University Of California-Irvine

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY/ABSTRACT Optic neuropathies, a wide-ranging group of eye diseases, primarily target the optic nerve and frequently result in irreversible vision loss. Globally affecting millions, these conditions stem from a variety of causes such as glaucoma, ischemic, inflammatory, compressive, toxic, and hereditary factors, each with distinct pathophysiological traits. Characterized by the degeneration of retinal ganglion cells, these diseases lead to changes in the optic nerve head and visual field defects. The diverse onset and myriad underlying causes of these neuropathies complicate early diagnosis, underscoring the necessity for advanced diagnostic tools. This project proposes leveraging deep learning-based morphometric analysis in optical coherence tomography (OCT) to develop innovative biomarkers for optic neuropathies. OCT, a non-invasive imaging technique, has revolutionized the diagnosis and management of these conditions, providing detailed retinal and optic nerve head imagery. However, its efficacy is limited by device-dependent variability, signal quality dependency, and insufficient sensitivity of current thickness markers in chronic disease monitoring. This project proposes to overcome these limitations by employing advanced computational techniques such as deep learning, neural fields, and geometric modeling. These methods excel in extracting complex patterns from medical images and enhancing the accuracy of morphometric analyses. Geometric deep learning adapts to the neuroretina's geometric structures, offering novel insights into the optic nerve head and macula. Neural field image registration enhances OCT image co-registration accuracy, crucial for longitudinal disease monitoring. The project aims to revolutionize the diagnosis and management of optic neuropathies through three interconnected objectives. The first aim is to employ deep generative models for mapping structure-function relationships in optic neuropathies, focusing on predicting visual field outcomes and tracking disease progression using advanced deep learning techniques. The second aim is to pioneer the next generation of retinal morphometric OCT biomarkers using deep learning, enhancing the precision in identifying retinal changes and improving the longitudinal analysis of optic nerve head and macular structures. Finally, the third aim is dedicated to leveraging deep learning models for the classification of various types of optic neuropathies directly from retinal OCT scans, aiming to significantly increase the accuracy and efficiency in distinguishing these conditions. This research proposes a multidimensional strategy to significantly improve the diagnostic and management capabilities in the field of neuro-ophthalmology through innovative applications of deep learning to OCT imaging. By integrating advanced imaging techniques with deep learning models, it aims to unveil novel biomarkers and predictive models, offering insights into the progression and treatment of these complex eye diseases. The success of this project could lead to earlier detection, personalized treatment strategies, and ultimately, better outcomes for patients with optic neuropathies.

NIH Research Projects · FY 2026 · 2024-07

PROJECT SUMMARY/ABSTRACT Adverse Childhood Experiences (ACEs) constitute a serious public health issue, impacting almost half of adolescents and over 60% of adults in the United States. High ACEs exposure (i.e., four or more ACEs) may result in self-dysregulation (i.e., challenges managing cognitions, emotions, and behaviors) and lead to early initiation of alcohol and substance use (e.g., self-medication hypothesis) and other biopsychosocial responses, such as cardiometabolic risks (e.g., lowered heart rate variability [HRV], increased weight and blood pressure, and sleep disturbance), and emotional and/or cognitive dysregulation. Health inequities resulting from self- dysregulation are highest among minoritized and impoverished populations, who experience disproportionately higher exposure to ACEs, and early adolescence is a time in which experimentation with alcohol and drugs occurs. Although not all adolescents who experiment with drugs are later diagnosed with a substance use disorder, those who engage early (i.e., before the age of 14) and regularly are at greater risk. Youth with four or more ACEs may experience a unique type of adversity characterized by chronic, unpredictable stress shaping their perception of and responses to stress. However certain strategies, called Shift and Persist, can mitigate these exposures where one shifts their attention from adverse experiences to future-directed behaviors (e.g., healthy habit adoption, stress management), resulting in improved self-regulation and lower cardiometabolic risks. GRIT is a community health worker (CHW)-delivered psychoeducational health coaching intervention that promotes coping with high exposure to ACEs to regulate the stress response using self-regulation techniques and the development of healthy habits recommended by the California Surgeon General (e.g., supportive relationships, quality sleep, physical activity). We propose conducting a 2-arm Randomized Controlled Trial (RCT) (GRIT vs an active control [i.e., digital citizenship]) with 210 adolescent-caregiver dyads to determine GRIT’s impact on preventing the early initiation of regular use of alcohol and cannabis among adversity-impacted adolescents ages 11-14 who do not regularly use alcohol or cannabis at baseline. The specific aims will: Aim 1. Examine the effect of GRIT on preventing the early initiation of regular alcohol and cannabis use over time. H1: Adolescents enrolled in GRIT will have lower rates of regular alcohol and/or cannabis use at post- intervention, 6-, and 12-month follow-ups compared to adolescents in the active control group. Aim 2. Examine the role of youth and caregiver self-regulation in mediating the effect of GRIT on adolescent rates of alcohol and cannabis use. H2: Youth and caregiver self-regulation will mediate youth initiation of regular alcohol and cannabis use. This community-based study seeks to establish efficacy for a brief, accessible secondary prevention program. Once efficacy is established and the mechanism of action is identified, larger confirmatory efficacy studies and effectiveness trials using innovative in additional settings offer the opportunity to scale and decrease the research-to-practice gap for adversity-impacted youth.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY/ABSTRACT Vision begins in photoreceptor cells with light activation of the visual pigment, rhodopsin, which triggers a transduction cascade to produce the cellular electrical response. A wide range of blinding disorders have been associated with mutations in rhodopsin. From these, mutations of Glycine 90 to Aspartate (G90D) and to Valine (G90V) have been reported to cause congenital stationary night blindness (CSNB) and retinitis pigmentosa (RP), respectively. Structural and biochemical in vitro studies have shown that the G90D/G90V mutations cause rhodopsin destabilization that could interfere with normal light detection. However, despite decades of research, the mechanisms by which these mutations cause vision loss remain unclear and effective treatments for people with these mutations are not available. To address these questions, we have created G90D and G90V rhodopsin knockin mice. We will perform comprehensive analysis of these mice to determine the phenotype of their rod photoreceptors. These experiments will include morphological analysis and in vivo eletroretinography and single- cell suction electrode recordings to determine the physiological properties of the mutant rods, combined with microspectrophotometric and biochemical analysis to determine the molecular properties of the mutant mouse rhodopsins (Aim 1). We will perform experiments to determine the molecular mechanisms by which the G90D and G90V rhodopsins cause blindness by evaluating the stability of their covalent bonds between opsin and chromophore, the binding and release of chromophore, and the equilibrium between chromophore-free and chromophore-bound mutant opsins (Aim 2). Finally, we will also test the efficiency of genome editing for rescuing the function of rods with the G90D or G90V rhodopsin mutations (Aim 3). Together, these experiments will establish the unique disease mechanisms of two distinct human visual disorders caused by mutations in the same residue of rhodopsin and will develop therapeutic approaches for reversing their effects that could eventually be used in human clinical studies. Analyzing our G90D and G90V mutant mice side by side will also help understand why these two similar mutations produce distinct clinical phenotypes.

