University Of Illinois At Chicago

NSF Awards · FY 2025 · 2025-06

This award supports the participation of US-based graduate students and postdoctoral researchers to a conference titled “Singularities in Algebra and Geometry” being held June 15-21, 2025, in Guanajuato, Mexico. The conference will take place on the premises of Centro de Investigación en Matemáticas in Guanajuato, which has a long tradition of successful international events. Algebraic Geometry and Commutative Algebra are among the oldest yet most vibrant branches of mathematics, and have important applications throughout the sciences in light of the rich structure and computational elegance of polynomial equations. The conference “Singularities in Algebra and Geometry” will bring together leading experts in these and related areas, fostering an exchange of ideas and methodologies and further enriching this dynamic field. This conference will also include substantial mentoring and training for young researchers, helping to stimulate collaboration and cultivate peer-support networks. This will enhance retention, improve future job opportunities, and foster their future success in the STEM disciplines. The specific focus of the conference is on recent advances in Commutative Algebra, Algebraic Geometry, and related areas including Arithmetic Geometry and Noncommutative Algebra, with a common theme being the study of singularities. Over the past decade, these fields have experienced spectacular advances due to the cross-fertilization of techniques and perspectives. These developments have also made significant impacts in other areas, including cluster algebras and number theory, while at the same time borrowing heavily from insights in those fields. More information can be found on the conference website: https://sites.google.com/view/singularitiesalggeom2025. 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 · 2025-06

Project Summary/Abstract: (30 lines of text maximum) Innate lymphoid cells (ILC) are the innate counterparts of CD4+ T helper cells and are particularly abundant in mucosal tissues where they contribute to tissue immunosurveillance, immunoregulation, tissue repair, and the maintenance of homeostasis or tissue inflammation. Based on transcriptional regulation and cytokine profiles, three distinct types of ILCs have been proposed and identified: T-bet+ ILC1s that produce IFNg, GATA3+ ILC2s that secrete IL-5 and IL-13, and RORgt+ ILC3s that release IL-22 and IL-17A/F. However, ILC numbers and functions are believed to vary in a context-dependent fashion such that single-cell RNA-Seq and flow cytometry- based analyses including a range of markers have revealed high levels of ILC heterogeneity arising due to the plasticity of these cell populations. However, the molecular mechanisms and environmental cues governing this plasticity remain to be elucidated, in part due to a lack of appropriate animal models. We thus generated ILC3- specific reporter and Cre recombinase-expressing mice in which we identified GATA3+ exILC3s which were previously ILC3s but has converted into the ILC2s. Using this model, the goals of this study are to examine (1) the mechanistic basis for transdifferentiation between ILC3s and ILC2s and (2) the roles that these plastic ILCs play in vivo. To accomplish these goals, we have formulated two specific aims. In Aim 1, we seek to understand the environmental factors and mechanisms that regulate the maintenance of ILC3 identity and plasticity. Using ex vivo and in vivo models with fate mapping approaches, we will evaluate the environmental cues such as gut inflammation and gut damage associated with transdifferentiation and will elucidate the physiological roles of transdifferentiated cells during gut inflammation. By gathering phenotypic, transcriptomic, and chromatin accessibility data, we will capture the functional status and transdifferentiation potential of cells with distinct identities. While our supporting data clearly indicate that ILC3s can undergo conversion into ILC2s, when, where, and how ILC3s actively convert into ILC2s remain to be established. In Aim 2, we thus propose to elucidate the active conversion from ILC3s to ILC2s in response to tissue-specific factors under ILC2-intensive conditions and/or when the identity of ILC3s is decreased. To do this, we will adapt our ILC3-fate mapping mice to models of helminth infection and type 2 immunity-mediated colonic inflammation and will explore ILC3s conversion into ILC2s. We will also clarify the roles of GATA3+ exILC3s under steady-state conditions and in inflammatory settings. Through the conditional deletion of GATA3 only in the converted ILC2s from ILC3s or the reconstitution of ILC2-depleted mice with GATA3+ exILC3s or naturally generated ILC2s derived from their precursors in the bone marrow, we will interrogate their roles during helminth infection and type 2 immunity-mediated inflammation in the colon. These studies will advance our current understanding of ILC plasticity under specific circumstances. The insight gained from these analyses will better enable us to control the balance among ILCs in vivo, leveraging such plasticity under ILC-intensive settings of infection, inflammation, and the repair of intestinal damage.

