University Of California Berkeley

NIH Research Projects · FY 2024 · 2022-08

Neural mechanisms of active vision in the fovea In many ways human vision is like a camera, with a lens that forms an image on a spatially arranged sensor (the retina). However, it is unlike a camera because the sensor has uneven sampling and is constantly moving with the eyes. Recent behavioral and theoretical work suggest these eye movements serve a faciliatory role in high acuity vision – where the eye movements are part of the computations and enhance spatial resolution. However, the neurophysiological mechanisms to support this facilitation remain unknown. More broadly, little is known about the neural mechanisms that integrate across the retinal motion generated by eye movements, especially in the central visual field (the fovea). This is particularly important because over 8 million Americans suffer from central vision loss due to retinal disorders. Even if the retinal signals could be repaired, it is imperative to understand how the brain reads out foveal signals to ensure recovery of high-acuity visual processing, and fixational eye movements are a part of that process. The proposed career development plan aims to address these questions by measuring visual processing in the foveal representation of primary visual cortex (V1) during natural visual behavior. This proposal uses custom high-resolution eye-tracking, a novel visual foraging paradigm, largescale neurophysiology, and state-of-the-art machine learning to make these measurements possible. The proposed research will not only generate fundamental understanding of how eye-movements facilitate visual processing, but also will integrate the experimental and theoretical tools required to support neurophysiological studies of active visual processing without a loss of rigor or detail. The candidate has extensive expertise in awake- behaving neurophysiology and computational modeling and the training plan is designed to support his further training in statistical modeling, high-resolution eye-tracking, and modern machine-learning techniques for analyzing neural population data. The primary mentor, Dr. Daniel Butts, is a world expert in statistical models of neural activity during active vision; Co-mentor, Dr. Michele Rucci, is a world leader in high-resolution eye tracking and theoretical approaches to active vision; and Co-mentor, Dr. Jude Mitchell, is a pioneer in establishing the marmoset model of visual neuroscience and an expert in neurophysiology of visual attention. Together, they will provide the guidance to establish the candidate’s transition to a successful independent research career.

NIH Research Projects · FY 2025 · 2022-08

One of the biggest challenges facing cancer drug discovery is that >90 % of the proteome is currently considered “undruggable” because most proteins do not possess known binding pockets or “ligandable hotspots” that can be pharmacologically and functionally targeted for therapeutic benefit 1. Tackling the undruggable proteome requires the development of innovative technologies for ligand discovery AND the discovery of novel therapeutic modalities to functionally manipulate the undruggable proteome for therapeutic benefit. The Nomura Research Group is focused on reimagining druggability by advancing and applying chemoproteomic platforms to tackle the undruggable proteome, towards developing next-generation therapies and therapeutic modalities for cancer.

NIH Research Projects · FY 2026 · 2022-07

PROJECT SUMMARY Childhood obesity is a growing public health epidemic that is disproportionally affecting Hispanic children and associated with morbidity and downstream health disparities. Early-life adversity and childhood psychosocial stressors have been shown to contribute to obesity risk, with stronger effects reported among children growing up in lower-income households. The period of fetal development and early-life are marked by dynamic and rapid changes in fetal DNA methylation programming, epigenetic maturation of immune system-related genes in early- childhood and general physiological development. A poor and adverse social environment in early life has been hypothesized to contribute to epigenomic “weathering” leading to accelerated decline in health, aging and eventual health disparities, including obesity. A leading hypothesis for the origins of health disparities is the biological embedding of adversity on the epigenome due to chronic adversity exposure. While emerging evidence indicates that psychosocial stressors and adversity are associated with epigenetic biomarkers like DNA methylation, significant limitations remain in the field. Namely, most studies to date have been cross-sectional, used candidate gene approaches, not investigated changes or trajectories in epigenetic biomarkers throughout development, or functional consequences in gene expression. The proposed project will leverage data and samples from The Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS), a long- term study of low-income Latinx, predominantly Mexican American, mother-child pairs living in the Salinas Valley of California. We have repeated measurements and samples for DNA methylation analyses at birth, 7, 9, 14 and 18 years in approximately 300 mother-child pairs, genetics, and stabilized RNA for sequencing at 14 years of age. We will investigate both pre- and postnatal early-life adversity measures to 1) determine if adversity measures are associated with blood DNA methylation trajectories and subsequent variation in gene expression; 2) evaluate if adversity measures influence epigenetic aging clocks and biomarkers and their trajectories and if longitudinal changes are prospectively associated with obesity risk; and 3) determine if DNA methylation or epigenetic aging mediate associations with obesity and if an epigenetic adversity score can be constructed from children’s blood methylome. Our study will address critical gaps in the field by testing hypotheses prospectively over 18 years and addressing questions of persistence and embedment of pre- and postnatal adversity. We will test if epigenetic changes influence gene expression with untargeted RNA sequencing at 14 years. We will evaluate if DNA methylation can serve as a reliable biomarker of adversity in early-life and or alternatively if these biomarkers are causal for the relationship between adversity and obesity risk with mediation and mendelian randomization methods. Our approach will yield rigorous data to test the biological embedment of social adversity and its consequences in a Latinx, low-income birth cohort with high obesity prevalence.

NIH Research Projects · FY 2025 · 2022-07

Project Summary/Abstract The UC Berkeley/UCSF joint Training Program in Metabolic Biology (TPMB) offers unique opportunities for trainees to gain a strong foundation in rigorous, reproducible science, and to acquire the professional skills and knowledge to support future leaders in the field of human metabolic health and disease research. Built around an inter-departmental, trans-institutional training program, it brings together world-leading researchers and mentors from UCB's Department of Nutritional Sciences and Toxicology (NST) and UCSF's Diabetes Center (DC) to offer an unparalleled training experience for predoctoral fellows. TPMB seeks to attract a diverse group of highly qualified students from various academic backgrounds including biochemistry, cell and molecular biology, nutrition, and physiology. Our curriculum is build around development of scholarship and skills in research, teaching and professional service with the goals of establishing early research independence and laying a foundation for research integrity and responsibility. In addition to taking TPMB specific courses that emphasize human health and disease topics in metabolic regulation, research design and reproducibility, data analysis and interpretation, as well as ethical conduct, students will be able to rotate through laboratories both on the UCB and UCSF Parnassus campuses in their first year. TPMB students will experience a nurturing, diverse, and exciting environment that has build a well-established and integrated community of program leadership, researchers and preceptors across the two campuses and is well aware of the opportunities and potential challenges this approach offers. In order to make informed choices for their rotations incoming students will be exposed to the variety of metabolism centered research in the program through introductory lectures given by all TPMB faculty and participate in the programs joint annual retreat offering talks, posters, and social interactions with faculty, students, and postdocs. A central strength of TPMB is the quality of our faculty and the breath of human health and metabolism focused research topics ranging from central regulation of feeding behavior to adipocyte biology and ß-cells and state-of-the-art technical approaches from single-cell-sequencing, to metabolomics, genetics, stem cell biology, and bioengineering and the ability to pursue research in both clinical and preclinical settings. This wide range of expertise and approaches foster collaborative science and prepare TPMB students to successfully transition into independent careers in academia, industry, and government to tackle problems central to the mission of NIDDK and to improve human health and wellbeing.

