University Of California, San Diego

NIH Research Projects · FY 2025 · 2024-03

PROJECT SUMMARY The blood-brain barrier (BBB) is characterized by a series of properties that tightly regulate the transport of ions, molecules and cells between the blood vessel lumen and the brain parenchyma. This BBB is critical to control the environment of the brain to allow for proper neuronal function, and to protect the brain from injury and disease. Dysregulation of the BBB has been implicated in a variety of disorders including stroke, Alzheimer’s disease, multiple sclerosis, and epilepsy. In addition, the BBB is a key obstacle to central nervous system (CNS) drug delivery. The BBB has been extensively studied in a small number of model organisms (mouse, zebrafish) in which endothelial cells form this barrier. Interestingly, several species have a BBB formed instead by glial cells including invertebrates, elasmobranchs (sharks, rays and relatives) and sturgeons, but very little is known about the molecular mechanisms of BBB function in these species. Furthermore, a lack of correspondence between phylogenetic relationships and endothelial versus glial BBB suggests that the BBB evolved independently several times. Hypotheses that may explain these observations include an ancestral vertebrate with a glial BBB and independent evolution of the endothelial BBB at least six times (hypothesis A), an ancestral vertebrate with an endothelial BBB and independent re-evolution of the glial BBB at least twice (hypothesis B), or an ancestral vertebrate in which endothelial and glial cells each accomplished aspects of BBB function, with current BBB diversity a result of a “push-and-pull” toward either extreme (hypothesis C). Detailed molecular knowledge of the BBB in non-model organisms is required to better understand the mechanisms underlying BBB function in vertebrates and their evolution. To achieve this we will employ single nucleus RNA-sequencing (snRNA-seq) of brain tissue in fish species with an endothelial BBB (hagfish, trout, zebrafish, and lungfish) and fish with a glial BBB (shark, ray, and sturgeon). We will also profile mouse and octopus as outgroup comparators. This will allow us to define the molecular characteristics of endothelial and glial cells in each species and perform a cross-species comparison of BBB-forming cell types. Furthermore, we will examine BBB function and ultrastructure by injecting horseradish peroxidase (HRP) systemically into each species and visualizing HRP localization with electron microscopy. Together, the proposed study will provide unprecedented new information related to the molecular foundations of BBB function across life and will yield new information on the evolution of the BBB. The resulting information may also reveal novel molecular targets for CNS drug delivery and for treating BBB dysfunction in CNS disorders.

NIH Research Projects · FY 2026 · 2024-03

SUMMARY Intellectual and developmental disabilities (IDD) are a heterogeneous group of disorders characterized by deficits in cognitive and adaptive functioning, with onset before adulthood. Individuals with IDD face substantive social, healthcare, and health disparities. In recent years, multiple studies have reported an increased risk of adverse maternal, birth and infant outcomes associated with any IDD diagnosis. To date, the risk associated with specific diagnoses and the underlying causes of these excess risks have not been elucidated, although researchers have hypothesized that chronic disease, adverse reproductive factors such as smoking or inadequate prenatal care, and pregnancy complications could explain the risk. Without quantifying these mediating pathways, it is unclear where to target intervention efforts to optimize maternal and infant outcomes. To address this gap, we propose a study with the overarching objective to (1) leverage large-scale administrative data to elucidate the factors contributing to adverse maternal and infant outcomes for women with IDD, and (2) conduct causal mediation analyses, accounting for multiple mediators, to establish empirically derived intervention targets. In order to achieve this objective, we will do the following: characterize the pathways between IDD subtypes and adverse maternal outcomes (Aim 1); characterize the pathways between IDD subtypes and adverse birth and infant outcomes (Aim 2), quantify the multiple factors that mediate maternal and infant outcomes among women with IDD diagnoses (Aim 3). We will use data from the Study of Mothers and Infants, an administrative birth cohort consisting of all live born (n=6.7 million) and stillborn (n=26,922) deliveries in California between 2007-2021 in which birth records are linked to maternal and infant hospital summaries, infant and fetal death records, and in a subset, California Medicaid records. This will allow us to perform causal mediation analyses to quantify the extent to which chronic comorbidities, reproductive factors, or prescription medications mediate associations between IDD subtypes and adverse maternal and birth outcomes. Through this research, we will greatly expand the conceptual framework of reproductive health in women with IDD, allowing for targeted interventions to be interrogated in future work.

NIH Research Projects · FY 2025 · 2024-02

Osteoarthritis (OA) is the most common form of arthritis and affects millions of people in the United States. No disease-modifying drugs exist. Hence, treatment is currently limited to pain management, exercise and weight loss, or ultimately total joint replacement. Approaches which can identify early signs of OA and OA progression are critically needed for drug development. To better understand OA and to help identify genes associated with OA which might be targetable for drug development, genome-wide association studies (GWAS) have been conducted. As GWAS typically require large sample sizes, meta-analyses have commonly been used to combine data from OA-specific and large-scale population studies reaching close to a million samples. However, endpoints for such studies are generally defined by radiographic diagnosis of OA, total joint replacement, ICD codes, or self-reported OA. Hence, complicating the differentiation of genetic associations with early signs of OA progression from genetic associations with later OA disease stages. Several studies indicate the utility of image biomarkers for GWAS; but these imaging genetics (IG) studies only use relatively simple image biomarkers (such as bone shape, bone area, alpha angle, or minimum joint space width). On the other hand, deep learning approaches (DL), which can use image information in a more comprehensive way, have been successfully applied to segment cartilage and bone from images at scale and have shown promise for disease prediction. Hence, this project will develop advanced image biomarkers and related statistical approaches to improve OA GWAS results and to identify druggable genes associated with early OA disease stages. By learning image biomarkers from longitudinal data we will directly link biomarkers to progression. Unfortunately, while OA image datasets amenable to IG exist, those are typically either relatively small, not OA-specific, or provide heterogenous imaging modalities and acquisitions. This project will therefore develop computational approaches which can take advantage of such heterogeneous datasets. We will base our analyses on the Osteoarthritis Initiative, Johnston County, and UK Biobank datasets resulting in over 100,000 patients. We will focus on knee OA for which no IG studies exist and will extract image biomarkers from DXAs, radiographs, and 3D MRIs, including from longitudinal data to develop progression-sensitive biomarkers. Our resulting image analysis and statistical approaches will be general and therefore applicable beyond knee OA. To assure reproducible results we will provide all our analysis approaches in open-source form. They will be easy to use and will simultaneously be targeted at users wishing to build upon our approaches as well as users who want to use them for their own analyses. We will provide zero-install web-based data exploration capabilities to simplify analyses and quality control. Our analysis approaches will be developed based on industry-strength software engineering, will dramatically improve OA IG analysis capabilities, will benefit the entire research community, and will effectively democratize OA analyses.