NIH Research Projects · FY 2026 · 2025-06

ABSTRACT The development of pulmonary hypertension is associated with oxidative stress, endothelial dysfunction, and pulmonary vascular remodeling. Pulmonary vascular remodeling is involved in proliferation and phenotypic transformation of pulmonary endothelial cells and smooth muscle cells. And endothelial dysfunction influences endothelial cell proliferation, and differentiation, leading to endothelial apoptosis-resistant hyperproliferation underlying the pathogenesis of pulmonary hypertension. The voltage-gated proton channel Hv1 has been shown to promote the production of NADPH oxidase (NOX)-derived reactive oxygen species (ROS) and plays an essential role in the regulation of cell proliferation and apoptosis. Here we discovered that Hv1 was implicated in pulmonary hypertension. The expression of Hv1 was significantly upregulated in the lungs of multiple rodent models of pulmonary hypertension and pulmonary hypertension patients. Moreover, deficiency of Hv1 reduced pulmonary hypertension burden in mouse model of hypoxia-induced pulmonary hypertension. To explore the role of Hv1 in the pathogenesis of pulmonary hypertension, we will apply transgenic mice and complementary in vivo approaches to delineate the contributions of Hv1 to the development of pulmonary hypertension. We plan to examine the molecular mechanisms of Hv1-mediated pulmonary hypertension and determine how Hv1 regulates the progression of pulmonary hypertension. Additionally, the Hv1 blockers will be applied to assess the translational potential of targeting Hv1 for treatment of pulmonary hypertension.

NIH Research Projects · FY 2025 · 2025-06

Misfolded and hyperphosphorylated tau are hallmarks of the tauopathies, including Alzheimer’s disease (AD) and Related Dementias (ADRDs), such as Progressive Supranuclear Palsy, Cortical Basal Degeneration, Pick’s disease, Frontotemporal Dementias and Chronic Traumatic Encephalopathy (CTE), among others. To understand these diseases, we need to know what makes pathological tau toxic and how this relates to normal functions of tau. Our central hypothesis is that pathogenic forms of tau represent misregulation of a normal biological function for tau as a scaffold for localization and regulation of multiple kinases and phosphatases. Our discovery of a biologically active motif in tau (called the Phosphatase Activating Domain, PAD) that activates protein phosphatase 1 (PP1) and glycogen synthase kinase 3b (GSK3b) provided a common molecular basis for increased kinase activities in tauopathies and supports the contention that tau acts as a scaffolding protein to regulate signaling pathways. This function is disrupted by disease-related tau changes. Exposure of PAD is normally carefully regulated and transient but becomes constitutively exposed in pathological tau. Recent studies show that specific pathological forms of tau also activate casein kinase 2 (CK2) and c-Jun N-terminal kinase (JNK) pathways, which represent novel mechanisms that are a central focus of this proposal. We propose that toxicity of pathological tau may be modulated by disease-specific patterns of tau posttranslational modifications (PTMs), isoforms and mutations that affect tau conformation and lead to disruption of neuronal functions via dysregulated CK2 and JNK signaling. Aim 1 will define effects of tau PTMs on tau function and pathology. In addition to multiple phosphorylation sites, several other tau PTMs are known, including acetylation, cross- linking and polyamination, among others. We will evaluate the effects of PTMs (single sites and combinations of sites) on presentation of PAD and SH3-binding domains that affect CK2, JNK and PP1/GSK3b signaling pathways regulated by tau. Aim 2 will determine the role of disease-related forms of tau using models of sporadic and inherited tauopathy. We will evaluate how mutations in tau may lead to differential exposure of PAD and SH3-binding domains to dysregulate CK2, JNK and PP1/GSK3b pathways. Aim 3 will identify molecular mechanisms for tau-mediated activation of novel neuronal signaling pathways. We will characterize the mechanisms underlying tau-mediated regulation of CK2 and JNK pathways by manipulating motifs in each protein and using a host of biochemical and in-cell protein-protein interaction assays. Aim 4 will define physiological roles for tau in developing and mature neurons. We will evaluate how regulation of tau isoforms and PTMs play critical roles in neuronal development as well as pathogenesis in AD and ADRDs. These studies will have significant impact by identifying novel mechanisms regulating exposure of biologically active motifs involved in tau’s role as a scaffolding protein that regulates signaling pathways critical for neuronal function and that are disrupted by disease-associated aggregation, PTMs and mutations.