NIH Research Projects · FY 2026 · 2022-07

Project Summary Most mammalian retrotransposons are strictly silenced in development and physiology, yet induction of some retrotransposons can be observed during specific developmental processes. Interestingly, a portion of the reactivated retrotransposons, particularly LTR retrotransposons, confer a gene regulatory role, at least in part, by acting as alternative promoters to drive chimeric transcripts with proximal protein-coding genes. Such retrotransposon promoters frequently alter gene structure and/or gene expression, yet their functional importance remains largely unclear. Mammalian preimplantation embryos are an excellent experimental system to probe the functional importance of retrotransposons. Dynamic induction of retrotransposons in preimplantation embryos have been observed in all 8 mammalian species examined, and the global retrotransposon expression profiles across mammalian species are similar. Using published single-cell RNA-seq data from mouse, human, primate and livestock preimplantation embryos, we discovered hundreds of retrotransposon promoters, which drive preimplantation-specific, proximal gene isoforms. Interestingly, most retrotransposon sequences and integrations are species specific, yet many retrotransposon promoters yield gene isoforms that encode evolutionarily conserved proteins. Hence, these data suggest that retrotransposon promoters can regulate conserved protein sequences and bestow them with species-specific gene regulation. One of such evolutionarily conserved retrotransposon driven gene isoform, Cdk2ap1N(MT2B2), encodes an N-terminally truncated isoform for Cdk2ap1, a negative regulator for cell proliferation by repressing Cdk2. Cdk2ap1N(MT2B2) is generated by an MT2B2 promoter, whose deletion in mice yield reduced cell proliferation, impaired implantation and embryonic lethality. This is among the first study demonstrating an essential function of a retrotransposon element in development. Here, we hypothesize that retrotransposon-mediate gene regulation play an essential role in mammalian preimplantation development. Using bioinformatics prediction combined with experimental validation, we propose to comprehensively and accurately categorize retrotransposon-promoters in mouse, primate and livestock preimplantation embryos, and elucidate the diverse molecular mechanisms for retrotransposon-mediated gene regulation. Additionally, we will employ a highly efficient CRISPR technology, CRISPR-EZ, to generate mouse deletion mutants for selected retrotransposon promoters or for the corresponding canonical gene isoforms. We will compare the roles of retrotransposon-dependent gene isoform and the canonical gene isoform, elucidate the molecular mechanisms of their action and explore the evolutionary significance of such regulation. Taken together, these proposed studies will generate a comprehensive atlas of retrotransposon-dependent gene regulation during preimplantation development, and provide a new paradigm to investigate retrotransposon functions both computationally and experimentally.

NIH Research Projects · FY 2025 · 2022-07

PROJECT SUMMARY The human genome is regulated through interactions between DNA and proteins in the nucleus that define and maintain the epigenetic state of cells. Therefore, large consortia such as the Encyclopedia of DNA Elements (ENCODE) are dedicated to comprehensively mapping regulatory elements such as transcription factor binding or histone modification so that we may understand regulatory processes that guide development, disease, and the everyday functioning of cells in our body. However, current methods for genome-wide measurement of protein-DNA interactions are unable to map regulatory elements in highly repetitive regions of the genome because they rely on high-throughput, short-read DNA sequencing platforms. This limitation prohibits comprehensive investigation of roughly 8% of the human genome including centromeres and ribosomal DNA arrays, which play essential roles in chromosome segregation and nuclear organization. Furthermore, these methods typically lack the sensitivity to profile the epigenetic landscape of single cells, preventing high-resolution measurements of regulatory variation in complex tissues. The goal of this research program is to expand the toolbox for mapping protein-DNA interactions genome-wide and extend capabilities to long-read sequencing and single-cell sequencing technologies with the development of two methods: (1) Directed methylation and long- read sequencing (DiMeLo-Seq) and (2) single-cell directed methylation and sequencing (scDiMe-Seq). To record the genomic position of protein binding or histone modification, a methyltransferase fused to protein A will be directed to the targeted regulatory element with a primary antibody. Upon activation, the methyltransferase will methylate adenines in proximal DNA sequences. DiMeLo-Seq will implement long-read DNA sequencing technologies such as nanopore sequencing to directly detect the position of these modifications on long molecules of DNA, taking advantage of the differential signal generated by methyl-adenines as they pass through the nanopore. This approach will produce sequencing reads of up to hundreds of kilobases long, providing high- confidence mapping of regulatory elements to regions of the genome that are unmappable with short-read sequencing. To detect these modifications with single-cell sensitivity, scDiMe-Seq will enrich genomic loci containing methyl adenines through targeted digestion, adapter ligation, and PCR amplification. These enriched fragments will then be sequenced using standard high-throughput sequencing. This project aims to develop DiMeLo-Seq and scDiMe-Seq through rigorous protocol optimization of the directed methylation strategy and sequencing library preparation for long and short-read sequencing. The methods will then be characterized and validated by targeting well studied features such as lamina associated domains, and CTCF landscapes, as well as H3K9me3 and CENPA which are both enriched in centromeres. The overall goal of this project is to produce two robust and scalable methods that may shed light on regulatory mechanism in previously unexplored regions of the genome and aid in Human Cell Atlas initiatives by providing epigenetic information for single-cell analysis.

NIH Research Projects · FY 2026 · 2022-06

Project Summary/Abstract The University of California, Berkeley (UCB) is a world-class research institution with a large number of biomedical science undergraduates who are underrepresented minority, are first-generation college students, come from low-socio-economic backgrounds or are disabled. The overarching goal of the UCB MARC program is to prepare highly motivated students from these underrepresented (UR) groups to apply and succeed in Ph.D. programs, helping to address the nation's need for a diverse scientific workforce. The program will address barriers that deter UR students from pursuing research careers using three strategies. First, the program will place students in labs run by PIs known for their scientific rigor and undergraduate mentoring skills. Second, the program will provide a series of scientific and professional development workshops, journal clubs and research seminars that will enhance the trainees' written and oral communication skills, their ability to ask important scientific questions and to design rigorous experiments to address these questions, and to critically evaluate the scientific findings. Third, the program will build a cohort of students and mentors who will support each other and help the trainees achieve their career goals. Together, these strategies will enhance the self-efficacy and science identity of the trainees and produce a group of gritty and rigorous young scientists with promising futures. The program will engage evaluation and assessment tools to ensure that these strategies are successful in achieving the its goals and to provide the flexibility to improve the program as it evolves. The program will support UR junior and senior students with an intention to pursue a Ph.D. in the biomedical sciences. Over the course of this five-year grant, we propose to support 78 MARC Scholars. Our goal is to have >75% of MARC Scholars to matriculate into Ph.D. programs within two years of graduation from UCB. The proposed MARC Program will also serve as a model for programs seeking to increase diversity and support the success of undergraduate students from UR groups in research careers and share best practices with programs that have overlapping goals.

