022-08

PROJECT SUMMARY/ABSTRACT Chronic pain (CP) is one of the most common and debilitating medical conditions resulting in substantial morbidity, lower quality of life and tremendous health care costs. With ongoing and tragic consequences, opioids were overprescribed creating a surge in opioid use disorders and overdose deaths. Although non- pharmacologic interventions have a strong evidence base, these interventions are rarely available and expensive. The common co-morbidities of psychiatric and substance use disorders trigger further stigma and lower quality care. Subjective reports of pain symptoms and the cultural meanings ascribed to them create a situation ripe for health care disparities driven by multilevel biases on individual, provider, and systemic levels. These biases are manifested in stigmatizing language and the denial of interventions to reduce pain and alleviate suffering. Multiple studies have shown that racial and ethnic minorities with CP are especially mistreated. It is essential to accelerate the creation of hybrid CP management programs that improve access to treatments while simultaneously addressing the stigma, bias, and mistrust that further harm and isolate patients with CP. The INSPIRE CP intervention creates a hybrid blend of tailored cognitive-behavioral therapy, physical therapy, mindfulness, and pain education delivered via a trilingual mobile app and supported by a telehealth pain coach providing essential care coordination with PCPs within the EHR. PROs for pain, depression, anxiety, substance use, and a range of social risks and needs will be regularly collected, summarized in the coaching dashboard, and shared with PCPs. The intervention builds on an existing, in person pain program for marginalized patients but significantly improves reach, expands cultural and linguistic adaptations, and directly addresses multilevel bias and stigma through intensive community engagement, individual and group support, and the provision of “tech tutoring” to improve digital health literacy. The two year R61 development phase includes 3 specific aims with matched milestones: 1) creation of the digital tool and coaching protocol using intensive community engagement, 2) iterative development of educational and implementation strategies for health care staff and providers, and 3) a 3 month pilot test to further assess acceptability and feasibility. The three year R33 validation phase includes 3 additional specific aims 1) perform a pragmatic RCT with n=586 patients comparing INSPIRE to enhanced usual care, 2) analyze secondary outcomes and the treatment effects model, and 3) a mixed method evaluation of implementation outcomes using Normalization Process Theory to better design strategies for future scale.

NIH Research Projects · FY 2025 · 2022-08

ABSTRACT The proposed work will fund two postdoctoral scholars from varied disciplines each for 3 years to focus on equity in Alzheimer’s disease and related dementias. This application will create a training program for early career researchers from the United States (U.S.) who are passionate about brain health for underserved communities. We will leverage two outstanding programs at the University of California at San Francisco’s (UCSF). The Global Brain Health Institute (GBHI) led by MPD/PI, Victor Valcour, which leads a 12-month international training program in equity and dementia with a particular focus on low and middle income countries. This 12-month course enrolls international and inter-professional trainees and provides an equity-based curriculum in Alzheimer’s disease and related dementias, leadership training, career mentoring and a robust alumni experience to advance their careers. The UCSF Memory and Aging Center (MAC), led by MPD/PI, Bruce Miller, has a remarkable record in training successful academic behavioral neurologists with a T32-funded behavioral neurology training program (BNTP). This remarkable environment provides outstanding research opportunities for trainees supported by the current T32 application to research Alzheimer’s disease and related dementias. Although GBHI does not exclude applications from the US and has a track-record of successful engagement of U.S. citizens, the one-year curriculum is insufficient for early-stage trainees (e.g. postdocs) who typically require 2-3 years of support in order to successfully transition to academic posts. The two-year BNTP fellowship accepts only doctors, is neurologically-focused and does not specifically focus upon brain health equity. This T32 will fill this gap in both programs by intentionally targeting multi-disciplinary early career patient-oriented researchers and by providing 3-years of support. These T32 trainees will leverage the most robust aspects of coursework and environment provided by the curriculum at GBHI and the MAC while also working with faculty across multiple departments at UCSF as they advance trajectories toward independence. Our application includes substantial novelty in that trainees will be working with other international trainees who are in later stages of their career and will serve as experts for work in diverse immigrant communities in the U.S. Our long-term goal is to contribute to the pool of academic research working together to better understand disparities in Alzheimer’s disease and related dementias and create culturally appropriate solutions to optimize diagnosis and care for underserved groups.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY Alzheimer’s disease (AD) and related dementias represent a growing public health concern with tremendous impact on patients and their families. Efforts to treat AD effectively are partially confounded by different hypotheses regarding its initiation and progression. The varying hypotheses are reflected in the range of highly informative imaging methods used to study AD and its progression, such as positron emission tomography (PET) targeted to specific cerebral proteins. In this project we will develop a novel [18F]-labeled PET imaging tracer, RP-115, to evaluate changes in astrocytes in healthy versus cognitively impaired AD patients by quantitative PET imaging of the excitatory amino acid transporter 2 (EAAT2) that is primarily localized on astrocytes and is significantly down-regulated in select cerebral regions of AD brain. The project hypothesis is that regional cerebral decreases of RP-115 tracer binding to astrocyte EAAT2 detected by PET imaging in live human brain can be used as an early and sensitive measure of AD onset and progression. The first-in-human project objective is composed with two translational development goals: 1) to establish RP-115 tracer human safety, and 2) to utilize the tracer to assess regional cerebral EAAT2 tracer binding differences in healthy vs. Ab-, pTau- and cognitively-defined AD patients; and compare the EAAT2 AD data to existing AD FDG and MAO-B astrocytic-related PET profiles. We will test the hypothesis and satisfy the translational project objective by accomplishing three Specific Aims. Aim 1: Establish RP-115 safety in the clinic with male and female PET imaging. Aim 2: Acquire RP-115 EAAT2 imaging data in well-defined male and female healthy control and AD patient cohorts. Aim 3: Analyze the PET imaging data.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY/ABSTRACT In 2017, 1.7 million Americans suffered from opioid use disorders (OUD), which led to 47,000 American deaths from opioid overdose. Social determinates of health (SDoH) affect patients' OUD risk level and physicians' opioid prescribing. Physicians lack the tools to quickly and accurately assess SDoH associated with OUD, and lack knowledge of relevant resource for intervention. Clinical decision support (CDS) could quickly assess a patients' SDoH factors associated with OUD risk and provide actionable recommendations, which would reduce OUD risk assessment time and address knowledge gaps. In 2018, UCSF researchers created the Compendium of Medical Terminology Codes for Social Risk Factors that maps SDoH risks to medical vocabularies. However, most SDoH are documented in clinical notes. My long-term career goal is research independence with expertise in: 1) OUD risk assessment, 2) SDoH research, and 3) intervention development, implementation, and evaluation. Related to these goals, this study will use natural language processing (NLP) to identify SDoH in clinical notes, examine associations between SDoH and OUD, and develop a CDS tool to assess OUD risk. We will then assess usability, acceptability, and feasibility of using the CDS tool in clinical settings. This research will help physicians quickly and accurately assess OUD risk, intervene earlier, and improve care. Our research aims include: Aim 1. Use NLP to identify SDoH in clinical notes and examine associations between SDoH and OUD. We will use the Compendium and NLP to extract new SDoH in clinical notes. Two raters will manually validate the new SDoH, and use descriptive statistics to characterize associations between SDoH and OUD. (training goals 1 and 2). Aim 2: Develop a CDS tool to assess OUD risk. We will use SDoH and OUD associations from aim 1 to develop a supervised machine learning algorithm for our CDS tool. We will validate the CDS tool by measuring its ability to correctly assess OUD risk in patients' EHR data (training goals 1 and 2). Aim 3: Test the usability, acceptability, and feasibility of physicians' use of the CDS tool. 40 physicians will be asked to assess sample patient cases, then given CDS results on those same cases. Physicians will indicate whether they would follow the CDS's recommendations. Additionally, participants will be asked to complete an interview and questionnaire to evaluate usability and acceptability. We will assess feasibility by examining recruitment, implementation, and metadata. (training goal 3). These aims are achievable because I have experience in NLP and machine learning and my mentors are experts in OUD research, SDoH research, and intervention design; and have an outstanding record in career development. This K01 will help me achieve researcher independence by providing a) skills to develop an OUD risk assessment intervention; b) expertise in a novel growing SDoH field; c) an innovative trial-ready scalable intervention; and d) preliminary data for an R01.

