University Of California, San Diego

NIH Research Projects · FY 2026 · 2022-02

SUMMARY Per- and polyfluoroalkyl substances and their derivatives (PFAS) are industrial chemicals that are wide- spread in the environment, including blood serum of wildlife and humans. Their pervasiveness and long half-life raises the questions about their toxicity, especially with regards to the effect on the developing fetus. Several studies have demonstrated that these compounds cross the placenta, are found in the umbilical cord blood, and can cause neurodevelopmental abnormalities in the offspring of the exposed mothers, including early pregnancy loss, low birth weight, hyperactivity, decreased head circumference and behavior problems. However, the molecular mechanisms following PFAS exposure, such as dysregulated genes and pathways, especially in the context of human brain development, remain unexplored. Here, we are proposing to use human induced pluripotent stem cell (iPSC) derived models such as neural progenitor cells (NPCs), spheroids and brain cortical organoids, to fill in this knowledge gap. We hypothesize that PFAS impact early brain development by dysregulating transcriptional programs of NPCs that are involved in proliferation, cell cycle and survival. We also hypothesize that these early alterations will have significant impact on the formation of cortical networks. We are proposing the following Specific Aims to test these hypotheses: (1) Investigate dose- dependent impact of PFAS on neural progenitor cell cycle, cell viability and proliferation; (2) Perform genome- wide pooled genetic screens with CRISPRi/a sgRNA libraries to identify modifier genes and pathways upon PFAS treatment; (3) Validate the impact of PFAS on long-term neurodevelopment in cortical organoids models and identify cell populations impacted by PFAS. Our study will identify genes, molecular and cellular pathways dysregulated by PFAS exposure across various stages of brain development, modeled in vitro. It has a potential to uncover new mechanisms behind PFAS exposure, and to predict the impact of PFAS on developing human brain network function.

NIH Research Projects · FY 2026 · 2022-02

Abstract Asthma affects over 300 million individuals worldwide. An estimated $81.9 billion dollars were spent on the diagnosis and management of asthma in the U.S. in 2013. Uncontrolled asthma is associated with a doubling of direct costs; it has been estimated that 20% of the subjects with asthma contribute 80% of the economic costs of asthma. For severe asthma, multiple new FDA approved biologic therapies exist, but they remain very expensive and there are a significant proportion of nonresponders. Current biomarkers may not distinguish reliably between responders and non-responders; ~40% of those expected to respond continue to have exacerbations and ~40% of those not expected to respond become symptom free. In this proposal, we will use novel genomics approaches to assess and predict responses using therapy-induced phenotypes across a spectrum of asthma severity and endotypes. We hypothesize that comprehensive characterization using clinical metrics, ‘omics’ approaches, and novel systems biology approaches will generate more precise treatment response biomarkers, further define disease heterogeneity, and uncover novel biologic mechanisms as related to the therapy of moderate to severe asthma. To address this hypothesis, we have specified three specific aims, centered around the combination of a well-characterized, within-person evoked phenotype clinical cohort, including subjects with both type 2 (i.e. those expected to respond based on current biomarkers) and non-type 2 moderate to severe asthma, to anti-IL5 (benralizumab) and anti-IL4/IL13 (dupilumab) with deep genomic interrogation, including single cell and bulk RNA sequencing in both sputum and blood across each of the biologic interventions. The first aim will be to identify, and subsequently validate, pharmacogenomic transcripts that predict response to each therapy, thereby yielding clinically relevant biomarkers for response to asthma biologics. Our second aim takes advantage of the biologic interventions as immunomodulators of specific pathways serving as “human knockdown models” to elicit the underlying mechanistic response at the level of the single cell to the biologic therapies. The final aim will provide novel insights into cohort via the characterization of genomic signals that influence clinical asthma subtypes and via the identification of molecular endotypes, which will be compared to the tradtional clinical subtypes and evaluated for their response to the biologics. Analyses for each aim with include both traditional statistical models as well as novel systems medicine and network biology approaches. The strengths of our study include a melding a unique longitudinal clinical evoked phenotype cohort with state of the art genomics analyses. Successful completion of this study will drive understanding of severe asthma response to biologics to an unprecendented level, provide novel therapeutic biomarkers leading to direct clinical application, and detail previously unknown cellular and genomic pathway mechanisms underlying severe asthma.

NIH Research Projects · FY 2026 · 2022-02

ABSTRACT Pancreatic cancer (PC) is an aggressive malignancy where surgical resection is the most effective curative option. Reliance on bright light visualization and tactile cues limit the efficiency of surgical resection for PC and its premalignant precursor lesions and contribute to unfavorable outcomes. Intraoperative fluorescence guidance improves both stagings as well as the accuracy of oncologic surgeries and results in lower local recurrence rates and improved survival. The success of fluorescence-guided imaging is dependent on the sensitivity and specificity of a marker being utilized for detecting PC and its precursor lesions. Multiple studies from our laboratory and others have established the differential expression of MUC4 in pancreatic pathologies. While it is undetectable in the normal pancreas, de novo overexpression of MUC4 is restricted to high-risk-precursor lesions and invasive PC and its expression increases progressively disease advancement. An in-house generated monoclonal antibody (mAb) against MUC4, 8G7, which recognizes repetitive epitopes in the tandem repeat domain, has emerged as a useful tool for ultrasensitive detection and defining the role of MUC4 in tumor progression and metastasis. High MUC4 expression in PC is associated with poor survival, while in precursor lesions, MUC4 expression is a predictor of malignant risk. Our preliminary studies indicate that systemically administered mAb 8G7 labeled with NIRF dye IRDye800CW can very sensitively illuminate MUC4-expressing subcutaneous and orthotopic tumors in vivo. Further, we have developed a unique animal model that recapitulates MUC4-driven IPMN-to-invasive PC progression. In this model, pancreas-specific inducible expression of human MUC4 in conjunction with oncogenic KrasG12D results in the development of premalignant IPMN and PanIN lesions that progress to invasive PC. The proposal seeks to develop and evaluate MUC4- targeted NIR probes for optical surgical navigation of PC and its premalignant precursor lesions in the preclinical models. We hypothesize that intraoperative use of MUC4-targeted Near-Infrared Fluorescent (NIRF) imaging probes will improve the resection of PC and its high-risk precursor lesions. To test this hypothesis, two specific aims are proposed. Studies in Aim 1 focus on the synthesis, characterization, and (pre) clinical safety profiling of MUC4-targeted near-infrared fluorescent conjugates. Aim 2 studies evaluate the preclinical efficacy of MUC4-targeted imaging probes in patient-derived orthotopic xenograft (PDOX) models, human MUC4 transgenic GEM models, and clinical specimens. Overall, the development of targeted imaging probes can improve both the detection and margin-free resection of precursor lesions and PC. The studies proposed in this application will develop and test high-performance NIR probes targeting MUC4 (a top differentially overexpressed membrane mucin in PC) for surgical navigation in PC and its precursor lesions. Successful accomplishment of study goals will pave the path for a Phase I clinical trial for urgently needed imaging probes for improved detection and surgical resection of PC and its high-risk precursor lesions.