NIH Research Projects · FY 2026 · 2024-07

PROJECT SUMMARY Transposable elements (TEs) are widespread genomic parasites that occupy nearly half of the human genome. The selfish replication and movement of TEs are generally harmful to organisms, and eukaryotic hosts primarily defend against these adverse effects by depositing repressive epigenetic marks at TEs to silence them. Our recent investigations suggest an evolved balance of this process—the epigenetic silencing of TEs needs to be strong enough to reduce TEs’ harmful replicative movement, yet weak enough to avoid inadvertent spreading of repressive marks to TE-adjacent functional sequences. Interestingly, growing evidence shows that epigenetic modifications can be altered by diet, because dietary metabolites and nutrients can act as substrates, cofactors, or inhibitors for enzymes responsible for such epigenetic modifications. However, a critical knowledge gap remains regarding how diet-mediated changes in epigenetic modifications may influence the epigenetic silencing of TEs and, thus, organismal health. We hypothesize that dietary changes can negatively impact organismal health by perturbing the evolved balance of TE epigenetic silencing through both weakened and enhanced TE silencing. We will leverage TE natural variation and combine that with functional genomics and experimental genetics to address our evolution-driven hypothesis. Drosophila will be used as a model system for its ease of handling for large screens, its shared mechanisms of epigenetic regulation with mammals, and its unique TE features that offer an informative model for human TEs. We will conduct large screens to identify dietary factors that alter the balance of TE epigenetic silencing and the involved epigenetic modifying enzymes. This effort will use our newly developed fluorescence reporter system that enables efficient quantification of the strength of TE silencing (Aim 1). We will perform epigenomic and transcriptomic analyses of wildtype strains fed control and altered diets to characterize varying dietary responses of TEs across the genome. This genome-wide profiling will use natural polymorphism of TEs and compare the epigenetic states of homologous sequences with and without a TE insertion, pinpointing diet- mediated changes at individual TEs. Using these functional genomic data under altered diets, we will also investigate the predicted functional outcomes of perturbed TE silencing—elevated TE activity due to weakened silencing or excessive spreading of repressive marks to TE-adjacent genes due to enhanced silencing (Aim 2). Finally, by using pharmaceutical intervention to revert the functional outcomes of perturbed TE silencing, we will directly quantify dietary fitness impacts that are mediated by altered TE silencing (Aim 3). By exploring dietary factors that influence how organisms defend against TEs, and the subsequent impacts on genome function and organismal fitness, this project will reveal previously unknown mechanisms by which diet acts through epigenetic modifications to influence individual health. Our findings will provide a novel perspective for gauging the full impacts of the ongoing and rapid shifts in human diets on our health.

NIH Research Projects · FY 2025 · 2024-07

Project Summary Depression, addiction, and disordered eating are common mental health disorders that affect millions of people worldwide, and all involve dysregulated reward circuitry leading to abnormally low, or abnormally high reward pursuit. While there are some effective treatments for these disorders, not all individuals respond well to these treatments and some experience significant side effects. Therefore, it is vital to develop new therapies that induce behavioral changes quickly and remain effective for extended periods. Recently, clinical trials using psychedelic drugs to treat these disorders and others have shown promising and long-lasting results, and trials are now underway using psilocybin to treat eating disorders such as anorexia nervosa and binge eating disorder. Although these findings are exciting, it remains a concern that little is known about the mechanisms by which psychedelics may have therapeutic effects, other than that their actions require agonism of the serotonin (5-HT) 2A receptor. Animal models are useful to study these mechanisms and establish their causal effects, but animal models of depression, and especially of psychedelic drug actions, are to say the least challenging in rodents. Here we capitalize on our well-validated, translationally relevant rat early-life adversity (ELA) model, which causes long-lasting and sex-dependent alteration in reward circuitry, such as anhedonia in males and excessive pursuit of rewards in females. Parallel findings emerge in our model and in men and women who experienced low socioeconomic status, trauma, or chaotic early-life environments, allowing us to interrogate in rodents the responsible brain mechanisms, and potential therapeutics. My project will examine the effects of psychedelic 5-HT2A agonist drugs DOI and psilocybin on ELA- induced alterations to food-seeking behavior and reward circuit function in rats. We acknowledge that these drugs may act differently in rats and humans, but nonetheless our preliminary data suggests that at least some ELA-induced changes in reward pursuit are persistently reversed by a single dosing of DOI when it’s administered in a familiar and reward-filled “set and setting.” The current proposal aims to replicate and extend these exciting findings, determining the effective DOI dose range, and determining whether DOI effects also occur with the more readily translatable 5-HT2A agonist psilocybin. Further, we investigate whole-brain regional activity associated with ELA-induced anhedonia/hyperhedonia, and of its reversal by psychedelics. These studies may help develop a new animal model of the therapeutic effects of 5-HT2A stimulation, leveraging established models of developmental adversity, multiple 5-HT2A agonist drugs, and behavioral procedures modeled to the extent possible on human treatment protocols. We hope these studies will contribute to the sorely-needed body of basic research on psychedelic drug effects, and provide new insights that could be capitalized upon when developing maximally effective, but minimally disruptive therapeutic strategies.