NIH Research Projects · FY 2025 · 2022-06

PROJECT SUMMARY Humans and other animals are able to seamlessly integrate sensory and mnemonic information. As a medial temporal lobe structure at the apex of high-level sensory cortices, perirhinal cortex (PRC) is ideally situated to support perceptual-mnemonic integration. Indeed, PRC has been shown to play a causal role in diverse behaviors, including familiarity-based recognition, visual object perception, and fear conditioning. Yet this confluence of functions has proven difficult to formalize, and there is considerable debate over the mechanisms that enable PRC to play a role in these diverse behaviors. By integrating traditional neuroscientific methods within a novel deep learning computational framework, this proposal aims to formalize and evaluate computational theories of PRC function. I have three specific aims: Aim 1. My graduate work has already laid the foundation to formalize PRC function. By integrating lesion, electrophysiological, and behavioral data within a deep learning framework, this work resolves decades of seemingly inconsistent experimental findings surrounding PRC involvement in visual object perception. More specifically, I find that a biologically plausible computational proxy for the primate ventral visual stream (VVS) approximates the visual discrimination behaviors of PRC-lesioned (human and non-human) primates, directly from experimental stimuli. Conversely, PRC-intact participants are able to outperform PRC-lesioned behaviors, as well as these computational proxies for the VVS—a finding that implicates PRC in these behaviors. Aim 2. The work proposed during the F99 phase will build upon my previous work to include a computational account of PRC-dependent visual discrimination behaviors. First, I will develop biologically plausible computational models of PRC-intact visual behaviors able to achieve the performance of PRC-intact human participants on concurrent visual discrimination tasks. Then, I will identify which of these PRC-models best fit in- vivo (fMRI) measurements of PRC function. This will provide extensive training in building deep learning models of visual behaviors, alongside neuroimaging expertise, harnessing resources available at my graduate institution. Aim 3. Work proposed in the K00 phase will build upon these perceptual models to include PRC's known mnemonic functions. I intend to gain extensive experience with reinforcement learning (RL) models of mnemonic behaviors. By integrating deep learning and reinforcement learning within a biologically plausible computational framework, I will build towards an integrated model of PRC-dependent perceptual-mnemonic behaviors. Collectively, this proposal offers a novel framework for characterizing typical and atypical perceptual-mnemonic behaviors, promising new insights into the neurobiology of perception and memory, while outlining the training I need to be an independent researcher at the forefront of computational cognitive neuroscience. It is my hope that this framework may provide a foundation for future clinical applications to address memory-related disorders.

NIH Research Projects · FY 2026 · 2022-05

Checkpoint therapy is remarkably effective against many malignancies that were previously devoid of effective treatment options. Nevertheless, even for the types of cancer where it is effective, many patients do not respond, or their cancers recur. The therapy is ineffective in many other types of cancer. Evidence has accumulated that ineffective checkpoint therapy is often due to either the dearth of neoantigens in a given type or example of cancer, or acquired resistance to therapy, which is frequently due to loss of MHC I antigen presentation or neoantigen expression. Therapeutics that mobilize NK cells may dramatically complement T cell mediated anti- tumor mechanisms, because NK cells do not depend on neoantigens, and are especially effective against MHC- deficient tumors, which arise during checkpoint therapy. Preliminary data show that innate agonists, such as a STING agonist, dramatically synergize with an IL-2 superkine called H9-MSA, leading to NK-dependent indefinite long term tumor free survival in mice with established MHC I-deficient tumors, including the cold B16-B2m-/- model and the MC-38-B2m-/- model, which were otherwise refractory to each therapy alone. Strikingly, this therapy combination was also effective in “curing” mice of MHC I+ B16 tumors, mediated by CD8 T cells, and primary methylcholanthrene (MCA)-induced sarcomas, a highly stringent autochthonous model of cancer that was also refractory to checkpoint therapy, where both T cells and NK cells mediated antitumor effects. In the latter model, the addition of checkpoint therapy led to long term remissions in ~half the animals. In clinical trials, STING agonists alone have been disappointing in cancer patients, but our new evidence of great synergy of STING agonists and IL-2 superkine suggests that the combination may have great potential for applications in human cancer therapy. We will interrogate the mechanisms of synergistic efficacy of this combination, including whether STING agonist, via IFN, protects NK cells from fratricide induced by the superkine, or cooperatively prevents NK desensitization. We will further address the impact of checkpoint therapy on top of or preceding this therapy combination, including understanding how T cells and NK cells cooperate. We will model the acquired resistance of tumors to checkpoint therapy via selection of MHC-loss variants expression in a tumor transfer model. Finally, we will employ the MCA sarcoma model undergoing therapy to test the roles of T cells in selecting MHC I deficient or other NK sensitive variants, and of NK cells in potentially selecting T cell sensitive variants. The culmination of these studies will provide a strong basis for understanding and applying this form of combination therapy in human patients with cancer.

NIH Research Projects · FY 2026 · 2022-05

Project Summary/Abstract Alzheimer’s disease is severely under-studied in Sub-Saharan Africa: the few existing estimates suggest that prevalence is currently low but changing risk factors predict that it could double in the next 20 years. We propose to study risk factors for Alzheimer’s disease and related dementias (AD/ADRD) in the Kenya Life Panel Survey (KLPS), a unique, richly phenotyped cohort of Kenyan adults who have been followed since childhood, and who were participants in a randomized child health intervention (school-based deworming). The existing dataset contains information on health, cognition, educational, demographic, social attitudes, and labor market outcomes for over 6,500 Kenyans first surveyed in 1998 (at ages 8-15) through 2021 (ages 31-39). KLPS thus provides an unusual opportunity to study cognition, and the determinants of AD/ADRD and related risk factors, over the life course, with direct measurement during childhood, young adulthood, and midlife. This project proposes an additional field interview in the KLPS Round 5 Aging Module (KLPS-5A) to collect detailed “midlife baseline” cognition and aging-related health data, as well as information on AD/ADRD risk factors, among participants, who will be 35 to 43 years old at the time of survey. One novel aspect is the ability to link these midlife measures to rich existing longitudinal data from childhood and early adulthood, including cognitive assessments (achievement and cognitive test scores), as well as educational outcomes, health status and behaviors, and economic outcomes (e.g., earnings, migration, occupational complexity) collected contemporaneously rather than via recall in later life. By combining state-of-the-art cognitive measures at this new midlife timepoint with the extensive cognitive measures and exposures already collected, we hope to establish KLPS as the premier African study of life-course dementia determinants. There are very few surveys globally that include such detailed data from childhood to old age, and these data would open up multiple avenues for investigating dementias tied to life-course disadvantages. We will make all data publicly available to researchers across disciplines. Another notable feature is the ability to utilize experimental variation from a randomized child health intervention that has been documented to meaningfully affect adult living standards and several risk factors for dementia, to better understand pathways over the life course and the scope for public health interventions to reduce AD/ADRD risk. The Primary School Deworming Program provided deworming medication to randomly-selected schools starting in 1998 in a region with high worm prevalence (>90%): 10 to 20 years after treatment, the intervention had positive effects on self-reported health, educational attainment; adult living standards; urban residential status, and occupation in the non-agricultural sector. This setting offers an unusual opportunity to experimentally test the extent to which an effective child health intervention can affect AD/ADRD risks and midlife health and cognition, as much of the associational literature suggests.