NIH Research Projects · FY 2026 · 2022-02

In response to RFA-MH-21-170, we propose to expand and enhance a longstanding scientific resource, the CNS HIV Antiretroviral Effects Research (CHARTER) project. The new longitudinal resource, CHARTER Plus, will enable research on the neurologic, cognitive, psychiatric, and drug use disorders that afflict people with HIV (PWH) across their lifespan. The resource will be guided by scientific themes that reflect the priorities of the Office of AIDS Research and the funding agencies. By combining extensive assessments that focus on the Research Domain Criteria (RDoC) framework and the collection of multiple biospecimens (including cerebrospinal fluid), CHARTER Plus will provide an unparalleled weapon in the fight against neuroHIV. Approved requestors will receive data, biospecimens, and scientific expertise from the resource to support innovative research. To extend the existing rich resource, we propose to comprehensively assess a cohort of 500 adults twice over five years. The cohort will consist of four subgroups: 1) 200 PWH who have been followed in CHARTER for nearly two decades and previously underwent comprehensive assessments; 2) 100 new PWH diagnosed within the past 10 years on suppressive antiretroviral therapy (ART); 3) 100 new people without HIV (PWoH) with comparable demographic and risk behavior characteristics, including drug use; and 4) 100 new PWoH older than 50 years, particularly those at elevated risk for Alzheimer’s disease and related disorders. Combined, these subgroups will enable users of the resource to address many of the key knowledge gaps that currently exist in the neuroHIV field. Our longitudinal evaluations will use domain-based cognitive, behavioral, emotional, and neuropsychiatric assessments that map onto the RDoC framework. Assessments will also include neuromedical data; drug use characterization; mechanistic biomarkers, viral and host genetic data, including indicators of HIV activity; and neuroimaging on a subset of 200 participants. The CHARTER Coordinating Unit will provide central support of study operations including training and certification of personnel; coordination of recruitment, assessments, and retention; data entry, storage, and quality control/assurance; and biospecimen management. We have a nearly 20-year history of managing CHARTER and processing investigator requests in collaboration with the National NeuroAIDS Tissue Consortium (NNTC) Data Coordinating Center (DCC), with which we have worked since its inception. The need for this resource is clear. Even though therapeutic advances have greatly benefitted PWH, their healthspan remains markedly compromised; they experience medical, neurological, and psychiatric disabilities much more frequently than PWoH. Experts debate whether these poor outcomes result from HIV itself, its immunological effects, premature senescence, syndemic conditions such as drug use, or combinations of these and other factors. The biological mechanisms underpinning these disorders remain incompletely defined, and effective therapies beyond ART are sorely lacking. The proposed resource responds well to RFA-MH-21-170 and will be a critical tool for advancing future neuroHIV research.

NIH Research Projects · FY 2026 · 2022-02

Project Summary. In complex ecosystems, microbes use secondary metabolism as a means to communicate within and control their local environment. Some of these products have had profound utility for the treatment of human diseases, particularly infectious disease, where a large percentage of currently prescribed antibiotics are based on or derived from natural products of microbial origin. This program develops, evaluates and implements a new activity-based single cell genomics approach for the discovery of antibiotic candidates from host-associated marine microbes. The research in this collaborative program involves sample collection, single cell genomics, bioinformatics analysis of genomic data with focus on antibiotic producing gene clusters, engineering the most promising clusters into host strains, and flow cytometry-based guided production of these compounds. Using three marine soft-bodied macroorgansims as models (nudibranchs, tunicates and sponges), our team will use a new synthase-selected approach to identify unexplored PKS producing symbiotic microbes, evaluate their genomes for PKS systems and use this genomic data to guide the reconstruction of PKS production in laboratory tractable hosts. The expected results will advance the discovery of novel antibiotic candidates from the microbiomes of marine animals.

NIH Research Projects · FY 2026 · 2022-02

PROJECT SUMMARY: Persistent post-viral olfactory dysfunction (PVOD) is associated with a large spectrum of viruses with significant adverse impacts on quality of life. The molecular and cellular changes in the olfactory epithelium in cases of persistent PVOD have not been well characterized. Specifically, we are interested in studying the response of the olfactory stem cells which are responsible for peripheral olfactory neurogenesis and the regeneration of olfactory epithelium (OE) following injury. In the olfactory system, constitutive TNF-mediated inflammation suppresses stem cell differentiation while elevated levels of IL-6 are correlated with persistent olfactory loss. These findings raised the possibility that prolonged anti-viral signaling will inhibit olfactory stem cell differentiation and thus impair OE regeneration and result in olfactory dysfunction. In our preliminary data, we show evidence of increased type I and II interferon signaling in the olfactory mucosa of patients with SARS- CoV-2 infection and elevated expression of interferon signaling genes in the olfactory stem cells of mice infected with H1N1 influenza A. Furthermore, Notch signaling is known to be important in maintaining horizontal basal cells (one of the olfactory stem cell populations) in an undifferentiated state. Thus, we hypothesize that persistent PVOD may be related to an anti-viral olfactory epithelial response driven by the host innate immune system that translates to a chronic upregulation of inflammatory signaling genes in the olfactory stem cells and an upregulation of Notch signaling to result in stem cell quiescence and impaired regeneration of the olfactory epithelium. In the proposed studies, we will investigate the chronic anti-viral and pro-inflammatory signaling pathways in the local olfactory epithelial environment and olfactory stem cells through cytokine analysis and single cell transcriptomic sequencing (Aim 1). We will correlate expression levels of these cytokines and interferon stimulated genes with objective measures of olfactory function in humans with PVOD. Furthermore, we will assess the effects of cytokines directly on cultured olfactory stem cells in vitro. In Aim 2, we will assess the impact of viral infection on the Notch signaling pathway in olfactory stem cells using individual cell fate mapping with quantitative immunostaining and single cell transcriptomic sequencing. In vivo testing of Notch antagonists using a mouse model of viral infection will help determine the reversibility of the viral impact and the efficacy of therapeutic targeting of the Notch pathway. The incorporation of both mouse and human models in this study will allow for precise genetic manipulation and functional testing to assess olfactory epithelial cell fate as well as permit direct translation of post-viral changes in gene expression on clinical outcomes of olfaction. Together, these studies will help elucidate the cellular and molecular mechanisms for persistent post-viral olfactory loss that may shed light on potential pathways for future therapeutics.