NIH Research Projects · FY 2026 · 2024-02

Project Summary Our goal is to determine the connection among genes, brain structure and neuropsychiatric disorders. These disorders are common and increasing in incidence worldwide. Lower costs of both genotyping and magnetic resonance imaging (MRI) acquisition have provided an unprecedented opportunity to understand how genetic factors shape brain morphology. Given that structural brain measures may reflect intermediate phenotypes of neuropsychiatric disorders on the pathway between genotypes and clinical phenotypes. These findings in turn may help us better understand the pathogenesis of neuropsychiatric disorders. Data released by UK Biobank and ABCD Study (Adolescent Brain Cognitive Development Study) containing individual-level genotypes and rich phenotype variables allow genome-wide association studies (GWAS) in brain imaging phenotypes to identify genetic variants associated with brain morphology. Our study and work from other groups in brain imaging GWAS have confirmed that many identified genes are related to neurodevelopmental processes. The first objective in the current study is to uncover genetic variants associated with brain imaging phenotypes (Aim 1). Our second objective is to test genetic heterogeneity between the sexes in association with brain morphology and to include the X chromosome in the analysis (Aim 2). Our third objective is to determine the impact of neuropsychiatric genetic risks on the brain (Aim 3). Previously we produced the genetic atlases of the human cortex based on MRI data of twins using fuzzy clustering. Our most recent work demonstrated the value of using the atlases to determine genetic variants influencing brain structure. In this proposal, we will leverage an increased sample size with both MRI and single nucleotide polymorphism (SNP) data. The larger sample increases power for discovering and replicating SNPs associated with individual brain structures and will enable us to examine genetic heterogeneity between the sexes. Many GWAS loci are located in non- coding genomic regions thus it is hard to have functional interpretation of GWAS findings. We will use new methods for SNP-to-gene mapping to tackle this daunting challenge. We will also characterize pleiotropy among multiple brain regions. This will provide insight into shared and distinct genetic influences among brain regions, given that different brain regions have previously been implicated in neuropsychiatric disorders (Aim 1). Second, we will include the X chromosome in the association analysis with brain structure and determine X- linked dosage compensation (Aim 2). Third, building on improved genetic knowledge of the brain, we will determine its genetic relationship with neuropsychiatric disorders. We will estimate effects of neuropsychiatric genetic risks on brain structure and how the disorders are mediated by brain structure. (Aim 3). This current project has potential to significantly increase our understanding of the genetic basis of the human brain, to determine shared genetic influences on brain structure and neuropsychiatric disorders, and ultimately to advance therapeutic development for neuropsychiatric disorders.

NIH Research Projects · FY 2025 · 2024-02

Project Summary Heart disease remains the leading cause of mortality in the United States and in the developed world. Arrhythmogenic cardiomyopathy (ACM) in particular is a leading cause of sudden cardiac death in both young people and athletes, remains difficult to diagnose, and has no currently effective treatments. ACM is termed a disease of the desmosome, a cell-cell junctional protein complex critical to cardiomyocyte adhesion, as 40-50% of underlying genetic mutations known to be pathologic for ACM affect a core desmosomal gene component. Importantly, the loss or reduction of any singular desmosomal protein component at the intercalated disc is associated with a “domino effect,” where adjacent desmosomal protein expression is lost, compromising cellular attachment and gap junction electrical conductivity in the heart. Our hypothesis is that the dysregulation of desmosomal protein content homeostasis is directly correlated to ACM disease progression and can be leveraged to identify viable therapeutic targets which could be translated into patient care. Here I will employ both molecular and theoretical approaches to screen for differential transcriptomics and proteomics related to reduction and loss of the core desmosomal component plakophilin-2 (PKP2). In addition to these unbiased approaches, I will leverage human induced pluripotent stem cell (iPSC) and mouse models of PKP2-mutant ACM to characterize candidate regulatory pathways of disease progression. These models each contain distinct splice acceptor site mutations, and have displayed sufficiency to recapitulate disease phenotypes, providing first-of- their-kind platforms to address how RNA alternative splicing and post-transcriptional dysregulation may drive ACM. We further show preliminary studies demonstrating that gene therapy reintroduction of the gap junction protein connexin-43 (Cx43) rescues both early- and late- stage disease phenotypes in spite of the continued absence of the desmosomal core component desmoplakin. Here I will assess whether Cx43 itself may serve as a master regulator of desmosome protein content at the intercalated disc by applying Cx43 gene therapy in the novel context of PKP2 loss, and characterize the broad applicability of this therapeutic approach. My goal for this project is to provide a comprehensive characterization of desmosomal protein regulation across multiple platforms, leveraging predictive systems-level computational molecular models and state-of- the-art RNA binding protein pull-down techniques to identify essential mediators in this signaling network, while assessing the efficacy of Cx43 candidate gene therapy in ACM rescue using physiologically relevant tissue engineered models of human disease and in mice, to establish a generalizable mechanistic model to treat the array of ACM disease presentations in the clinic. Understanding common regulatory pathways controlling desmosomal protein expression at the intercalated disc could be critical to preventing, mitigating, and treating ACM in humans.

NIH Research Projects · FY 2026 · 2024-02

PROJECT SUMMARY/ABSTRACT The mesothelium is an overlooked cell type that is also ubiquitous: it is the most external cell layer that encapsulates all internal organs and lines the body cavities. The best-known canonical function of the mesothelium is to produce lubricant to facilitate organ sliding past each other and the body wall. The mesothelium is composed of a single layer of large and flat squamous epithelial cells that is derived from the mesoderm lineage. In the lung, aside from being the site of asbestos-induced mesothelioma, the role of this fundamental cell layer in lung development and injury repair is poorly understood, and is the focus of this study. Our entry point to studying the mesothelium is Myelin Regulatory Factor (MYRF), a transcription factor. Variants in the MYRF gene have been identified in congenital diaphragmatic hernia (CDH) patients. CDH carries a high mortality rate at birth largely due to respiratory distress. In the lung, MYRF is expressed in the mesothelial cells and alveolar type I cells, two large and flat cell types of the mesenchyme and epithelium, respectively. In mice, while inactivation of Myrf in the lung epithelium led to no discernable phenotypes, inactivation of Myrf in the mesenchyme led to a clear CDH phenotype, including organ herniation, lung hypoplasia and lethality at birth. Later inactivation of Myrf bypassed embryonic lethality, revealing a striking subpleural fibrosis phenotype in the postnatal lung. In the adult, bleomycin treatment of these mutant lungs led to exaggerated injury compared to control, implicating subpleural myofibroblasts as a possible contributor to fibrosis progression. In this study, we will use MYRF as an entry point to investigate mesothelium function as a signaling center in lung growth (Aim 1), as an active barrier in homeostasis (Aim 2), and as an instigator of pathogenesis in lung repair (Aim 3). Our findings will delineate the fundamental role of the mesothelium and its quintessential transcription driver MYRF in lung development, homeostasis, injury and repair.

NIH Research Projects · FY 2026 · 2024-02

Project Summary The excessive accumulation of cholesterol in vascular macrophages is regarded as a leading factor in the development of vascular inflammation, plaque instability and clinical manifestations of atherosclerosis. However, recent advances in single cell analyses and our studies suggest that inflammatory genes are predominantly expressed in macrophages that accumulate cholesterol in the plasma membrane rather than in lipid droplet- laden macrophage foam cells. Cholesterol and many receptors governing inflammatory responses colocalize in the ordered plasma membrane microdomains, often designated as lipid rafts. Upon activation, lipid raft resident and recruited proteins assemble and initiate signaling cascades leading to inflammation. We introduced the term inflammarafts, defined as enlarged, clustered lipid rafts harboring activated receptors and adaptor molecules and serving as a scaffold to organize cellular inflammatory responses. We found inflammarafts to be surprisingly stable in macrophages isolated from atherosclerotic lesions. We further identified apoA-I binding protein (AIBP) as a key regulator of cellular cholesterol metabolism, which can selectively target inflammarafts via its binding to TLR4, without disrupting physiological lipid rafts. In preliminary studies, we found that non-foamy macrophages but not macrophage foam cells expressed inflammarafts, which correlated with atherosclerosis burden. In addition, hypercholesterolemic AIBP deficient mice, which we created, developed exacerbated atherosclerosis. In contrast, the AAV-mediated expression of a secreted form of AIBP in the liver reduced atherosclerosis. In addition, mitochondria in AIBP-deficient cells were morphologically distorted, with a characteristic hyper- branched and cupped shape, typically associated with oxidative stress. The goal of this proposal is to delineate mechanisms governing differential inflammaraft dynamics and related mitochondrial dysfunction in macrophage foam cells and in non-foamy macrophages in atherosclerosis. Specifically, we will test the hypothesis that reversal of inflammarafts in non-foamy macrophages reduces vascular inflammation and is atheroprotective. The hypothesis will be tested using genetic and AAV tools to achieve constitutive, macrophage-specific and/or inducible loss-of-function or gain-of function of cholesterol transporters ABCA1/G1 and/or AIBP and its variant that does not bind TLR4. In addition, we will test the hypothesis that AIBP protects macrophages from mitochondrial dysfunction and oxidative stress in atherosclerosis. We will examine mitochondrial architecture and function in macrophages with loss- and gain-of-function of different forms of AIBP and/or ABCA1/G1. Methods will include serial block-face scanning electron microscopy (EM) and multi-tilt EM tomography, along with measures of bioenergetics by Seahorse. To assess the relevance of our hypotheses and the findings to human cardiovascular disease, we will characterize macrophage inflammarafts and mitochondrial dysfunction in coronary arteries from explanted hearts of patients with heart failure due to atherosclerotic coronary artery disease or due to non-ischemic cardiomyopathy, which undergo heart transplant surgery.