NIH Research Projects · FY 2026 · 2022-05

PROJECT SUMMARY This project proposes to study the roles of specific amacrine cells (ACs) in the visual signal processing performed by the mammalian retina. Electrophysiological recordings of light evoked activity will be made from ACs, ganglion cells (GCs), and bipolar cells in intact in vitro whole- mount and slice preparations of mouse retina maintained at photopic adaptation levels. The functional properties of the cells will be probed using images projected onto the photoreceptors through the microscope objective. Patch-clamp recordings from amacrine and ganglion cell somas will be performed to measure the stimulus-evoked postsynaptic currents, postsynaptic potentials, and spiking responses. The project focusses on the elucidating the synaptic mechanisms underlying the receptive field properties of 3 genetically labelled amacrine cell types. Aims 1 and 2 examine the functional properties of two types of amacrine cells, so called NOS-1 and NOS-2 amacrine cells, which are identified by their expression of nitric-oxide synthase (NOS). Aim 1 will test the hypothesis that the NOS-1 ACs are key interneurons for controlling the strength of surround antagonism in GCs at scotopic light levels and that they exert their effects via GABAergic synaptic connections to AII ACs. We will make dual recordings between the NOS- 1 ACs and specific types of GCs, to directly test for indirect synaptic connections consistent with the proposed circuit. Aim 2 will examine the role of NOS-2 ACs in conferring motion-sensitivity to specific type of small-field GCs in the mouse. We will use optogenetic stimulation of ChR2 expressing NOS ACs to identify the postsynaptic targets. The postsynaptic targets will be identified morphologically and physiologically and inputs arising from NOS-2 ACs will be confirmed by paired recordings. Aim 3 focuses on a novel amacrine cell type that is one of 2 AC types that can be identified by their expression of the gene Gbx2. We will focus on the Gbx2+ ACs that stratify in sublamina 3 (S3) of the inner plexiform layer. The S3-Gbx2+ ACs are highly unusual because they appear to express none of the conventional inhibitory or excitatory neurotransmitters, indicating that they represent novel populations of so-called non-GABAergic, non-glycinergic (nGnG) ACs. Preliminary data show that these nGnG ACs are tracer coupled to bipolar cells. We will quantify the spatio-temporal receptive field properties of these nGnG S3- Gbx2+ ACs and will test the hypothesis that they make output via electrical synapses with bipolar cells. To do so, we will make patch-clamp recordings from cone bipolar cells in slice and measure depolarizing responses elicited by optogenetic stimulation (ChR2 expression) of the S3-Gbx2+ ACs. Overall, the results will reveal the functional properties and connectivity of the three AC types and will determine their roles in visual processing in the retina.

NIH Research Projects · FY 2025 · 2022-04

ABSTRACT / PROJECT SUMMARY The goal of this proposal is to establish a high-priority research network to identify mechanisms through which soft tissue manipulation (STM), such as massage, exerts biological effects on the nervous system, non-neural cells and tissues. Neuromusculoskeletal pain afflicts up to half of the adult U.S. population and is the most commonly cited health reason for receiving massage. Soft tissue manipulation has been shown to promote relaxation and functional change, reduce anxiety, attenuate pain and mitigate inflammation. STM also offers non-addictive alternatives to pharmacological interventions for short-term pain relief. Although STM has been used widely since ancient times, the underlying mechanisms of STM’s beneficial effects are not well understood, and STM interventions are not optimized based on rigorous and compelling scientific evidence. Although mechanistic studies over the past decade have identified molecular, cellular and circuit mechanisms of discriminative touch sensation in mammals, how these neural pathways are engaged by STM is unknown. Moreover, the cells and circuits that mediate affective components of touch sensation have not been defined. To enable mechanistic research into therapeutic effects of STM, interdisciplinary research and new resources are needed. The field requires collaboration between manual therapists, neuroscientists, engineers, and cell biologists. Scientific conferences or other networking opportunities that bridge these disciplines do not currently exist. This application in response to RFA-AT-21-006 will create a cross-disciplinary research network of scientists and clinicians with the shared goal of developing technologies and collaborations to break barriers to progress. First, few quantifiable standards exist to rigorously measure either how therapists apply hands-on manipulations, or how these manipulations alter stress/strain fields in receiving tissues. Second, the field lacks technologies and computational models to quantify the spatiotemporal dynamics of STM techniques. Third, how non-neural signals and cell types, including cytokines, immune cells, fibroblasts, and epithelial cells, promote restorative repair versus fibrotic healing have not been defined. Our team consists of scientists and clinicians whose expertise spans physical therapy, neuroscience from molecules to circuits in the mouse and human nervous systems, engineering and tissue mechanics, and extraneural tissues including the immune, myofascial and integumentary systems. To advance mechanistic research on STM and mechanosensory signaling, the Network aims to 1) Organize a Conferences Program to promote cross-disciplinary networking and collaborations, draw a broad spectrum of researchers and clinicians to the field, and seed mechanistic, multi-scale research on the neurobiology of mechanotherapies. 2) Implement a Pilot Project Program to generate new tools for quantifying force-based manipulations, testable hypotheses, and new mechanistic knowledge. 3) Rapidly and feely disseminate high-impact research to advance the field by sharing innovative concepts and technologies that define neural mechanisms underlying beneficial effects of STM.

NIH Research Projects · FY 2026 · 2022-04

Host factors and viral determinants mediating flavivirus NS1 tissue-specific endothelial dysfunction and vascular leak ABSTRACT The flavivirus (FV) genus contains medically important mosquito-borne human pathogens that cause a major global disease burden. While dengue (DENV), yellow fever (YFV), and Zika (ZIKV) viruses are systemic, and West Nile (WNV), Japanese encephalitis (JEV), and Zika viruses cause neurotropic infections, each FV can cause severe disease characterized in part by endothelial barrier dysfunction – the most classic example being vascular leak in severe dengue. This may result from overproduction of vasoactive cytokines as well as viral factors. The highly conserved FV non-structural protein 1 (NS1) is secreted from infected cells and circulates in the blood of infected humans. We and others have shown that FV NS1 can trigger endothelial barrier disruption in vitro and vascular leak in mice, independently from virus infection. In our current R01, we showed that endo- cytosis of FV NS1 into endothelial cells (ECs) followed by activation of key enzymes such as cathepsin L and heparanase leads to disruption of the endothelial glycocalyx layer (EGL) as well as mislocalization of intercellular junction proteins, both critical for maintaining endothelial barrier integrity. Interestingly, we found that FV NS1 proteins display exquisite tissue tropism, triggering EC dysfunction in vitro and in vivo in a manner reflecting tissue tropism and disease manifestations of each virus. While FV NS1 tissue tropism was determined by differential EC binding and internalization, downstream activation of key enzymes and signaling pathways required for pathogenesis appear to be conserved across FVs. However, host factors, viral determinants, and mechanisms mediating these processes are unknown. We hypothesize that distinct host factors on tissue- specific ECs mediate FV NS1 cell binding and internalization, leading to endothelial barrier dysfunction, virus dissemination, and different FV disease manifestations. In contrast, once a FV NS1 protein is internalized, we hypothesize that downstream steps of EC dysfunction are comparable – thus pointing the way to a pan-FV intervention. Here, we expand our previous work by identifying and characterizing host glycans, proteins, and NS1 determinants required for tissue-specific cell binding and internalization of NS1 in human ECs, mouse models, and clinical samples. We also define common mechanisms by which FV NS1 proteins trigger pathology. In Aim 1, we will identify and characterize host glycans and FV NS1 determinants required for differ- ential binding to tissue-specific ECs. In Aim 2, we will identify proteinaceous NS1 receptors required to initiate EC dysfunction and define mechanisms by which FV NS1 proteins mediate disruption of the EGL and intercellular junctions in tissue-specific ECs in vitro and in vivo. Aim 3 investigates the impact of FV NS1-mediated endothelial dysfunction on FV dissemination and pathogenesis in mouse models and human clinical samples from severe dengue and YF patients in Vietnam, Nicaragua and Brazil. This work is supported by experts in glycobiology, FV structural biology and biochemistry, vascular biology, FV pathogenesis and animal models, and clinical investigation and should identify biomarkers of severe FV disease and novel viral and host therapeutic targets.