NIH Research Projects · FY 2026 · 2022-01

This proposed project will develop tests and methods for assessment of cognitive status in deaf older adults (aged ≥65), focusing primarily on those who use both American Sign Language (ASL) and written English to communicate. In spoken language bilinguals, sensitivity to Alzheimer’s disease (AD) is maximized when testing occurs in the dominant language, but it is not known if this applies to bilingual deaf seniors, a group that presents many challenges for assessment and diagnosis. Few tests have been developed for administration with deaf signers, and vanishingly little is known about the behavioral presentation of AD in this population. In Aim 1 we will develop tests of language proficiency, list memory, and executive function (i.e., Stroop) that can be administered in ASL or English. We will investigate which language maximizes test performance in deaf ASL-English bilinguals, information we believe is critical for avoiding a false-positive diagnosis of AD. Many seniors who were pre-lingually deaf suffered language deprivation that could alter the behavioral presentation of AD since they lacked full access to a spoken language and their use of sign language was discouraged. In Aim 2 we will test a small sample of deaf signers with probable AD to determine which language of testing maximizes differences between patients and controls (tested in Aim 1), and if deaf signers with probable AD exhibit patterns of impairment found in hearing AD (including reduced delayed recall, reduced primacy effects, increased proactive interference on list memory tests, and increased errors on Stroop tests). We will also conduct a detailed exploratory linguistic analysis of proficiency narratives, aiming to identify how AD affects production of more complex and naturalistic forms of language in deaf signers. In Aim 3 we will examine the possible effects of language deprivation and speech/sign bilingualism on cognitive reserve by recruiting 2 additional comparison groups of cognitively healthy monolingual seniors: those with normal hearing and those with late-onset aging-related deafness. Individuals who lost their hearing late-in-life have reduced exposure to linguistic interactions because of their hearing loss, and this increases their dementia risk. Comparison of these groups will provide a unique lens on the possible effects of early versus recent language deprivation on cognition. Participation of seniors with aging-related deafness will also increase the potential significance of the proposed work by providing data on written English tests which may be useful for assessment of monolingual seniors with late-life hearing loss. This project will constitute a major advancement in tests and procedures for cognitive assessment of older deaf signers, a historically disadvantaged group, will improve understanding of how diverse linguistic backgrounds may alter the behavioral presentation of AD, and will contribute to the NIA mission to “Understand health disparities related to aging and develop strategies to improve the health status of older adults in diverse populations” (in Strategic Directions for Research, Goal F).

NIH Research Projects · FY 2026 · 2022-01

PROJECT SUMMARY/ABSTRACT Transfer RNAs (tRNAs) are critical adaptor molecules that physically link amino acids to codons, decoding mRNA transcripts during translation. The mammalian genome contains hundreds of tRNA genes which are classified into families based on their anticodon. Each family contains multiple tRNA genes, suggesting that these genes may be buffered against the impact of deleterious mutations. Recently, we have demonstrated that a mutation that impairs processing of n-Tr20, a tRNAArgUCU gene, or its complete loss, alters gene expression and physiological responses at both the cellular and organismal level, despite the existence of four additional, functional tRNAArgUCU genes in the mouse genome. More specifically, loss of this highly expressed, neuron- specific member of the tRNAArgUCU family decreases the susceptibility of mice to seizures and alters the excitatory-inhibitory balance in the hippocampus. Loss of n-Tr20 leads to ribosome stalling on cognate AGA codons, along with changes in the transcriptional and translational landscape, characterized by decreased mTORC1 signaling and activation of the integrated stress response. Transgenic overexpression of the other members of the tRNAArgUCU family genes restored seizure susceptibility, in a manner which correlated with the level of tRNA expression from the transgene, suggesting that the phenotypes in n-Tr20-/- mice are due to a decrease in the tRNAArgUCU neuronal pool, to which n-Tr20 is the major contributor. Our results provide the first demonstration that mutation of an individual member of a multicopy, nuclear-encoded tRNA family can alter the molecular landscape and physiology of neurons and provide an impetus for future investigations of tRNA mutations in the maintenance of cellular homeostasis and in disease. This proposal expands upon our findings in several ways. In Aim 1, we will determine the cellular mechanisms underlying the altered excitatory-inhibitory balance upon n-Tr20 loss by conditionally deleting n-Tr20 in either inhibitory or excitatory neurons during or post-development. We will also investigate the effect of genetically increasing mTOR signaling in n-Tr20-/- neurons on synaptic transmission. To further understand these physiological changes, we will analyze the translatome in excitatory and inhibitory neurons of n-Tr20-/- and wild-type mice and determine whether n-Tr20 deletion disrupts local translation. In Aim 2, we will test our hypothesis that phenotypes derived from tRNA loss are due to the decreased level of the pool of tRNAs with the same anticodon, and we will investigate whether the identity of the depleted tRNA family impacts these phenotypes. We will perform ChIP- Seq from several major cell types in the brain, utilizing a novel mouse model that can conditionally express an epitope-tagged allele of RNA Polymerase III. Based on this data, we will identify and delete other highly expressed tRNAs and investigate the effect of their loss on major cell types in the mouse brain. Finally, we will extend our work into humans by investigating the impact of tRNA loss on the translatome and physiology of iPSC-derived neurons.

NIH Research Projects · FY 2026 · 2022-01

PROJECT SUMMARY/ABSTRACT Since becoming an Associate Professor two and a half years ago, I think back to my years as an Assistant Professor and realize that my greatest moments of joy came from my mentee’s successes. Moments where they were awarded their first grant, obtained their first faculty position and a high-impact first authored paper was accepted all shine brightly in my memories. Equally important were the moments where a trainee came to see me because they were feeling unsuccessful or unmotivated, and they felt they were not going to succeed in academics, and through our conversation they arose, reassured about their good ideas, skill set and ability to move forward in a positive and productive way. Looking forward, I worry about the amount of time committed to administrative and clinical efforts and believe that obtaining protected time via this K24 will directly lead to development and enrichment in three areas: 1. Mentoring, 2. Conducting cutting-edge novel research, and 3. Learning new patient oriented research skills. I truly believe that expanding my time dedicated to mentorship will have the greatest impact out of the three, because enhancing and supporting the training of passionate, clever, dedicated trainees will lead to broader effects across medicine and academics relative to my research alone. In terms of research, e-cigarettes are drug delivery (vaping) devices that entered the country in 2007 and have exploded in terms of use, especially in adolescents and young adults whom have never smoked. We have no longitudinal data on the health effects of vaping, particularly on lung and systemic inflammation. By leveraging our existing cohort of young e-cigarette vapers at UCSD, the research proposed here can obtain longitudinal data by having these subjects return at 1 and 2 years, thus giving 3 timepoints across which changes in airway inflammation, microbiome and reactivity, and systemic inflammation can be defined. These data will help us understand which chronic diseases will arise from chronic e-cigarette use. Asthmatics are using e-cigarettes at a high rate, most likely because of the successful advertising campaigns tobacco companies have run, convincing many of the lack of adverse effects of these devices. But patients with asthma have airways and systemic inflammation, thus they are likely to be more susceptible to the pro-inflammatory and immunomodulatory effects of vaping. By again leveraging the ongoing patient-oriented research conducted by our team, I propose here to recruit vaping and non-vaping subjects with TH2-high allergic asthma to assess the effects of e-cigarette aerosol inhalation on their underlying disease state. Finally, I propose to dive deeper into clinical research design and analysis, to improve my ability to conduct high level patient oriented research and thus yield the highest quality, relevant data possible. With the support of my own mentors (Drs. Atul Malhotra and Victor Nizet), the support of UCSD, my existing fantastic research team and the mentees to come, I believe the support of this K24 will make it possible to thrive as a mentor, researcher and life-long learner.