NIH Research Projects · FY 2026 · 2024-02

ABSTRACT People with schizophrenia (PwS) have high rates of cognitive dysfunction and associated disability, especially with aging, and there is a lack of effective treatments to improve cognition in PwS. Obstructive sleep apnea (OSA) is a key modifiable risk factor for cognitive deficits in PwS as it is often underdiagnosed and undertreated. Untreated OSA may cause cognitive decline and dementia, which can be particularly dire in middle-aged and older PwS due to lower cognitive reserve stemming from the onset of illness. The inflammatory mechanisms by which OSA leads to cognitive deficits may intersect with the pathobiology of schizophrenia. Thus, inflammatory biomarkers may be a key surrogate biomarker of OSA-related cognitive deficits. There is a critical unmet need for interventions to improve cognition in PwS. However, to design and power future OSA intervention trials in PwS, the proposed observational naturalistic study is needed to gather relevant data in PwS and a non-psychiatric comparison (NC) group and include objective assessments of OSA, cognitive functioning, and comprehensive inflammatory assessments. The overall objectives of the proposed study are: (1) to assess the contribution of OSA to cognitive impairment, (2) to comprehensively investigate inflammation as a surrogate marker of OSA and cognitive deficits, and (3) to identify key cognitive correlates among PwS. The expected outcome of this proposed project is to lay the groundwork necessary for future OSA treatment trials in PwS. We propose a cross-sectional case-control study of 150 PwS with and without untreated OSA and 150 non- psychiatric comparison subjects with and without OSA, age 40-70 years. The research plan aims to: 1) examine differences in cognitive functioning in PwS and NCs with and without co-morbid OSA; 2) examine the relationships of inflammatory biomarkers with OSA and with cognitive functioning; and 3) explore how general and schizophrenia-related OSA risk factors affect cognitive functioning. The innovative approach of this proposal includes a comprehensive multi-level inflammatory assessment that incorporates systemic biomarkers and gene expression to highlight specific mechanistic pathways and immune cells and the use of mobile cognitive testing that may be more sensitive to OSA-related changes. The team for this proposed project includes expertise in aging in schizophrenia (Ellen Lee, MD), OSA physiology and assessment (Atul Malhotra, MD; Christopher Schmickl, MD, PhD), neurocognitive functioning (Barton Palmer, PhD), mobile cognitive assessments (Raeanne Moore, PhD), psychoneuroimmunology and sleep (Michael Irwin, MD), comprehensive inflammatory assessments (Steve Cole, PhD), and biostatistics (Xin Tu, PhD). Ultimately, this work’s positive impact will be future development of personalized, biologically-based interventions to improve cognition among middle-aged and older PwS.

NIH Research Projects · FY 2026 · 2024-02

PROJECT SUMMARY/ABSTRACT Type 1 diabetes (T1D) is characterized by autoimmune destruction of insulin-producing beta cells in pancreatic islets where there is currently no prevention or cure. The processes driving T1D initiation and progression in the pancreas are poorly understood, and improved understanding of these processes in the pancreas is critical to gain new insight into disease mechanisms and identify novel biomarkers and therapeutic targets. A wealth of data has been generated in human pancreas donors in initiatives supported by the Human Islet Research Network (HIRN) which can be used to address open questions in T1D, yet these data are currently both under- utilized and in formats inaccessible to many researchers which prohibits insights. To address this gap, we have assembled a team of highly accomplished researchers to create a pancreatic knowledge base PanKbase leveraging our expertise in computational biology and data science (Gaulton, Flannick, Voight), type 1 diabetes (Rich, Atkinson, Anderson, Gauton, MacDonald), islet biology (Gloyn, MacDonald), immunology (Anderson, Atkinson), knowledge base engineering (Flannick, Gaulton), engagement and outreach (Burtt, Westley), and rigor and reproducibility (Grethe, Martone). For this proposed project we will in Aim 1 develop a database that comprehensively aggregates and harmonizes data in HIRN repositories and other repositories containing human pancreas data based on our existing CMDGA platform. We will further derive high-quality summary resources from these harmonized data that are of value to the community. In Aim 2 we will implement an analytics library of tools that address impactful questions in T1D by performing statistical modeling and machine learning of data and resources, and that extrapolate knowledge learned from these data into large, independent datasets, as workflows in multiple formats including Github repositories, Jupyter notebooks, WDL pipelines, and pre- computed results. In Aim 3 we will create an open science platform accessible to any user that provides user- friendly interfaces to customizable workflows that address impactful questions, an analysis sandbox to run advanced workflows and pipelines, and APIs and code repositories for full customization, based on the HuGeAMP and Terra platforms. In Aim 4 we will form collaborations and working groups with investigators leading HIRN repositories to develop standards and pair experts with data scientists to integrate domain knowledge into resource creation and machine learning applications using our expertise coordinating consortia. In Aim 5 we will establish engagement and outreach programs for the broader research community to improve data, workflows, and user experience in PanKbase and identify new key questions in the field by applying our extensive expertise in developing outreach for AMP-CMD and the digital platform the (sugar)science. Together this proposal will provide a knowledge base of the pancreas which will enable researchers across all expertise levels to extract novel insight and relationships from data in HIRN and other pancreas donor repositories, which will expedite the development of biomarkers, therapies, and prevention strategies for T1D.