NIH Research Projects · FY 2026 · 2024-07

PROJECT SUMMARY Regulatory regions of the genome play crucial roles in ensuring appropriate spatiotemporal expression of genes. Like other regions of the genome, regulatory DNA sequences exhibit variations that could influence their functions. Yet, there is a significant gap in our understanding of how variants in non-coding gene regulatory regions alter gene expression and what impact these variants have on an individual’s development or fitness. In particular, some rare variants confer gain-of-function enhancer activity, causing ectopic gene expression that contributes to limb malformations, intellectual disabilities, and autism among other congenital conditions. Determining how these gain-of-function enhancer variants cause ectopic gene expression and adverse outcomes is critical for understanding the etiology of underlying diseases. The main objective of this project is to use limb development as a model to uncover transcriptional mechanisms of pathogenic Sonic Hedgehog (SHH) activation in anterior limb bud cells that occurs in patients with rare variants in the ZRS limb enhancer of SHH. More than 30 independent rare variants in ZRS are linked to human polydactyly. However, these gain-of-function enhancer variants are challenging to study because cell culture- or organoid-based models typically do not recapitulate ectopic gene expression observed in vivo. In preliminary studies, we used our newly developed, reproducible transgenic mouse assay to show that most of these rare variants cause ectopic enhancer activity in the anterior margin of developing mouse limb buds, suggesting a common mechanism for pathogenic enhancer de-repression. The proposed project will dissect the mechanism(s) by which gain-of-function enhancer variants result in pathogenic developmental phenotypes. We will utilize a modified version of our novel transgenic assay, which enables visualisation of pathogenic enhancer activity in live embryos, together with our enhancer variant knockin mouse model that faithfully recapitulates limb malformations observed in patients, to delineate transcriptional mechanisms that cause ectopic Shh expression and pathogenic phenotypes. In Aim 1 we will characterize chromatin and spatial mechanism of ectopic gene activation resulting from gain-of-function mutations in the ZRS enhancer. In Aim 2 we will identify transcription factors that cause ectopic Shh activation. The high-resolution and rigorous quantitative characterization of novel genetic factors that contribute to enhancer pathogenicity will significantly advance our knowledge of enhancer malfunction in disease. Ultimately, this knowledge can be used in combination with information about epigenome state from single-cell studies to predict the clinical significance of novel non-coding variants emerging from rapidly expanding whole-genome sequencing studies.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY In the United States, early-life adversity (ELA) is frequently reported and is strongly linked to later-life repercussions. Research highlights a significant association between neuropsychiatric disorders and adverse or traumatic events during early life, indicating ELA as a potential common root cause. This association has been identified as a precursor to various neuropsychiatric disorders, including anxiety, depression, and addiction. These conditions are of considerable global concern, as they not only diminish overall quality of life but also have adverse effects on societal functioning. A pivotal aspect of ELA involves stress and the processing of sensory signals during early stressful events. These signals undergo decoding by cortical layers in the brain, subsequently being transmitted to midbrain regions responsible for regulating behavioral responses. The dorsal striatum plays a central role in this process by processing cortical inputs and establishing connections with key brain regions that influence behavioral adaptability. Our recent research has unveiled functional impairments in corticostriatal synapses in adult mice following ELA. Specifically, we observed a decrease in glutamate release from the anterior cingulate cortex to the dorsomedial striatum in male ELA mice, contrasting with an increase in females. Furthermore, males exposed to ELA displayed behavioral inflexibility, while females exhibited no impairments. This represents the first direct functional evidence of the impact of ELA on this brain circuit. The current proposal will focus on this circuit and evaluate the potential mechanism underlying ELA. Previous findings revealed increased metabotropic glutamate receptor 5 (mGluR5) expression after ELA, however, their role in ELA-induced effects on corticostriatal synapses and behavioral adaptability remains unknown. Our pilot study revealed that ELA disrupts mGluR5-mediated synaptic transmission (i.e., depolarization-induced suppression of excitation, DSE). Based on our published and pilot work, our central hypothesis is that ELA elevates mGluR5 activity and expression, disrupting dorsomedial striatum (DMS)-mediated functions. We aim to demonstrate this by investigating mGluR5's impact on ELA-induced impairments and its potential rescue through mGluR5 inactivation. Understanding these ELA-induced effects on corticostriatal synapses is crucial, as it sheds light on the potential development or progression of psychiatric disorders. The contrast in glutamate release and behavioral responses between genders emphasizes the need to further study this brain circuit to intervene effectively and mitigate the risk of psychiatric disorders. The proposed studies will address critical gaps in understanding ELA-induced impairments, offering potential targets for treatment.

NSF Awards · FY 2024 · 2024-07

This project examines why some states make national citizenship accessible and others do not, and whether democratic pressure propel states towards broader definitions of citizenship. Citizenship laws are important to study because they simultaneously define who can participate in a national election and who belongs in the nation. And while autocratic contexts may not provide opportunities to formally participate like democracies, shaping a cohesive nation remains an important goal. Are citizenship laws more participatory in democracies than autocracies? To examine the political factors that determine citizenship policy, this project collects global data of laws for gaining and losing citizenship, across countries and over time. With this comparative view, the project examines the relationship between regime values and how states define their national communities. This project advances prosperity and welfare, especially in terms of how obtaining citizenship can create security and opportunity for immigrants and diasporic communities. This project theorizes that regime-level factors create meaningful contexts for understanding variation in citizenship policy settings. As a result, democracies and autocracies may both maintain similarly accessible (or restrictive) citizenship laws but be motivated by distinct reasons. To test this and related arguments, the project conducts statistical analysis and tests several hypotheses with original data, obtained by building an expanded Global Citizenship Law Dataset, which describes laws for gaining and losing citizenship, across 191 countries over time. This research will make significant contributions to scholarly literature on citizenship and migration, public policymaking, welfare, immigration policy, and democratization. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-07

The project resides at the intersection of the fields of mathematical analysis, partial differential equations, and geometry. Specific questions to be investigated concern the inverse spectral problem, the structure of Laplacian eigenfunctions, and the asymptotic behavior of Bergman kernels. These topics are crucial for understanding how geometric structure influences spectral properties, and are deeply connected to various concepts in mathematics and mathematical physics. The inverse spectral problem investigates how much information about the shape of a (not necessarily round) drum can be obtained solely from its frequencies of vibration. This is a classical question famously popularized by Mark Kac with the phrase `Can one hear the shape of a drum?’ A second set of problems focuses on the shape and the size of the set (`nodal set’) on which an eigenstate of the Laplacian operator vanishes. The size (in the sense of Hausdorff measure) of the nodal set is conjectured to be comparable to the frequency of the eigenstate. Finally, the Bergman kernel is an essential concept in the fields of complex analysis and complex geometry. Bergman kernel approximations arise naturally in mathematical physics, especially in string theory, where they have been proposed as a tool for the search for geometrically well-behaved complex metric structures. The broader impacts of the project contribute to education and diversity. The principal investigator actively supervises graduate students and postdoctoral researchers. Additionally, the PI participates in outreach activities such as organizing math competitions for middle school students and mentoring students from diverse backgrounds through summer research programs. The planned research lies in three main areas. Building on previous work with Steve Zelditch, in which nearly circular ellipses were shown to be spectrally unique among smooth domains, the PI aims to generalize such results to generic ellipses and to domains with constant width. Another direction of interest resides in strong inverse spectral results for generic polygons. Next, recent work by the PI resulted in new explicit upper bounds for the Hausdorff measure of nodal sets of eigenfunctions on compact Riemannian manifolds with Gevrey or quasianalytic regularity. The PI seeks to extend these results to manifolds with boundaries and to improve the current upper bounds using innovative methods. Finally, in collaboration with Hang Xu, the PI investigates asymptotic properties of Bergman kernels. This includes establishing new off-diagonal asymptotics for smooth Kaehler potentials and improving extant upper bounds for Bergman kernels. In addition, the PI will explore convergence properties of the Fefferman expansion for domains with real analytic boundaries. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-07