NIH Research Projects · FY 2026 · 2025-05

Approximately 16-24% of those who are American Indian/Alaska Native (AI/AN) exhibit post-traumatic stress disorder (PTSD). Left unresolved, trauma is believed to be associated with marked differences in health outcomes, including higher rates of community and interpersonal violence, suicide, and child and substance abuse in AI/AN communities. The Yurok tribe, residing in Humboldt and Del Norte County, California, have a history of forced displacement, cultural disruption, and documented traumatic events, which have been shown to manifest in high rates of trauma and are associated with increased rates of adverse behavioral and health outcomes. Importantly, rates of suicide and drug overdose deaths are higher in Humboldt County than national rates. Further compounding these elevated rates is the rural location, absence of trauma-focused treatment, and shortage of mental healthcare providers. Narrative Exposure Therapy (NET) is an evidence-based form of trauma therapy that can be performed with lay counselors. Our program of research seeks to adapt and implement NET with Yurok lay counselors. However, prior to adaptation and implementation, community data on trauma and its effect is necessary. Aim 1: Characterize trauma (type, severity, and frequency of symptoms) and assess the relationship between trauma, harmful behaviors, and cultural engagement. Aim 2: Conduct in-person qualitative semi-structured interviews with Yurok tribal members to contextualize findings from Aim 1 and obtain an in-depth understanding of the relationship between trauma, harmful behaviors, and factors that promote recovery. The proposed study aligns with the National Institute of Nursing Research’s (NINR) interest in population and community health outcomes. The results will be the first to document and characterize trauma and its effect in this community as well as identify factors that promote resilience and recovery. The results will inform the next steps of our program of research by providing essential information to adapt and implement a NET intervention within the Yurok tribe. Successful implementation of NET will address barriers to mental healthcare access for this community and will be an important step toward improving access to effective mental health care for the Yurok.

NIH Research Projects · FY 2026 · 2025-05

PROJECT SUMMARY/ABSTRACT Infertility is estimated to affect 1 in 6 people worldwide, with 25% of infertility cases being attributed to ovulatory dysfunction. Despite the significant economic burden of treating ovulatory dysfunction and associated morbidities, our ability to successfully treat ovarian causes of infertility is limited by an incomplete mechanistic understanding of the development of the ovarian follicle, the functional unit of the ovary. Recently, our group was the first to describe salt-inducible kinase 3 (SIK3) as a critical determinant of fertility. Strikingly, global knockout of SIK3 in mice results in complete infertility. Our preliminary data shows that tissue-specific knockout of SIK3 in the steroidogenic granulosa cells of the ovarian follicle in a mouse model resulted in sub-fertility, a significantly reduced ovulatory response, follicle growth defects, and decreased markers of granulosa cell FSH-induced differentiation. Further, our preliminary RNA-seq data from SIK3-deficient granulosa cells in vivo showed significant alterations in lipid and glucose metabolic pathway gene expression. However, the cellular mechanisms by which SIK3 acts in the granulosa cells are currently unknown. We propose two aims to elucidate SIK3’s upstream regulation, downstream targets, and role in metabolism in FSH-induced granulosa cell differentiation. In Aim 1, I will characterize the changes in SIK3 kinase activity in response to FSH in primary mouse granulosa cells, and correlate activity to changes in SIK3 phosphorylation via phosphopeptide mapping. In Aim 2, potential upstream regulators and downstream targets of SIK3 will be identified via proximity labeling and a phospho antibody array. Finally, I will investigate whether SIK3 regulates FSH-induced differentiation via the class IIa HDACs—important SIK targets and transcriptional repressors—or other targets of interest that we identify. In Aim 3, the role of SIK3 in granulosa cell metabolism will be determined by comprehensively interrogating the effects of the loss of SIK3 on key metabolic pathways via performing metabolomics and assays measuring nutrient consumption, secretion, and utilization. Upon completion of this project, we expect to gain a foundational understanding of the mechanisms by which SIK3 regulates fertility, which may inform future work on new potential therapeutic strategies for treating infertility or developing contraceptives. This proposal was designed by my strong team of mentors and myself to broaden my expertise and toolkit, allowing me to learn, for the first time, metabolism and metabolomics, proteomics, and bioinformatics, which I hope to bring to my future career as an academic physician-scientist in pediatric endocrinology.