NIH Research Projects · FY 2026 · 2022-08

PROJECT SUMMARY/ABSTRACT This proposal describes a 5-year research and career development plan that will enable Dr. Jarish Cohen to achieve his long-term goal of becoming an independently funded physician-scientist studying how regulatory T cells (Tregs) protect cutaneous epithelial stem cells during development, homeostasis, and disease. Currently, very little is known about the mechanisms skin-resident immune cells use to safeguard cutaneous epithelial stem cells in inflammatory dermatoses and alopecias. The proposed research will focus on uncovering the mechanisms by which Tregs protect hair follicle stem cells (HFSC) from attack by autoreactive T cells. Dr. Cohen has generated a novel experimental in vivo model of Treg-mediated protection of HFSC from autoimmune attack, that closely resembles a highly morbid form of human scarring alopecia. Additionally, he has pioneered a highly innovative topical technique to delete genes specifically in skin-resident Tregs, which will allow him to resolve organ-specific mechanisms of Treg-mediated immunoprotection of stem cells. In Aim 1, Dr. Cohen will elucidate the spatial and temporal kinetics of Treg-mediated HFSC protection and dissect the mechanism of skin Treg localization to the HFSC niche. Aim 2 will focus on elucidation of the distinct mechanisms that Tregs in the skin and lymph nodes employ to safeguard against HFSC destruction. In Aim 3, Dr. Cohen will leverage comprehensive transcriptomic and cutting-edge imaging technologies to identify molecules and pathways of Treg dysfunction and altered patterns of Treg localization in human scarring alopecias. The aggregate data will provide a major advancement in our understanding of how Tregs promote immune tolerance of epithelial stem cells and have the potential to identify novel therapeutic strategies to treat human dermatoses. During his post-doctoral work and as a Clinical Instructor in the University of California, San Francisco (UCSF) Dermatopathology Service, Dr. Cohen has strategically sought out additional training and mentorship in cutaneous immunology. Under the mentorship of Dr. Michael Rosenblum, M.D., Ph.D., an expert in skin Treg biology, the candidate, co-mentors (Drs. Jason Cyster, Ph.D., and Ophir Klein, M.D., Ph.D.), and scientific advisors (Drs. Boris Bastian, M.D., Ph.D., and Abul Abbas M.D., Ph.D.) have developed a career development plan for Dr. Cohen to gain additional experience in state of the art immunology and cutting-edge imaging techniques, biostatistics, epithelial stem cell biology, and scientific communication. To enhance Dr. Cohen's training, a multidisciplinary advisory committee consisting of mentors, scientific advisors, and Dr. Jayanta Debnath, M.D., chair of the UCSF Department of Pathology, will meet biannually to review his progress and support his career development. The proposed training program draws on the combined resources of the Rosenblum Laboratory, the UCSF Immunology Training Program, and the UCSF Departments of Dermatology and Pathology. This will provide an ideal setting for Dr. Cohen's transition to an independent investigator.