NIH Research Projects · FY 2025 · 2024-01

Project Summary This study seeks to understand early health effects in those exposed to toxins following the Feb. 3, 2023 East Palestine, Ohio (EP) train derailment and subsequent (Feb. 6) controlled burn of toxins. It seeks to assemble a cohort for longitudinal follow-up, securing survey information on exposures, symptoms and health effects and in-depth information on relevant covariates to adequately incorporate potential confounders and effect modifiers. It seeks to assess laboratory tests in a subset, tests previously reported to be affected by EP- relevant toxins. It separately secures phlebotomy samples for archiving as a resource to benefit future investigations. Additionally, it seeks to initiate longitudinal follow-up of symptoms/health outcomes. It then seeks to assess how outcomes relate to EP exposures and to effect modifiers, to identify vulnerabilities and protections. We bring to bear our critical expertise from our longstanding work on chronic health consequences of mixed toxin exposures in Gulf War illness (GWI). We hypothesize that, beyond possible specific effects of EP toxins, shared mitochondrial toxicity mechanisms that transcend specific chemical class will lead to shared health consequences. Our early EP findings already support this – with evidence of GWI-like multisymptom illness and emergence of burn pit-compatible respiratory conditions. Proposed shared mechanisms also have implications for factors that may mitigate development and severity of health problems. Some such factors can be assessed as effect modifiers in analysis. It is our work that documented mitochondrial foundations for GWI – and also affirmed randomized trial benefit of treatment (CoQ10) addressing this. Indeed, a critical benefit of the study is a focus on vulnerable subgroups – which may be strongly affected even when an overall population is not – and protective factors that may guide development of preventions and treatment. Significant progress has already been made in the early stages of this project. A prerecruitment survey has been conducted, identifying scores of EP residents who have expressed their interest in participating. Furthermore, interviews with affected EP residents have been carried out, enabling the development of a comprehensive survey instrument. Importantly, the study has received approval from the UCSD IRB. Moreover, the acquisition of a $15K start-up award from the UCSD Academic Senate has allowed for project pilot testing, troubleshooting, and refinement in advance. These proactive actions not only enhance cost efficiency but also bolsters the project's prospects for success. If granted NIH funding, the study will be poised for a "full speed ahead" launch, building on the foundation established during the jumpstart phase.

NIH Research Projects · FY 2025 · 2024-01

PROJECT SUMMARY/ABSTRACT SCD is a heritable disease, which affects a patient's red blood cells (RBCs). This monogenic disorder is caused by a single nucleotide polymorphism (SNP) within the HBB gene. Despite progress in the treatment of SCD regarding early screenings, prevention of infections, and blood transfusions, the life expectancy for SCD patients is still reduced by about 30 years. Currently, allogeneic hematopoietic stem cell transplantation (HSCT) is the only curative treatment available. Unfortunately, the process is invasive and associated with high risk of graft-versus-host-disease, infection, and infertility. CRISPR-based gene editing is a powerful therapeutic tool for potentially curing a wide variety of diseases. However, low editing efficiency can result in unedited HSPCs outcompeting edited ones, resulting in diminished therapeutic impact. Current methods for maximizing the percentage of edited cells rely on GFP or surface protein sequences to be contained within the homologous donor DNA, complex optical assays and cell sorting to establish cell populations with >85% editing efficiency. We propose to develop a versatile and easy-to-use platform to monitor and optimize the editing efficiency of CRISPR/Cas9 for SCD gene therapy applications. This in vitro platform utilizes multiplex CRISPR-transistors to quantify the amount of a specific sequence within an unamplified genomic DNA sample without the bias associated with the artifacts of library preparation like other sequencing-based methods. The electronic platform provides rapid readout with low sample input requirement. By combining the programmability of RNA-guided CRISPR-Cas technology with the scalability of nano-electronics, the proposed project provides a flexible, and simple to use ex-vivo monitoring solution for a comprehensive and effective gene therapy quality control. We will expand CRISPR-transistor design in Aim 1 to yield a sensor which employs a variety of gRNA designs and RNA-guided Cas nucleases to electronically detect and quantify single nucleotide changes using SCD as a genetic model. In Aim 2, we will scale up this technology design and fabricate a multiplex gFET capable of analyzing a single sample with up to 16 different RNA-guided Cas complexes simultaneously without amplification. In Aim 3, we will utilize this multi-plex CRISPR-transistor platform to rapidly assess the ex-vivo CRISPR/Cas9 HBB editing efficiency of HSPCs from patients with SCD. In addition, we will leverage the flexibility of CRISPR-transistor to establish an ON/OFF-target evaluation of the RNA-guided Cas nuclease in the presence of chromatin structures and compare against existing technologies for off- target screening, like CIRCLE-seq and genome wide. This project will demonstrate a facile, general platform for quantification of editing efficiency that has the potential to shorten the processing time, reducing sample and complexity necessary to ensure high quality of ex-vivo gene therapy.

NIH Research Projects · FY 2025 · 2024-01

PROJECT SUMMARY Fungal infections impact hundreds of millions of people and kill >1.5 million individuals annually. The recent emergence of resistance against all three major classes of antifungals in pathogens such as Candida auris presents a grave threat to human health. Indeed, with mortality rates ~60%, C. auris is now classified as a “superbug” by the Centers for Disease Control (CDC). This program will address this therapeutic need via the discovery of small molecules that inhibit novel Cu-only superoxide dismutases (SODs). During infection, the host can produce a toxic burst of superoxide (O2-•) to attack microbes. However, fungal pathogens produce extracellular SODs that disproportionate O2-•. The co-I (Culotta, JHU) has discovered a new class of extracellular, Cu-dependent SOD metalloenzymes that are unique to fungi, distinct from human SODs, and essential for the virulence of widespread fungal pathogens. These ‘Cu-only’ SODs are highly conserved in fungal kingdom and our data suggests they are a promising, untapped antifungal targets. This exploratory effort (R21) will identify inhibitors of fungal Cu-only SODs using an innovative approach to metalloenzyme inhibitor discovery developed in the laboratory of the PI (Cohen, UCSD). This approach utilizes metalloenzyme fragment-based drug discovery (mFBDD) and does not involve removal of the metal ion from the enzyme active site. The laboratory of the PI has a strong track record of identifying first- or best-in-class inhibitors of metalloenzymes by using mFBDD. In this effort, we will focus on Cu-only SOD5 from the fungal pathogen C. albicans, followed by validation of our approach with Cu-only SOD4 from drug resistant C. auris. Promising MBP hits will be developed in a hit-to-lead effort into inhibitors that will be screened for activity against fungal infections in vitro and in vivo. Ultimately, this program will discover first-in-class inhibitors of fungal Cu-only SODs and demonstrate their utility as a novel therapeutic target against these life-threatening infections.

NIH Research Projects · FY 2025 · 2024-01

PROJECT SUMMARY/ABSTRACT Despite rising incidence and prevalence of inflammatory bowel diseases (IBD), including Crohn’s disease and ulcerative colitis, in Hispanic population in the United States, there is limited understanding of the natural history and treatment outcomes for this vulnerable population, who are vastly underrepresented in clinical trials. The principal investigator’s (PI) long-term goal is to inform evidence-based management of IBD in Hispanic population, using large-scale epidemiologic studies and novel comparative effectiveness research using real world data. The overall objectives of this proposal are to understand patterns and drivers of disease and treatment outcomes in Hispanic patients with IBD, specifically focusing on social and structural determinants (SDoH) and biological determinants of health. The central hypothesis is that Hispanic patients experience a complicated IBD course with high disease burden and inferior treatment outcomes, driven primarily by adverse SDoH, rather than biological differences in treatment effectiveness. The rationale for this proposal is that a comprehensive epidemiological assessment of the natural history, social and biological predictors of outcomes and real-world comparative effectiveness and safety of targeted immunomodulator (TIM) therapies in Hispanic patients with IBD will directly and decisively inform management of IBD in a timely manner in this population just as the disease is at an inflection point in the US. The central hypothesis will be tested by pursuing three specific aims: (1) characterize natural history and treatment outcomes, and compare the effectiveness and safety of TIMs, in Hispanic patients with IBD using large-scale epidemiologic studies and novel target trial emulation methodology; (2) understand impact of area-level SDoH and patient-level social risk factors on adverse disease and treatment outcomes in Hispanic patients; and (3) understand the impact of specific genetic (HLA-DQA1*05 variants) and tissue transcriptomic (oncostatin M) factors on treatment outcomes with TIMs in Hispanic patients with IBD. The context for this proposal is a contemporary, electronic health record-based registry of patients with IBD seen at 7 large health systems in California with ~14,000 Hispanic patients that the investigator team have developed, a large commercial insurance claims database (OptumLabs Data Warehouse, ~18,000 Hispanic patients with IBD), and robust infrastructure of an established Cedars Genetics Research Center and biorepositories at UCSD. These large cohorts allow for efficient and cost-effective large-scale analysis in this health disparity population. The research proposed in this application is innovative, utilizing tools of applied clinical informatics, innovative causal inference methodology and combined evaluation of biological and non-biological determinants of health, to conduct the largest study on Hispanic patients with IBD in the United States. The proposed research is significant because it is expected to fill a key evidence gap in understanding the natural history and treatment outcomes in Hispanic patients with IBD, providing timely information on evidence-based management.