NIH Research Projects · FY 2025 · 2022-04

Project Summary The higher burden of cardiovascular disease (CVD) in rural areas, particularly in Appalachia and the Mississippi Delta is alarming, yet virtually nothing is known about the underlying factors contributing to this rural health penalty. Prior research has shown that neighborhood environments are important drivers of CVD risk and racial/ethnic disparities in CVD; however, this work has been conducted almost exclusively in urban cohorts, leaving ~20% of the population understudied in regard to the #1 cause of mortality in the US. It remains unknown whether traditional features of neighborhood environments (e.g., food access, crime, social cohesion) operate similarly in rural areas to impact CVD risk, and this must be investigated rigorously. There is also an urgent need to better understand the role of more unique features of rural communities, such as geo- spatial isolation of residences, distance between businesses and retail outlets, and social networks operating in these contexts. It is important to characterize these unique rural neighborhood typologies and to investigate which subgroups may be most vulnerable to the cardiovascular health impacts of different neighborhood archetypes. We will examine whether associations are more deleterious among those who are psychosocially vulnerable – those with high levels of childhood trauma or inadequate social support. Finally, factors that contribute to cardiovascular resilience have also been understudied and we have a unique opportunity to investigate the multi-level factors that may contribute to CVD resilience (optimism, purpose in life, resilient coping). Thus, the overarching goal of the proposed study is to: 1) examine the relationship between neighborhood factors and unique neighborhood typologies on cardiovascular health (CVH) in rural communities, 2) determine which groups are most psychosocially vulnerable, and 3) determine whether the impact of adverse neighborhood typologies on CVH and subclinical CVD is mitigated by psychological resilience. The final, exploratory goal of this study is to 4) assess if associations are modified by age, sex, or race/ethnicity. To achieve these goals, we will leverage existing data from the Risk Underlying Rural Areas Longitudinal Study (RURAL) that will recruit 4,600 individuals ages 25-64 from 10 rural counties in Appalachia and the Mississippi Delta of the United States. We will augment this rich rural cohort by linking new data sources (e.g., geo-spatially referenced databases) and creating new measures in order to provide a comprehensive database of indicators of neighborhood physical and social environments. All in all, this work may help provide a more nuanced understanding of the multi- level determinants of both CVD risk and resilience and may help to identify novel levers of intervention to improve cardiovascular health in rural communities.

NIH Research Projects · FY 2026 · 2022-03

The lysosome, the main hub for cellular degradation and recycling processes, is emerging as a crucial signaling platform that controls cell metabolism. It is now clear that lysosomal signaling plays an important role in a variety of cancers. The Transcription Factor EB (TFEB), a master regulator of lysosomal biogenesis and autophagy, is both a substrate and a regulator of the mTORC1 lysosomal kinase complex, which drives growth and whose hyperactivation is broadly associated with cancer. Overexpression or constitutive activation of TFEB results in kidney cancer in two distinct disease entities: MiT-TFE Renal Cell Carcinoma (RCC) and Birt- Hogg-Dube' (BHD) syndrome, an inherited disease caused by mutations of folliculin (FLCN), a crucial regulator of TFEB activity. The goal of this proposal is to elucidate the mechanisms underlying TFEB-mediated kidney tumorigenesis. Emerging evidence suggest that such mechanisms may be involved in other disorders associated to kidney cancer, such Tuberous Sclerosis. Using sophisticated kidney-specific mouse transgenic models and CRE-fluorescent reporters, we will perform metabolic, biochemical, cell biology, omic and tumorigenesis assays both in vivo and in renal cultured cells with the aim of identifying the metabolic and signaling programs that underlie BHD and MiT-RCC tumorigenesis. In particular, these studies will allow us to dissect TFEB-regulated pathways that drive kidney tumorigenesis in both an mTOR- dependent and independent manner. To dissect these oncogenic programs in mechanistic depth, we will perform a detailed molecular characterization of FLCN- and mTORC1- dependent TFEB phosphorylation, coupled with candidate-based and high throughput genetic screens for novel TFEB regulators. Together, these studies will shed light on the pathogenesis of kidney tumors, and point the way toward new targets and therapeutic strategies.

NIH Research Projects · FY 2026 · 2022-02

PROJECT SUMMARY / ABSTRACT California is the most populous state in the nation but, in contrast to the racial and ethnic diversity of the Californian population, the research workforce in the biological science is relatively homogeneous. One of the reasons lies in the limited number of underrepresented minority (URM) students who enter PhD programs. To address this issue, a Post-Baccalaureate Research Education Program (PREP) will be developed at UC Berkeley to provide URM and disabled students, who want to pursue a career in biomedical research, with the intensive research experience and academic enrichment necessary to prepare them successfully for graduate school application and their subsequent careers in academia. The goals of this application are three-fold: (1) P rovide exceptional research opportunities to underrepresented recent college graduates; (2) Establish strong mentoring relationships and community building through a mentoring system providing the trainees with the support network they need to flourish in the program and beyond; and (3) Provide state of the art professional development tools and coaching to support scholars’ development and optimally prepare them to succeed in a biomedical research career. Annual support is sought for 6 “post-bac” students who will be placed in productive research laboratories which are actively funded by federal grants. Throughout the year long program, scholars will participate in enrichment activities including: writing personal statements for graduate applications; mock interviews; assistance in completing graduate applications; GRE Preparation; travel to scientific meetings; and improvement of communication skills. To achieve the success of this program, the Program Directors Prof. Gian Garriga, Associate Dean of Equity and Inclusion in the Biological Sciences, and Dr. Schaletzky, Executive Director of the Center of Emerging and Neglected Diseases (CEND) at UC Berkeley have recruited 38 faculty members to provide, not only intensive laboratory research training, but also relevant professional development guidance. An asset for the program, CEND is known within UC Berkeley for excellence in administration and a commitment to enhancing participation of underrepresented groups in STEM. CEND will bring excellent management and leadership and individual mentoring to the program and also provide a comprehensive career development program, involving individual development plans supported by a variety of career development workshops tailored to participating scholars. We are confident that scholars graduating from this program will be in an excellent position to successfully compete for graduate schools, contributing to equal representation of all groups in STEM and strengthening the innovation capacity of the scientific community in a sustainable fashion.

