University Of California, San Diego

NIH Research Projects · FY 2026 · 2023-09

PROJECT SUMMARY/ABSTRACT Mitochondria provide 90% of our energy; defects in mitochondria lead to a wide range of diseases including seizures, stroke, heart disease, neurodegeneration, and cancer. Far from their static kidney-bean shaped depiction in many textbooks, mitochondria form a dynamic three-dimensional network that spans the entire volume of the cell. This network undergoes continuous remodeling through fission and fusion, motility, biogenesis and clearance. Under stress or disease conditions, the mitochondrial network fragments and changes its dynamic equilibrium. Understanding this equilibrium, and its changes and adjustments to disease, is an archetypical question in quantitative cellular organelle biology. The dynamic mitochondrial network has so far evaded experimental interrogation and modeling as mitochondria were too small and too fast for volumetric fluorescence microscopy. Fortunately, recent advances in imaging technology, namely lattice light-sheet microscopy (LLSM), have changed that. Substantial preliminary data in this application supports the working hypothesis that a combination of quantitative LLSM image processing, and particle based spatial modeling can succeed in creating the first four-dimensional (4D) spatiotemporal model of the mitochondrial network. The goal of the proposed work is to elucidate the fundamental biophysical principles of mitochondrial network homeostasis. We have outlined three aims that will enable us to close this knowledge gap. Aim 1 will test the hypothesis that deep learning-based mitochondria segmentation will demonstrate more accurate extraction of the 4D mitochondrial network from LLSM data as compared to traditional methods. New deep neural network architectures will be developed to test this hypothesis. It is expected that a tool will be delivered that generalizes across diverse imaging conditions and diverse mitochondrial form and function impaired conditions. Aim 2 will test the hypothesis that graph-based topological linking will demonstrate the first temporal tracking of the 4D mitochondrial network. New linear assignment problem-based algorithms will be developed to precisely track the mitochondrial network backbone as well as its fission/fusion events. It is expected that a tool will be delivered that can track the mitochondrial network in a variety of imaging conditions and mitochondrial form and function impaired conditions. Aim 3 will test the hypothesis that morphology, dynamics, and function of the mitochondrial network are linked and can be predicted. A new particle-based polymer simulation model will be developed based on 4D graph temporal analysis of experimental data. It is expected that the first 4D spatio-temporal model of the mitochondrial network will be developed that can predict form and function observables and their time evolution from first principles.

NIH Research Projects · FY 2025 · 2023-09

SUMMARY Resolution in skin wound healing is coordinated by intercellular communication processes that include extracellular vesicles (EVs) containing biologically active protein and nucleic acid. In injury models, EVs have been shown to be important mediators of tissue repair, although the mechanisms underlying the formation of specific EV subsets, loading of EV payloads, and cell- type specific EV uptake remain poorly understood. We address this knowledge gap with a comprehensive genetic approach to modify the regulation of EV biogenesis to change the EV Profile, Payload and Activity in cutaneous wound models that have well-defined biological relevance. We have recently established that genetic tools regulating EV biogenesis `re-program' EV payload. Moreover, over-expression of specific pro-reparative payloads that were identified by mass spectrometry can be engineered and delivered to promote resolution in models of impaired wound healing. With a focus on the discovery of novel EV mediators of crosstalk between immune and epithelial cells in the wound bed, we have focused on the biology of EVs in mediating intercellular signaling in EVs formation (Project 1-EV Biogenesis), the engineering of biologically active payloads (Project 2-EV Payloads), and identifying specific cell types that internalize EVs in the wound bed (Project 3-EV Uptake). Together, these Projects address the over-arching goals of creating therapeutic EVs with a systematic approach that is optimized for specific cell types based on an understanding of 1) How and where EVs are made?; 2) How EVs are loaded and whether they are biologically active ?; and 3) Which cells uptake EVs to promote durable tissue repair.

NIH Research Projects · FY 2025 · 2023-09

Changes in interactions between neurons enable diverse computations and flexible behaviors. Such changes can occur very rapidly by rerouting information flow through existing connections, or more slowly by updating connections. The proposed project will study how local and brain-wide dynamics arise during learning of goal-directed behaviors. Experiments will use novel ‘all-optical’ experimental techniques to causally map network interactions at cellular resolution in combination with data-constrained computational models, to follow the learning process in the living brain with unprecedented detail. The investigation will focus on learning mechanisms in several novel memory-guided behavioral tasks, that either do not require learning, or specifically tailored for studying learning within and over days. This will fundamentally advance the understanding of how different learning mechanisms shape brain-dynamics and behavior. Aim 1: Mapping changes in causal interactions (effective connectivity) between neurons in local cortical circuits. Modeling and experiments will allow disentangling contributions of synaptic plasticity and gating to changes in network interactions and representations during learning. Aim 2: Investigating unique properties of cortex-wide neural activity. Preliminary work, based on cellular-resolution mesoscopic imaging of ~1,000,000 neurons, led to the discovery that spatial and temporal scales of brain-wide dynamics follow a power-law. Intriguingly, the most dominant modes of activity are global and fast, differently from any existing network model. The proposed work will uncover biological mechanisms supporting the emergence of these newly discovered cortical states during learning. Aim 3: Investigating functional implications of learned neural network dynamics studied in Aims 1 and 2. To test the hypothesis that such dynamics enable animals to perform flexible memory-guided behaviors, work will focus on modeling the effect of targeted optogenetic perturbations of neural activity on different spatial scales on network dynamics and behavior. Overall, the proposed collaborative study will leverage the PIs complementary expertise, to deepen the understanding of mechanisms and function of neural dynamics on different spatial scales. The experimental and theoretical methods developed as part of this proposal will provide insight for brain-wide control of memory-guided behavior, and will serve as a road-map for future studies of other behaviors controlled by distributed brain networks.

NIH Research Projects · FY 2026 · 2023-09

SUMMARY Overall The overall purpose of the Center Core Grant for Vision Research is to provide core services and resources to enhance and accelerate the productivity and impact of the vision research community at the University of California, San Diego. Specifically, the Center Core Grant for Vision Research will leverage the outstanding basic science and clinical research expertise of National Eye Institute funded investigators by providing important resources and services organized into the following five distinct cores. 1. The Vision Biostatistics Core provides dedicated statistical expertise for the vision research community at UCSD. There are several common analysis themes and statistical issues that can be addressed effectively and efficiently by having a dedicated biostatistician familiar with eye research to analyze vision-related data and to ensure rigor and transparency of the results. 2. The Animal Structure and Function Core will provide shared instrumentation and a technician to assist with ocular structural imaging and functional imaging in animals. 3. The Computational Ophthalmology and Biomedical Informatics Core provides i) dedicated high- performance CPU and GPU computing resources ii) 3 computer programmers, iii) institutional software licenses, iv) electronic health record data extraction services, v) cloud-based data management infrastructure, and vi) secure file sharing and backup services to support UCSD’s cellular, animal and human vision research studies. 4. The Histology, Tissue Processing and High Content Microscopy Core provides rapid characterization of eye tissue with respect to histology, immunohistochemistry and high content microscopy for drug screening and histologic specimen imaging by supporting instrumentation and a technician who is familiar with ocular anatomy and techniques required to properly process ocular tissues. 5. The new Viral Production and CRISPR Engineering Core provides centralized dedicated space, equipment and personnel for the production, isolation and titering of adeno-associated virus (AAV) and lentivirus (LV) vectors and assistance with non-viral CRISPR gene editing. These cores will improve the efficiency and productivity and impact of UCSD vision scientists by providing core services that are unavailable or not easily accessible to individual investigators. The core grant infrastructure and resources also leverage the expertise of each participating investigator to enhance multidisciplinary collaboration for the benefit of the entire UCSD vision research community.