Autonomous vehicles (AVs), commonly referred to as self-driving cars, have been gaining popularity in recent years, as demonstrated by over 50 companies developing autonomous driving software (ADS). AVs are expected to bring convenience and other benefits, for example for those who cannot drive. Despite well-known companies making advances in autonomous driving, the technology is not as safe as it should be -- with widely publicized accidents from major companies in the AV industry. Over the past few years, software engineering research in the domain of ADS has yielded tools that can generate virtual scenarios for testing. However, reusing these tools is challenging as it requires sufficient experience with installation and complex interoperability issues, as well as costly hardware investments. To overcome these issues, this project aims to develop CADRI (Cloud-based Autonomous Driving software Research Infrastructure), a first-of-its-kind cloud-based ADS research infrastructure to ease software research in the context of ADS testing. CADRI will be delivered as a tool suite comprising three principal components: (1) a cataloged library of cutting-edge ADS testing approaches; (2) pre-configured ADSes and simulators on the cloud that allow new approaches to be easily evaluated; and (3) a dataset repository and benchmark that is accessible through a web-based graphical user interface. CADRI will be the first software research infrastructure of its kind with the goal of improving accessibility and reusability of ADSes, relevant simulators, and ADS testing approaches. It will provide an effective, community-wide platform for ADS research and practice through the continuous integration of diverse tools. The planning activities supported through this award include prototype library development, community planning workshops, prototype software development, and pilot studies. CADRI has the potential to improve the future of ADS research and development by making AVs safer and more comfortable. It will facilitate the discovery and adoption of cutting-edge techniques and tools that are best suited to the problems at hand. CADRI will also foster more effective university-industry collaboration. The project will result in a lower barrier to entry for researchers in the domain of ADS. Through collaborations with the Autoware Foundation, Toyota, and Zoox, this project will work toward building the infrastructure in a manner that leverages ADS testing in industry. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2025 · 2024-06

Project Summary/Abstract Culturally competent assessment tools are a crucial component in providing bilingual Latinx children with a free and appropriate public education. However, many assessment tools used with culturally and linguistically diverse children are based on WEIRD norms. Health disparities occur when children’s linguistic skills are measured up against WEIRD norms rather than practices from their own linguistic and cultural communities. This research will (1) provide documentation of storytelling practices and styles for bilingual Latinx children and (2) compare the utility of using measures derived from within the linguistic community with measures derived from WEIRD language norms. Ethnographic observations, interviews, and surveys will serve as the main methods to gather what storytelling practices bilingual Latinx children with DLD are typically exposed to. Narrative sample analysis will be utilized to analyze children’s narratives. Two scoring systems will then be used: one derived from the data gathered in (1) and the other will be based on extant, traditional measures of narratives. By documenting the storytelling practices of bilingual Latinx children with DLD, we can utilize culturally and linguistically appropriate descriptions of linguistic backgrounds for linguistically minoritized children with disabilities. By comparing performance based on community-generated measures with extant measures of narratives, we can learn which methods best fit culturally specific ways of telling stories in narrative performance. This will allow us to understand normal linguistic processes in culturally and linguistically diverse communities that we can then use to understand disordered linguistic processes in these communities, thereby reducing health disparities. This fellowship includes mentorship and training opportunities with researchers across California, including a data collection site in Santa Ana, CA. The training goals for this fellowship include training in qualitative research methods and psychometrics.

NIH Research Projects · FY 2024 · 2024-06

Project Abstract Funding is requested to acquire a state-of-the-art mass spectrometer for MALDI Imaging Mass Spectrometry (MALDI IMS) in support of multiple NIH-funded programs at UC Irvine. The instrument is based on a AP-MALDI-QTOF design optimized for imaging by high-speed, high resolution acquisition of mass spectra from raster laser scanning of matrix-coated 2D specimens. MALDI IMS provides a proven technique capability of retaining spatial information alongside high dimensional ion mass detection. Supported projects originate from researchers in the Schools of Physical Sciences, Biological Sciences, Engineering, Medicine and Pharmacy & Pharmaceutical Sciences. The instrument will, therefore, be truly a shared inter-disciplinary resource. Projects of the major users include, 1) neuropathological proteins and lipid phenotyping in Alzheimer’s disease models, 2) investigating metabolic heterogeneity in tumors, 3) evalauting ECM composition of engineered cartilage, 4) defining age/environmental changes of lens cyrstallins, 5) spatial plant metabolomics and 5) assessing lipid/protein distributions in dry eye syndrome. All the projects are pursuant of highly defined goals where the spatial organization of biomolecules (metabolites, lipids, peptides/proteins) is a critical component for understanding the molecular organization and function or dysfunction of tissues. For optimal access, maintenance and expert operational support, the instrument will be placed in UCI’s Mass Spectrometry Core Facility. UCI has long supported the MSF with permanent funding for full-time facility staff members: a PhD-level director with >30 years experience as a multidisciplinary research scientist, complemented by a proteomics specialist with expertise in MALDI and LC-MS techniques, and an instrument operator. Normal facility operational funds are obtained though a well established stable recharge system. Additional extended service support is provided through pledged institutional funds. All 20 instruments in the Facility are intensively used, particularly for small molecule analysis, top down proteomics and metabolomics with most available 24/7 as walk-up open access instruments. In fiscal year 2021-2022 the facility analyzed >35K samples by 300 users, with many users receiving advanced instrument training. The MALDI-IMS instrument will be run as a staff-operated service but also made accessible to qualified trained users to maintain a high sample throughput and maximum use. The research outlined in the proposal highlights an urgent need for an advanced but user-friendly instrument that is not currently available at UCI; a fast MALDI-QTOF IMS system for high quality biomolecular spatial phenotyping.

NSF Awards · FY 2024 · 2024-06

This project explores the process of property formation following a major disaster. While much attention has been given to the rapid privatization of land following disaster (a process commonly referred to as disaster capitalism), this project focuses on the post-disaster period when the form of property is not yet determined, private or otherwise. Indeed, after the emergency phase of the disaster has passed, property often remains in flux, caught up in local resistance efforts, political wrangling, and contested legal matters. By focusing on this interim period, this research is able to study the way in which law and legal decisions come to matter in differing claims to property. Privatization is neither a facile nor foregone process, and law is neither always nor the only way that different societies relate to land and their claim to it. As the severity and frequency of disasters has escalated, this research has broad implications by building an understanding of how law impacts society at large and marginalized communities more specifically as they recover and reclaim property. This early concept grant for exploratory research (EAGER) project investigates the process of property formation in the aftermath of natural disaster. The guiding research questions are: how does landownership take shape following a major disaster? And how are laws and legal decisions taken up (or not) when making a claim to a particular model of property? To answer these questions, the researcher will conduct a series of three ethnographic research trips over the course of 18 months. The site of the research is a community that was directly affected by a major hurricane several years ago and is now actively negotiating the shape that property will take in the wake of the disaster, recent landmark legal decisions, and an external push to privatize. The researcher will conduct interviews, participant observation, and media and social media analysis. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2025 · 2024-06