NIH Research Projects · FY 2026 · 2024-01

Project Summary Persistent pain secondary to tissue and nerve injury involves key roles for DRG neurons, macrophages, and spinal microglia. Therapies targeting single components of this tripartite pain axis have not proven clinically efficacious, suggesting a strategy is needed that addresses all three components in concert. We have exciting new findings that suggest one such therapeutic strategy may be to target the subset of cellular membrane cholesterol rich lipid rafts that contain Toll-like receptor 4 (TLR4-rafts). Membrane lipid rafts are a fundamental organizational nidus in all cells for numerous membrane channels, receptors and enzymes that regulate reactivity and excitability. The TLR4-raft subtype is special as these are specifically localized in the three key cellular elements regulating the excitability of nociceptive signaling. Following tissue inflammation or nerve injury, TLR4rafts transform from small diffuse labile membrane structures into markedly enlarged and persistent complexes supporting the formation of homo and hetero dimers of several excitatory channels and receptors, underpinning the transition from an acute to a persistent pain phenotype and to establishing a “primed state” after an initial system activation. Specific disruption of these neuraxial TLR4-rafts has profound effects upon injury induced pain behavior. While we have gained insight into mechanisms by which TLR4-rafts regulate microglial function, we know little about the mechanisms by which TLR4-rafts regulate excitability of DRG neurons and macrophages. To address this knowledge gap, we propose three specific aims: i) Define time dependent changes in TLR4-rafts and pain behavior induced by trauma, inflammatory and neuropathic pain, and the effects of targeted TLR4-raft disruption on pain behavior in these models; ii) Determine baseline molecular architecture of DRG neuronal and macrophage TLR4-rafts and then how this architecture and function is altered with tissue trauma, inflammation and nerve injury; and iii) Define role of DRG neuronal TLR4-raft localized receptors in regulating excitatory phenotype in mouse, rat and human DRG neurons and effects of TLR4-raft disruption in modifying this excitatory phenotype. This is a large multi-PI / multi-center study that defines mechanisms by which neuraxial TLR4-rafts affect multiple pain-related signaling processes, integrated pain behavior and the molecular anatomy underpinning this signaling and the degree to which these mechanisms are conserved between rodents and humans, across differing pain phenotypes. This work will have a sustained impact on understanding the neurobiology of a largely unexplored cellular element regulating post injury afferent excitability. In sum, this proposal centers on the unifying thesis that neuraxial TLR4-rafts are a common facilitatory element of the persistent pain facilitated states observed following tissue and nerve injury and that this effect is mediated by TLR4 rafts not only on DRG macrophages, and spinal microglia but unexpectedly by the TLR4-rafts expressed on the DRG nociceptor.

NIH Research Projects · FY 2026 · 2024-01

Abstract Maintaining the fidelity of the cell’s transcriptome is critical to a cell’s viability and biological function. As such, there are many mechanisms the cell has in order to detect and degrade aberrant RNA transcripts. Dysfunction in these mechanisms can lead to physiological issues in the cell’s function on a micro-level and if unchecked, can lead to disease states affecting the whole organism. Therefore, it is critical that we understand these mechanisms of RNA quality control. In recent years, RNA modifications have emerged as key regulators of RNA functions. One of these modifications is a 3’ end modification found in both coding and non-coding RNAs: the 2’,3’-cyclic phosphate. The 2’,3’-cyclic phosphate is involved in many important biological pathways; however, despite the importance of these cyclic phosphate intermediates in RNA processing and quality control, the metabolism of this modification is still poorly understood. Recently, two developments have emerged that now allow us to approach an understanding of the metabolism of the 2’,3’-cyclic phosphate: identification of two proteins, Angel1 and Angel2, as cyclic phosphatases and the development of a 2’,3’-cyclic phosphate-based ligation assay which utilizes tRNA ligase and makes it possible to identify RNAs modified with a 2’,3’-cyclic phosphate. While the new information regarding both Angel1’s and Angel2’s activities as cyclic phosphatases is exciting, there is still a paucity of information regarding the biological role that each play in 2’,3’-cyclic phosphate metabolism. My research in the Lykke-Andersen lab seeks to resolve these issues by taking advantage of the tRNA-ligase based capture of RNAs terminating in 2’,3’-cyclic phosphate. In specific aim 1, I will define Angel1’s biological role in the ribosome-associated quality control pathway (RQC). Previous studies conducted by the Lykke-Andersen lab reveal that Angel1 associates with members of the RQC and eIF4E and its catalytic activity acts as a rate-limiting factor for decay of RQC substrate mRNAs. Thus, I will identify where in the RQC Angel1 is acting as a cyclic phosphatase as well as define the importance of its interaction with and potential action as an inhibitor of eIF4E. Additionally, through my second aim I will identify the biological role of Angel2 in RNA processing. Previous studies have shown that overexpression of Angel2 causes accumulation of tRNA ligase substrates. Thus, through this specific aim, I will probe for Angel2’s activity as a potential inhibitor of tRNA ligase. I will once again take advantage of the tRNA ligase-based capture assay to verify targets of Angel2 in the tRNA ligase pathway. By identifying and defining the biological roles of the Angel1 and Angel2 cyclic phosphatase, the research proposed in this fellowship will work to unravel the previously understudied role that the 2’,3’-cyclic phosphate has in regulating the cell’s transcriptome.