NSF Awards · FY 2025 · 2025-05

This project seeks to develop responsible language models (LMs) with rigorous guarantees. LMs have significantly advanced deep learning, reshaping the modeling and resolution of predictive tasks, yet in the real world, their deployment often results in errors. This undermines trust in artificial intelligence (AI) technologies and necessitates the development of advanced AI algorithms that address the unique complexities and emergent capabilities of LMs. New research underscores the inherent relation between uncertainty and various responsible AI principles, highlighting the critical role of uncertainty estimation in ensuring reliable decision-making, especially in sectors like healthcare and autonomous driving. This project will explore uncertainty's decisive yet largely unrecognized role in enhancing LM reliability. Considering the unique characteristics of LMs that present new opportunities and challenges beyond the scope of traditional uncertainty estimation methods, this project uses conformal prediction, which uses past experience to help determine confidence in new predictions. It leverages conformal prediction’s advantageous features like lightweight design, rigorous approach, and informative output. It further integrates these qualities with the emergent properties of LMs to enhance their performance and reliability. The successful outcome of the project will expand the fundamental understanding of responsible LMs, enable effective LM-augmented tools, and advance conformal prediction research to a new frontier, thus positively impacting the overall value of various large-scale data and foundation models and responsible AI education. This project is structured around three interconnected research aims. The first aim quantifies uncertainty for LMs with theoretical guarantee, exploring conformal prediction across different LM settings, including closed-source, open-source LMs, and scenarios challenging the fundamental exchangeability assumption in conformal prediction. It will then demonstrate how conformal prediction can be applied to detect and mitigate hallucinations to improve LM reliability. The second aim focuses on merging conformal prediction's robust uncertainty estimation with LMs' self-correction capabilities, using reliable prediction sets to iteratively refine LMs and reduce uncertainty through conformal prediction-guided Chain-of-Thought reasoning and external knowledge integration. The third aim introduces an uncertainty-based reliability measures and develops processing error mitigation strategies that utilize conformal prediction to strategically enhance responsible AI in both closed and open-source LMs, ensuring more equitable outcomes across a range of application scenarios. 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 · 2025-05

Abstract The enclosed application seeks to add a dual source ion mobility hybrid mass spectrometry system for biomedical research at the University of Illinois Chicago (UIC), a federally designated minority serving institution. This instrumentation would enable state-of-the art measurements for researchers at UIC as well as their collaborators in the Midwest, nationally and internationally. The instrument will be housed and maintained in the Department of Chemistry Instrumentation Core and will be the first high-resolution mass spectrometer in the Core and will replace current MALDI-MS instrumentation that is more than a decade old, currently being used for mass spectrometry imaging which is owned and shared by the PI. The major and minor user group reflects the diverse biomedical research on the UIC campus and span cancer, neurodegeneration, public health and more. Moreover, users are members of multiple NIH funded research centers (e.g. P01 and P30) on the UIC campus. The major applications of this new instrumentation are proteomics, lipidomics, and metabolomics workflows. Approximately half of the user group will also utilize the MALDI mass spectrometry imaging capabilities. Addition of this new instrumentation will enable new discoveries owing to the improved analytical performance of the Bruker timsTOF Flex including the dual ESI/MALDI source design, trapped ion mobility separation, improved sensitivity and resolution, as well as increased speed for performing complex measurement. The PI has more than 18 years of mass spectrometry experience and will work closely with the user groups, advisory group and core instrumentation specialist for streamlined access and utilization for biomedical research.