PROJECT SUMMARY Host defense and immunity are initiated by pattern-recognition receptor (PRR) binding to pathogen- or danger- associated molecular patterns. Activation of immune cells in response to microbes or damaged tissue results in the induction of antimicrobial processes, the production of inflammatory mediators, and activation of adaptive immunity. Triggering Receptor Expressed on Myeloid cells 2 (TREM2), is a scavenger receptor that is predominantly expressed on the surface of monocytes, macrophages, dendritic cells, and microglia. TREM2 binds to a diverse array of host and pathogen anionic molecules, including phospholipids, DNA, and lipoproteins, and contributes to sensing tissue damage. Given the myriad endogenous and microbial ligands that become accessible during tissue damage and infection, TREM2 activity in vivo is complex. Signaling through TREM2 in association with its adaptor protein DAP12 activates the tyrosine kinase Syk and can result in beneficial or detrimental outcomes for the host, depending on the context. Despite its broad expression on myeloid cells and its genetic association with neurodegenerative and metabolic diseases, the function of TREM2 in host defense and immunity during infection in vivo remains incompletely understood. Using a CRISPR knock-out strategy, we recently discovered a role for TREM2-DAP12-Syk signaling in human monocyte activation during infection with Toxoplasma gondii. We also found that TREM2 knock-out (KO) mice are acutely susceptible to T. gondii, with increased mortality and elevated parasite burden compared to control wild-type (C57BL/6) mice. These preliminary data support the hypothesis that TREM2 plays a key role in immunity against T. gondii. The objective of this proposal is to determine how TREM2 functions in human innate immunity and in protection against T. gondii in vivo using human immune cells and a mouse model. The first aim will examine the outcome of TREM2 activation in human immune responses by examining the signal transduction pathways that are activated and the production of cytokines and chemokines during infection or phagocytosis using control or TREM2 KO human monocytic cells and human induced pluripotent stem cell (iPSC)-derived microglia. The second aim will define the role of TREM2 in myeloid cell immunity in vivo by comparing antimicrobial host defense and protective immune responses during infection of myeloid- specific and microglia-specific TREM2 KO mice. The proposal involves the use of innovative single-cell proteomic technology and human iPSC-derived microglia. This research is significant because it has the potential to reveal a new receptor involved in innate immunity to T. gondii. In addition, an enhanced understanding of how TREM2 functions in the periphery and in microglia in the brain during infection may inform the development of strategies to increase its protective activities during disease.

NIH Research Projects · FY 2026 · 2024-06

Project Summary Prostate cancer (PCa) is the second most common cancer in American men and is responsible for 3% of total deaths and 10% of deaths by cancer. Most patients experience a slow-progressing disease and are assigned to active surveillance. These patients are spared immediate radical prostatectomy (RP) or radiation that is used for patients that have more advanced disease. Because assignment to active surveillance is imperfect, some patients are unnecessarily overtreated, with the burdens of unnecessary side effects, cost, and lower quality of life, whereas a few patients that need prompt radical treatment may experience delays. The limited treatment options available for aggressive disease usual fail within a few years. Thus, there is an unmet clinical need for low toxicity preventive/interceptive agents or natural products that prevent PCa progression either during active surveillance or after RP or radiation treatment. S phase kinase-associated protein 2 (Skp2) is a putative oncogene that targets several tumor suppressors for degradation. The Skp2 gene is amplified in several human cancers. In PCa, Skp2 is overexpressed in pre- malignant high-grade prostatic intraepithelial neoplasia (HG-PIN) and in primary tumors, suggesting a role in the early stages of PCa. Skp2 deletion blocks tumorigenesis in Rb1, p53, or Pten deficient mouse models, suggesting that Skp2 may serve as an “Achilles' heel” drug target against pRb, p53 and/or Pten-deficient cancer. However, inhibitors that disrupt Skp2 protein-protein interactions or cause degradation through the proteolysis targeting chimera (PROTAC) have had limited success. Thus, we propose to instead screen directly for natural products that target Skp2 for degradation. In a collaboration with the National Center for Advancing Translational Sciences (NCATS), we will use 500,000 natural product samples that are known to include highly diversified chemotypes with cancer-preventive properties. To implement the screen, we have developed a cell-based luciferase assay for degradation of Skp2 and several other resources including our large PCa patient cohort, our prostate-specific human Skp2 knock-in mouse model of early prostate carcinogenesis, our PCa patient-derived organoid cultures, and patient-derived xenograft (PDX) models. In Specific Aim 1 (UG3) we will optimize our cell-base luciferase assay, develop a prototype HTS assay for screening skp2 degraders, and perform mechanistic studies of products that have potential utility. In Specific Aim 2 (UG3) we will quantitate Skp2 protein in PCa progression. This is a step towards identifying patients that would benefit from interception via a Skp2 degrader, which will be important for developing a novel clinical trial. In Specific Aim 3 (UH3) we will complete a full-scale HTS of up to 500,000 natural products with NCATS. We will perform activity-based characterization and bioassay-directed isolation, structural elucidation, and perform mechanistic studies of leads generated during screening. In Specific Aim 4 (UH3) we will determine the in vivo chemopreventive efficacy, toxicity, and mechanisms of two confirmed compounds through dietary administration in a novel prostate-specific human Skp2 knock-in mouse carcinogenesis model and in PDX models. Impact: Positive results from this study will identify novel natural products for interception of progression in early stage PCa. Measuring Skp2 in a large PCa patient population will allow identification of patients most likely to respond, allowing development of a novel clinical trial.

NIH Research Projects · FY 2025 · 2024-06

Project Summary / Abstract Dementias from Alzheimer’s disease (AD) and age-related cognitive impairments are a major health and socio- economic concern in the US and worldwide. AD remains resistant to treatment based on earlier research efforts. Approximately 20% of the US population will be 65 or older by year 2030; roughly 8 million of these individuals are expected to suffer from AD. The neural circuit aspects of AD are an emerging new research area with tremendous potential for growth and progress. The UC Irvine Center for Neural Circuit Mapping (CNCM) research program has quickly established strong federal funding that supports our transformational projects with significant clinical translational potential. The ongoing acceleration of our understanding of the nervous system will drive the development of new therapeutic strategies to treat AD and other brain diseases over the next decades. Our new CNCM research program has unified multidisciplinary investigators from multiple academic units across UC Irvine including the Schools of Medicine, Biological Sciences, Pharmacy and Pharmaceutical Sciences, Engineering, and Information and Computer Science. Our T32 program is designed to train the next generation of researchers focused on neural circuit studies of brain disorders including AD and related dementias. The proposed training program will be administered by the CNCM and will be supported by CNCM investigators who have fostered a highly collaborative environment exemplifying interdisciplinary team-based research. Our exciting and diverse group of faculty members will mentor and support predoctoral and postdoctoral trainees in neural circuit studies using a range of interdisciplinary approaches combining analysis of mouse genetic models and post-mortem human brain tissues with state-of-the-art technologies that include viral genetic mapping, in vivo neural ensemble recording/imaging, single-cell genomics, engineering and computational modeling. Our faculty mentors and trainees will expand our mechanistic understanding of Alzheimer’s disease and other disorders and develop tools that enable early detection and diagnosis. Our training plan is well defined; trainees are required to take courses and seminars related to cutting-edge neuroscience and AD research with a neural circuit focus. We anticipate four trainees per year (2 pre- and 2 postdocs) whose training will continue until they complete their respective programs. Critically, we will teach our trainees to develop their own unique tools and methodologies to address scientific questions that others cannot. We include training in rigor and reproducibility, statistics and data analysis training, and professional development. The expected outcome of our T32 program is to establish a successful training pipeline to prepare trainees with career-long experimental and quantitative skills as future research leaders who will focus on neural circuit analysis of Alzheimer’s disease and related dementias.