NIH Research Projects · FY 2026 · 2024-01

Project Summary High titers of anti-NMDAR1 IgG autoantibodies in brain cause anti-NMDAR1 encephalitis that exhibits psychosis, impaired memory, and many other psychiatric symptoms in addition to neurological symptoms. We found that blood circulating anti-NMDAR1 IgG autoantibodies are sufficient to impair spatial working memory (p=2.02E-08, power: 1) with a large effect size (d=2.3) in the integrity of the blood-brain barriers (BBB). Low titers of natural anti-NMDAR1 autoantibodies, predominantly IgM or IgA isotype, were reported in the blood of ~5-10% of the general human population and psychiatric patients. It is unknown whether chronic presence of these natural anti-NMDAR1 autoantibodies may impact human cognitive functions. After quantifying the levels of plasma natural anti-NMDAR1 autoantibodies in 143 Marines, we found that Marines with higher levels of natural anti-NMDAR1 autoantibodies have significantly better cognitive functions in both Continuous Performance Test (reaction time in CPT, p=0.00029) and Short Letter N-Back test (reaction time in SLNB, p=0.00091) than Marines with lower levels of the autoantibodies. Consistent with the pro-cognition, high levels of natural anti-NMDAR1 autoantibodies protect (p=0.048) from the development of TBI-associated symptoms. Anti-NMDAR1 autoantibodies had been reported to provide protections against neuronal excitotoxicity caused by excessive glutamate in neurological diseases. Therefore, it appears that blood circulating anti-NMDAR1 autoantibodies may have two opposing effects. Synaptic NMDARs are essential for cognitive function and their activation promotes neuronal survival, whereas activation of extrasynaptic NMDARs is responsible for neuronal excitotoxicity. Unlike small IgG, IgM antibodies (diameter of ~30 nm) are physically too large to enter synaptic cleft (width: 20-30 nm) to suppress synaptic NMDAR-mediated neurotransmission but are restricted to bind extrasynaptic NMDARs and therefore specifically inhibit neuronal excitotoxicity. Hence, we hypothesize that blood circulating anti-NMDAR1 IgM autoantibodies are both neuroprotective and pro-cognitive, whereas blood circulating anti-NMDAR1 IgG and IgA autoantibodies are detrimental to cognitive functions. We propose two specific aims for this 3-year R01 application. In Aim 1, we will validate pro-cognitive and neuroprotective functions of pre-existing IgM anti-NMDAR1 autoantibodies by quantifying plasma anti-NMDAR1 IgM, IgA, IgG autoantibodies, respectively, in humans. In Aim 2, we will cross-species validate pro-cognition and neuroprotection of IgM anti-NMDAR1 autoantibodies by generating mice carrying either IgM or (IgG and IgA) only anti-NMDAR1 autoantibodies. Immunogold electron microscopy will be used to validate that IgM anti- NMDAR1 autoantibodies can only bind extrasynaptic NMDAR1 but not synaptic NMDAR1 in brain. Success of the proposed studies will open up a new avenue for the development of therapeutic IgM anti-NMDAR1 autoantibodies that can promote cognitive functions and protect from neuronal excitotoxicity in many neurological diseases and psychiatric disorders including TBI, PTSD, and schizophrenia.

NIH Research Projects · FY 2025 · 2024-01

PROJECT SUMMARY Cardiovascular disease is a leading cause of mortality and morbidity worldwide. Currently, echocardiography (i.e., ultrasound imaging of the heart) is the standard-of-care for optimal assessment and measurement of patient heart function. Both transthoracic and transesophageal echocardiography are commonly used in hospitalized patients, but they have limitations. Transthoracic echocardiography is non-invasive but data is only collected while the probe is manually positioned on the patient's chest, which may result in missing important changes in a patient's clinical course and windows for potential intervention. Transesophageal echocardiography provides real-time measurement of different indices of cardiac function, but requires general anesthesia or deep sedation. To address these limitations, this proposed project aims to develop a wearable ultrasonic imager for continuous, non-invasive monitoring of cardiac functions in real-time via a transthoracic approach. Based on our previous work in wearable ultrasound blood pressure and flow sensors, the proposed device will utilize a stretchable ultrasonic device with reduced transducer element pitch, enabled by a multilayered, highly stretchable and highly integrated liquid metal electrode. The small pitch allows high transducer frequency and thus enhanced imaging performance. The device will be designed to monitor the heart in two orthogonal planes simultaneously and will use associated algorithms for B-mode imaging. To map the transducer locations on the dynamic human body, we will use shape sensing multicore optical fibers to acquire the exact coordinates of each transducer and use these location data for beamforming . We will use the wide-beam compounding transmission strategy, which can enhance the signal-to-noise ratio of ultrasound signals and therefore overall imaging performance of the device. The results will be benchmarked against those from a clinical ultrasound probe. We will construct a deep learning model based on Fully Convolutional Networks to process the acquired cardiac images automatically. We will extract the left ventricular wall motion waveforms and left ventricular volume, from which critical indices, such as stroke volume, ejection fraction, and cardiac output, can be generated continuously. The performance of the device will be evaluated on a commercial phantom and tested on human subjects. After verifying the safety of the proposed device, we will use it to collect the cardiac images from 138 healthy and patient subjects. The accuracy of the results collected by the proposed device will be compared and analyzed statistically with that obtained by a clinical-grade ultrasound machine. Our team is composed of highly interdisciplinary expertise that is required for the success of the proposed research. If successful, this technology has the potential to significantly improve cardiovascular monitoring and open new use cases for monitoring other critical visceral organ, which will exert a sustained and powerful impact on many NIH-related research areas s.

NIH Research Projects · FY 2026 · 2024-01

PROJECT SUMMARY/ABSTRACT The objectives of this K08 proposal are to foster the development of critical scientific and professional skills that will allow the candidate, Dr. Mona Alotaibi, to advance toward her goal of becoming an independent investigator; and to investigate the role of metabolic dysregulations and bioactive molecular markers of endothelial dysfunction in modulating pulmonary arterial hypertension (PAH) progression in human studies and experimental models. This will be achieved through a comprehensive training plan and extensive laboratory experience and course work, which will provide Dr. Alotaibi additional expertise in experimental design, laboratory procedures, large data handling and laboratory leadership skills. Pulmonary arterial hypertension is a rare but life-threatening condition, that if left untreated leads to right ventricular failure and death. Despite advances in therapeutics, PAH mortality and morbidity remains unacceptably high, motivating efforts to identify circulating biomarkers and mechanistic targets that could improve tailored treatment approaches and outcomes. Central to PAH pathobiology is endothelial dysfunction governed by imbalance between endothelial derived relaxing and contracting factors. These factors include circulating small bioactive lipid mediators, eicosanoids known to exhibit vasoactive properties including vasocontraction or vasodilation in context dependent matter. Sensitive methods for comprehensively detecting and quantifying distinct eicosanoid species have been limited with prior studies in PAH focusing mainly on cyclooxygenase pathway. We have shown that distinct lipoxygenase (LOX)-eicosanoid dysregulations exist in animal models with severe pulmonary hypertension and these metabolites associated with mortality and worse clinical outcomes in human. The overall goal of this proposal is to utilize our newly developed mass spectrometry approaches together with comprehensive, complementary study design that include human biosamples, PH murine models and cell culture experiments to provide an unprecedented view into the role and mechanism of LOX-eicosanoid derangements in PAH. We hypothesize that endothelial LOX intermediates play an important role in the development and progression of PAH through sustained pulmonary vasoconstriction and concentric pulmonary vascular remodeling, and particularly via activation of mechano- sensitive and receptor-operated cation channels in both pulmonary arterial smooth muscle and endothelial cells. We will test this hypothesis in three Specific Aims: 1) To determine the relation of LOX-derived eicosanoids with PAH disease progression and outcomes; 2) To examine whether LOX-HETEs induce spontaneous PAH or enhance PH in animal models; 3) To examine whether LOX-HETEs activate or upregulate mechanosensitive, or receptor operated cation channels in pulmonary arterial vasculature. Successful implementation of these Specific Aims will provide a rigorous training program for Dr. Alotaibi, laying the groundwork for R01 submission, and will allow us to answer a fundamentally important question about the role of LOX-eicosanoids as specific biomarkers for disease risk and target for future interventions.