NIH Research Projects · FY 2026 · 2022-08

Project Summary/Abstract The objective of this proposal is to provide a robust course of training for Fei Jiang, Ph.D., a candidate with an excellent foundation in statistical and machine learning research, to enable her to become an independent investigator in the field of quantitative data analysis and statistical/machine learning methods development for neuroimaging research. The proposed research aims to extract dynamic resting-state functional connectivity from multimodality imaging and use them for the prediction of cognitive decline. The central hypothesis is that the resting state functional connectivity changes over the imaging acquisition period, and this dynamic pattern is crucial for the optimal prediction of cognitive decline. Towards proving this hypothesis, a unique machine learn- ing framework is proposed to (1) robustly extract dynamic resting-state functional connectivity from multimodality imaging; (2) identify the important features that are associated with individuals' cognitive scores; and (3) predict cognitive decline using the identified important features. Successful completion of the proposed research will provide the next generation machine learning framework for the extraction and analysis of dynamic resting-state functional connectivity and lead to potential endpoints that can be used in the assessment of treatment effects. Recognizing the multidisciplinary nature of the work proposed, the author will be mentored and work closely with an expert committee from multiple scientific areas of relevance to the project (Neuroimaging, Neurodegenerative disease, Biostatistics): Srikantan Nagarajan (primary mentor), Ph.D., Department of Radiology and Biomedical Imaging, Ashish Raj (co-mentor), Ph.D., Department Radiology and Biomedical Imaging, William W. Seeley (ad- visor), M.D., Ph.D., Department of Neurology, John Kornak (advisor), Ph.D., Department of Epidemiology and Biostatistics, Marilu Gorno Tempini (collaborator), M.D., Ph.D., Department of Neurology, Charles McCulloch (collaborator), Ph.D., Department of Epidemiology and Biostatistics. This committee will be coordinated by Dr. Nagarajan. The goal is that by the end of the K25, Dr. Jiang will have the requisite knowledge, technical skills, and expertise to submit a successful R01 proposal that integrates her expertise in statistical and machine learn- ing methods with a knowledge of the questions and approaches pertaining to imaging in neuroscience, acquired through this training period.

NIH Research Projects · FY 2025 · 2022-08

The major barrier to long term survival following lung transplantation is a progressive loss of lung function, termed chronic lung allograft dysfunction (CLAD), for which constrictive fibrosis in small airways is a pathologic hallmark. CLAD affects over half of lung transplant recipients by 4 years post-transplant and negates much of the quality of life and functional improvements associated with transplantation. Pitt, Toronto, and UCSF Lung Transplant programs have refined transcriptional analysis of small airway brushings from lung transplant recipients as a novel technique to understand the gene expression changes at the anatomical site where CLAD pathology develops. We have published gene expression changes associated with CLAD validated across our centers. This proposal leverages this innovative approach to understand mechanisms of CLAD pathogenesis. Our preliminary data show an early upregulation of hypoxia pathways in airway brushings including genes that recruit and activate cytotoxic T lymphocytes using both airway epithelial cell culture in hypoxic conditions and pathway analysis of airway brush transcriptomes. This hypoxia signaling may reflect disordered microvasculature, absent bronchial circulation, and vascular inflammation associated with lung transplant. In recruited T lymphocytes, we also observed upregulation of tumor necrosis factor superfamily (TNFSF) genes, which are major drivers of apoptosis in lymphocyte targets. Our data show preferential apoptosis in airway club cells, the protectors and progenitors of small airways, in association with upregulated TNF-related apoptosis- inducing ligand (TRAIL) expression. Our single cell investigations in airway brushings and bronchoalveolar lavage (BAL) fluid show the segregation of these pathways across epithelial and lymphoid cell types. Based on these data, we hypothesize that airway hypoxia precedes TNFSF gene expression and T cell-mediated airway club cell apoptosis that drive CLAD pathogenesis. To test this hypothesis, we will generate parallel cohorts investigating bulk and single cell transcriptomes of CLAD versus controls across three centers, allowing for rigorous cross-validation of gene expression signatures. We will complement these studies with cell culture- based methods to determine mechanisms driving these gene expression changes. In Aim 1, we will quantify hypoxia-related transcripts in airway brush cells with respect to CLAD and determine how hypoxia can promote lymphocytic inflammation. In Aim 2, we will determine the cellular sources and kinetics of TNFSF co-stimulatory molecule expression in CLAD using airway brushes and BAL fluid. In Aim 3, we will investigate whether TRAIL preferentially induces club cell apoptosis. The synergy of three large lung-transplant translational research programs with world-class cross-institutional biostatistical infrastructures provides a unique opportunity to address this hypothesis rigorously. The cell-specific gene expression signatures over the time course of CLAD development that will be generated through this study are critically needed as surrogate biomarkers to support clinical trials of targeted therapies and to pioneer a novel approach to CLAD diagnosis.