NIH Research Projects · FY 2025 · 2024-06

PROJECT SUMMARY Peritoneal carcinomatosis (PC) is the deadliest form of colorectal cancer (CRC) and gastric cancer (GC) metastasis, with a median survival of 10-18 months for CRC and less than this for GC. PC is a common form of metastasis in both CRC and GC, each with an incidence of between 10 and 50%. Unfortunately, there are few treatments available, and there exist large regional and ethnic disparities in each of these diseases, emphasizing the need for increased research on developing improved therapies. This development is slowed by the absence of appropriate in vitro models and the gaps in our knowledge of how metastasis occurs. Our application is focused on improving this situation. Here we propose to characterize and utilize a recently-developed in vitro PC model (the Vascularized Micro-Peritoneum, VMP) for use as a therapeutic development tool. The model is based on our vascularized micro-tumor (VMT) platform, a microphysiological system (MPS) that allows direct observation of living cells that are proliferating, metabolizing, migrating, and dying in a complex 3D environment. This application is in response to the Funding Opportunity Announcement PAR-22-099 titled “Cancer Tissue Engineering Collaborative: Enabling Biomimetic Tissue-Engineered Technologies for Cancer Research”, the stated goal of which is to “support the development and characterization of state-of-the-art biomimetic tissue- engineered technologies for cancer research.” In general, systemically-delivered drugs have not been especially effective against PC as much of the early growth occurs on the surface of the peritoneum, somewhat distant from the underlying blood vessels and so hard to target with high doses of drug. Most patients now receive neoadjuvant systemic therapy followed by cytoreductive surgery and hyperthermic intra-peritoneal chemoperfusion (HIPEC), which has resulted in a general increase in patient survival. Despite this improvement, most patients still develop recurrent disease in less than a year and the majority die due to disease by 5 years. Hence there is a huge unmet need for new and improved therapies for patients with PC, and repurposing drugs approved for other cancers might be a promising approach. Our hypothesis is that: A microphysiological system platform can be used to help identify improved therapies for peritoneal carcinomatosis. To test this hypothesis we will pursue the following aims: 1. Characterize a dual-tissue platform that models peritoneal carcinomatosis 2. Correlate platform performance to in vivo data in a prospective Clinical Study 3. Test drug sensitivities of PC tumors in the VMT/VMP

NIH Research Projects · FY 2026 · 2024-06

There is an unmet need to obtain natural product-derived medicines in a scalable and reliable manner. Natural products are small molecules produced by biological systems, but often in low quantities. Synthetic biology promises to move the biosynthetic pathways of these medicinal small molecules from their native producers into heterologous hosts such as bacteria and yeast or into a bioreactor, so that large-scale, low-cost, industrial processes can be developed to produce them. The long-term goal of my research program is to address the ultimate challenge in chemical biosynthesis, namely to precisely control the flow of electrons, carbon, and energy. Over the past five years, we have made substantial strides toward this goal, by establishing unnatural electron currency which operates in parallel to Nature's universal cofactor. This design is inspired by Nature: Catabolism and anabolism, two opposing metabolic systems responsible for breaking down and building up cell components, respectively, are insulated from each other because they each have a designated redox cofactor, NAD and NADP, respectively. We have demonstrated that our unnatural cofactor can indeed precisely channel reducing power only to the desired pharmaceutical producing reactions inside the cells while silencing all side-reactions, effectively insulting the biosynthetic pathway from the host's complex native metabolism. Importantly, we have also developed universal, high-throughput, growth-based selection platforms to readily obtain enzymes that can use the unnatural cofactor. Through these efforts, general enzyme design principles also start to emerge which paves the way for our proposed work in the next five year. Through the MIRA support, we will develop methods to drastically improve the efficiency of the unnatural cofactor technology; make it easy to adopt by bioengineering community; bring this technology to bear on difficult high-reward biosynthesis challenges; broaden the category of unnatural metabolic currencies from electron- to carbon- and energy-carriers and distill translatable design principles; use this project as a vehicle to include and promote diverse STEM researchers at K-12, undergraduate, graduate, and post graduate stages. The proposed work is transformative because it directly targets life's universal metabolic infrastructure and therefore can have extremely broad impacts in biomedicine and synthetic biology.

NIH Research Projects · FY 2025 · 2024-05

Abstract Botulinum neurotoxins (BoNTs) with its seven major serotypes, BoNT/A-G, are the causative agents of neuroparalytic disease botulism. BoNT/A and BoNT/B in particular pose the most serious threats to humans because of their wide prevalence, high potency, and persistence. Each BoNT molecule has a modular architecture consisting of a ~50 kDa catalytic light chain (LC) and a ~100 kDa heavy chain (HC). The HC serves as BoNT’s delivery vehicle, which has high specificity for motor neurons and, following its uptake, subsequently translocates the LC into the neuronal cytosol. The LC is the warhead of the toxin, which acts in the cytosol as a sequence-specific protease to cleave soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNAREs). This blocks the fusion of synaptic vesicles and prevents the release of acetylcholine at neuromuscular junctions (NMJ), resulting in paralysis of the affected muscles and death by asphyxiation in severe cases. Currently the only available therapeutics for botulism are equine or human antitoxin serum products that can prevent further intoxication by neutralizing the circulating toxins, but these antibodies have no effect on the internalized LC that is mainly responsible for BoNT’s neurotoxic effects. Therefore, there is an urgent need for an effective treatment for post-exposure therapy for botulism patients. Here we strive to develop a platform for intra-neuronal delivery of nanobodies (aka single-domain antibodies such as camelid VHHs) targeting the LC to neutralize the toxin inside the intoxicated neurons and accelerate recovery of the paralyzed muscles. The general principle of our antidote design is to create genetic fusion proteins consisting of three modules: a LC-inhibiting VHH as the payload, the translocation domain of diphtheria toxin as a delivery module for cytosolic translocation, and a targeting module for highly specific neuron targeting. We propose two Specific Aims to explore two different design types. In Aim 1, we will develop antidotes using the receptor-binding domain of BoNT/A (HcA) as the targeting module for intra-neuronal delivery of VHHs that inhibit the LC proteases of BoNT/A and BoNT/B, respectively. HcA binds neuron-specific synaptic vesicle glycoprotein 2 (SV2) and is solely responsible for neuron-targeting of BoNT/A. These fusions proteins will be subjected to comprehensive biochemical and functional characterization to optimize their designs followed by mouse efficacy studies. In Aim 2, we will develop and characterize novel VHHs that bind SV2 to replace HcA as a neuron-targeting domain for the antidotes, which will expand the flexibility of this delivery vehicle and also minimize the immunogenicity concern. We will then test this second type of antidotes for efficacy in animals. Successful completion of this work will result in the identification of novel antidotes for BoNT/A and BoNT/B that can be further developed as therapeutics to treat post-exposure botulism. The versatile intra-neuronal delivery platform is amenable for quick optimization and flexible enough to expand to develop antidotes for other BoNT serotypes, or to selectively deliver nanobody or other protein therapeutics, including gene editing components, to treat neuronal diseases.