NIH Research Projects · FY 2024 · 2023-09

PROJECT SUMMARY Hematopoietic stem cells (HSCs) regenerate all blood and immune cells throughout life. Aging HSCs exhibit diminished regenerative function, reduced lymphoid potential, and clonal outgrowth that is associated with compromised immunity as well as an increased incidence of anemia, bone marrow failure, and hematological malignancies in older adults. The regulation of protein homeostasis (proteostasis) has recently emerged as a fundamental process required to promote HSC self-renewal. Loss of proteostasis is considered one of the hallmarks of aging, but to what extent it contributes to stem cell aging is largely unknown. An essential pathway in maintaining proteostasis is the Heat Shock Response, which is regulated by the master transcription factor Heat shock factor 1 (Hsf1). Hsf1 induces expression of heat shock proteins that aid in proper protein folding, trafficking, and degradation. At steady state, Hsf1 is typically sequestered in the cytoplasm, but translocates into the nucleus in response to cellular and proteotoxic stress. Previously, we demonstrated that HSCs undergo cellular stress when cultured ex vivo and Hsf1 activation can alleviate this stress to maintain HSC regenerative activity. Hsf1 is highly expressed in young and old adult HSCs but is specifically activated during aging in middle- aged and old adult HSCs. Aging is a notably stressful process associated with the accumulation of genetic mutations, inflammation, and oxidative stress. Based on these preliminary results, the central hypothesis of this proposal is that Hsf1 activation promotes HSC function and proteostasis during aging. To test this hypothesis, Aim 1 will examine the role of Hsf1 in aging HSC function and proteostasis using conditional Hsf1 knockout mice. HSC function will be assessed in competitive transplantation assays and proteostasis will be assessed by quantifying protein synthesis, proteasome activity, misfolded protein, unfolded protein, and protein aggregate abundance. I expect that there will be less reconstitution in aged Hsf1-deficient HSCs and more protein synthesis, misfolded and unfolded proteins, and aggregates. While Hsf1 activation is hypothesized to be important for HSC function during aging, the mechanism underlying heterochronic Hsf1 activation is unknown. Preliminary RNA-sequencing results revealed that Transglutaminase 2 (Tgm2), involved in Hsf1 activation, is significantly upregulated in old adult HSCs. Thus, Aim 2 will examine if age-related Hsf1 activation depends on Tgm2 upregulation. Hsf1 activation, HSC function, and proteostasis will be assessed in conditional Tgm2 knockout mice. I expect that loss of Tgm2 in aging HSCs will disrupt proteostasis and exhibit an associated decline in fitness and function due to a decrease in Hsf1 activation. Collectively, these studies will provide deeper insights into mechanisms that regulate proteostasis during stem cell aging. These findings will uncover new therapeutic targets to promote HSC fitness during aging.

NIH Research Projects · FY 2025 · 2023-09

Abstract Chronic obstructive pulmonary disease (COPD, which includes chronic bronchitis and emphysema) and obstructive sleep apnea (OSA) are both common diseases with major cardiovascular sequelae. The concomitant presence of COPD and OSA is referred to as overlap syndrome (OVS), which has a very poor prognosis with his risk of cardiovascular mortality. Our data demonstrate an association between OSA treatment and improved mortality in individuals with OVS, but to date data are not definitive and underlying mechanisms are undefined. In theory, in individuals with baseline (sustained) hypoxemia, further intermittent hypoxemia due to OSA may promote pulmonary vasoconstriction and elevated pulmonary vascular resistance. Thus, the right ventricle (RV) may be particularly affected by OVS. Of note, we have robust preliminary data showing the impact of OVS on the RV and reversibility with intervention. To investigate these concepts further, we propose two specific aims. First, we will perform a cross-sectional study to compare specific markers of cardiovascular risk among those with OSA vs. COPD vs. OVS. This aim will test the hypothesis that OVS has worsen endothelial function as compared with individuals afflicted with either disease alone. We will quantify other markers of cardiovascular risk such as cardiac MRI and plasma biomarkers including novel microRNAs. We have recent prominent publications suggesting a major role of miR-210 in the pathogenesis of OSA induced vascular risk. We will also employ novel imaging methods to assess potential biomarkers for mechanistic insights and to identify robust surrogate outcome measures for subsequent studies. Second, we will perform a mechanistic clinical study to compare the improvement in RV mass among individuals who receive bi-level positive airway pressure (PAP) as compared to individuals who receive oxygen (O2), which is the current standard of care. This aim will test the hypothesis that bi-level PAP therapy improves markers of cardiovascular risk as compared with O2 therapy. In addition to cardiac MRI we will assess other biomarker of cardiovascular risk as in Aim 1. Such findings will lay the groundwork for a multicenter randomized controlled trial, which we believe will be required to change the current standard of care. Our proposal will also inform basic research on the interactions of sustained plus intermittent hypoxemia. Given the high vascular risk among these individuals, the very high population prevalence of disease and the lack of current data, further mechanistic research is imperative.

NIH Research Projects · FY 2024 · 2023-09

Project Summary Cerebral blood vessels are critical to deliver oxygen and nutrients to the brain, and to remove carbon dioxide and other waste products. Although just 2% of the body’s weight, 20% of the circulation is directed to the brain, highlighting the importance of the cerebral vasculature to the health and function of the brain. Blood vessels that vascularize the central nervous system (CNS) harbor distinct physical, transport, metabolic, and signaling properties, termed the blood-brain barrier (BBB). Manifested within the endothelial cells (ECs) that line the lumen of the CNS vasculature, these BBB properties stringently regulate the movement of molecules, ions, and cells between the blood and the brain, allowing for proper neuronal function and safeguarding the neural tissue against injury and disease. As such, many neurological diseases are associated with BBB disruption, including multiple sclerosis (MS), epilepsy, and stroke. Recently it has been suggested that BBB dysfunction may contribute to the pathogenesis of Alzheimer’s disease (AD); however, the extent, nature, and contributions of this dysfunction to AD pathophysiology remains enigmatic. To identify nuanced changes to the brain vasculature in AD, a vascular-specific proteomic approach was employed. This approach revealed down-regulation of many enzymes involved in fatty acid and lipid biosynthesis, namely ELOVL fatty acid elongase 7 (ELOVL7), in the cortical vasculature of AD patients compared to controls. From here, this proposal will test the hypothesis that aberrant vascular lipid metabolism is a critical component of AD pathophysiology. Many classes of lipids have been implicated in regulating the trafficking and proteolytic activity of disease-relevant enzymes in AD. As lipid signaling is critical to brain homeostasis, vascular integrity, and AD etiology, identification of the lipidomic changes occurring at the BBB during AD could give important insight about the pathogenesis of AD and potentially identify novel therapeutic targets that can be used to normalize the BBB in AD patients. While ELOVL7 has never been studied in brain ECs or in the context of AD, previous studies have revealed that ELOVL7 is uniquely enriched in brain ECs in both mice and humans. Further, brain EC-specific transcriptomic approaches have shown dynamic loss of ELOVL7 expression in neuroinflammatory mouse models with known BBB disruption. Data such as these, taken together with the finding that ELOVL7 is decreased in the brain vasculature of patients with AD, steers this proposal towards the hypothesis that ELOVL7 may be critical to BBB function and that its downregulation may contribute to AD etiology. This hypothesis will be tested in vivo by conditional deletion of ELOVL7 within brain ECs of mice. Understanding the role of ELOVL7 at the BBB may elucidate crucial mechanisms of AD pathophysiology, and its downstream fatty acid metabolites may prove to be viable therapeutics to normalize the brain vasculature in AD.