NIH Research Projects · FY 2026 · 2022-01

SUMMARY Over 37 million people worldwide are infected with HIV and as many as 50% are affected by some form of neurological dysfunction. Despite effective antiretroviral therapy (ART), treatments to reduce the prevalence of HIV-associated neurocognitive disorder (HAND) are lacking. Recent findings suggest that increased mitochondrial activity in reactive astroglia play a causal role in mitochondrial dysfunction in neurons and this may be a targetable mechanism underlying neuronal dysfunction in virally suppressed people with HIV (PWH). Early during HIV infection, HIV-infected monocytes enter the brain and spread infection to resident microglia that then release HIV, HIV proteins, and inflammatory cytokines, all of which stimulate a proinflammatory phenotype in astroglia. Reactive astroglia are a hallmark of postmortem brain tissues from PWH with HAND even when on suppressive ART. Astroglia have many homeostatic functions, which are likely disrupted by chronic low-level HIV infection and long-term exposure to ART. One such function of astroglia is to buffer the concentrations of metabolic substrates (glucose, lactate, and glutamine) available to neurons in the extracellular space. Despite this crucial function to maintain bioenergetic homeostasis in the brain and the well-documented evidence of bioenergetic deficits during HAND, little is known about how these processes are affected in reactive astroglia. We’ve recently discovered that HIV and ART stimulate a switch in astroglia from being primarily glycolytic and secreting the byproduct lactate, to relying on oxidative phosphorylation to meet energy demands. To achieve this increase in mitochondrial activity, reactive astroglia increase levels of the mitochondrial biogenesis factors (TFAM), which is associated with a reduction in TFAM expression and viability in neurons. Importantly, this neurotoxicity is blocked by anti-inflammatory compounds that inhibit mitochondrial activity and reduce the reactive phenotype of reactive astroglia. However, the mechanistic link between increased mitochondrial activity in reactive astroglia and the reduction in mitochondrial biogenesis in neurons is not understood. We will investigate the role of astroglial metabolism in HAND by testing the hypothesis that increased mitochondrial activity in reactive astroglia compromises mitochondrial function in proximal neurons. AIM 1 will test in human brain cells how TFAM knockdown alters mitochondrial activity in and neurotoxicity conferred by reactive astroglia. AIM 2 will investigate in postmortem brain tissues from PWH with and without HAND and HIV- controls the location and changes in mitochondrial biogenesis and dynamics factors and lactate transporters in reactive astroglia and neurons. In AIM 3, mouse brains exposed to the HIV protein gp120 and ART drugs will be used to investigate mitochondrial biogenesis and dynamics factors and lactate transporters in astroglia and neurons. These AIMs address the Office of AIDS Research Priorities to 1) Address HIV-Associated Comorbidities; and 2) Advance Cross-Cutting Areas of research in the basic and behavioral sciences.

NIH Research Projects · FY 2026 · 2022-01

Summary/Abstract Intellectual disability and autism spectrum disorders are devastating disorders thought to arise from a combination of synaptic dysfunction and altered neural progenitor modulation for which there are no effective treatments. Mutations or deletions in one allele of myocyte enhancer factor 2C (MEF2C) result in MEF2C Haploinsufficiency Syndrome (MHS), a disorder characterized by a severe phenotype with intellectual disability, repetitive motor behaviors, and difficulties with communication and social interaction on the autism spectrum. We have found that MEF2C is highly expressed in human microglia during neurodevelopment and have identified MEF2C as a core transcription factor involved in the microglial cell fate. Furthermore, MEF2C expression is regulated by the brain environment and decreases during aging. Microglia have not been extensively investigated in the pathogenesis of neurodevelopmental disorders, but there is increasing evidence for their impact on brain development suggesting they may contribute to especially the social and behavioral deficits in autism. The central hypothesis is that microglial MEF2C has a crucial role in human brain development and contributes to neurodevelopmental disorders including intellectual disability and autism pathogenesis and the resulting behavioral phenotype. We will utilize novel in vitro and in vivo methods to ascertain the role of microglial MEF2C in brain development including synapse retention and pruning, modulation of the neural progenitor pool, and microglial development. The project goal is to test the hypothesis that MEF2C specifically in human microglia contributes to brain development and reduced expression contributes to neurodevelopmental deficits found in intellectual disability and autism. Delineating MEF2C transcriptional and environmental targets using epigenetic techniques will yield novel insight into human microglial transcriptional networks and expand on our knowledge of autism associated genes with the potential to yield novel therapeutic targets. The long-term goal is to generate and validate methods using human microglia specifically which can be utilized for drug screening and to generate preclinical data in order to ultimately identify novel potential therapeutic targets to improve the outcomes for children with autism.

NIH Research Projects · FY 2025 · 2022-01

Nicotinic acetylcholine receptors are therapeutic targets for neurodegenerative disorders, addiction, and mental illness. These pentameric ligand-gated ion channels are prototypical members of the Cys-loop receptor superfamily, which mediate fast neurotransmission throughout the central and peripheral nervous systems. Fundamental questions about nicotinic receptor biophysics and pharmacology remain, due in large part to the limited high-resolution structural information. We propose to determine high-resolution structures of two archetypal nicotinic receptor subtypes using single particle cryo-electron microscopy and investigate structure- based mechanistic hypotheses using molecular dynamics simulations and electrophysiology. Our first target is the muscle-type nicotinic receptor, the founding member of the pentameric receptor superfamily. Mutations in the channel, as well as autoimmune antibodies to the receptor, cause myasthenic syndromes. Our second target is the human α7 nicotinic receptor. α7 is exceptional among nicotinic receptors in several ways: it assembles physiologically as a homopentamer, it is expressed abundantly in the brain but also in non- electrically excitable cell types, it has a high permeability to Ca2+, and it desensitizes in microseconds. The receptor is a target in neurodegenerative disease, addiction and inflammation. We propose to use single particle cryo-electron microscopy combined with mutagenesis, electrophysiology and molecular dynamics simulations to elucidate mechanisms of channel activation, ligand recognition and ion permeation in these two distinctinctive nicotinic receptor subtypes to define general mechanisms and idiosyncratic properties.