NIH Research Projects · FY 2025 · 2024-05

Pertussis or whooping cough, despite widespread vaccination, remains a major human health problem. Pertussis is highly infectious and is most dangerous for newborns, where 1/3 of infected infants under one year old are hospitalized and one in a hundred of hospitalized babies die. In the last decades, we have seen a resurgence in pertussis cases, which is believed to stem from decreased efficacy of the vaccine. The current vaccine is composed of cellular components of the causative agent of pertussis, Bordetella pertussis; a major component is the protein Filamentous hemagglutinin protein (FHA). FHA is a virulence factor in Bordetella and is essential for adherence and colonization in human hosts. FHA is the mature form of FhaB, following the loss of a signal peptide and FhaB’s C- terminal region whereby it was proposed that this C-terminal region had no function. Notably, FhaB has striking similarities to CdiA, the toxin carrying component of contact dependent growth inhibition (CDI), whereby the C-terminal toxin domain of which is translocated into target bacterial cells upon contact. Our recent work has shown that extreme C-terminal of FhaB (FhaB-CT) is delivered into human cells, where it acts as a microtuble (MT) binding protein. Thus, FhaB-CT likely has a role in Bordetella virulence. While FhaB is translocated into eukaryotic cells and CdiA is translocated into bacterial cells; these similarities lead us to hypothesize that FhaB is part of an uncharacterized anti-eukaryotic CDI system. This proposal aims to characterize the interaction of FhaB-CT with MTs and identify other Gram-negative bacterial FhaB-CT domains with anti-eukaryotic activities. First, we will determine the structure of the complex of FhaB-CT with MT using cryo-EM. Secondly, we will identify other anti-eukaryotic FhaB-CT domains through in silico analysis. We will test these domains for eukaryotic entry and toxin/adhesion activity. The results of this study will (1) lay the groundwork to further explore Bordetella virulence and the activity of B. pertussis FhaB-CT, and (2) identify other FhaB-CT proteins that target eukaryotic cells and characterize their activity. Not only could these results aid the development of a new pertussis vaccine, but with an improved understanding of the interaction between FhaB- CT and MTs we may also offer a new target for pertussis therapeutic development. Lastly, with the discovery of FhaB-CT activity and a novel anti-eukaryotic CDI system, we have found a new branch of CDI systems with direct correlation to human health that require investigation.

NIH Research Projects · FY 2026 · 2024-05

Project Summary Alzheimer’s disease (AD), the most common dementia, currently affects ~6.7 million individuals in the U.S. alone and is expected to grow to 13 million by the year 2050. A major component of its devastation is the progressive loss of the patient’s ability to form memories. Treatments for rescuing memory function in AD patients do not exist, due in part to insufficient research performed to characterize the activity of memory-supporting neural circuits compromised by the disease. The effort to develop memory-restorative therapeutics that intervene in neural circuits requires investigation of which circuit-level functions are impacted during pathophysiological progression, and how they relate to memory performance. Neurons in the entorhinal cortex (EC) act as a gateway for sensory inputs feeding into the hippocampus. This EC-hippocampus circuit is critical for memory formation and retrieval. Inside the EC, the lateral entorhinal cortex (LEC) is a primary site of atrophy and activity loss in the early phases of AD. Despite its significance to AD pathophysiology, it remains unclear what type of activity is lost in the LEC of AD patients or animal models. Our laboratory’s pioneering previous research has developed exciting preliminary results that suggest a path forward. We have found in healthy rats that LEC neurons develop reward-associated spike representations during associative learning. Recently, using optogenetic circuit analyses, we found in healthy wild type (WT) mice that (i) LEC layer 2a neurons categorize rewarded vs. unrewarded sensory cues when mice are performing associative learning, and (ii) this categorization activity is facilitated by dopamine inputs from the ventral tegmental area (VTA) to the LEC. Our overall hypothesis is that dysfunction of LEC neuronal activity for memory encoding causes associative memory impairment in APP knock- in mice. To test this hypothesis, we will (Aim 1) determine cell types that show activity dysfunction in the LEC, (Aim 2) determine if dysfunction of LEC dopamine causes associative memory impairment, and (Aim 3) determine if LEC 20-40Hz oscillation deficit underlies associative memory impairment. The project is expected to yield advances toward the development of therapeutics to rescue memory function in the LEC.

NIH Research Projects · FY 2025 · 2024-05

Pathophysiology of vascular contributions to cognitive impairment and dementia (VCID), including vascular cognitive impairment, remains enigmatic, and this project will take a novel focus by addressing the possible role of calcification of the intracranial vasculature. We will analyze the consequences of neurovascular calcification (NVC) on brain parenchyma and subsequent impact on cognition in a high-risk population of aging and chronic kidney disease (CKD) subjects/patients. We will delineate the specific pattern of calcification (intimal vs medial arterial/arteriolar and capillary) and analyze ischemic and hemorrhagic injury in autopsy human brain. We will also examine the process of NVC in mouse brain, its impact on parenchymal injury and cognitive impairment, and determine how it may be treated or prevented. Vascular calcification is age-dependent, and we will focus on aging in our studies. Because CKD is known to profoundly advance calcification of vasculature, we will also focus on CKD in our studies. The project team has expertise in stroke neurology, vascular neurobiology, nephrology, neuropathology, and biostatistics, all relevant to the proposal: Specific Aim 1: To determine the relationship between NVC and microvascular disease in CKD of aging. Hypothesis 1A: NVC (medial vs intimal/capillary) predicts microvascular ischemic injury in autopsy brain of aged CKD subjects. Hypothesis 1B: NVC (medial vs intimal/capillary) predicts microvascular hemorrhagic injury in autopsy brain of aged CKD subjects. Specific Aim 2: To determine a) the effects of NVC on brain parenchyma and cognitive performance, and b) the mechanistic treatment of NVC, in aged CKD mice. Hypothesis 2A: NVC worsens microvascular parenchymal injury and VCID with cognitive decline in aged CKD mice. Hypothesis 2B: Anti-calcification therapies decrease NVC and parenchymal injury and improve cognitive performance in aged CKD mice. Our proposed project combines human autopsy investigation with a relevant mouse model, designed to produce project synergy in which observations from the human study inform the mouse investigation and mouse studies suggest targetable mechanisms of NVC in human brain. Incorporation of the mouse model provides the advantage of a trial of targeted therapy for NVC, which is to the best of our knowledge the first such attempt. Our human autopsy study will compare CKD vs non-CKD subjects, and thus insights will be generated for both the CKD and non-CKD population. Completion of this project by our unique mutli- disciplinary team should pave the way for more comprehensive studies of NVC and its treatment, providing new directions in the scientific approach to ameliorating VCID, including vascular cognitive impairment.