NIH Research Projects · FY 2025 · 2023-09

PROJECT Summary Lp(a) is a highly prevalent, independent, genetic and likely causal risk factor for cardiovascular disease. The population at risk represents 20-30% of individuals in the United States, or >100,000,000 people, and an estimated 1.4 billion people globally. Lp(a) is associated with increased CVD risk in primary prevention settings and in patients on statins and PCSK9 inhibitors in secondary prevention settings. Lp(a) is a preferential carrier of OxPL, the content of which in plasma can be measured by the assay OxPL-apoB. There are no approved pharmacological therapies to treat elevated Lp(a). In primary prevention settings, clinical equipoise exists in the use of aspirin in adults with elevated Lp(a) (>30 mg/dL or >75 nmol/L), and physicians do not have enough information to treat such patients with aspirin, particularly those with a strong family history of CVD. We hypothesize that elevated Lp(a) will identify a large subgroup of individuals that may benefit from aspirin in primary prevention settings and propose to test this hypothesis in the ASPREE and ASCEND trials. We propose to test the hypothesis that aspirin modifies the risk of incident atherothrombotic CVD events in high-risk primary prevention settings to a different extent in people with high Lp(a) or OxPL-apoB levels than in people with lower Lp(a) levels. SubAim 1 will test this hypothesis in elderly individuals in the ASPREE trial. SubAim 2 will test this hypothesis in individuals with type 2 diabetes in the ASCEND trial. We will also perform a meta-analyses of the effects of aspirin on the risk of incident atherothrombotic CVD events in high-risk primary prevention settings in people with high versus lower Lp(a) levels and in people with high versus lower OxPL-apoB levels in the ASPREE and ASCEND trials, using the most comprehensive relevant outcome in each trial, as used in Aim 1 and Aim 2.

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY One in fifty Americans will be diagnosed with melanoma in their lifetime and skin cutaneous melanoma is the deadliest skin cancer. Cancer immunotherapy is a breakthrough approach to treat this disease and cytotoxic CD8+ T-cell tumor infiltration is a critical factor to immunotherapeutic success. As such, identifying effective strategies to increase the magnitude and functionality of the patient’s tumor-specific CD8+ T-cell response remains an important goal. Inhibitory molecules on CD8+ T cells are imperative to T-cell signaling and immune homeostasis. However, elevated expression of these molecules is correlated with dampened antitumor effector response as well as poorer patient survival. FcγRIIB is an inhibitory Fc receptor recently discovered on a subset of CD8+ T cells. FcγRIIB+ CD8+ T cells exhibit increased expression of activation markers, higher proliferative ability, and secrete more proinflammatory cytokines than their FcγRIIB- counterparts in mice and humans, making them imperative to the antitumor response. Recently, we discovered that an immunosuppressive cytokine, fibrinogen-like protein 2 (Fgl2), is a ligand that binds FcγRIIB on CD8+ T cells and induces FcγRIIB- mediated apoptosis of CD8+ T cells. The goal of this research is to interrogate the mechanism by which Fgl2 regulates tumor-specific FcγRIIB+ CD8+ T cells using syngeneic mouse models via the following aim. AIM 1 (F99): Determine the cellular and molecular mechanism by which Fgl2 critically regulates tumor-specific CD8+ T cells. Our studies show that both Foxp3+ regulatory T cells and CD8+ T cells express Fgl2 at the tumors of mice and humans. Thus, we will determine if Fgl2 secreted by these cell types is necessary and/or sufficient for FcγRIIB-mediated CD8+ T-cell apoptosis, findings which would provide the impetus for subsequent therapeutic targeting of this cell type. Additionally, as we have discovered that FcγRIIB-Fgl2 binding induces apoptosis, the upstream requirements of apoptosis (e.g. T-cell receptor stimulation, proteins recruited to the intracellular domain of FcγRIIB) are proximal items of investigation in the latter part of Aim 1. Piecing together the pathway by which FcγRIIB induces apoptosis via Fgl2 could uncover a new CD8+ T cell pathway readily harnessed for future immunotherapies. AIM 2 (K00): Identify novel mechanisms of T cell resistance to cancer immunotherapy. After the F99 stage, I intend to transition to the K00 stage to begin postdoctoral studies. Numerous studies highlight the role of elevated checkpoint molecule expression (PD-1, TIM-3) as well as decreased proinflammatory cytokine production (IFNγ, TNF) in mediating resistance to ICB. The current paradigm in cancer immunotherapy revolves around the suppressive impact of the tumor microenvironment on T cells, but the existence and impact of immunosuppressive factors secreted by effector CD8+ T cells themselves is incompletely understood. The impact of the proposed aims is considerable as they will identify novel targets, that could rescue a population of memory CD8+ T cells that are crucial to the immune response to tumor.

NIH Research Projects · FY 2026 · 2023-09

PROJECT SUMMARY/ABSTRACT Physical activity (PA) has been listed as a promising intervention to delay or prevent Alzheimer’s disease (AD) and related dementias (ADRD), however most studies used self-reported PA. Our preliminary data show that, among older women, higher amounts of accelerometer-measured moderate to vigorous intensity PA and steps/day are associated with lower risk of rigorously adjudicated incident mild cognitive impairment (MCI) and ADRD. However, the molecular mechanisms through which PA influences ADRD risk are unclear. The plasma proteome is a promising target for identifying the molecular mechanisms of PA because proteins regulate biological processes, capture disease mechanisms, and may identify intervention targets. Machine learning (ML) methods have been applied to derive PA proteomic signatures, proteomic aging clocks, and ADRD proteomic clocks. However, few studies have systematically applied and compared ML methods to derive PA proteomic signatures. The objective of this research is to enhance our understanding of PA, proteomics, and how they relate to ADRD. I propose leveraging an NIA-funded study (RF1AG079149) that will use the SOMAscan platform to measure ~7,000 clinically relevant plasma proteins and plasma AD biomarkers in a case cohort of 2,836 (n=1,336 incident MCI/ADRD cases) women in the richly phenotyped and racially/ethnically diverse Women’s Health Initiative (WHI) Memory Study (WHIMS) from samples collected in 1995-1998 (n=2,836) and 14-18 years later in 2012-2013 (n=1,000; 500 incident MCI/ADRD cases) and the WHI Objective Physical Activity and Cardiovascular Health (OPACH; R01HL105065) study which collected accelerometry in 2012-2014 among 6,489 women, including the 1,000 WHIMS women in RF1AG079149. WHIMS contains longitudinal annual cognitive assessments and rigorously adjudicated MCI/dementia over 27 years of follow-up. In the R00 phase, I propose obtaining plasma biomarkers of AD pathology from 600 Black and Hispanic/Latina OPACH women. Study results will be replicated in the Atherosclerosis Risk in Communities study to extend findings to men and women. Our Aims are: (1a) Apply and compare ML methods to derive PA proteomic signatures, (1b) Examine the overlap of PA proteomic signatures, proteomic aging clocks, and ADRD proteomic clocks, (1c) Relate PA proteomic signatures with MCI/ADRD and cognitive functioning, (2) Determine the role of PA-associated plasma proteins in our observed PA-MCI/ADRD associations, and (3) Determine the associations of PA (self-reported and accelerometer-measured) and PA- associated plasma proteins with plasma AD biomarkers among Black, Hispanic/Latina, and White women. This research will advance understanding of the molecular mechanisms linking PA, aging, and ADRD. The addition of plasma AD biomarker data to OPACH will have an enduring impact by enabling broader studies of accelerometry and AD pathology in relation to aging-related phenotypes.