NIH Research Projects · FY 2026 · 2025-05

Project Summary Asthma is a chronic airway disease in which diverse immune cells participate in the development and eventual resolution of allergic lung inflammation. Among these immune cells, conventional dendritic cell type 2 (cDC2) plays a fundamental role in bridging innate and adaptive immunity. However, recent studies show that the cDC2 population is diverse and heterogeneous, unlike the more homogenous cDC1. Our group has characterized the heterogeneous cDC2 subsets with distinct transcriptomic features in the lung and demonstrated that a unique pro-inflammatory cDC2 subset, CSF1R+cDC2, is necessary for sensing inhaled allergens. Our supporting data for this proposal show that CX3CR1 is predominantly expressed by cDC2 but not cDC1 in mouse and human lungs, indicating that CX3CR1+cDC2 is another unique cDC2 subset. In mice, we compared the gene expression patterns between CX3CR1+cDC2 and their receptor-negative counterparts. Remarkably, the gene expression pattern of CX3CR1+cDC2 was skewed towards anti-inflammatory pathways. This corresponds with prior reports indicating an immunoregulatory role for CX3CR1 expressing myeloid cells, and our own published data showed that CX3CR1+ lung macrophages facilitated the resolution of allergic lung inflammation. This proposal aims to examine the mechanisms by which CX3CR1+cDC2 has the role of a contrasting anti-inflammatory role in allergic lung inflammation. To analyze the functions of the CX3CR1+cDC2, we generated several novel transgenic mice to deplete them selectively or knockout CX3CR1 in a cDC2- specific way. Our data show that depletion of CX3CR1+cDC2 results in a marked reduction in CD4+Foxp3+ regulatory T cells (Tregs) and the delayed resolution of allergic lung inflammation with delayed resolution. In addition, CX3CR1+cDC2 expressed higher levels of the co-inhibitory molecule PD-L1 compared to their receptor-negative counterparts. These data strongly suggest that lung CX3CR1+cDC2 is an anti-inflammatory subset of cDC2, which plays an essential role in the resolution of allergic lung inflammation. In this proposal, we will characterize the anti-inflammatory role of the lung CX3CR1+cDC2 subset and determine the immunologic mechanisms by which the CX3CR1+cDC2 regulates allergic lung inflammation. To do so, we will first determine whether CX3CR1+cDC2 drives Treg development. Next, we will characterize the molecular signalings via MHC classes and PD-L1, contributing to CX3CR1+cDC2-mediated anti-inflammatory function. Finally, we will seek to elucidate the human relevance of this unique lung cDC2 as an anti- inflammatory subset, using human BAL cells and intrathoracic lymph nodes obtained by bronchoscopy. In summary, these proposed experiments are designed to uncover a novel anti-inflammatory role of the CX3CR1+cDC2 subset in the resolution of asthmatic inflammation. These data will significantly expand the understanding of the processes involved in the resolution of allergic lung inflammation and delineate novel treatment options.