NIH Research Projects · FY 2026 · 2022-01

PROJECT SUMMARY/ABSTRACT This experimental therapeutics R61/R33 proposal responds to RFA-MH-18-704. The goal of this project is to evaluate a new technology-supported blended intervention aimed at reducing social isolation and improving social functioning in serious mental illness (SMI). Social isolation is common in SMI and leads to morbidity and limits functional recovery. Unfortunately, few available interventions specifically target social isolation and its determinants in SMI, which include anxious social avoidance, defeatist attitudes toward interactions, and social anhedonia. Moreover, intervention development in this area is limited by imprecise measurement of social interactions, processes, and related constructs. Our new blended intervention, mobile Social Interaction Therapy by Exposure (mSITE), blends brief in-person psychotherapy with context-triggered mobile smartphone intervention and remote telephone coaching. mSITE builds on preliminary work indicating that blended mobile interventions are acceptable and both strengthen and shorten cognitive behavioral intervention. Recent work by our group and others indicates that contexts, such as being at home or alone, exacerbates social defeatist attitudes and perceptions of social threat. mSITE is unique in that it uses smartphone sensors (e.g., GPS, conversation sensing) to trigger intervention content tailored to specific social contexts, such as when home alone for extended periods or after a social interaction in the community, in order for cognitive and behavioral interventions to be delivered at the “right place, right time.” In addition, the study will be the first to examine passive sensing measures as outcomes in a clinical trial in SMI, by deriving objective digital markers of negative symptoms and social engagement using smartphone sensors (GPS and microphone) to monitor distance traveled, time spent at home, and conversations. In the R61 phase, we will recruit people with SMI who have limited social engagement. We will then conduct an open trial of mSITE, evaluating whether the intervention leads to clinically significant changes in the frequency of social interactions (the target mechanism). We will also determine the dose of app plus remote coaching necessary to achieve this effect, by evaluating change at 12, 18, or 24 weeks. If go/no go criteria are met (medium effect size increase in social interactions and < 20% dropout) in the R61 phase, the R33 phase will include a randomized trial contrasting mSITE with a therapist and device time-equivalent supportive contact (SC) condition. We will evaluate whether mSITE leads to greater improvement in social interactions, negative symptoms and social functioning relative to SC. We also predict that increases in social interactions will mediate improvements in experiential negative symptoms and social functioning. Our project responds directly to NIMH Strategic Aim 3.1, by evaluating a new behavioral intervention that targets functional improvement and by validating new digital biomarkers for objective measurement of social processes. Our project is also responsive to the NIMH Digital Health Priority Area by advancing digital assessment and context-aware mobile interventions, which are designed to be scalable to community settings.

NIH Research Projects · FY 2026 · 2022-01

PROJECT SUMMARY Molecular mechanisms of nucleic acid recognition and maintenance in meiosis and innate immunity I am a biochemist and structural biologist with a strong interest in the molecular mechanisms of genome maintenance. Since starting my own laboratory in 2011, I have made major contributions in the areas of chromosome organization and recombination in eukaryotic meiosis, in particular defining the molecular architecture and assembly mechanisms of the meiotic chromosome axis. My laboratory also determined the structure and mechanism of TRIP13, an ATPase regulator of HORMA domain signaling proteins in mitosis, meiosis, and DNA repair. As an Associate Professor and Vice Chair of the UC San Diego Biomedical Sciences graduate program, I contribute significantly to graduate teaching and advising. I am also active in the broader scientific community, having participated in grant review for NIH, graduate fellowship review for NSF, and having served on an NIH Center for Scientific Review workgroup in 2019-2020. My laboratory's work over the next five years will focus on a diverse but conceptually related set of questions in genome maintenance and protein-nucleic acid recognition. Our primary interest is in meiosis, the specialized two-stage cell division program that gives rise to haploid gametes and is crucial for sexual reproduction in eukaryotes. Building off our work defining the architecture of the chromosome axis, we will determine how the axis interacts with and controls the activity of DNA-binding cohesin complexes, and how the axis recruits and controls recombination proteins to drive the formation of inter-homolog crossovers. Next, we are pursuing collaborative projects to understand the structural basis for sequence- and structure-specific RNA recognition in two contexts. With Gene Yeo (UCSD), we are developing a new generation of programmable sequence-specific RNA binding proteins to target and degrade disease-associated mRNAs in diverse diseases from cancer to neurodegeneration. With Matt Daugherty (UCSD), we are determining how IFIT proteins in the mammalian innate immune system cooperate to specifically recognize viral RNAs and inhibit their translation. Finally, my laboratory has begun a new effort aimed at determining the molecular mechanisms of novel bacterial defense systems in which canonical genome-maintenance machines have adapted to new roles. In our first work in this area, we have found that the condensin/cohesin-like MksBEFG system protects its bacterial hosts from plasmid transformation by specifically recognizing and cleaving closed-circular DNA. I am fascinated by molecular machines, particularly those that maintain genome integrity in the face of constant internal and external assault. My research program is aimed at understanding the molecular basis for genome maintenance in diverse contexts, and in exploring how the proteins responsible for genome maintenance have adapted to new roles throughout evolution.

NIH Research Projects · FY 2025 · 2022-01

ABSTRACT Obstructive sleep apnea (OSA) is a common condition affecting >10% of the adult population and 2-3% of children in the USA. OSA is considered as an independent risk factor for the development of cardiovascular and lung disorders but the underlying mechanisms are still largely unknown. In particular, the role of intermittent hypoxia and hypercapnia (IHC, the integral components of OSA) in inducing or promoting cardiovascular conditions remains obscure. Recent advances in sequencing technology and microbial and metabolomic bioinformatics have shed light on an important relation between the gut microbiome and cardiovascular diseases. Since OSA is a critical risk factor for these disorders, and our preliminary studies have demonstrated that IHC alters the ecology of gut microbiome and have a strong impact on metabolism, we hypothesize that IHC induces specific alterations in the gut microbiome and microbial-derived metabolites, and these changes causally promote atherosclerosis. Indeed, we have obtained strong candidate microbial families and metabolites that can affect vascular integrity under IHC. For example, we have found that a) IHC accelerates the formation of atherosclerosis in ApoE-/- mice; b) IHC changes the gut microbiome ecology of families such as Verrucomicrobiaceae, Ruminococcaceae and Erysipelotrichaceae; and c) IHC alters microbial-derived metabolites (such as bile salts (BAs)). In the current application, we focus on these microbiota and metabolite candidates to investigate their role in atherosclerosis. First, we will isolate specific gut microbial strains that were altered by IHC treatment and determine the role of these specific microbial strain(s) in the development of cardiovascular disease in vivo using germ-free ApoE-/- mice that were currently created and established in our laboratory. Second, we will delineate the role of the major bile acid receptors (i.e., FXR and TGR5) in mediating the effect of candidate bile acids in IHC-induced cardiovascular disease in vivo using ApoE-/-/FXR-/- and ApoE-/-/TGR5-/- double knockout mice strains as well as the mice strains carrying cell specific conditional deletion of FXR and TGR5 on ApoE-/- background. And third, we will dissect the mechanisms underlying the role of specific IHC-altered bile acids (i.e., TβMCA and UDCA) in IHC-induced macrophage foam cell formation in vitro using primary cell cultures that are derived from mice with ApoE-/- /FXR-/- and ApoE-/-/TGR5-/- double deletion. This project will delineate novel mechanisms regulating OSA- induced cardiovascular disease and provide potential novel targets and strategies to improve treatment or prevent disease.