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY The practical goal of this project is to obtain high-resolution genetic and epigenetic maps that reveal the evolutionary relationships and dynamics over space and time in Barrett’s esophagus (BE). Barrett’s is the precursor to esophageal adenocarcinoma (EAC) therefore patients undergo surveillance exams to detect early cancers. Our study will provide an unprecedented level of molecular detail that has not been achieved in any previous study of pre-cancer evolution in BE. Importantly, the proposed experiments and analyses will define a BE patient’s “tissue phylogeography”, including significant features of clonal expansions that are predictive of BE progressing to future EAC. To this end, we will leverage a rich set of serially collected tissue samples and genomic data from patients in the Seattle BE natural history cohort that includes cancer outcome patients and an age-matched group of patients with non-cancer outcomes, sampled at multiple time points. The unique design of this case-control study enables us to identify (epi)genetic markers prognostic of progression using data from advanced multi-omic platforms. Computational modeling and phylogenetics will be used to extract the elusive but essential information on when BE arises in a patient, how fast particular clones spread in BE, and how dispersive these clones are within the tissue. Ultimately, we will use these evolutionary quantities to forecast outcomes of cancer versus non-cancer in a well-documented prospective patient population. The long-term goal of the project is to assess the feasibility and performance of data-driven predictive models that can be translated to improved clinical care. Notably, this project will quantify the utility of robust molecular markers for EAC risk to improve the current practice of relying solely on histopathologic features that are difficult to assess and interpret. To facilitate this goal, we will parameterize the inferred space-time dynamics in phylogeographic reconstructions of this pre-cancer, and embed these measurements in a multiscale model framework for progression from BE to EAC in a population. This multiscale approach explicitly models the stochastic clonal expansions at the cellular level over a patient’s lifetime, within the spatial constraints of the esophagus. The three specific aims for our project are: 1) Measure how new clones arise and spread within Barrett’s glands; 2) Measure how glands move and grow through the Barrett’s lesion by quantifying epigenetic drift to estimate Barrett’s tissue age and constructing phylogeographies to infer how Barrett’s clones spatially evolve; and 3) Integrate spatiotemporal measurements from multi-region Barrett’s samples into a multiscale model of EAC development. The proposed project is innovative because we will infer evolutionary parameters, such as rates of stem cell replacement and TP53 two-hit inactivation in BE, from (epi)genomic data for the first time. This research is significant because it is expected to provide predictive models that incorporate dynamic biomarkers of EAC progression in BE patients to potentially offer new strategies of risk-based surveillance.

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY/ABSTRACT Stigma is a pervasive barrier to preventing HIV among persons who inject drugs (PWID). Kyrgyzstan is part of the world’s most rapidly expanding HIV epidemic in the Eastern Europe and Central Asia (EECA) region, where HIV is predominantly concentrated among PWID. Our previous work with PWID in Kyrgyzstan found experiences of HIV, drug use, and drug treatment (i.e. methadone) stigmas were associated with greater HIV risk behavior and low use of evidence-based HIV services, including syringe service programs (SSP) and methadone to treat opioid use disorder (MMT), which limited, timely HIV diagnoses. Following the launch of pre-exposure prophylaxis (PrEP) services in Kyrgyzstan, PrEP awareness increased among PWID with limited uptake but was not associated with stigma suggesting integrating PrEP referrals in stigma reduction programming may increase PWIDs engagement in PrEP and other evidence-based HIV services. Yet there is little to no evidence base on the potential effectiveness and implementation needs of evidence-based stigma reduction strategies that address HIV-related intersectional stigma at multiple levels with PWID in the EECA region. In line with NIDA and OAR priorities, the long-term goal is to rapidly advance evidence-based stigma mitigation efforts among PWID to improve HIV service uptake and turn the tide on the rapidly expanding EECA HIV epidemic. To achieve this goal, the current study will use the ADAPT-ITT model to adapt and refine effective community-level and health facility-level HIV stigma reduction strategies to intervene on intersecting drug use, MMT, and HIV stigma in the local context among PWID and MMT clinic staff (AIM 1). We will pilot the resulting multilevel stigma reduction intervention – LIFT – using a randomized waitlist control trial study design to evaluate the preliminary effectiveness of the LIFT intervention on stigma reduction and MMT/PrEP use (AIM 2) among 68 PWID and all staff from two MMT clinics. In parallel, a sequential mixed methods design will evaluate LIFT implementation outcomes and needs among our local implementation partners and 25 key stakeholders (AIM 3) to develop implementation strategies that can accelerate the pace and scale up of EECA stigma reduction efforts. To reduce risk of contamination via injection and treatment networks, we will conduct all community- and health facility-level intervention and waitlist control activities in distinct geographic districts in the capital city of Bishkek. This R34 pilot is the first EECA study to evaluate intersectional stigma mitigation efforts among PWID to reduce HIV transmission risk. This R34 is significant because stigma remains a fundamental driver of HIV transmission globally. This R34 pilot is highly innovative because it extends the current state of HIV stigma intervention research by integrating strategies that target intersecting stigmas at multiple levels to improve the impact of evidence-based HIV services and advance the use of implementation science models, methods, and measures to accelerate our understanding of how to close the stigma reduction research to practice gap.