NIH Research Projects · FY 2025 · 2022-08

Project Summary/Abstract The study of the genetic basis for type 1 diabetes (T1D) has benefited tremendously from examination of rare individuals with likely monogenic forms of the disease. Combined with GWAS, a number of polymorphisms in immune regulatory genes have been defined that contribute to genetic risk for T1D. Using whole exome sequencing of individuals with T1D enrolled in a monogenic diabetes registry, we identified an individual with a gain-of-function mutation in the SKAP2 gene, as well as several other T1D patients with potentially pathogenic variants in other leukocyte integrin signaling genes. These patients tend to have a number of autoimmune manifestations in addition to T1D, indicating defects in critical pathways of immune tolerance. Multiple GWAS studies have identified a strong genetic linkage between SKAP2 polymorphisms and T1D (at a frequency of ~20%), however the mechanisms by which alteration of SKAP2 could lead to autoimmune T1D are unknown. SKAP2 is expressed primarily in myeloid cells, where it functions as an adapter protein in the integrin signaling pathway, linking cell surface integrins to WASP and actin rearrangements that occur following leukocyte adhesion. The SKAP2 G153R mutation in our patient resulted in constitutive association of SKAP2 with WASP leading to a hyperadhesive phenotype in macrophages cultured from the patient or macrophages engineered to contain the SKAP G153R substitution. To understand how activation of leukocyte integrin signaling may contribute to T1D, we have generated knock-in (KI) mice containing the G153R substitution in murine Skap2, on the NOD genetic background. Female NOD.SKAP2 KI mice have a higher incidence and earlier onset of T1D than do NOD.WT animals; male NOD.SKAP2 also develop T1D (incidence ~50%) while male NOD.WT do not develop frank hyperglycemia. Initial analysis of these mice reveals evidence of ongoing inflammation early in life with development of a broad spectrum of auto-reactive antibodies. Dendritic cells from NOD.SKAP2 KI mice have increased antigen presenting activity to islet-specific transgenic T-cells while neutrophils from these mice show evidence of increased integrin signaling. These observations demonstrate that the NOD.SKAP2 KI mice appropriately model the autoimmune T1D disease observed in our patient. The project proposes to complete the analysis of these mice, under the hypothesis that increased cell adhesion in dendritic cells leads to prolonged DC-T cell interactions, which drives selection of auto-reactive T-cell clones leading to development of T1D, associated with broad spectrum autoimmunity. We will test this hypothesis in a variety of adoptive cell transfer experiments, by generation of conditional knock-in mice and by imaging of DC-T cell interactions in the inflamed islets. Similar studies will be performed for other candidate leukocyte integrin signaling mutations identified in the monogenic T1D registry. This study will address whether dysregulation of leukocyte integrin signaling may constitute an unrecognized genetic risk factor for T1D, suggesting potential alterative therapeutic approaches for these patients.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY The goal of this proposal is to develop novel PARP inhibitor nanomedicine and a companion PET biomarker for treatment of prostate cancer. Despite recent advances, metastatic castration resistant prostate cancer remains a lethal, incurable disease with poor outcomes. Recently, PARP inhibitors have demonstrated great promise in this disease in patients bearing enabling mutations. We have developed a novel nanomedicine, star-PEG-TLZ4, with a cleavable linker which enhances delivery of talazoparib, a PARP inhibitor, to tumors while reducing potential toxicity. We have also developed a cognate molecular imaging tool, [89Zr]DFO-star-PEG-TLZ3, which enables imaging of the delivery of this nanomedicine. In this proposal, we develop [89Zr]DFO-star-PEG-TLZ3 and star-PEG-TLZ4 as novel imaging agent and drug combination in prostate cancer. The central hypothesis of this proposal is that the star-PEG backbone will enable enhanced delivery of PARP inhibitors and the imaging agent to prostate cancer, both in animal models as well as in a pilot translational study. In order to test this hypothesis, we have assembled an experienced team of chemists, imaging scientists, physicists, and physicians to evaluate this method in preclinical models and to perform initial feasibility testing in men with metastatic prostate cancer. In specific aim 1, we test the biodistribution of [89Zr]DFO-star-PEG-TLZ3 in prostate cancer preclinical models including patient derived xenografts. In specific aim 2, we test if [89Zr]DFO- star-PEG-TLZ3 can serve as a companion biomarker of star-PEG-TLZ4 mediated talazoparib delivery, and test the efficacy of star-PEG-TLZ4 in prostate cancer models bearing enabling mutations. In specific aim 3, we perform a translational study in men with prostate cancer, to determine the feasibility of star-PEG mediated drug delivery and imaging in men with that disease. These experiments will help aid the development and implementation of star-PEG mediated PARPi delivery, thereby improving patient care for men with prostate cancer.

NIH Research Projects · FY 2025 · 2022-08

Abstract Immune dysfunction associated with co-infection and AIDS-related cancers is commonly observed in HIV-infected individuals. In particular, gene expression programs in the immune system are often abnormally regulated in these individuals. We and other groups have recently discovered that the positive transcription factor b (P-TEFb), a critical cellular factor required for productive elongation of transcription, is severely down-regulated in quiescent and aberrant T cells. In resting CD4+ T cells, representing major latent HIV reservoirs, the expression of the cyclin T1 (CycT1) subunit of P-TEFb is diminished post-transcriptionally via currently unknown mechanisms, this being a main cause of HIV latency and tumor-specific T cells' defective response to check-point inhibitors and/or CAR-T cell therapies. Since increasing CycT1 is a prerequisite and mandatory step for optimal HIV reactivation and proper immune response against other pathogens and tumor cells, understanding the mechanism of CycT1 down-regulation is crucial. We have recently demonstrated that P-TEFb assembly regulated by phosphorylation determines the stability of CycT1. Also, we have identified all key players, including E3 ligases, involved in CycT1-degradation. Therefore, we hypothesize that increasing CycT1 proteins in resting and aberrant CD4+ T cells by manipulating cellular pathways to regulate P-TEFb assembly will reverse HIV latency and improve immune functions in HIV-infected individuals. In the proposed study, we will manipulate the cellular pathways regulating P-TEFb assembly and CycT1 stability to control HIV latency and improve immune functions. We will also identify previously uncharacterized "CycT1-degradation complexes", which will serve as new therapeutic targets. Successful completion of the proposed study will result in a new concept of T cell regulation modulated by the protein level of a master transcriptional regulator.