NIH Research Projects · FY 2026 · 2022-02

Abstract In the U.S., there are currently 22.7 million people living with asthma with a large cost to society estimated at $89 billion. Environmental exposures have been identified as playing a role in asthma etiology and lung function growth and the relationship with air pollution exposure is well established in more urban areas. Pesticide exposure has also been related to asthma and decline in lung function in workers. In the Center for the Health Assessment of Mothers And Children Of Salinas (CHAMACOS) Study, a longitudinal study of Latino farmworker families in Salinas California, we observed that early life exposure to several pesticides, as measured by biomarkers or residential proximity to agricultural use, were associated with childhood asthma and poorer lung function at age 7. It is unknown if these relationships persist into adulthood. Few studies have examined the impact of exposure to mixtures of pollutants such as particulate matter and pesticides. Methylation of DNA from nasal cells has been related to asthma and airway inflammation and there is evidence of differential methylation with exposure to pollutants, suggesting a possible link between environmental exposures and respiratory health. The long-term goal of our research is to identify modifiable factors related to respiratory health in a birth cohort that has reached young adulthood. We will leverage the unique CHAMACOS prospective birth cohort study to address these questions. Participants are currently 21 years of age and 500 participants still live near the Salinas Valley, and 250 completed lung function testing at 7 years of age. Our objectives in this proposal are to determine whether early life exposure to pesticides continue to impact their respiratory health in adulthood, identify the relative importance of pesticide and air pollution exposures, periods of susceptibility (prenatal, early life and childhood/adolescence), factors that modify these relationships and potential mechanisms involving the methylation of nasal cells. We hypothesize that higher exposure to pesticides and air pollutants in early life will result in poorer respiratory health and that DNA methylation will be a biomarker of these relationships. We will conduct spirometry testing at 22y and estimate pesticide exposure using California’s unique Pesticide Use Report data for the prenatal, early life (0-3y), childhood/adolescence (4-20y) and recent (previous year) periods. We will estimate exposure to particulate matter air pollution by combining remote sensing and air monitoring data. We will measure methylation in DNA collected from nasal swabs. We will assess whether associations observed in the CHAMACOS cohort between pesticide exposure and respiratory health at 7y persist into early adulthood and determine associations of exposure to a mixture of pesticides and particulate matter with respiratory symptoms, asthma, allergy, and lung function. We will characterize associations of DNA methylation with environmental exposures and respiratory health. In this study, we expect to identify the most important exposures and periods of exposure related to adverse respiratory health. Our findings will help inform future policies related to pesticide use and air quality designed to protect respiratory health.

NIH Research Projects · FY 2025 · 2022-02

Project Summary Visual information is processed through a set of neural circuits that organize into functional maps distributed throughout the thalamus, midbrain, and cerebral cortex. However, little is known about how circuits develop and organize in the retina, where this information processing begins. The goal of this proposal is to determine the mechanisms underlying the development of the circuits that mediate direction selectivity (DS) in the retina. Classic studies show that the distribution of preferred directions, referred to as the DS map, align with the cardinal axes–– superior-inferior and anterior- posterior. However, recent characterization has shown that the DS map follows the axes defined by optic flow. As a result, the DS map across the adult retina changes as a function of location, where the clusters are orthogonal to one another closer to the optic nerve and become skewed as distance from the optic nerve increases. This map is present at eye opening. How this complex organization arises prior to eye opening is not known. This prompts an investigation of the developmental factors that contribute to the formation of DS maps. Direction-selective ganglion cells (DSGCs) respond robustly to motion in a preferred direction and weakly to motion in the opposite, or null, direction. In order to achieve this computation, DSGCs receive greater synaptic inhibition during null direction motion from starburst amacrine cells (SACs) via precise wiring patterns. Interestingly, during the developmental period where DSGCs are wiring up with SACs, the retina is spontaneously active. This activity presents itself as waves propagating across the surface of the retina––termed retinal waves. In this proposal, I will explore the role of retinal waves, specifically waves driven by cholinergic signaling, in the development of DS maps. Additionally, I propose to investigate the synaptic basis underlying the formation of this distinct organization across the retinal surface. As a first step towards understanding whether retinal waves influence DS map formation, I will use two-photon population calcium imaging, genetic tools, and pharmacology to assess how the DS map develops in the presence and absence of patterned spontaneous activity across development. To achieve this, I will use a mouse model where cholinergic waves are severely disrupted by knocking out the β2 subunit of the nicotinic acetylcholine receptor (Aim 1). Moreover, given the extent to which asymmetric inhibition is necessary for directional tuning, I propose that the tuning of inhibitory inputs onto DSGCs will change at varied locations in the retina, to account for the skewing of preferred directions. To test this, I will use two-photon-targeted voltage clamp recordings to unmask the synaptic basis of this organization (Aim 2). These findings will provide key insights into the mechanisms that underlie this precise organization during development.

NIH Research Projects · FY 2025 · 2022-01

Project Summary Frontotemporal dementia (FTD) is an early onset neurodegenerative disease, and the second most common cause of dementia in patients 60 years or younger. The majority of familial FTD are caused by intronic hexanucleotide (CCCCGG) repeat expansion in chromosome 9 open reading frame 72 (C9orf72) gene and by dominant mutations in the Progranulin (GRN) gene, causing haploinsufficiency in both genes, abnormal protein aggregate formation in neurons. Several functional and transcriptomic studies have shown that mice with null mutation in C9orf72 or Grn show abnormal microglia (resident CNS immune cells) activation mediated pathogenesis of neurodegeneration in FTD. While the exact functions for C9orf72 and Progranulin (PGRN [protein]) are still unclear, several studies have implicated both in autophagy and endolysosomal pathways in neurons and microglia, and concurrent mutations resulting in increased brain atrophy in patients. These results suggest a possible interaction between C9orf72 and PGRN in neurodegeneration during brain aging The goal of my project is to investigate the synergistic interaction of C9orf72 and Grn genes in glial homeostasis and neuronal degeneration using mouse models. In support of this, my preliminary data showed that C9orf72-/- ;Grn-/- DKO mice have significantly shortened lifespan, much shorter than C9orf72-/- mice, Grn-/- mice and control mice. Brain pathology examination in C9orf72-/-;Grn-/- DKO mice showed age-dependent gliosis as well as neuronal TDP-43 aggregates that are more pronounced and wide-spread than those in C9orf72-/- or Grn-/- mice. These results support my hypothesis and further indicate that loss of C9orf72 and Grn synergistically disrupt glia-neuron homeostasis and lead to more pronounced neurodegeneration phenotype. For the F00 phase, I propose to uncover the mechanism of C9 and PGRN in neurodegeneration in the aging brain via single-cell and bulk RNA-sequencing in 7 and 12 months old control, C9orf72-/-, Grn-/- and C9orf72-/-;Grn-/- DKO brain to determine how loss of these two FTD genes disrupts the homeostasis in glia-neuron interaction (Aim 2a). These transcriptomic data will be validated using in situ hybridization, immunohistochemistry and western blots (Aim 2b). Finally, I propose to develop in vitro cultures, including neuron-only cultures and glia-neuron co-cultures, which will provide more insights into the synergistic interaction between C9orf72 and PGRN in the autophagy- lysosome pathways and in glia-mediated toxicity to neurons (Aim 2c). For the K00 phase of this fellowship, I plan to develop induced pluripotent stem cells (IPSC)-derived 3D brain organoids as model systems to investigate disease mechanism and identify therapeutics for neurodegeneration. To identify signaling pathways that could be affected by diseases, I plan on using single-cell transcriptomics on patient IPSC derived glia-neuron organoids, followed by CRISPR/Cas9-based manipulation strategies on the signaling pathways dysregulated in these brain organoids to elucidate the diseases progression mechanisms.