NIH Research Projects · FY 2024 · 2023-09

PROJECT SUMMARY/ABSTRACT The parent grant leverages the rich, longitudinal data from the Atherosclerosis Risk in Communities (ARIC) Study and Baltimore Longitudinal Study of Aging (BLSA) and uses a data-driven approach to characterize the cognitive heterogeneity of subtle cognitive difficulties in older adults who do not yet show cognitive impairment consistent with mild cognitive impairment (MCI) or dementia. We are then examining the mid- and late-life vascular, physical activity, and Alzheimer’s disease and related dementia (ADRD) biomarker predictors of subtle cognitive decline phenotypes (e.g., low-executive, low-memory) as well as rates of decline on ADRD outcomes. The current proposal for a research supplement to promote diversity in health-related research would provide funding for Fareshte Erani to complete a postdoctoral fellowship in my lab. Through this supplement, she is proposing to extend the parent RF1 to conduct a novel examination of mid- and late-life depressive symptoms on cognitive and biological outcomes in older adults. Her long-term career goal is to be an ADRD researcher with an independent research program focused on the intersection of neuropsychiatric factors, neural networks, and cognitive decline in order to guide individualized intervention efforts. Support from the diversity supplement will leverage her existing expertise while also providing Ms. Erani with advanced training and mentorship in ADRD research, depression and relevant cognitive outcomes and mechanisms, skills to conduct longitudinal statistical analyses, and tools to submit an NIA K-award application. Depression has been associated with lower cognitive performance in older adults and increased risk for dementia; however, there is likely considerable heterogeneity in causal mechanisms since longstanding, chronic depression could be a causal link to subsequent cognitive impairment and/or late-life depression could be co- occurring with an ADRD process. The proposed study will use ARIC and BLSA data to investigate the role of depression onset and cognitive decline by examining associations of mid- and late-life onset depressive symptoms with cognitive and biological outcomes. Specifically, we will 1) examine the extent to which mid- and late-life depressive symptoms among cognitively unimpaired older adults predict late-life subtle cognitive decline phenotypes and progression to MCI/dementia and 2) examine the associations of mid- and late-life depressive symptoms with fronto-cingulate regions on neuroimaging, markers of inflammation, and ADRD plasma markers. We will also explore neuroimaging, inflammatory, and ADRD biomarker variables that mediate the associations of mid- and late-life depressive symptoms and subtle cognitive decline. Examining the associations between depressive symptom onset, profiles of subtle cognitive difficulties, and the neural mechanisms that link depressive symptoms and cognitive decline will enhance our understanding of the directionality of depression- cognition associations and identify targets for personalized treatment plans.

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY/ABSTRACT With each inhalation, exhalation and across development, maturation, aging and pathogenesis, the lung is constantly under mechanical tension. How the biophysical force is sensed and responded to remains poorly understood. In the gas exchange region that bears the front of this force, tension is distributed across the vast alveolar surface. In this study, we will investigate the central premise that mechanical tension, sensed by alveolar epithelial cells, triggers a molecular feedback loop that drives the generation and regeneration of the gas exchange surface area. At the center of this feedback loop is Piezo, a large membrane localized channel that is a quintessential mechanosensor. First discovered and studied in neurons, Piezo genes are also widely expressed in the lung. Our preliminary data show that while loss of Piezo genes in the lung mesenchyme or the endothelium did not lead to discernable alveolar structural defects, inactivating these genes, especially Piezo2, in the lung epithelium led to alveolar simplification in the early postnatal lung. In the adult lung, Piezo2 loss in the alveolar epithelium led to drastically increased susceptibility to alveolar damage, leading to fibrosis. In this study, we will investigate the nature of this mechanosensory circuit in development (Aim 1) and injury repair (Aim 2). The findings will advance our knowledge on how mechanosensation could tune the size and composition of the alveolar surface.

NIH Research Projects · FY 2024 · 2023-09

Project Summary Mechanistic target of Rapamycin (mTOR) complex 1 (mTORC1) integrates inputs from multiple pathways and senses diverse signals to regulate cell growth, protein translation, and proliferation1,2. Given that spatial compartmentalization can enhance signaling specificity and efficiency3,4, spatial regulation of mTORC1 appears to be critical for this multifaceted signaling complex5 as it has been reported at many subcellular locations6–9. For example, mTORC1 at the lysosome is regulated by both amino acids and growth factors and functions to promote translation and suppress autophagy10. The complex has also been identified at peroxisomes, where mTORC1 responds to reactive oxygen species7. However, the roles of mTORC1 at other subcellular locations where its presence has been reported, in particular in the nucleus, are not well understood. A major limitation in the field is the availability of tools to assess the activity and function of spatially compartmentalized signaling enzymes in living cells. Using a genetically encoded fluorescent biosensor to monitor mTORC1 activity, the Zhang lab has previously discovered a pool of nuclear mTORC1, which has yet to be defined in function. Based on our preliminary data, we hypothesize that nuclear mTORC1 regulates pro-inflammatory transcription. We will test this hypothesis by combining targeted inhibition of mTORC1 with a phosphoproteomics experiment and biochemical assays. Lastly, since genetic mutations activating phosphoinositide 3-kinase(PI3K)/protein kinase B (Akt)/mTOR signaling are prominent alterations in oral squamous cell carcinoma (OSCC)11,12 and mTORC1 inhibition can induce tumor regression13,14, we will study the role of subcellular mTORC1 signaling in the growth and drug resistance of OSCC cells in vitro and in vivo in mice. We hypothesize that inhibiting mTORC1 in the nucleus or the cytosol will differentially effect cell growth and EGFR inhibitor resistance in OSCC. The proposed project will elucidate the function of the previously undefined pool of nuclear mTORC1 and clarify the roles of subcellular mTORC1 in the growth and drug resistance of OSCC.

NIH Research Projects · FY 2024 · 2023-09

PROJECT SUMMARY Ultrastructural molecular/sub-molecular level aging-induced degradation in cellular assemblies makes them dys- functional leading to cellular dysfunction that causes and exacerbates the aging-related problems. However, no investigation has been carried out to explore such degradations due to the lack of imaging modalities that are sen- sitive enough to capture the sub-molecular level features inside the cells in situ. One such assembly is the Nuclear Pore complex which creates a conduit in the nuclear membrane essential for cytoplasm-nucleoplasm trafficking, chromatin silencing, transcriptional control, and other vital cellular processes. NPC is a highly dynamic assembly formed of extremely long-lived aging-affected proteins, whose composition, structure, and function deteriorate with aging. This deterioration then negatively impacts their critical cellular functions, causing a decay in the health and function of the cells, which is especially relevant for non-dividing, non-rejuvenating, and aging-prone cells like neurons, thereby contributing to neurodegeneration. Cryo-focused ion beam milling and electron tomography (cryo-FIB-ET) imaging is a novel and emerging imaging modality that allows us to peek into the cells at the sub-molecular level, enabling in situ structural biology. Complementing cryo-FIB-ET imaging, single-molecule imaging can be used to explore the identification of the building blocks of massive cellular assemblies and also the molecular mechanism of its assembly. Using cryo-FIB-ET, Dr. Singh recently identified the in situ architecture of the NPC (Cell (2022)). He has also contributed to the development and application of cryo-FIB-ET imaging with contributions to 4 publications in his postdoc. During Ph.D., Dr. Singh trained in single-molecule imaging to study the molecular mechanism of CRISPR enzymes and T4-bacteriophage motor with 11 publications, including 6 as first/co-first. By leveraging his dual expertise in cryo-FIB-ET and single-molecule imaging and a broad collaboration effort within UCSD, around UCSD and with his collaborator and co-mentor at Rockfeller, Dr. Singh will determine: • The structures and isoforms of aged NPCs to map its aging-accumulated degradations (K99 phase). • Aging-induced changes in composition of NPC and its building blocks (K99 to R00 transition). • The assembly process of the NPC to understand how aging affects it (R00 phase). Dr. Singh will receive the needed training under the mentorship of Drs. Elizabeth Villa and Michael Rout. These mentors have demonstrated excellence in research leadership and have trained multiple trainees who have transitioned to independent fulfilling careers in sciences. In addition, an excellent team of collaborators and advisory committee (Drs. Andrej Sali, Nan Hao, Elizabeth Villa, Michael Rout) has been assembled to assist Dr. Singh’s research and provide additional training and career support through the K99-R00 phase. The R00 Award phase will set the foundation for Dr. Singh’s long-term career goals of establishing a rigorous research program that seeks to merge two powerful imaging modalities to understand the cellular level changes caused by aging at the molecular level.