NIH Research Projects · FY 2025 · 2022-08

Project Abstract Dr. Christopoulos is an infectious disease physician and Associate Professor of Medicine in the Division of HIV, ID, and Global Medicine at UCSF. Her research over the past ten years has focused on improving engagement in HIV care for underserved urban populations by identifying those at risk for poor engagement, understanding barriers to and facilitators of engagement, and developing interventions to support engagement. She has mentored numerous early career investigators, including pre-doctoral students, post-doctoral fellows, and junior faculty but now seeks the protected time of the K24 award to increase the depth and scope of her mentorship, undertake dedicated mentorship skills training, and grow her program of patient oriented research. The COVID-19 pandemic has highlighted further the need for rigorous evaluation of the impact of innovations in HIV care delivery to ensure their use does not widen HIV health disparities. In this application, Dr. Christopoulos proposes a comprehensive mentoring, research, and career development plan to promote the equitable delivery of HIV care and treatment in a post-COVID landscape. Leveraging the infrastructure of the CFAR Network of Integrated Clinical Systems (CNICS) and her role as UCSF site PI, the research proposed in this application seeks to investigate the impact of advances in HIV care and treatment, i.e., telehealth, long- acting injectable antiretroviral therapy, on retention and viral suppression. In addition to the resources of CNICS, which include a mentoring core, Dr. Christopoulos will utilize an implementation science R01 on long- acting injectable antiretroviral therapy, training and career resources at UCSF, and a robust network of multidisciplinary collaborators to provide mentees with training opportunities, preliminary data, and platforms on which to build new research. Through the guidance of an experienced senior mentoring team, formal didactics, and mentee feedback, she will augment and formalize her mentoring abilities and approach with additional training in mentoring across differences and supporting under-represented minority (URM) investigators, building an equity focus in her mentoring as well as her research. The K24 is instrumental to achieving her long-term career goals of becoming an international leader on the topic of engagement in HIV care and maximizing the impact of her scientific pursuits by training the next generation of researchers focused on optimizing HIV care engagement.

NIH Research Projects · FY 2025 · 2022-08

PROJECT ABSTRACT Lung transplantation aims to extend survival, relieve disability, and improve health-related quality of life (HRQL). Although many do well, perioperative complications have increased, one third of patients die within the first three post-transplant years and 20-40% of survivors do not report improvements in patient-reported outcomes (PROs) such as functioning and HRQL. Reasons for this lack of improvement are generally unknown. As a result, RFA- 022-002 highlights body composition and PROs as key priority areas for further investigation and intervention. In earlier work using BMI, CT scans, and DXA, our group showed that obesity and sarcopenia are prevalent in lung transplant candidates and are risk factors for frailty, primary graft dysfunction (PGD), and mortality. We also highlighted, the challenges to more widely implementing these modalities and introduced bioelectrical impedance (BIA) as a method of advanced body composition quantification that overcomes these challenges. We demonstrated that obesity and sarcopenia by BIA are risk factors for PGD, and wait-list death. Our preliminary data suggests that sarcopenic obesity may be a novel phenotype at heightened risk for perioperative complications. After transplant, PGD and other perioperative complications contribute to disability, poor HRQL, and death after transplant. Despite the clinical primacy of PROs, the only empirical data on the impact of perioperative complications on PROs comes from our single-center work. Data on which PROs are responsive to perioperative complications is lacking, hindering informed selection of PROs for use in future research. Finally, defining the factors and events from before through early after transplant that impact PROs can identify and prioritize targets for intervention and improve clinical trial efficiency through prognostic enrichment. To address these problems, we will enroll 803 lung transplant candidates and, in Aim 1, will define the impact of sarcopenic obesity, sarcopenia, and adiposity on peri-operative and PROs at 6-months. We hypothesize that sarcopenic obesity will confer heightened risk for perioperative complications, including PGD, even in patients with normal BMI. In Aim 2, we will define the responsiveness of PRO measures to PGD and other perioperative complications. Aim 2 will provide the foundational empirical data needed to inform appropriate PRO selection for future observational and interventional studies. Aim 3, will develop landmark prediction models accounting for pre-, peri- and early post-operative factors to identify groups with worse post-operative PROs at 6-months and time to graft failure up to 3-years after transplant. Developing new modeling of peri- and early post-operative outcomes to predict which individuals are at risk for poor outcomes will inform the prognostic enrichment strategies needed to improve clinical trial efficiency in lung transplant. In sum, we address key priorities in RFA HL-22-022 by examining body composition in an innovative and scalable manner; identifying high yield PROs for future studies and generating foundational knowledge to inform future studies and trials in lung transplantation.