NIH Research Projects · FY 2025 · 2021-09

PROJECT SUMMARY / ABSTRACT Lipid droplets (LDs) are neutral lipid storage organelles that act as cellular hubs of lipid homeostasis. Dysregulation in LD function has been implicated in prevalent metabolic diseases such as obesity, diabetes, cardiovascular disease, and non-alcoholic fatty liver disease (NAFLD). Indeed, the pathological hallmark of NAFLD is the accumulation of large hepatic LDs. In addition to metabolic diseases, LDs have also been implicated in cancer proliferation and survival, host-pathogen interactions, and neurodegeneration. Thus, understanding how LDs are regulated has the potential to broadly impact our understanding of human health and disease. LDs are ER-derived organelles that have a unique ultrastructure, consisting of a core of neutral lipid surrounded by a phospholipid monolayer decorated with integral and peripheral proteins. While recent findings have advanced our understanding of LD biogenesis, how LDs are regulated under different metabolic conditions and how the composition of the LD proteome remain poorly understood. To overcome these critical gaps in knowledge and define the mechanisms that regulate neutral lipid storage, we performed a series of CRISPR-Cas9 screen in human cells using a fluorescence-based neutral lipid reporter under different metabolic conditions. We also employed genetic screens to examine the mechanisms that regulate PLIN2, a near ubiquitous Class II LD protein that plays important roles in regulating LD stability. Our findings establish a compendium of neutral lipid storage regulators, revealing interesting novel regulators that are condition specific. Furthermore, we identify several ubiquitination factors that influence neutral lipid storage and the stability of PLIN2. The current proposal aims to build on the foundation provided by our extensive preliminary data to characterize new mechanisms of LD regulation. In aim 1, we will complete our validation experiments to establish an extensive, phenotypic-rich resource for the community that is hypothesis generating. We will also examine the concept that metabolic state-dependent regulation of LDs is a significant contributor to cellular lipid homeostasis. Finally, we will characterize high priority candidates in iPSC-derived hepatocytes and examine the hypothesis that a subset of regulators governs LD stability as part of a host response to pathogens. In Aim 2, we will define the role of new ubiquitination pathways in regulating lipid homeostasis, examining the hypothesis that the identified factors regulate LD stability by controlling the degradation of PLIN2 during lipolysis. These findings will provide new global and mechanistic insights in to LD proteome remodeling and regulation under different metabolic conditions.

NIH Research Projects · FY 2026 · 2021-09

PROJECT SUMMARY Stroke-causing illness, disability, and early death is set to double worldwide within the next 15 years. Despite physical therapy, about 50% of stroke survivors have impaired hand function, which strongly impacts activities of daily living and independence; novel treatment methods are urgently required. While most pre-clinical research addressing stroke recovery and rehabilitation focuses on restoring damaged descending movement pathways, dexterous hand function is also reliant on the brain receiving ascending somatosensory input and being able to use it to guide movements. Clinically and in animal models, deficits in somatosensory cortices predict worse recovery of hand function following stroke, though the functional mechanisms by which somatosensory signals support hand function remain poorly characterized. In this proposal, we aim to uncover how somatosensory signals drive motor activity during the acquisition and performance of dexterous manipulation behaviors in intact and post-stroke non-human primates. The main experimental approach of this proposal includes simultaneous high-density, high channel-count acute electrophysiological recordings from the somatosensory thalamus, primary somatosensory cortex, and primary motor cortex in intact and post-stroke non-human primates performing complex manipulation tasks. The main analytical approach includes modeling motor activity evolution as a combination of intrinsic motor cortical dynamics and inputs from somatosensory thalamic and somatosensory cortex. The hypothesis of this proposal is that somatosensory input signals guide the identification of effective motor activity trajectories that become frequently used and less input-dependent with improved manipulation skill. Thus, somatosensory signals are critical for improvement of manipulation skill and recovery of dexterity post-stroke. Completion of this proposal will identify nodes and functional interactions within the sensorimotor system that could be targeted with novel therapies for improving recovery of hand function following stroke. I will complete these aims with the guidance of an exceptional mentoring team led by Dr. Karunesh Ganguly and including Dr. Joni Wallis, Dr. Robert Morecraft, and Dr. Aaron Suminski. During the mentored phase of the award at UCSF, I will develop a state-of-the-art high channel-count, multi-area electrophysiological approach for monitoring the sensorimotor network. I will also conduct the proposed experiments in animals performing object manipulation tasks, pilot a haptic brain-machine-interface task, and focus on professional development in order to facilitate a successful transition into an independent faculty position at an academic institution.

NIH Research Projects · FY 2025 · 2021-09

SUMMARY Chronic and/or excess glucocorticoid (GC) exposure, such as prolonged stress and long-term GC therapy, causes metabolic disorders including hyperglycemia. Intracellular GC receptor (GR) has been shown to directly stimulate the transcription of gluconeogenic genes, such as Pck1 and G6pc, to promote gluconeogenesis. However, chronic GC exposure can induce additional mechanisms to further enhance hepatic gluconeogenesis. Our preliminary studies found that chronic GC exposure elevated hepatic sphingosine-1-phosphate (S1P) levels. S1P is exported to the extracellular surface and binds to membrane S1P receptors (S1PRs) to exert its actions. We found that reducing S1PR2 expression in mouse liver attenuated chronic GC exposure-promoted gluconeogenesis. Activating S1PR2 in hepatoma cells enhanced GC-induced Pck1 and G6pc expression. Chromatin immunoprecipitation assay found that GC-induced GR recruitment to the GC response elements (GREs) of Pck1 and G6pc was reduced by hepatic S1PR2 knockdown. Global gene expression analysis identified that RAR-related orphan receptor C (Rorc) expression was reduced by hepatic S1PR2 knockdown. Rorc antagonist attenuated GC-induced gluconeogenic gene expression in hepatoma cells and overexpressing Rorc in the liver of hepatic S1PR2 knockout mice enhanced GC-induced GR recruitment to the Pck1 and G6pc GREs as well as their expression. Intriguingly, GC suppressed Rorc expression, which was antagonized by S1PR2 signaling. Based on these results, we hypothesize that chronic GC exposure activates S1PR2 signaling to enhance GC-induced gluconeogenesis by inhibiting GC’s suppressive effect on the expression of Rorc, which can act with GR to strongly augment gluconeogenic gene transcription. In Aim 1, we will test if altering intracellular S1P levels in hepatocytes affects chronic GC treatment-induced hyperglycemia by overexpressing or knocking down Sphk1 and Sphk2 (both convert sphingosine to S1P), Sgpl1 (hydrolyzes S1P) and Spns2 (exports S1P to extracellular space) in mouse liver. In Aim 2, we will establish Rorc’s in GC-induced hepatic gluconeogenesis by reducing hepatic Rorc expression or treating mice with Rorc antagonist. Notably, 4a- carboxy, 4b-methyl-zymosterol (4ACD8), a metabolite of cholesterol biosynthesis, has been shown to be a Rorc agonist. We will investigate whether reducing the expression of Sc4mol, an enzyme generating 4ACD8, attenuates the GC effect on hepatic gluconeogenesis. In Aim 3, we will identify signaling molecules activated by S1PR2 that participate in GC regulation of gluconeogenic genes and Rorc expression. We will also analyze the role of Rorc in GR regulated global hepatic gene transcription. Finally, how GC and S1PR2 signaling regulate Rorc expression will be investigated. Overall, the proposed studies will establish a novel S1PR2-Rorc axis induced specifically upon chronic GC exposure to enhance GC activated gluconeogenesis. Not only will this knowledge advance our understand on pathophysiology of chronic GC exposure, but it also will provide novel targets for therapeutic intervention against steroid induced hyperglycemia.