NIH Research Projects · FY 2026 · 2021-12

Project Summary The University of California San Diego (UCSD) Microbiome and Metagenomics Center (MMC) as part of the Nutrition for Precision Health (NPH) consortium will provide rapid, robust stool sample processing, high-quality metagenomic and metatranscriptomic data generation, and best-in-class bioinformatic analysis. We will optimize our protocols for DNA and RNA extraction from stool, metagenomic and metatranscriptomic library preparation, sequencing, and bioinformatics for ultra-high resolution taxonomic and functional profiling of the microbiome, including bacteria, archaea, eukaryotes, and viruses. We will offer analytical services and expertise on study design, sample collection, statistics, artificial intelligence, and host-microbe data interpretation to support other NPH centers and develop standard operation procedures with the Research Coordinating Center (RCC). Our team has developed uniquely innovative approaches to provide metagenomic and metatranscriptomic data at a cost that facilitates application to all 17,500 samples provided by the BioBank, with robust quality control to ensure high-quality raw and processed data products. We are also able to provide absolute quantification of microbial load through our recent innovation in synthetic DNA ‘spike-ins', which also facilitates rigorous assessment of contamination and extraction efficiency. Beyond bringing cutting edge technology that we have developed to the consortium, we also propose 3 Pilot Projects: (i) long-read data assembly; (ii) multiplexed metaproteomics; and (iii) automated stool sample collection and processing, so as to improve the taxonomic and functional resolution of profiling and improve biomarker detection sensitivity using dense timeseries. Importantly, our team is also optimally positioned to develop community consensus for the analysis strategies agreed on during the planning year, as well as to address the challenges of integrating microbiome data into the NPH consortium, due to our: existing high-throughput sample processing, sequencing, and data analysis cores; tight integration among disciplinary groups; access to supercomputing infrastructure; data visualization expertise; and tight coordination with an international braintrust of scientists who have been selected based on their complementary expertise in different areas of microbiome and precision nutrition research. This center will also benefit from cross-campus institutional commitment to provide 4 undergraduate, 5 postgraduate, and 6 postdoctoral fellowships, enabling faculty engagement and the development of innovative technologies and algorithms to advance NPH consortium goals. Additionally, our existing community outreach experiences can further support the NPH consortium’s goal to provide respectful, accessible and engaging feedback to the participants. Essential to the success of the MMC is the 35% time-commitment of the PI who has an outstanding track record in leading similar scale efforts. As a key part of the NPH consortium, we aim to democratize microbiome data by reducing cost, time, and computational requirements and coordination of multidisciplinary expertise required for data analyses and interpretation to achieve the ambitious goals of precision nutrition.

NIH Research Projects · FY 2025 · 2021-12

Anterior temporal lobectomy (ATL) is a highly sucessful treatment for eliminating seizures in patients with temporal lobe epilepsy (TLE). However, ATL-induced memory decline is frequent and often severe, having a deleterious impact on quality of life and functional outcomes. Stereotactic laser amygdalohippocampectomy (SLAH) has been introduced as a minimally-invasive alternative that could minimize risk of memory decline. However, it is unclear which patients would benefit the most from SLAH and whether SLAH decreases risk for critical aspects of episodic memory decline compared to ATL. During the previous grant funding period, we demonstrated the clinical value of combining information from structural (sMRI), diffusion- weighted (dMRI), and functional (fMRI) imaging to better characterize the neural networks that underlie preoperative language and memory impairment and (re)organization and in TLE. We propose that the same multimodal imaging (MMI) approach can be used to quantify risk for postoperative memory decline. In this R01, we extend our MMI approach, combining sMRI/dMRI/fMRI with intracranial recordings (iEEG), enabling us to delve deep into the spatial and temporal dynamics of episodic memory networks in TLE. We employ multimodal associative learning tasks with real-world implications (i.e., pairing a face with a name) that have not before been studied in the surgical context. In addition, we draw from cognitive neurosicence models of hippocampal functioning that may inform why many patients struggle to make fine-grain distinctions in memory (i.e., impaired pattern separation), even when simple item memory appears intact. We propose that our MMI approach will yield a more complete characterization of episodic memory networks in TLE, reveal patterns of structural and functional reorganization in individual patients, and enable a personalized approach to risk assessment when considering surgical options. Finally, we will track cognitive and imaging changes post-ATL and SLAH and identify patient-specific factors that promote reorganization and improved cognitive outcomes. The goals of this renewal are perfectly aligned with the 2020 NINDS Benchmarks for Epilepsy Research (Part IV), which stress the critical need for reseach to limit or prevent adverse consequences of seizures and their treatments across the lifespan. Our renewal directly addresses this request, striving to improve surgical decision-making, which will have an immediate and sustained impact on patient care. Epilepsy is a common neurological disease that costs the healthcare system approximately $15.5 billion annually and can negatively impact quality of life, employment, and health status. The current project has strong implications for public health because it strives to improve health outcomes in patients with epilepsy by using advanced, noninvasive technology to identify individual predictors of memory decline that can help to guide surgical decisions and possibly reduce morbidity associated with removal or ablation of eloquent brain regions.

NIH Research Projects · FY 2025 · 2021-12

Project Summary By 2030, 73% of people with HIV will be ≥ 50 years of age and 78% will have cardiovascular disease. People with HIV have a 50% increased risk of acute myocardial infarction, a 61% higher risk of heart failure with reduced ejection fraction and > 4 fold higher rates of sudden cardiac death compared to the general population. In addition to traditional risk factors, HIV-associated features such as chronic inflammation and immune dysregulation in the setting of treated HIV infection are strong predictors of cardiovascular disease. However, studies elucidating the pathogenesis of heart failure in HIV have been largely descriptive and have thus provided limited insight into the underlying mechanisms of these disease processes. Thus, we propose to address the pathogenesis of heart failure in people with HIV through investigating the impact of HIV, immune activation and antiretroviral therapies on the broad range of cell types comprising the human heart. Overall, the proposed studies will illuminate underlying mechanisms of HIV cardiomyopathy, which may be translated to the creation of cell-type specific therapies for HIV-related cardiac diseases.