NSF Awards · FY 2024 · 2024-01

Terabit-per-second data rates will enable next-generation wireless cellular applications, including extended reality, holography, haptic feedback, and wireless cognition. These applications provide, in part, the means to create an immersive experience for work, education, and healthcare which helps to bridge the gap in experience between in-person interaction and video telephony. Achieving the high data rates, though, requires going to higher radio frequency bands than are currently used for cellular communications. In the last five years, cellular communication has embraced the lower millimeter wave spectrum, which refers to radio frequencies from about 25 GHz to 100 GHz. Indeed, millimeter wave communication has become one of the defining features of fifth generation cellular communication systems. Going to terabit-per-second data rates will require higher bandwidths that are available above 100 GHz, in what is known as the sub-THz band. This collaborative project establishes fundamentals that will help realize sub-THz communication and drive the future of wireless technology. It develops new hardware and algorithms that help to create the required high data rate communication links to serve the applications highlighted above. For example, it develops technology that helps sub-THz communication signals better go around obstacles, by instrumenting the environment with smart reflective surfaces and reconfigurable antenna arrays. The results of the project will contribute to the development of new wireless technologies that are beneficial for personal communication, safety applications and industrial deployments. Industry impact and technology transfer will occur through frequent communication with the partners of the sixth generation North Carolina program. The project will lead to more undergraduate and graduate students with expertise on new and important technologies for wireless communications. Sub-THz Augmented Routing and Transmission for 6G is a collaboration among experts in wireless communications at North Carolina State University (NC State) and Yonsei University (YSU). It addresses the design of reflective surfaces and reconfigurable arrays for multiple-input multiple-output (MIMO) communication at sub-THz frequencies. It devises methods for configuring the beams formed or reflected from those arrays in a way that routes around obstacles. It creates algorithms that exploit new levels of reconfigurability in the arrays to obtain higher throughput and more robust communications. Finally, it results in the creation of joint real-time hardware (H/W) and software (S/W) testbeds for sub-THz communications. The uniqueness of this project lies in the multi-domain approach for improving sub-THz communications. The intellectual merit will occur in several directions. (a) Intelligent reflective surfaces constructed from state-of-the-art meta-materials / meta-devices. (b) Reconfigurable antenna arrays with adaptable structures that are mechanically and electrically controlled. (c) Directional-beam-based initial access and beam routing algorithms that leverage channel map information. (d) Models of reconfigurable antennas arrays and performance limits of those arrays. (e) Algorithms that leverage true time delays to reconfigure those arrays to support high bandwidths. (f) A suite of evaluation scenarios that test the developed hardware and algorithms. The immediate impact will be to identify the most relevant approaches for enabling large arrays for communication and reflective applications, as well as algorithms that leverage those arrays to enhance communication at sub-THz frequencies. The long-term impact will be in the development and realization of sub-THz communication as part of 6G wireless communications. 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 2026 · 2024-01

PROJECT SUMMARY Glaucoma is a neurodegenerative disease defined by the injury of retinal ganglion cell (RGC) axons at the optic nerve head, leading to cell death and irreversible vision loss. Current therapies center around lowering intraocular pressure (IOP) although this can be challenging in some patients. In order to advance towards a neuroprotective strategy that could complement IOP-lowering, we have been identifying potential neuroprotective targets in primary RGCs using high- throughput functional genomic screening. We initially identified dual leucine zipper kinase (DLK) and its paralog, leucine zipper kinase (LZK) as being key upstream activators of JUN N-terminal kinase (JNK) and axon injury signaling. We showed that DLK/LZK inhibition provides robust and durable protection to RGCs in multiple rodent models of optic neuropathy and, more recently, validated the survival effect in a nonhuman primate model of glaucoma. Despite their central role as neuronal messengers of axonal injury, little is known about the regulation of DLK/LZK. Moreover, inhibition of DLK/LZK prevents axon regeneration and has only modest effects on distal axon degeneration. Using chemical genetic- and clustered regularly interspaced short palindromic repeat (CRISPR)-based screens, we have identified two subgroups of Sterile 20 (STE20) kinases, including thousand and one amino acid (TAO) and germinal center kinase IV (GCK-IV) kinases which seem to regulate the interpretation and duration of the DLK/LZK axon injury signal. Moreover, inhibition increases rather than decreases axon regeneration and has a much greater impact on distal axonal degeneration. Based on insights from cancer biology, we recognized that similar STE20 kinases converge to regulate Hippo signaling, a developmental growth pathway not previously linked to axon injury signaling. We show that inhibition of the central kinases of Hippo signaling, large tumor suppressor (LATS) 1 and 2, robustly protects primary mouse RGCs and we attempt to demonstrate that the canonical Hippo transcription factor, transcriptional coactivator with PDZ-binding motif (TAZ) modulates DLK/LZK signaling by affecting JUN-dependent transcription. The central theme of this proposal is that combinatorial inhibition of STE20 kinases can be leveraged to generate robust somal and axonal protection combined with long-distance, sustained axon regeneration and that a key molecular mechanism involves Hippo signaling. In Specific Aim 1 (SA1), we focus on the role of STE20 kinases in axon degeneration and evaluate the potential for pancellular and functional RGC protection in a rat model of glaucoma. For this, we built a novel all-in-one adeno-associated virus (AAV)/CRISPR reagent capable of disrupting multiple kinases. In SA2, we test the role of combinatorial STE20 kinase inhibition in axon regeneration. We also use transcriptomic assays to dissect the mechanism by which DLK/LZK and STE20 kinase inhibition differs with respect to axon regeneration. Finally, in SA3, we explore the role of Hippo signaling in both mouse and human RGC survival and its link to STE20 and DLK/LZK signaling. Together, we anticipate this proposal will lead to a robust RGC neuroprotective strategy for combined axonal and somal preservation and a deeper understanding of the key axon injury pathway in RGCs.

NSF Awards · FY 2024 · 2024-01

Cellular communication systems continue to incorporate new multiple-antenna technologies. In particular, third, fourth and fifth generation cellular systems saw advancements in the use of multiple antennas at the base-station infrastructure and multiple antennas in the devices. A main application of these antennas was to support multiple-input multiple-output (MIMO) communication, which is known to increase spectral efficiency and thus the data rates that can be achieved by devices in a given bandwidth. The numbers of antennas and the ways the antennas are used can vary across device models even from the same manufacturer. At the same time, the types of devices supported in cellular systems is growing beyond smartphones to include other highly mobile platforms like aerial vehicles, automobiles, and robots. The differences in the hardware between devices, coupled with the high device mobility, makes it challenging to configure the antennas to provide MIMO communication with the highest performance. This project develops machine learning-inspired solutions to empower devices to learn optimal configurations collaboratively. System-wide Operation via Learning In-device Dissimilarities is a cooperation among experts in wireless communications at North Carolina State University (NC State) and Tampere University (TAU). The overall objective of the proposal is to employ machine-learning-assisted collaborative solutions for MIMO beam prediction and codebook optimization in a large-scale dynamic system. The key challenge of such networks is the extreme diversity of the devices’ hardware (e.g., antenna designs and configurations). The existing distributed ML approaches do not explicitly include this type of client heterogeneity and do not fully support the temporal and spatial heterogeneity of data, network resources, and deployments. The project team will develop a novel integrated-learning and wireless-networking framework, which will enable the design and optimization of advanced MIMO beam-management solutions specifically tailored to the highly diverse and dynamic system. This project will result in new algorithms for collaborative device-centric beam management for 5G+/pre-6G MIMO communications in non-stationary environments with highly mobile and heterogeneous agents. The specific technical contributions occur in several directions: (a) Distributed user-centric learning for optimizing codebook-based MIMO communications; (b) Novel representation of device heterogeneity in an ML-friendly way; and (c) Network-resource optimization to facilitate distributed learning. The immediate impact will be improved communication efficiency in 5G+/pre-6G networks. The longer-term impact will be the establishment of the core principles for designing fast and reliable methods of distributed ML training deployed over wireless systems with diverse hardware and resources. 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 2026 · 2024-01