NIH Research Projects · FY 2026 · 2025-05

The overall goals of this project in the R00 phase are to (1) test the efficacy of CM-PST vs CM alone in a 2-arm pilot RCT, and (2) assess neural mechanisms associated with CM-PST treatment effects in young adults with Alcohol Use Disorder (AUD). AUD is a chronic disease of impaired ability to stop or control alcohol use,1 and is a major public health problem, most prevalent in young adults (aged18-24 yr).2 AUD cost about 95,000 lives and $249B annually in the US as of 2010.3 About 70% of young adults engage in risky drinking,1,4 predisposing them to AUD.5 AUD has adverse whole-life health implications, especially among young adults, by virtue of their age. Heavy alcohol consumption impairs brain structure and function, more severely in young adults than in older adults.6 However, evidence-based treatments for AUD in young adults are lacking, and the neural mechanisms following available behavior treatments are poorly understood. The proposed study therefore aims to begin to overcome these gaps, by developing and testing an integrated AUD intervention, among young adults, to improve treatment efficacy, and inform about the neural mechanisms of treatment. One recommended treatment for AUD is contingency management (CM), a behavior therapy that rewards individuals for evidence of positive change,7 but CM has never been specifically tested in young adults. Prior randomized clinical trials (RCTs) of CM in AUD8–11 have shown only modest effects, but we hypothesize this is because CM is mediated by reward circuitry,12 a system impaired in persons with AUD.13–15 Therefore, to overcome this barrier so as to improve treatment efficacy, we will innovate by combining CM with a complementary approach that engages a neural circuit that may not rely on the reward system, but rather, involves reframing using cognitive control. To do so, we will integrate CM with Problem-Solving Therapy (PST), a brief psychotherapy proven beneficial in multiple health problems across different age groups, including young adults.16–20 Ma et al.’s mechanistic pilot trial showed that PST can engage both negative affect and cognitive control circuits.21,22 PST has been tested as enhancement strategy in combination with behavioral treatments such as motivational interviewing in related patient populations with substance (smoking, alcohol) use disorders,23,24 but these studies have not specifically assessed the efficacy of combining PST with CM. The proposed study's goal (StuDy AimED at Increasing AlCohol AbsTinEnce; DEDICATE) is to test the preliminary efficacy of CM-PST, vs. CM alone, to improve treatment efficacy and inform about neural mechanisms of treatment effects in young adults with AUD. Central hypothesis: Combined CM-PST can 1) improve alcohol abstinence (tested by urine alcohol screening; primary outcome) and other AUD outcomes (e.g., AUDIT, RAPI scores), and 2) increase activity in positive affect and cognitive control regions, decrease activity in negative affect regions, and enhance connectivity between these regions (exploratory outcome).

NIH Research Projects · FY 2025 · 2025-04

Abstract Sickle cell disease (SCD) affects more than 100,000 people in the United States and causes a significant burden to affected individuals, their families, and national healthcare systems. Pain is the hallmark symptom of SCD, and such pain is frequently poorly managed and adversely affects coping and psychological well-being as well as health-related quality of life. In a mouse model of SCD our team showed that the gut microbiome plays a prominent role in pain. The composition of gut microbial communities and their metabolic function is dynamic and modifiable, making it a prime therapeutic target for reducing pain in SCD. A Mediterranean diet (MedDiet) has anti-inflammatory, antioxidant, and pain-relieving benefits, with positive effects on the gut microbiome in non-SCD populations. While diet is thus viewed as critical for managing SCD and its severity, there is a shocking lack of studies examining diet as an approach to managing SCD symptoms including pain. In this R21, we propose to conduct a randomized crossover study of a 4-week MedDiet compared to usual diet (control) among 24 adults with SCD and chronic pain (30 will be recruited). The aim of the feeding study is to explore the effect of a MedDiet compared to usual diet in altering the gut microbiota and microbial metabolites and reducing chronic pain. We will collect blood and stool samples throughout. We will also apply a reverse translational approach: transplanting fecal samples from the human participants before and after the MedDiet intervention to sex concordant SCD mice. The goal of this aim is to investigate the role of diet-induced changes in gut microbiota in altering the metabolic profile and sensitivity to pain by evaluating fecal microbiota transplant of human samples to SCD mice. We will apply an interdisciplinary approach with a high probability of success due to our team of highly productive investigators, who bring expertise in hematology, pain management, nutrition, basic pain neurobiology, pharmacology, microbiome research in both human and mouse models, and clinical care in SCD management. In the future, we anticipate further testing and broadly disseminating evidence of the effectiveness of a MedDiet for mitigating chronic pain in SCD and understanding its underlying mechanisms for a high national public health impact.