NIH Research Projects · FY 2026 · 2021-12

Cerebral Cavernous Malformations (CCMs) are common neurovascular lesions made of endothelium clusters filled with blood surrounded by gliosis. CCMs affect ~1/200 children and adults, causing a lifetime risk of hemorrhagic strokes and neurologic deficits for which there is no current effective pharmacologic therapy. Loss of function mutations in three CCM genes propels brain vascular changes. However, the propensity of CCM lesions to form in the central nervous system (CNS) parenchyma relative to other tissues has not been fully explained, and the heterogeneity in disease severity suggests that environmental or biological factors (e.g. other genes, neural cells) act as disease modifiers. We and others have demonstrated that increased vascular endothelial growth factor (VEGF) signaling and associated vascular leakage are significant contributors to CCM disease. Our preliminary data show that hypoxic conditions contribute to an aggressive onset and progression of CCM disease. We observed that hypoxia acts as an accelerant of CCM disease by exacerbating the number and size of brain vascular lesions in CCM animal models. We also observed that mouse and human CCM tissue results in increased hypoxia-inducible factor 1 alpha (HIF-1a) activity, and that proliferative astrocytes influence CCM pathogenesis. The proposed study will test the hypothesis that hypoxia exacerbates CCMs through hypoxic programs from astrocytes and endothelium, leading to abnormal vascular development and stroke due to intracranial hemorrhage. Moreover, we hypothesize that intermittent hypoxia (that occurs with patients with obstructive sleep apnea) will further exacerbate CCMs. Specific Aim 1 will test the hypothesis that hypoxia exacerbates CCM formation by elevating hypoxia-driven genes in astrocytes in murine CCM. We will investigate the effect of hypoxia on astrocyte gene expression (e.g., hypoxic program, VEGF) by profiling translated mRNAs obtained from the purification of the EGFP-tagged ribosome in astrocytes in the presence or absence of CCM lesions. Co-culture in vitro models will be used to define the interaction between CCM endothelium and astrocytes that propels vascular dysfunction. Specific Aim 2 will test the hypothesis that hypoxia exacerbates CCM formation by HIF-1a protein stabilization in the brain endothelium in murine CCM. We will investigate the role of endothelial HIF-1a on changes in the endothelial barrier function, gene expression, VEGF signaling using CCM mouse models. Specific Aim 3 will test the hypothesis that intermittent hypoxia exacerbates murine CCM. We will investigate the role of intermittent hypoxia-driven CCM lesion burden, using mouse models of CCM under intermittent hypoxia that partially recapitulates nocturnal oxygen profile in patients with obstructive sleep apnea (OSA). The proposed research may lead to a new therapeutic approach (e.g., combination therapies for activated astrocytes and CCM endothelium) and preventive measures by defining how environmental (e.g., high altitude) or pathological factors (e.g., OSA, chronic lung disease) that alter oxygen levels may act as risk factors for patients affected with CCMs.

NIH Research Projects · FY 2026 · 2021-12

PROJECT SUMMARY A growing body of evidence implicates oxidative stress in Amyotrophic Lateral Sclerosis (ALS). Nevertheless, it is currently unknow if it is a cause, a by-product or a consequence of disease. The effects of oxidative stress on cellular damage caused by reactive oxygen species is usually attributed to modifying proteins and DNA. However, RNA oxidation occurs ten times more often than DNA oxidation. Importantly, high levels of oxidized RNA are detected in relevant neuronal tissues of patients with ALS while, mouse models of ALS show increased RNA oxidation in motor neurons of the spinal cord at an early pre-symptomatic stage. What remains lacking, however, is an understanding of the functional relationship between RNA oxidation and ALS onset and progression. Thus, there is a critical need to identify which motor neuron transcripts are oxidized in early, pre- symptomatic stages of ALS and how this dysregulation contributes to neuronal death and other molecular hallmarks of ALS. I believe that there are many, yet to be discovered, RNA Binding Proteins (RBPs) that are crucial for controlling the fate of oxidized RNAs. I hypothesize that RNA oxidation drives motor neuron degeneration in ALS by dysregulating proper RNA processing by RBPs. I will test this hypothesis by (1) elucidating, in iPSC-derived motor neurons, the RNA targets and the consequences of depletion of known RBPs that interact with oxidized RNAs and identify novel ones; (2) identifying and comparing oxidized RNAs in iPSC- derived motor neuron models; and (3) investigating, at a single cell resolution, the effects of RNA oxidation on transcription, translation and RBP-RNA interactions in iPSC-derived spinal organoid ALS models. If successful, this project will generate the foundational methods and insights to enable early, pre-symptomatic-stage diagnostic approaches and interventions to reduce RNA oxidation levels in high-risk individuals. My background in DNA damage and repair and single cell transcriptomics together with the Yeo lab’s expertise on RNA processing and neurodegeneration make me an ideal candidate to accomplish the research proposed above. These three aims will serve as a basis for my independent academic position generating the foundational methods and insights to study the effects of RNA damage. The Yeo lab at UCSD is an ideal environment to perform this research and complete my training towards pursuit of an independent academic faculty position, as it has consistently been a leader in developing both experimental and computational methods to characterize RNA processing and RBP regulation. Additionally, the location of the Yeo lab proximal to outstanding researchers at UCSD, the Salk Institute, and other research institutes and biotechnology companies in La Jolla will provide ample opportunities for mentored training in performing research and developing an independent research program.

NIH Research Projects · FY 2025 · 2021-09

PROJECT SUMMARY/ABSTRACT The HEALthy Brain and Child Development (HBCD) Study is entering a critical period in the evolution of this unprecedented research endeavor. While the Study has achieved success in recruitment of participants and is exactly on target with approximately 4,200 mother/child pairs enrolled, participant retention has been identified as an overarching challenge that is critical to address in Year 5. For a variety of reasons, HBCD families may withdraw from the study, decline to attend one or more study visits, or fail to complete one or more study measures within a visit. Original projections for the Study included expected rates for such missingness. However, at this point, mid-way through the overall recruitment period, it is essential to ensure that adequate retention is maintained throughout the remaining course of this complex study. With this Supplement, we propose to take a three-pronged approach to measuring, understanding, intervening on, and evaluating retention and measure completion rates across the study. First, we will offer Opportunity Pool funds, through an application process, to the HBCD recruitment sites to support implementation of evidence-based strategies to improve retention and measure completion rates overall and within specific vulnerable subgroups. Second, the HBCD Administrative Core will develop and disseminate centrally available tools, trainings, additional tailored communication materials, and monitoring activities to assist sites in meeting their retention objectives. Third, we will assign a dedicated Senior Project Manager to develop, maintain, integrate, and evaluate metrics for retention across the study administrative and data teams as well as through individual site leadership and personnel. In addition, with this Supplement, and for purposes of expediency, we propose to ensure that a necessary core measure of child dietary intake be developed and implemented within the HBCD Administrative Core so that this measure can be deployed across the study sites when it will be required for the first study participants.