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY / ABSTRACT Lipoprotein(a) [Lp(a)] is a lipid-carrying particle that contributes significantly to cardiovascular disease risk when at elevated levels (estimated 30% of the population), but has limited options for therapy, especially for primary prevention. Anti-platelet therapy with aspirin has become controversial for the primary prevention of cardiovascular events, but people with elevated Lp(a) may represent a subgroup that derives benefit due to the unaddressed risk associated with elevated Lp(a), Lp(a)’s interaction with platelets, and Lp(a)’s interaction with fibrinolysis which may result in lower overall bleeding risk. This proposal seeks to address the hypothesis that daily low-dose aspirin therapy will reduce atherosclerotic cardiovascular disease (ASCVD) events in people with elevated Lp(a). We will perform secondary analyses of the ASCEND trial of diabetic participants (Aim 1) and the ASPREE trial of healthy elderly participants (Aim 2) by measuring Lp(a) on stored blood samples and evaluating the effect of aspirin therapy on ASCVD events by Lp(a) level while preserving randomization. Additionally, we similarly aim to evaluate this hypothesis in multi-ethnic American prospective cohort studies (Aim 3) to study a population with enhanced ethnic diversity that is more reflective of the population in the United States and worldwide. Preliminary data using genetic polymorphisms from the ASPREE trial provides robust evidence of an anticipated benefit of aspirin therapy for primary prevention in people with elevated Lp(a). I have expertise in internal medicine, cardiology, epidemiology, and statistics. My career goal is to become an independent investigator in preventive cardiology with a focus on epidemiology, risk stratification and preventive therapies in association with thrombosis and lipid disorders, particularly Lp(a). This award and the described career development plan will allow me to achieve these goals by completing the proposed studies and by building on my previously established foundation by completing the training plan to further develop skills in lipidology, biostatistics and genetic epidemiology. Through this plan, I will develop the tools to ask novel questions related to lipidology using advanced methods in epidemiology and biostatistics. UC San Diego is a world-renown academic institution with an incredible array of resources for completing this training and performing research, as well as collaborators in every possible field to work with. Additionally, as an Assistant Professor, the Division of Cardiology has committed to supporting my research career by providing me with 75% protected research team, dedicated office space and startup funding to conduct research ($25,000 per year) through a KL2 grant.

NIH Research Projects · FY 2025 · 2023-08

PROJECT SUMMARY Speech is a closed-loop behavior which requires the brain to continuously perceive and produce acoustic signals in real time. Current neurobiological theories of speech posit that neural population activity across auditory and motor regions is dynamically coupled during speech production, but that speech perception relies on auditory processing alone. This sensorimotor integration hypothesis would allow the brain to exploit immediate auditory feedback to fine-tune the motor actions that elicit speech. Rigorous neurobiological tests of sensorimotor integration require (1) a model system that enables the control and measurement of sensorimotor behaviors, (2) the experimental expertise to conduct large-scale neural recordings simultaneously in sensory and motor regions, and (3) the computational abilities to develop population scale analyses that assess coordination in the distributed dynamics of individual neurons. This proposal presents a synergistic combination of experiments and analyses that meet these requirements: Simultaneous recordings and perturbations of both auditory and motor regions in European starlings during birdsong production and perception are combined with novel topological data analyses (TDA) to uncover the population mechanisms that instantiate sensorimotor integration. European starlings are an ideal organism for understanding neurobiological mechanisms that support sensorimotor integration; they produce and rely on complex vocal communication signals and have a long history of use in invasive electrophysiology studies. The overarching goal of this proposal is to investigate how distributed neuronal population activity integrates auditory and motor information during closed-loop behavior—specifically birdsong. The central hypothesis of this proposal is that auditory and motor population activity is uniquely coupled when birds sing, in contrast to when birds listen to song. This hypothesis will be tested through the following specific aims: In Aim 1, simultaneously recording auditory and motor regions while birds sing and listen to song will enable an understanding of how population activity is coordinated across regions. In Aim 2, recordings from auditory regions with concurrent optogenetic inhibition of motor regions while birds sing and listen to song will enable a delineation of causal interactions between regions. Novel TDA will be used to quantify the coordination of neural activity across regions and through time, enabling mechanistic insight into how population dynamics structure song behavior. Contrasting population activity across auditory and motor areas between singing and listening will allow for the identification of dynamics unique to sensorimotor integration. In the near-term, this proposal provides a mechanistic understanding of how neuronal populations coordinate to perform sensorimotor integration in the songbird system. In the long-term, this approach will enable future research into how brain network dynamics support closed-loop behaviors, such as speech. Ultimately, this proposal will enable the training and development of a unique and synergistic combination of skills that has the potential to provide novel insight into the neurobiological mechanisms of sensorimotor integration.

NIH Research Projects · FY 2025 · 2023-08

ABSTRACT The larynx is richly innervated with nerves, forming neuroimmune niches that constitute the basis for bidirectional interactions in mucosal defense and physiology. Idiopathic sensorimotor abnormalities of the larynx, such as acute vocal fold paralysis and chronic hypersensitivity (chronic cough, episodic laryngospasm) are attributed to upper respiratory tract infections with a viral etiology. However, a causal link for viral-induced laryngeal pathophysiology remains tenuous. In this application, I will employ an established model of influenza A virus (IAV) infection to interrogate laryngeal mucosal remodeling and map afferent/efferent neural circuits/cells in naïve and virus infected tissues. I will investigate the central hypothesis that viral infection of the larynx will activate neurosensory cells, remodel both afferent and efferent nerves, contributing to mucosal inflammation and hypersensitivity. I will test this hypothesis utilizing a combination of mouse genetics, whole tissue clearing and imaging, single-cell transcriptomics and live animal functional testing. We anticipate that these activated neural inflammatory signals are detected via a unique population of ASCL1+ neuroendocrine and CHAT+ cells that drive a neurosensory-immune circuit for laryngeal neuropathy. Together, these experiments are expected to ascertain neural sensorimotor circuits and reveal neuroimmune interactions for coordinating repair pathways following viral-induced mucosal inflammation. We expect findings will guide the field in new directions for innovating treatments for laryngeal and vocal fold inflammatory diseases and sensorimotor neuropathies.