NIH Research Projects · FY 2024 · 2021-09

PROJECT SUMMARY Innate immune receptors from the NLR protein family control basic organism-organism interactions across kingdoms, including incompatibility within a species. Current availability of genomic biodiversity allows us to examine patterns of innate immune receptor evolution. I propose that adaptive immunity has evolved by adopting subsets of proteins domains already present in innate immunity as well as their diversification mechanisms to act somatically in specialized cells. Testing this hypothesis through comparative genomics will be paradigm-shifting to our understanding of immune system evolution. To do this, we will examine evolution of protein domains involved in innate immunity across all available eukaryotic genomes, determine sources of genomic diversity and how they change with the re-current evolution of adaptive immunity across independent lineages. To test that there are targeted diversity generation mechanisms acting on NLRs at the population level, we will examine patterns of NLR evolution on multiple scales, including cross-kingdom analyses. We will test diversification mechanisms acting on them within species lacking adaptive immunity, including model plants and fungi. In parallel, we will experimentally test involvement of NLRs in fungal immunity, which has been proposed but yet to be experimentally validated. Finally, we will conduct experimental evolution on both NLRs and their ligands to collect data for modeling how new binding specificities arise on the population scale. Altogether, this project will fill in important gaps in understanding the evolution of innate immune systems, including our own.

NIH Research Projects · FY 2025 · 2021-09

ABSTRACT The integrity of a cell depends on the quality of its components. These components include proteins, which are responsible for executing most cellular functions, many through organization into stable complexes. A hallmark of aged cells is the breakdown of protein integrity, or proteostasis, which results from the damage to key proteins and complexes over time, leading to more accumulated damage, and ultimately cell dysfunction. The specific proteome components that are most susceptible to damage and that drive its accumulation remain unclear, but the survival of future generations depends on protection of one cell type—gametes—from inheriting damaged components from their precursor cell. During gametogenesis in the simple budding yeast, as a precursor cell is differentiated into gametes, we observe the degradation of many cellular structures and proteins, followed by their resynthesis and reorganization. This cellular restructuring is associated with an active rejuvenation program that allows equivalently young gametes to be produced from old or young precursor cells. The mechanisms that contribute to this natural rejuvenation program are not known, but it can be recapitulated by exogenous expression of a meiotic transcription factor in aged mitotic cells, suggesting that it is portable. Gametogenesis in yeast thus offers the opportunity to watch as the cell shows us what proteins and complexes it needs to reset and reorganize to ensure cellular youth, and the mechanisms it uses to achieve this. Of particular interest are proteins of basal or “housekeeping” function, including the ribosome, which are long- lived in mitotic cells, but degraded and replaced at great energetic cost during gametogenesis. We also observe reorganization of abundant housekeeping complexes, including the proteasome, during gametogenesis, and aggregation of some proteins, including superoxide dismutase 1 (Sod1), at the time of their degradation. Together, these observations suggest that yeast cells remodel their proteome during gametogenesis as a quality control measure. Here, we propose to identify the key set of cellular components, with a focus on “housekeeping” proteins, that are reset as gametes are created from precursor cells. We use a proteomic approach to globally define changes to protein complexes during gamete construction, and specifically determine proteasome remodeling and activity over time. We investigate the links between aggregation of proteins, including Sod1, and protein oxidation and degradation. Finally, we identify the specific degradation mechanisms that drive key aspects of proteome remodeling and test their necessity for gamete rejuvenation and ability to drive lifespan extension when exogenously activated. This project will build an atlas to reveal the proteins and complexes that are important enough for young cell identity to warrant the energetic cost of resetting them during gamete formation, as well as those that may be toxic enough to warrant their active removal. By identifying and manipulating the specific pathways used by gametes to selectively remodel their proteome, we will find strategies that can be co-opted to combat and prevent age-associated cellular damage.

NIH Research Projects · FY 2025 · 2021-08

SUMMARY It is increasingly recognized that global goals for HIV epidemic control cannot be realized without improving retention in HIV care and adherence to antiretroviral therapy (ART). Only 58% of people living with HIV (PLHIV) in eastern and southern Africa are virally suppressed, and adherence counseling provided to those with elevated viral loads results in viral suppression only 40-50% of the time. Financial incentives, first used for poverty reduction, have been shown to motivate behavior change and improve engagement in HIV-related services. However, there is a paucity of data about the effectiveness of incentive-based programs for people who have disengaged from HIV care as well as the proactive use of incentives for PLHIV struggling with adherence. This research gap limits our understanding of whether financial incentive programs are worthwhile investments to support lifelong care, which is essential to the success of ‘treatment as HIV prevention’ (TasP). The proposed research will advance global knowledge about the effectiveness of financial incentives for strengthening the continuity of HIV care. We will build on data from a pilot study we conducted in Tanzania which found that an intervention offering a one-time financial incentive to out-of-care PLHIV was feasible, acceptable, and preliminarily efficacious at motivating re-engagement in HIV care. Leveraging our established research program and expertise with behavioral economics, we designed a 5-year, mixed-methods, hybrid effectiveness-implementation study to evaluate the financial incentive intervention and describe its successful implementation, with the ultimate goal of closing the gap towards achievement of UNAIDS’ ‘95-95-95’ goals. We will first assess if a one-time financial incentive improves re-engagement in care and durable viral suppression at 12 months among 640 PLHIV in Geita and Kagera Regions who have disengaged from care (Aim 1). We will then measure the effectiveness of short-term financial incentives offered to 692 in-care PLHIV who are at risk of loss to follow-up or poor adherence, with durable viral suppression at 12 months as the outcome (Aim 2). A mixed-methods study will describe implementation successes and challenges and synthesize lessons learned to inform adoption of incentive programs for vulnerable PLHIV (Aim 3). The project is a collaboration of the University of California, Berkeley, Health for a Prosperous Nation, Rasello, Management and Development for Health, and the Tanzania Ministry of Health, Community Development, Gender, Elderly, and Children. At the conclusion of the project, we will have rigorously evaluated the incentive strategy and will understand whether it can mitigate the persistent challenge of disengagement from HIV care, consistent with NIH Office of AIDS Research priorities for implementation research on retention in care and adherence to ART. This information is highly relevant to the spectrum of incentive-based programs being implemented or under consideration to improve the health of PLHIV and to optimize TasP programs in UNAIDS Fast Track countries. 1