NIH Research Projects · FY 2026 · 2022-08

PROJECT SUMMARY/ABSTRACT This is a K23 career development award application for Dr. David Soleimani-Meigooni, a behavioral neurologist and Clinical Instructor who is establishing himself as a junior investigator at the University of California, San Francisco (UCSF) Memory and Aging Center (MAC). His long-term goal is to become a clinician-scientist who will lead an independent research program to advance the pre-clinical development/translation of novel PET tracers for diagnosis and monitoring of neurodegenerative diseases associated with frontotemporal lobar degeneration (FTLD) pathology. Through the K23 and the optimal training environment and resources of the MAC, Dr. Soleimani-Meigooni aims to achieve these training goals: 1. To become proficient in pharmacokinetic radiotracer modeling and optimization of PET image acquisition. 2. To become proficient in quantitative PET analyses. 3. To learn quantitative neuropathology techniques. 4. To gain advanced skills in study design and biostatistics. 5. To gain skills in clinical research operations, research ethics, and grantsmanship. 6. To implement his K23 training and findings into an R01 that will allow him to become an independent investigator involved in pre-clinical development/translation of novel PET tracers for FTLD. To achieve these training goals, Dr. Soleimani-Meigooni has assembled a world-class mentorship team including primary mentor, Dr. Gil Rabinovici, a behavioral neurologist and leader in PET neuroimaging of neurodegenerative diseases; co-mentor, Dr. William Jagust, a behavioral neurologist and expert in technical aspects of PET imaging, including radiotracer development and pharmacokinetic modeling; co-mentor, Dr. Lea Grinberg, a neuropathologist, co-leader of the UCSF Neurodegenerative Disease Brain Bank, and expert on FTLD and quantitative neuropathological measures; collaborator, Dr. Suzanne Baker, a scientist with technical expertise in PET imaging; and, collaborator, Dr. Isabel Elaine Allen, an expert biostatistician. This project will evaluate/validate new PET tracers to aid in diagnosis and monitoring of FTLD. Candidate PET tracers include a novel ligand that binds to non-Alzheimer tau proteins, [18F]PI-2620, and another ligand that binds to synapses, [18F]SynVesT-1. Further evaluation is needed to determine if [18F]PI-2620 can distinguish FTLD with tau pathology (FTLD-tau) from FTLD with TDP-43 pathology (FTLD-TDP), and if [18F]SynVesT-1 is a sensitive marker of synapse loss and disease state in FTLD. In this project, both tracers will be evaluated/validated by comparing patterns of tracer retention in patients with FTLD-tau to FTLD-TDP and other neurodegenerative diseases (Aim 1); correlating regional tracer retention to clinical measures and structural brain MRI changes (loss of cortical thickness or subcortical volume) (Aim 2); and performing quantitative PET-to-pathology correlations (Aim 3). This project provides critical data that could support the translation of these radiotracers for clinical use and application as clinical trial biomarkers.

NIH Research Projects · FY 2026 · 2022-08

PROJECT SUMMARY The overall goal of the proposed UC San Francisco – UC Berkeley Tuberculosis Research Advancement Center (UCSF-UCB TRAC) is to accelerate the pace of discoveries that improve our understanding of tuberculosis (TB) and lead directly to new tools for diagnosis, prevention, and treatment of TB. Addressing the complex problems of the current heavy burden and persistence of the TB epidemic requires partnerships across disciplines; mobilization of technology for identification, intervention, and prevention; and mentoring of future scientists and clinicians. The UCSF-UCB TRAC is uniquely positioned to address these challenges for radically new treatments, better diagnostics and an effective vaccine. UCSF and UCB represent a major hub of NIH-funded TB research with many labs across the wide spectrum of disciplines, and the UCSF-UCB TRAC will fill a critical gap in a prominent clinical and basic science research environment. Our proposed UCSF-UCB TRAC will allow us to, (1) attract and support New Investigators (NI) in the TB field by providing pilot awards, training, longitudinal mentorship and other key services and resources; and (2) attract and enable non-TB investigators to enter the field by providing awards, key resources and opportunities for multidisciplinary collaboration that support new directions in TB research. Further, our Center tightly integrates 4 cores: 1) an Administrative Core to provide leadership, infrastructure, administrative and communication support, advice and oversight to coordinate all UCSF-UCB TRAC operations; 2) a Basic Science Core to lower traditional barriers experienced by investigators to facilitate innovative, multidisciplinary, fundamental TB research through a suite of cutting edge technologies accessible in BSL-3/ABSL-3 facilities; 3) a Clinical Science Core to augment existing UCSF and UCB resources to accelerate clinical research by engaging new investigators and reducing the barrier to conducting high-quality, innovating clinical research; and 4) a Developmental Core to attract and develop scientific leaders in TB research via a platform of services to support a continuum of ideas to independence in TB research, offering mentoring, professional development, proposal support, and research funding. The UCSF-UCB TRAC will add value to the robust research enterprises of UCSF and UC Berkeley by bridging traditional silos between fundamental and clinical TB and by providing a nucleating factor for coordinated TB research resources and collaboration at the two campuses and at affiliated international research sites.