NIH Research Projects · FY 2024 · 2021-09

PROJECT SUMMARY/ABSTRACT The overall goal of this research is to understand how stress disrupts the ovarian cycle. Chronic undernutrition is a type of metabolic stress that impairs reproduction across species, and in women is implicated in the development of functional hypothalamic amenorrhea, an anovulatory disorder resulting from inadequate gonadotropin secretion. Although the tight coupling of energy balance to reproductive capacity is recognized in principle, the neuroendocrine loci and molecular mechanisms that mediate ovarian cycle dysfunction during undernutrition remain poorly understood. In females, ovulatory cyclicity is dependent on two populations of kisspeptin (Kiss1) neurons within the hypothalamus that coordinate gonadotropin-releasing hormone (GnRH) and luteinizing hormone (LH) pulses and generation of the preovulatory GnRH/LH surge. Disruption of either arcuate Kiss1 (ARCKiss1) control of LH pulses or anteroventral periventricular Kiss1 (AVPVKiss1) control of the LH surge would be anticipated to impair ovarian cyclicity in females. Our preliminary studies demonstrate that chronic undernutrition rapidly disrupts ovarian cyclicity in female mice via impairment of both pulsatile LH secretion and the LH surge. We show that these inhibitory effects on the ovarian cycle are recapitulated by activation of brainstem A2NE neurons or via central administration of urocortin 2 (UCN2), a neuropeptide that specifically activates corticotropin-releasing hormone receptor 2 (CRHR2). Our observations that antagonism of CRHR2 or knockdown of CRHR2 in Kiss1 cells diminishes reproductive suppression in response to undernutrition or A2NE activation provide the foundation to test this neural pathway mediating the effects of undernutrition on reproductive neuroendocrine function. Currently it is not known how undernutrition disrupts the cycle or the neural processes controlling pulsatile or surge LH secretion. We propose to fill this gap by testing the overall hypothesis: Chronic undernutrition disrupts the ovarian cycle and fertility via activation of a NE – UCN2 – Kiss1 neural pathway that impairs two modes of LH secretion: LH pulses and the preovulatory LH surge. Aim1 will utilize a genetic knockout approach to investigate the role of CRHR2 within Kiss1 cells as a mediator of disrupted cycles, LH pulses, and the LH surge during chronic undernutrition. Aim 2.1 will utilize a chemogenic approach to test the sufficiency of this brainstem population to impair the ovarian cycle, inhibit AVPVKiss1 control of the LH surge, and disrupt ARCKiss1 control of LH pulses. Aim 2.2 will determine the necessity of A2NE signaling for disrupted ovarian cyclicity and impaired neural pathways underlying pulsatile and surge LH secretion. This project will employ powerful physiological, anatomical, molecular and transgenic tools to advance our knowledge of integrated stress responses and the regulation of gonadotropin secretion. Results from this proposal will provide enhanced understanding of the metabolic control of reproduction that may influence the management and treatment for anovulatory disorders resulting from negative energy balance. All necessary animal models and methods are in place to complete these studies.

NIH Research Projects · FY 2025 · 2021-09

PROJECT SUMMARY People living with HIV (PLWH) are at the higher risk for impaired cognitive functions such as HIV-Associated Neurocognitive Disorder or HAND. Further, higher use of legal and illegal opioids among PLWH could affect their immune functions and exacerbate CNS impairment. However, little is known about the HIV harboring cell types in brain, effect of ART on specific CNS cell types, and the modification of brain functions by opioid use. The human brain is composed of an enormous diversity of cell types defined by distinct gene expression, morphology, connectivity, and physiology. Single cell sequencing assays enable cell type- specific analysis of the role of these cell types in healthy brain function and disease. The overall objective of this proposal is to reveal the single cell determinants of brain relevant to persistent HIV infection and opioid use disorder using snRNA-seq and snATAC-seq technologies, bioinformatics approaches, and validation studies. Opioids, as with other addictive drugs, affect nucleus accumbens (NAc) and prefrontal cortex (PFC) and both of these regions are also affected by HIV. We put forward an unprecedented concept and experimental system to identify single cell determinants of brain relevant to persistent HIV infection and opioid use disorder as well as potential opportunities to illuminate how genetic variation affects gene expression. Our project has two specific aims: Aim 1: Create a single nucleus transcriptomic atlas of PFC and NAc. snRNA-seq will be performed on these two regions isolated from post mortem brains. Aim 2: Create a single nucleus epigenomic atlas of PFC and NAc. snATAC-seq will be performed on these two regions isolated from post mortem brains. Successful completion of these innovative single-cell studies will generate cellular part list for two NIDA-relevant brain regions, PFC and NAc, and will illuminate novel insights into transcriptomic and epigenetic landscapes of CNS and how they are altered by HIV and opioid use.

NIH Research Projects · FY 2024 · 2021-09

PROJECT SUMMARY (See instructions): Overview: Progress in the characterization and treatment of retinal disease involves epidemiological and natural history studies which include genetic and environmental risk factor evaluation as well as clinical trials. As treatments advance, it is important to be able to scientifically analyze and interpret a large amount of information that can be procured from different areas and even points on the retina and evaluate retinal structure and function over time and in response to therapies. Currently there is a proliferation of technology to provide data and this data comes from many instruments and from different companies. It is increasingly difficult for any one person or reading center to evaluate this information. The goal of this proposal is to develop deep-learning based multi modal retinal image processing methods to help the ophthalmologist to quickly detect and diagnose diseases. Intellectual Merit: As treatments advance, it is important to be able to scientifically analyze and interpret a large amount of information that can be procured from different areas and even points on the retina and evaluate retinal structure and function over time and in response to therapies. Currently there is a proliferation of imaging technology producing images from many instruments and from different companies. It is increasingly difficult for any one person or reading center to reliably review the multiple types of imaging available in a patient with a retinal disease nor overlay these on each other to properly analyze retinal structure and function and determine correlations and predictive value of these tests to clinical outcomes and covariates like sex, age, race and concurrent medications. The ability to co-localize all of this data and use artificial intelligence (Al) to help with these analytics will advance the field of understanding and treating retinal disease. The objective of this proposal is to develop deep-learning based multimodal retinal image registration methods to help the ophthalmologist to quickly detect and diagnose retinal diseases.

NIH Research Projects · FY 2025 · 2021-09

ABSTRACT Gastroparesis is a chronic gastrointestinal motility disorder characterized by delayed gastric emptying, chronic abdominal pain, nausea and vomiting. Its incidence has increased 3-fold in the last decade, which has increased healthcare costs by 10-fold. It is suggested that immune dysregulation plays a role in the pathophysiology of the disease; however, the immune cellular mechanisms remain largely unknown, especially in humans. This is largely in part because of limited knowledge on the types and functions of immune cells present in the human stomach. This gap in knowledge presents a significant barrier to understanding the cellular mechanisms of disease, and for the rational design of novel therapeutic strategies. Our preliminary data using mass cytometry (CyTOF) shows that the human stomach harbors mononuclear phagocyte populations that are more diverse than previously appreciated. Our studies also point, for the first time, to a disease that affects not only the stomach muscularis as previously suggested, but also the stomach mucosa. Importantly, mononuclear phagocytes in the mucosa of gastroparesis patients are dysregulated in numbers and function, which correlates with delayed stomach emptying. Based on these data, our central hypothesis is that gastroparesis patients harbor dysregulated mucosa and muscularis mononuclear phagocytes that contribute to the pathophysiology of the disease. In three specific aims, we propose to resolve the identity and dysregulation of stomach mucosa and muscularis mononuclear phagocytes in gastroparesis patients at a resolution that has not been done until now. We will also explore the role of a neuronal peptide in modulating stomach mononuclear phagocyte function during gastroparesis. To achieve these aims, we will take advantage of approaches that allow for the identification of mononuclear phagocytes in an unbiased fashion. These approaches will be combined with ex vivo functional assays and a mouse model of stomach emptying with the goal of unraveling cellular mechanisms of disease. Our rationale is that by investigating the identity, i.e., phenotype and function, of human stomach mononuclear phagocytes, we can elucidate the cellular mechanisms underpinning delayed stomach emptying in gastroparesis. This proposal has the potential to impact the rational design of therapeutic strategies for gastroparesis.