NIH Research Projects · FY 2026 · 2025-04

PROJECT SUMMARY/ABSTRACT Anxiety afflicts more than 359 million people worldwide. Furthermore, >40% of individuals are refractory to conventional first-line treatments, leading to a 2.2-fold increase in mortality risk. An incomplete understanding of these conditions is a significant barrier to improving patient neuropsychiatric health. Until recently, efforts to clarify disease etiology and develop therapeutic interventions have centered around genetic and social factors, often neglecting environmental drivers that are increasingly linked to neurobehavioral dysfunction. However, a growing body of evidence suggests toxic metal/metalloid exposures contribute to adverse neuropsychiatric outcomes. For example, inorganic arsenic (iAs), a widespread environmental toxicant, increases anxiety/anxiety-like phenotypes in various epidemiological and experimental studies. Thus, environmental exposures to iAs may significantly contribute to the risk of anxiety across populations. Importantly, data indicate that anxiety disorders have neuroinflammatory origins, with microglia serving as causal mediators. Arsenic is known to accumulate in the brain and activate microglia. However, the mechanisms by which it contributes to neurobehavioral dysfunction remains incompletely understood. Our lab has shown that arsenic depletes the brain of the essential fatty acid docosahexaenoic acid (DHA). This is significant because DHA plays multiple homeostatic roles in the brain that are crucial for cognitive function, including effects on neurotransmission and microglial class-switching from pro-inflammatory (M1) to anti-inflammatory (M2) states. This proposal will use a complementary array of in vivo mouse studies and in vitro experiments in SIM-A9 microglia to interrogate our central hypothesis that DHA is essential for protecting neurobehavioral health from arsenic toxicity, and that targeted brain DHA enrichment via use of a novel lysophosphatidylcholine DHA (LPC-DHA) therapy mitigates environmental threats linked to anxiety. Unlike traditional triglyceride DHA that accumulates peripherally, LPC-DHA is preferentially shuttled across the blood-brain barrier by a unique transporter called MFSD2A. Thus, the research component of this training grant will provide the fellow with a rigorous depth and breadth of training in a complementary array of state-of-the-art techniques, including advanced behavioral assessments, electrophysiology, mass spectrometry imaging, and various assays to characterize microglial biology. These technical skills will be supplemented with highly engaged multidisciplinary mentorship and educational activities across the fields of neuroscience, environmental health, and clinical medicine. A central goal of this integrated training plan is to empower the fellow with skills to critically appraise, use, and analyze various models, methods, and data with a focus on translational therapeutic development. Collectively, this proposal will launch the fellow’s long-term success as a physician-scientist at the cutting-edge of environmental neuroscience with the knowledge and skills to develop new therapeutic approaches to improve human health.

NSF Awards · FY 2025 · 2025-04

The rapid growth of smart cities necessitates advanced solutions to improve traffic mobility and public safety. This project proposes a novel multi-camera surveillance system, leveraging a network of distributed smart cameras to capture and analyze streaming video data in real time. By combining the computational power of edge devices and the cloud, this system intelligently processes video streams to address challenges in smart city applications. The project emphasizes privacy-preserving techniques to ensure sensitive information, such as images of pedestrians and vehicles, is protected while fostering scalable, efficient, and resilient real-time systems. It bridges research domains in systems and networking, machine learning, computer vision, and security and privacy, creating a unified framework for advancing smart city infrastructures. The project delivers transformative contributions across multiple domains. It introduces innovative unsupervised learning models for tasks such as human and object re-identification and tracking, enabling accurate and efficient analytics in distributed, real-time systems. A novel real-time and resilient cyberinfrastructure is designed with full-stack configurability, addressing system scalability and network performance challenges for large-scale deployments. Additionally, lightweight cryptographic systems combining advanced cryptographic primitives and Trusted Execution Environments (TEEs) enable privacy-preserving computation for sensitive video data. Beyond technological contributions, the project promotes societal benefits by improving urban services, fostering public trust in privacy-conscious surveillance, and training a new generation of students with skills critical to the systems, networking, data science, and cybersecurity industries. 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 · 2025-04