NIH Research Projects · FY 2026 · 2024-05

PROJECT SUMMARY/ABSTRACT Muscular dystrophies (MDs) occur world-wide affecting all races with an estimated combined prevalence of ~20- 25 per 100,000. Muscle mass is ~65-85% of our body and there are many genetically distinct MDs that affect different body muscles. While mechanistic studies led to some promising therapeutic strategies to slow disease progression, these options are still limited and there is essentially no cure for MDs. Thus, it remains critical to understand the disease mechanisms and utilize the knowledge to develop innovative therapeutic strategies. At University of California, Irvine (UCI), we have strengths in 4 areas of muscle and MD research: (1) muscle immune response/inflammation, (2) muscle regeneration/stem cell biology, (3) epigenetics and gene regulation, and (4) robust clinical and translational research (with strengths in development of biomarkers, natural history studies, validating outcome measurements for interventional studies, and therapeutic development). Together, we believe we can build a robust training program to move the field forward. The major objective of this T32 grant is to cultivate future muscle biology and MD researchers through multidisciplinary training. Mentees will be three predoctoral students and one postdoctoral fellow per year. The T32 program will be affiliated with a newly formed Muscle Biology and Disease Research Center at UCI. UCI is a site for one of the highest number of clinical trials in the US for muscle-related therapy (immune myopathies, muscular dystrophies and rare and ultrarare genetic non-dystrophic muscle disorders). Eighteen mentors have complementary expertise in genomics, epigenetics, immunology, stem cell biology, tissue engineering and clinical research. Each trainee will be co-mentored by a clinician and a basic scientist. The trainees’ development will be supported through didactic teaching, journal club, seminar series, and research in progress meetings on campus as well as opportunities for research presentations at national and international conferences. The T32 program also provides rigorous training for responsible conduct of research and data reproducibility as well as support for career development. Trainees also have opportunities/exposure to the multidisciplinary muscle clinics at UCI (UCI hosts thematic half day clinics in muscular dystrophy, myositis, Pompe Disease and GNE myopathy). There will be opportunities to engage in activities with patient advocacy groups and industry, which would be important to help mentees to understand the impact and the process of possible application of their research in the MD community. Our goal is to train the next generation scientists who can perform rigorous translational research to help MD patients.

NIH Research Projects · FY 2026 · 2024-05

Project Summary/Abstract Background: Understanding the origin and fate of genetic variation relies on accurate measurement of that genetic variation. Until recently, whole genome sequencing approaches exhibited blind spots regarding vast swaths of genomes comprising repetitive regions, despite repeated demonstrations of the importance of mutations involving gene duplications, tandem duplications, TE insertions, and other structural changes that are associated with repeats. Indeed, such mutations are often targets of adaptation, are associated with variation in human traits, play causative roles in many genetic diseases, and often play key roles in important phenotypes in species that coexist with humans (e.g. conferring pesticide resistance to human disease vectors). Despite this, surveys of genetic variation typically continue to select techniques based on convenience and cost-effectiveness. Indeed, even standard long-read sequencing approaches fail to recover >15% of the genome. A better way would be to apply emerging methods capable of resolving all regions, particularly ensemble approaches combining highly accurate and ultra-long sequencing technologies and long-range scaffolding techniques. Such approaches have already proven capable both of reducing the uncertainty in inferring structural mutations and of saving analysis time. Projects can now plausibly aim to obtain accurate, full genetic catalogs of each chromosome, from telomere to telomere. Now is the ideal time to discover and make inferences on the full spectrum of genetic mutations. Proposal: The Emerson lab’s research focuses on the evolution of genome structure, particularly mutations that add, subtract, or otherwise refashion genome sequence on large scales. We apply cutting edge sequencing, computational, and statistical techniques to discover and interpret structural genetic variation in the most recalcitrant regions in the genome, using Drosophila melanogaster as a model system. Over the next five years, our goal is to identify all structural genetic variation in samples within and between species, infer the evolutionary forces acting on them, and understand their functional consequences. We will adapt cutting-edge telomere-to- telomere approaches to extend our reach into every region of the genome to obtain an exhaustive inventory of genetic variation within and between species, eliminating the thorny problem of genotype-based ascertainment bias and error in evolutionary inference. In doing so, we will develop tools to aid in genome assembly, structural variant genotyping, and evolutionary analysis. We will also use functional genomics techniques to understand how perturbing primary genome structure changes genome function. Finally, we will identify individual candidate mutations for functional characterization using reverse genetics. With such comprehensive surveys of genetic variation, we can finally meet the challenge of discovering all classes of genetic variation to study the evolution of genome structure and function.

NIH Research Projects · FY 2026 · 2024-05

PROJECT SUMMARY As humans age, their immune systems become dysfunctional. Specifically, aging impacts adaptive immunity leading to reduced response to vaccines. A productive immune response to vaccines is characterized by high affinity antibodies and an increase in antigen-specific memory B and T cells. Intense research efforts have determined the role of T cells in aging; however the role of B cells is less clear. We hypothesize that humans, like mice, have age-related B cells (ABCs) in blood that can be tracked by clonal expansion, and in within tissue, outcompete important tissue specific B cell types, therefore limiting the capacity of older adults to respond to vaccines. We have assembled a team that span topic areas and technical expertise to address difficult questions of human B cell dysfunction with age. We utilize longitudinal and cross-sectional design to assess B cell aging in blood and lymphoid tissues. Further, we leverage a novel in vitro human tonsil organoid model we developed that allows mechanistic testing of age-induced B cell decline of vaccine responses, a feat previously impossible. In Aim 1, we will identify human ABCs by mapping dysregulation of phenotypic and functional B cell signatures over time. We hypothesize that ABCs are memory B cells that accumulated epigenetic changes, leading to a transcriptional program consisting of muted BCR responsiveness, dysregulated expansion, and defective function. We will analyze peripheral blood B cells and serum from a healthy aged longitudinal cohort using high-parameter flow cytometry and bulk RNA sequencing and multiplexing to track changes in B cell subsets, transcriptional profiles, BCR repertoires, and cytokine and antibody secretion. In Aim 2, we will target age-related mechanisms of lymphoid tissue B cell dysfunction to improve effective flu vaccine responses. ABCs are thought to derive from expansion of memory B cells. Therefore, we hypothesize that lymphoid tissues with high antigen exposure will have higher prevalence of ABCs and increased signatures of aging. Furthermore, we anticipate that targeting ABCs using a human tonsil organoid platform will improve flu vaccine responses. With unparalleled access to multiple post-mortem lymphoid tissues, we will compare B cells from young and older adults. We will use high parameter flow cytometry to enumerate B cell populations and perform single cell RNA sequencing on sorted B cells across human blood and tissues. Additionally, we will assess metabolism and cytokine secretion of aging B cells across tissues using extracellular flux analysis and multiplex cytokine profiling. Lastly, we will use a novel in vitro human tonsil organoid model to determine the cellular and molecular mediators of impaired vaccine responses. Understanding how age impacts B cell function will allow for improvement of vaccine design to increase B cell antibody responses, and therefore better protect the aging population of the world.