ABSTRACT Current therapeutics, including the biologics, improve management of arthritic joints but often do not adequately address associated pain, suggesting multiple mechanisms. Delivery of antibodies/immune complexes in serum from a K/BxN mouse to a normal mouse yields a persistent, but reversible joint inflammation accompanied by early onset pain that persists long after resolution of inflammation. In the inflammatory phase, allodynia and the conditioned place preference respond to anti-inflammatory drugs and drugs that block spinal sensitization, while in the post-inflammatory phase, the pain phenotype responds to only to the latter agents. This profile is accompanied by changes in joint innervation, DRG and dorsal horn biology, revealing a transition over weeks in both sexes from an inflammatory to a polyneuropathic pain phenotype. The origin of this ongoing traffic and the appearance of a post-inflammatory pain phase in the preclinical rodent model reflects a major change in the phenotypic expression of channels and receptors within the DRG. Among the changes generated by inflammation and nerve injury are concurrent, time-variant, increases in nociceptive afferent expression of sodium channels (e.g., NaV 1.3,1.7,1.8,1.9) and down regulation of potassium channels (e.g., Kv1.4), changes which yield increased afferent excitability and ectopic activity. Here we will utilize the CRISPR-dCas9 system coupled with transcriptional activation domains or transcriptional repression domains to enable either activation or repression of the above genes epigenetically to systematically study their roles in modulating pain states. We have already extensively characterized the efficacy, duration, and safety profiles of epigenetic repression of NaV1.7 in DRG primary afferents via intrathecal (IT) AAV9 (CRISPR)-dCas9 delivery. Our work has shown, in vitro and in vivo after intrathecal delivery, titer dependent reduction in DRG NaV1.7 mRNA and allodynia in murine inflammatory and polyneuropathic pain models. We propose now, using this IT AAV CRISPR-dCas9 epigenome modifying platform to focus in male and female K/BxN mice on the inflammatory and poly-neuropathic joint pain component of repressing DRG NaV 1.3, 1.7,1.8,1.9 and increasing expression of Kv 1.4-channels. We will characterize these modifications in K/BxN and K/BxN- IT AAV9 (CRISPR)-dCas9 treated male and female mice on i) DRG target expression using RNA seq/RNA-FISH; ii) K/BxN driven allodynia / aversiveness (using conditioned place preference); iii) adverse event profile; iv) ectopic activity and membrane excitability (patch clamping) in primary DRG neuronal cell cultures and v) in vivo basal and evoked afferent substance P release. These aims provide mechanistic insights into the role of. these DRG-afferent channel populations in the inflammatory and post inflammatory arthritic pain phenotype accounting for the ongoing and evoked pain phenotype. These insights into regulation of multiple DRG channels will also guide improved engineering of potential therapeutic interventions.

NSF Awards · FY 2024 · 2024-01

Future wireless networks will integrate sensing and communication functions. The sensing capabilities can come from the sensors of the devices in the network. The radio communication signal itself can also be used for sensing, especially when operating at high carrier frequencies, with high bandwidths and large antenna arrays. Examples are cellular networks supporting automated vehicles or industrial robots equipped with radar, lidar or cameras. This project advances the fundamental technologies, from a hardware and software perspective, to enable integrated sensing, learning and communication (ISLAC) wireless networks, capable of obtaining and communicating accurate information about the environment, relevant for the users and for the network operation itself. The sensing accuracy provided by these technologies is critical, both to support a given use case, and to enhance the resilience of the network, enabling a fast respond to failures or mis-configurations. The outcomes of this project will improve cellular connectivity for people and devices, by providing higher data rates, with more reliability, in a way that embraces machine learning and the wealth of sensor data also being deployed in such networks. To establish the potential of integrated sensing, learning and communication networks to enhance their own resilience, this project develops: (a) the core enabling technologies for ISLAC networks, including hardware and signal processing algorithms for joint sensing and communications; (b) mathematical tools to measure resilience accounting for the particular propagation features and network operation at millimeter wave (mmWave) and sub-Terahertz (sub-THz) bands; (c) learning strategies that exploit sensing information to improve network adaptability; and (d) user-centric algorithms that exploit sensing information to improve network autonomy and increase. The developed strategies will be evaluated using a framework based on a combination of ray tracing, experimental measurements and models that mix the digital, physical, and virtual worlds. This methodology will enable the evaluation of the developed technologies in several relevant scenarios supported by cellular networks, including automated vehicles, automated factories, and immersive reality settings. 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 · 2024-01

SUMMARY/ABSTRACT Relapsed pediatric T-cell acute lymphoblastic leukemia (T-ALL) is often refractory to conventional therapy and is associated with a dismal survival rate of less than 25%. Thus, the development of novel therapies for relapsed T-ALL represents an urgent unmet medical need in children. Adenosine deaminase acting on RNA 1 (ADAR1) mediates the conversion of adenosine (A) to inosine (I) in the mammalian transcriptome. Malignant ADAR1 activation and over-editing was reported in extensively reported in adult cancer type. As a result, there is an intense interest to understand the mechanisms by which ADAR1-directed A-to-I RNA editing regulates gene expression, and how these editing events influence tumorigenesis. However, the global landscape of A-to-I RNA editing in pediatric cancer has not been systematically characterized. Fulfilling this knowledge gap will allow mechanistic and functional studies of these RNA editing modifications that can ultimately aid in formulating new therapeutic and preventive strategies. We discovered that 70% of T-ALL patients exhibit high expression of ADAR1, and this is associated with a significantly worse clinical outcome. Our RNA editing analysis of over 260 T-ALL patients revealed wide-spread A-to-I RNA mutations in the relapsed T-ALL cohort. Strikingly, we found that inhibiting ADAR1 impairs malignant T-ALL progenitor propogation. These discoveries need to be validated in a large cohort of T-ALL patients to further delineate the critical RNA editing “mutations” associated with relapse. The overall objective of this study is to leverage on the large sample size in Kids First Program to fully understand the heterogenous RNA editing landscape in T-ALL pathogenesis. Our central hypothesis that ADAR1 promotes unique A-to-I RNA editing changes in T-ALL which drives disease relapse and therapeutic resistance. In this proposal, we will 1) define the ADAR1-controlled A-to-I RNA editing landscape in 1,304 T-ALL patients by combining the Kids First and NCI TARGET datasets, 2) identify novel RNA editing events that predict disease outcome, and 3) compare the RNA editing landscapes in various molecular subtypes to reveal any critical link between RNA editing and genetic background. Our preliminary studies and the proposed work together will provide the first complete A-to-I RNA editing landscape in T-ALL that will be shared within the pediatric research community. In addition, we will provide new insights into the mechanisms and functions of ADAR1 in T-ALL pathogenesis and will substantially advance our understanding of the epitranscriptomic regulation in pediatric malignancies. The success of this work will reveal a comprehensive evaluation of the RNA editing network that provides advantages for leukemia expansion, and RNA hyper-editing events which may serve as an attractive therapeutic target.

NIH Research Projects · FY 2025 · 2024-01

Abstract Heart, Lung, Blood, and Sleep (HLBS) conditions such as heart failure, COPD, and pneumonia are among the most common causes of hospitalizations. Many of such hospitalizations are thought to be avoidable with early recognition and intervention. Today, patient-reported symptoms represent the primary means of detecting impending hospitalizations, but because symptoms are late indicators of disease, this results in days to weeks of delay in receiving care. We developed a non-contact adherence-independent longitudinal bed-sensing platform to detect early physiologic signs of impending hospitalizations before patients recognize or self-report symptoms. Preliminary results from our bed-based mechanical sensors suggest that the technology can learn patient-specific baselines during clinical stability and can recognize excursions from baseline in the early stages of developing illness. Here, we propose a milestone-based project aimed at collecting human training datasets and developing generalizable models that can recognize impending hospitalizations in the home with a focus on the underrepresented populations of San Diego and Imperial Valley counties. Doing so will encourage utilization and adoption across HLBS disease verticals and patient subpopulations.