NIH Research Projects · FY 2025 · 2023-08

People with HIV (PWH) remain vulnerable to central nervous system complications (e.g., neurocognitive impairment) despite antiretroviral therapy (ART) that suppresses viral replication. While many etiologies of these complications exist, damage to the blood-brain-barrier (BBB), inflammation, and mitochondrial dysfunction are consistently implicated, yet seldom studied simultaneously. PWH also use cannabis more frequently than the general population and recent evidence by our group and others indicates that cannabis may protect PWH from BBB damage by reducing inflammation and promoting mitochondrial homeostasis. The proposed multidisciplinary, translational project will combine a clinical observational study with two preclinical models: a) a technologically advanced brain chip model for BBB and b) personalized ex vivo/in vitro modeling of mitochondrial toxicity in BBB cells to determine the effects of cannabis use on the BBB in PWH. Using this multilevel approach, we will test the hypothesis that cannabis effects on the BBB vary based on patterns of use: moderate use will be associated with beneficial effects, due to the anti-inflammatory properties of cannabis, but chronic daily use will have detrimental effects. In a cohort of PWH and people without HIV (PWoH) across a range of cannabis use from naïve to daily users, we will measure in plasma and cerebrospinal fluid (CSF) a panel of biomarkers that reflect the BBB, inflammation, and mitochondrial dysfunction. These readouts will be correlated with advanced permeability and multicompartment diffusion magnetic resonance imaging that will identify global and regional variations in BBB leakage along with neuronal and glial microstructural properties (Aim 1). We will model the BBB using 3D microfluidic cultures of brain endothelial and parenchymal cell subsets to measure the effects of HIV and cannabinoids on BBB permeability, inflammatory gene expression, and markers of mitochondrial function (Aim 2). Because responses to HIV and cannabis are often specific to individuals or groups of individuals, we will use monocyte-derived macrophages and sera from the PWH and PWoH in the observational study to determine the effects of cannabis (and HIV) on BBB cellular components (astrocytes and endothelial cells), and on mitochondrial function, inflammatory gene expression, and BBB biomarker gene expression (Aim 3). Thus, the proposed project will provide innovative clinical readouts in a unique cohort alongside state-of-the-art modeling of the BBB and personalized investigation of pathogenic mechanisms. This highly innovative, multidisciplinary research proposal is very likely to generate impactful translational knowledge regarding mechanisms of pathogenesis and guide future therapeutic interventions. With our combined clinical and pre-clinical expertise in HIV infection, substance abuse, BBB biology and imaging, and mitochondrial homeostasis, we are uniquely suited to perform the proposed research.

NIH Research Projects · FY 2026 · 2023-08

Project Abstract Women represent the majority of people living with HIV in the world. Yet the underrepresentation of women in HIV research persists despite them experiencing greater societal/social disparities of health (SSDoH) including HIV care access and poorer HIV outcomes when compared to men. The coming together of substance (ab)use, violence against women and girls (trauma), and AIDS/HIV (known as SAVA) in the context of SSDOH contributes to excess HIV associated morbidity in women living with and at risk for HIV. This proposal aims to improve HIV outcomes in women living with HIV (WLWH) by evaluating the effectiveness and implementation of a combination intervention addressing substance use, trauma, and HIV. We will employ a randomized Type1 Hybrid study evaluating the effectiveness of acceptance and commitment therapy, exercise, and social support delivered by peer navigators. Implementation strategies that carry the potential to address SSDoH (economic insecurity, limited healthcare access, limited community) that WLWH experience and may enhance sustainability and dissemination will be evaluated. Community-based organizations in four Ending the HIV Epidemic jurisdictions will employ the intervention for a total of 48 weeks per site. The first 24 weeks (research effectiveness) will include a randomized study of 40 WLWH and will evaluate the impact on HIV (ART adherence, % continuous viral suppression), substance use (days and amount of use), trauma (trauma symptoms) and factors common to all three conditions (mood, social disconnection) over time. Weeks 24-48 will include a research implementation phase guided by the Exploration, Preparation, Implementation and Sustainment (EPIS) framework evaluating local barriers, facilitators, change in implementation strategies selected to address structural/social disparities of health and intervention adaptations using the the Framework for Recording Adaptations and Modifications-Enhanced (FRAME). The following aims will guide evaluation of our intervention referred to as women focused encounters for resilience, independence, strength and eudaimonia (WE RISE). Aim 1: Evaluate short (week 8) and longer term (weeks 12, 24) effectiveness of WE RISE on HIV (↑ ART adherence, ↑ % of participants with continuous viral suppression), trauma (↓ trauma symptoms), substance use (↓ days of substance use) and transdiagnostic factors such as mood (↓depression, ↓anxiety) and social connectedness. Aim 2: Document the WE RISE implementation process by characterizing reach, effectiveness, adoption, implementation and maintenance (RE-AIM) by site for 24 weeks. Aim 3: At completion of 24 and 48 weeks, transcreate alternate or additional implementation strategies that address local barriers and leverage facilitators to optimize the effectiveness, maintenance and broader dissemination of WE RISE and document site-specific adaptations FRAME.

NIH Research Projects · FY 2025 · 2023-08

PROJECT SUMMARY/ABSTRACT Anthracycline antibiotics are essential, lifesaving chemotherapies used in ~60% of pediatric cancer patients, but they confer a substantial dose-dependent risk of cardiac dysfunction and heart failure in long-term survivors. The standard heart failure management approach -- waiting for left ventricular ejection fraction decline and then starting afterload reduction therapy -- has been used for decades despite its limited success. Alternatively, an early, targeted treatment strategy guided by specific disease manifestations could improve outcomes. Adverse left ventricular remodeling (i.e., change in size and shape) precedes and may precipitate heart failure and could be used to guide such a strategy. However, there is a critical need to define the specific adverse features of left ventricular shape and to determine the relationship between remodeling and both modifiable risk factors and long-term dysfunction in childhood cancer survivors treated with anthracyclines. The overall objectives of this proposal are to define the anthracycline-related adverse features of left ventricular shape in childhood cancer survivors and to determine the associations between remodeling and both modifiable risk factors, including reduced physical activity, and dysfunction over time. The central hypothesis of this project is that anthracyclines cause specific adverse changes in 3D left ventricular shape; moderate to vigorous physical activity mitigates this remodeling process; and adverse remodeling is prognostic of subsequent dysfunction. To achieve these objectives, we will comprehensively analyze cardiac magnetic resonance imaging in cross-sectional and longitudinal cohorts of adolescent and young adult childhood cancer survivors. The Specific Aims are to 1) define the adverse features of left ventricular shape associated with anthracycline dose exposure; 2) determine the associations between left ventricular remodeling and modifiable risk factors, and 3) determine the relationship between left ventricular remodeling and subsequent dysfunction. The expected contributions of this research will yield new imaging-based disease markers; improve early detection, risk assessment, and clinical prognostication; and inform a future targeted intervention. Dr. Hari K. Narayan seeks this career development award to achieve his long-term goal of becoming an independent physician scientist focused on preventing anthracycline-related heart failure in childhood cancer survivors. Through the proposed training, he seeks to expand beyond his cardiovascular imaging and epidemiology background by developing skills in computational modeling and machine learning analysis, patient- oriented and physical activity research, and academic leadership. The mentorship team, which includes expertise in pediatric clinical trials, computational cardiac image analysis, physical activity in survivorship, and pediatric survivorship oncology, is optimally suited to guide him through training completion and his transition to independence. Dr. Narayan’s goal is to build upon the proposed training and research through the development of an early, targeted intervention to prevent anthracycline-related heart failure in childhood cancer survivors.