NIH Research Projects · FY 2024 · 2022-08

Project Summary/Abstract Alzheimer’s disease (AD) is significant health threat that is the fastest growing top 10 cause of death in the United States. AD currently costs Americans $280 billion dollars in direct health care costs annually. AD is characterized by, among other things, fibrils of aggregated microtubule associated protein tau. Tau in these fibrils is unique in several ways including truncation by caspases. The role of caspases and cleaved tau in AD has not been clearly defined, and two non-mutually exclusive hypotheses have been proposed. The first hypothesis is that caspases are being upregulated early in AD and cleave tau to a toxic species. A second possible explanation is that caspases are overexpressed in response to tau upregulation and cleavage of tau occurs after AD progression has been initiated. The overall goal of this proposal is understanding the role caspase cleaved tau plays in tau pathology. To date, several truncated tau products have been observed in vivo, but most efforts to understand the role of these products has revolved around genetic or chemical inhibition of caspases. Among all caspases, inhibition of caspase-3 and capase-6 have shown to alleviate tau pathology and cell death in cell and animal models. Knockout of caspase-3 is lethal in mice, but caspase-6 can be knocked out of mice without any adverse effects. This begs the question, is caspases-6 a potential therapeutic target for the treatment of AD? For the answer to this question to be yes, it must be shown why blocking caspase-6 alleviates tau pathology. Our central hypothesis is that caspase cleavage of tau results in a proteotoxic species that promotes tauopathy and cell death in AD. To demonstrate this, we will first characterize where caspases can cleave tau in a recombinant system. Next, we will characterize the stability, seeding propensity, cellular half-life, and toxicity of these cleaved tau proteins. Finally, we will show that cells expressing uncleavable tau are resistant to toxicity associated with caspase induction. These experiments will demonstrate that tau cleavage is necessary for neuronal cell death induced by caspase induction. When combined with previous the observations that 1) cleaved tau correlates with AD progression and 2) blockage of caspase activity alleviates tau pathology and cell death, the proposed research will provide a strong case for caspases as therapeutic targets in AD.

NIH Research Projects · FY 2024 · 2022-08

Project Summary (Abstract) We propose to separate scintillation and Cherenkov photons produced in scintillator crystals to improve the time and energy resolution of time-of-flight positron emission tomography (TOF-PET) detectors far beyond those achieved in state-of-the-art systems. With its pico-molar sensitivity and a few millimeters of spatial resolution, TOF-PET is the leading nuclear imaging modality for a number of diseases, from cancer to neurological and cardiovascular disorders. A significant improvement of the coincidence time resolution (CTR) and energy resolution would boost the signal-to-noise ratio and hence enhance image quality, resulting in more accurate diagnoses, lower patient doses and exposure times, and granting access to a new broad range of applications for TOF-PET. The ultra-fast picosecond emission of Cherenkov light has demonstrated to achieve the best CTR ever reached of 30ps FWHM using PbF2, a pure Cherenkov emitter. However, this provides a very poor energy resolution due to the low light yield of Cherenkov emission. The combination of Cherenkov and scintillation emission has been proposed as a way to obtain both good time and energy resolution, which has been demonstrated in bismuth germanium oxide (BGO), a high stopping power scintillator for PET, to obtain a CTR of 120ps FWHM with an energy resolution of 14%. The main reason why it is very challenging for BGO to reach CTRs of 30ps FHWM is due to the presence of the slower scintillation light and the inability of current detectors to disentangle between Cherenkov and scintillation. Additionally, the difference between the Cherenkov and scintillation light emission spectra, makes it very hard to obtain a BGO detector that provides both good time and energy resolution. We propose to separate Cherenkov and scintillation photons in order to provide a detector that can be optimized independently for each of the signals, maximizing time resolution with Cherenkov and energy resolution with scintillation without hindering each other. This separation can be achieved by exploiting the different emission spectra of each mechanism using dichroic filters, which are able to classify photons by wavelength with a negligible photon loss. This project aims to 1) obtain a CTR of 50ps FWHM and reduce the scintillation background by a factor of 5 through wavelength classification in BGO, 2) increase photon detection efficiency in BGO by at least a factor of 2 without compromising time resolution, and 3) reach a CTR of 30ps FWHM with a 7% energy resolution by leveraging the hybrid Cherenkov-scintillation concept with thallium chloride (TlCl). This project will pioneer the exploration of wavelength information as a way to dramatically improve TOF-PET performance. We will combine this technique with other cutting-edge technologies such as fast or high quantum efficiency photosensors, in order to demonstrate a novel a cost- effective approach to a next generation TOF-PET. Our goal is to enable a new technology that can bring CTR closer to the 10ps FWHM milestone with a good energy resolution in order to be further exploited in future projects for the construction of a full TOF-PET system.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY/ABSTRACT Pulmonary vascular disease (PVD) is a significant source of morbidity and mortality in neonates, infants and children with diverse heart, lung and systemic diseases. A major barrier to improving outcomes of children with PVD is the fundamental lack of understanding the differing pathobiologies among the spectrum of these disorders, which intersect between multiple clinical disciplines. This is compounded by the scarcity of training opportunities to develop and retain physician-scientists and scientists with expertise in PVD that allows for the successful translation of laboratory and clinical science across multiple disciplines. Thus, there is a need for well-trained scientists in Pediatric PVD who can perform collaborative and rigorous inter-disciplinary investigation to enhance the development of new treatment modalities. This novel application requests the resources to establish a unique two-year post-doctoral collaborative research training program in Pediatric PVD within the Departments of Pediatrics at the University of California, San Francisco, the University of Colorado, and Vanderbilt University. The goal of the program is to increase the number of highly trained, successfully funded and sustainable pediatric pulmonary vascular scientists, who will perform high level laboratory, clinical- translational, and/or health services research that will ultimately improve our understanding of the pathobiology of diverse pediatric PVD, design therapeutic plans that specifically target an individual’s underlying pathobiology, and thereby improve both short and long-term outcomes. To this end, this program aims to provide comprehensive scientific training through novel mentoring and collaborative approaches to enhance career development for physicians or post-doctorate scientists with an M.D., M.D./Ph.D. or Ph.D., who commit themselves to an academic career in pediatric PVD. The key and unique elements of this training program are: (1) a rich, diverse, mentored research experience; (2) interdisciplinary and inter-institutional experiences, including joint didactic learning opportunities, with direct integration into the North American Pediatric Pulmonary Hypertension Network and the associated Annual International Conference; and (3) continuous review and evaluation from academic leaders in the field. The centerpiece of the program for pediatric-scientists is the continuation of a 4-year fellowship training program (including but not limited to Pediatric Cardiology, Critical Care, Emergency Medicine, Neonatology, or Pulmonology), with 2 years devoted to intense research training in basic laboratory science, clinical-translational science, health services or epidemiology related to pediatric PVD. Exceptional faculty have committed their support as mentors, who lead and are affiliated with several of their universities’ research units and clinical programs, a represent a “critical mass” that few single centers can provide. Thus, the rationale for this novel proposal is based on the need for well-designed training programs in Pediatric PVD research, including the need to foster multi-disciplinary and multi-interdisciplinary collaborative approaches, and that these three institutions have the vision, experience, and collaborative infrastructure to train the next generation of leaders.