NIH Research Projects · FY 2023 · 2023-08

Patients with chronic pain are commonly treated with long-term opioid therapy (LTOT) despite risk of opioid-related harms including increased pain sensitivity, opioid misuse, overdose, and opioid use disorder (OUD). The risks of LTOT may outweigh its benefit for some patients. For instance, approximately 25% of individuals receiving LTOT for pain engage in opioid misusing behaviors such as unauthorized dose escalation or using opioids to alleviate negative emotions. Because opioid misuse confers risks for a range of other opioid-related harms, patients showing signs of opioid misuse need safe, flexible patient-centered opioid tapering approaches to reduce these risks. Patient-centered opioid tapering may be facilitated by adjunctive behavioral interventions. However, due to the complexity of the pathogenic mechanisms fueling the downward spiral from chronic pain to opioid misuse and OUD, few interventions have been shown to be efficacious in facilitating opioid tapering and safely reducing opioid-related harms among people with LTOT. Extant therapies may have limited efficacy because they fail to directly remediate dysregulation of brain reward systems underpinning this downward spiral of behavioral escalation. To address this gap, through a NIDA-funded integrative behavioral treatment development process we translated mechanistic findings from affective neuroscience into an innovative treatment for opioid misuse and chronic pain, called Mindfulness-Oriented Recovery Enhancement (MORE), that aims to enhance cognitive regulation of reward processes. In multiple randomized controlled trials (RCTs) patients treated with MORE reduced opioid dosing and opioid-related harms while evidencing improvements in chronic pain and quality of life. This opioid dose reduction was patient-initiated and occurred without explicit guidance from a physician. MORE has not yet been tested in combination with an explicit patient-centered opioid tapering approach. Given its demonstrated efficacy as a standalone intervention, we hypothesize that adding MORE to patient-centered opioid tapering will robustly reduce opioid-related harms while simultaneously improving chronic pain and quality of life. In primary care clinics in California, New Jersey and Utah we propose to conduct a hybrid 2 implementation-effectiveness RCT of MORE as delivered via an economically sustainable, insurance-reimbursable group medical visit (our key implementation strategy) as an adjunct to a patient-centered opioid tapering approach that leverages patient agency and therapeutic expectancy. The pragmatic nature of this study will provide high generalizability of findings. Informed by patients with lived experience, our trial design will determine whether MORE plus patient-centered opioid tapering can be implemented with effectiveness and fidelity by community providers, and will evaluate the implementation elements and intervention cost effectiveness that influence its uptake in the community.

NIH Research Projects · FY 2026 · 2023-08

PROJECT SUMMARY Autism spectrum disorder (ASD) is a clinically complex, heterogeneous condition affecting 1 in 44 children in the U.S. The identification of common etiologies across multiple forms of genetic and idiopathic forms of ASD will critically advance diagnostic biomarker discovery and therapeutic development. Dysregulation of cellular translation has emerged as a pathophysiological mechanism common to at least a subset of ASD forms. However, systematic investigation of the cellular mechanisms that converge onto the ASD phenotype has been hampered by a paucity of robust and reproducible human ASD cellular models and scalable experimental tools for cell-type resolved characterization at the level of translation. To address these bottlenecks and to directly address the role of translational dysregulation as a common feature in ASD, we have (1) used advanced genome engineering tools to generate an extensively validated, isogenic series of induced pluripotent stem cell (iPSC) lines modeling 15 syndromic forms of ASD caused by highly penetrant gene and genome variants, representing ~10% of the total ASD population (the largest such panel created to date, to our knowledge), (2) established a robust human iPSCs-derived cortical organoid model of brain development, and (3) developed ribo-STAMP, a method for translational profiling of individual cells in heterogeneous cell populations, which is the first and only method enabling translation to be measured at single- cell resolution. In this project, we identify common and divergent pathological mechanisms in genome- engineered isogenic stem cell based organoid models of ASD, using single-cell transcriptomic and translatomic approaches. We validate our findings using cellular and functional phenotypic assays and in patient-derived iPSC models. If successful, our study will identify common and unique translation-aware single-cell resolved gene expression signatures that predict cellular and functional outcomes. We anticipate that our datasets and insights into cell-type specific deficits in gene expression of genetic forms of autism will critically accelerate the development of a unified framework that enables molecular categorization of both genetic and idiopathic cases, facilitating the identification of biomarkers and the development of targeted therapies.

NIH Research Projects · FY 2024 · 2023-08

PROJECT SUMMARY Organisms use a variety of molecular mechanisms to adapt to their environments. RNA editing occurs widely across organisms and generates non-synonymous codon changes in mRNAs, thereby altering the amino acid sequence of proteins. In cephalopods and fungi, this ‘recoding’ generates incredible diversity in proteins across most cellular processes. However, the functions of RNA recoding in these organisms are largely unknown. How is RNA recoding used to support physiological needs and facilitate adaptation? The research proposed here investigates how cephalopod and fungal RNA recoding regulates the function of proteins involved in two core cellular processes: microtubule-based transport and DNA replication and repair. This work will illuminate how RNA recoding modulates protein function to support phenotypic plasticity and adaptation and will advance our understanding of the regulation and functions of highly conserved cellular machineries. In Aim 1, Dr. Rangan will investigate how RNA recoding diversifies the function of microtubule motor protein complexes. In the K99 phase, she will evaluate the effects of RNA recoding on dynein and kinesin motor complexes using in vivo cargo transport assays and single-molecule motility assays. She will also investigate how RNA recoding of motor proteins is coordinated at different temperatures in squid to facilitate transport. In Aim 2, Dr. Rangan will investigate how RNA recoding alters the function of DNA replication and repair proteins. In the K99 phase, she will characterize the effects of RNA recoding on DNA polymerases epsilon and zeta using assays for mutation rate, fidelity, and processivity. In the R00 phase, she will evaluate how temperature-dependent recoding of DNA polymerases alters function and extend this characterization to other proteins involved in DNA replication and repair. In Aim 3, Dr. Rangan will explore how RNA recoding of DNA replication machinery influences genomic mutation rate and bias in the filamentous fungus Neurospora crassa. In the K99 phase, she will use RNA-seq to evaluate temperature-dependent changes in RNA editing in Neurospora ascospores. During the R00 phase, she will perform mutation accumulation experiments with recoding site mutants and wild type fungi to elucidate the role of RNA recoding in mutagenesis. Dr. Rangan is committed to developing an independent research program centered around investigating how RNA editing in diverse organisms supports phenotypic plasticity and adaptation. To facilitate her transition to independence, she will attend diverse scientific conferences and participate in UCSD classes on topics of career development and lab management. She will receive guidance and support from her mentoring committee and her primary mentor, Sam Reck-Peterson. This development plan, combined with training in bioinformatics and computational genomics (with Ludmil Alexandrov, UC San Diego) as well as Neurospora biology and genetics (with Katherine Borkovich, UC Riverside) will prepare her for success in an independent career.