NIH Research Projects · FY 2025 · 2022-08

Medulloblastoma is the most common malignant pediatric brain tumor. After surgery, radiation and chemotherapy, five-year survival is 60-70% overall. Survivors show severe physical and cognitive disabilities, often unable to live independently. Medulloblastoma exists in four distinct molecular subgroups (WNT, SHH, Group3, Group 4). An incurable subgroup of SHH driven tumors show amplification of the MYCN transcription factor. How can we target N-myc in medulloblastoma? N-myc’s ability to regulate protein synthesis is tied both to its oncogenic potential and to interactions with the mTOR serine-threonine kinase. We hypothesize that N- myc hijacks the translational machinery regulated by the mTOR serine threonine kinase to drive transformation; and that targeting translation control represents a therapeutic strategy for N-myc driven cancers. Employing ribosome profiling technology, we surprisingly found that in addition to roles as a global regulator of protein synthesis, N-myc interacts with mTOR to regulate translation of 13 mRNAs belonging to the folding machinery, functionally important for N-myc driven medulloblastoma. The mechanisms by which N-myc directs the translation of these specific subsets of mRNAs to drive tumorigenesis and whether these potential vulnerabilities can be leveraged to develop targeted therapies remain outstanding questions. In this proposal, we will mechanistically dissect how N-myc hijacks the translational machinery for its oncogenic activity. Using novel genetic approaches, we will separately evaluate the importance of eIF4E and eIF4A in our N-myc driven genetically engineered mouse (GEM) models. We will also test new clinical drugs against eIF4A and eIF4E, analyzing GEM models, and patient derived orthotopic xenografts. Successful completion of these aims will delineate how N-myc interacts with mTOR to regulate key subsets of translational targets, and elucidates druggable mechanisms in N-myc driven medulloblastoma.

NIH Research Projects · FY 2025 · 2022-08

Project Summary/Abstract Engineered therapeutic T cells have shown transformative success in treating B cell cancers but applying this approach to solid tumors has proven far more difficult. There do not appear to be absolutely tumor-specific single antigen targets for solid cancers, and thus, CAR T cells that attack most tumor-associated antigens have led to toxic cross-reaction with normal organs that also express the antigen. If we are to successfully and safely treat solid tumors with CAR T cells, it will be essential to mitigate toxic cross-reaction with normal tissues. To prevent off-tumor toxicity of therapeutic T cells, we propose to engineer multi-receptor T cell circuits that can recognize a tumor based on a multi-antigen profile. In this proposal, we focus specifically on engineering NOT gate circuits -- circuits that can override and inhibit CAR T cell activation and killing upon detecting an antigen that is uniquely indicative of a cross-reactive normal tissue (i.e., antigen is absent in the tumor). Our recently published bioinformatic analysis shows that there are numerous tissue-specific antigens that could be used as signals to induce T cell inactivation in common cross-reactive tissues like the brain and lung. Nonetheless, there is currently a lack of robust NOT-gate circuits demonstrated to work well in tumor models. Thus, we will develop and test new NOT circuits that can inactivate a CAR T cell in an antigen-induced manner. Our specific aims are: Aim 1. Engineer, prototype and optimize new NOT gate circuits that use diverse mechanisms to block therapeutic T cell activation in antigen-induced manner Aim 1.1. T cell NOT gates using transcriptional repressors of CAR expression. Aim 1.2. T cell NOT gates that inhibit T cell proliferation by antigen-induction of cell death effectors. Aim 1.3. T cell NOT gates that locally induce production of secreted immunosuppressive factors (paracrine) Aim 2. Applying NOT gate circuits to prevent anti-GD2 CAR T cross-reaction with brain/CNS tissue. Aim 2.1. in vitro prototyping of NOT gate circuit targeting the brain antigen MOG to turn off anti-GD2 CAR Aim 2.2. Test if brain NOT gates block CNS toxicity of anti-GD2 CAR T cells in vivo, while maintaining efficacy against murine neuroblastoma xenograft models (GD2+). Aim 2.3. Test in vivo safety & efficacy of NOT gate CAR T cells in an immunocompetent model of neuroblastoma. This work should provide important general capabilities for engineering CAR T cells that selectively turn themselves OFF when they are in the wrong, cross-reactive tissue. These are much needed tools that are currently missing in the toolbox for T cell engineering, but which will be critical for engineering T cells that safely treat solid cancers.