PROJECT SUMMARY/ABSTRACT Aminoglycosides are a critically important class of antibiotics as designated by the World Health Organization, in part due to their activity against multidrug-resistant (MDR) Gram-negative bacteria. However, aminoglycoside use is currently impeded by the potential for resistance and dose-limiting toxicities to emerge during treatment. Aminoglycosides cause miscoding of the mRNA, leading to translation errors that contribute to their bactericidal effect. Although a majority of the antibiotics in this class bind to helix 44 (h44) of the ribosomal 30S subunit to cause miscoding, streptomycin can bind to an adjacent non-overlapping site on the ribosome. In preliminary studies, we found that combinations between aminoglycosides that bind separate sites on the ribosome (‘dual- aminoglycoside combinations’) were synergistic and bactericidal against MDR Enterobacter cloacae, Escherichia coli, and Klebsiella pneumoniae isolates. Dual-aminoglycoside combinations synergistically enhanced bacterial killing, suppressed resistance emergence, and caused higher rates of miscoding than individual aminoglycosides. These synergistic combinations may also retain their bactericidal activity at lower concentrations than monotherapies, which could enable the use of smaller doses that limit toxicity. Although other synergistic antibiotic combinations simultaneously bind to the ribosome (e.g., quinupristin and dalfopristin), there are no studies to evaluate activity of multiple aminoglycosides and the mechanism of their synergy is completely unknown. This structural, functional, and microbiological project will be the first to examine dual- aminoglycoside combinations against MDR Gram-negative bacteria, solve the structure of multiple aminoglycosides simultaneously bound to the bacterial ribosome, and provide critical insights into their mechanism of synergy. Our central hypothesis is that specific combinations of two aminoglycosides are synergistically bactericidal due to their ability to bind simultaneously to the bacterial ribosome and increase miscoding. To test this hypothesis, we will pursue the following specific aims. In Aim 1, we will identify dual- aminoglycoside combinations that are synergistic and maximally suppress resistance. An array of structurally unique aminoglycosides will be tested against a genetically diverse panel of MDR isolates to detect the most active combinations. Cytotoxicity of synergistic combinations will also be evaluated. In Aim 2, we will define the mechanism of synergy for dual-aminoglycoside combinations. We will determine X-ray crystal structures of the ribosome in complex with different aminoglycoside pairs, quantify miscoding in the presence of synergistic combinations, and define the importance of simultaneous binding for synergy. Structural insights will aid the development of next-generation aminoglycosides with unique binding sites. This project will deliver novel dual- aminoglycoside combinations and an understanding of their mechanism(s) of synergy, which will establish the foundation for future drug development and clinical explorations.

NSF Awards · FY 2025 · 2025-04

The 10th Lake Michigan Workshop on Combinatorics and Graph Theory will be held at the University of Illinois Chicago on April 5–6, 2025. The workshop will benefit graduate students and junior researchers in multiple subfields of discrete mathematics, working at institutions in the Great Lakes area and beyond. It is built around two sets of three tutorial lectures, focusing on state-of-the-art techniques and results on which the speakers are particularly qualified to expound. There will also be short talks by students and early-career researchers. There will be ample unscheduled time during the weekend, allowing new research collaborations to commence and active collaborations to be continued. Junior participants will establish valuable connections with more senior colleagues and receive guidance from them in a relaxed and informal environment. Combinatorics and graph theory are two very active areas of research within the broader field of discrete mathematics, with important ties to disciplines such as statistical physics, probability theory, and computer science. In the immediate vicinity of Lake Michigan there are a large number of researchers and students working on a variety of graph theoretical and combinatorial problems. This workshop will bring many of these scholars together. Through the tutorial lectures, short talks, and informal collaboration time, the workshop will train early-career researchers in important and emerging techniques of combinatorics and graph theory. The tutorial speakers for the 2024 workshop are confirmed to be Rose McCarty (Georgia Institute of Technology), Greta Panova (University of Southern California), and Mehtaab Sawhney (Columbia University). The PIs have selected tutorial speakers with the explicit goal of representing disparate subfields of combinatorics and graph theory, with McCarty as an expert in structural graph theory, Panova an expert in algebraic combinatorics, and Sawhney an expert in additive, extremal, and probabilistic combinatorics. The website for the workshop is https://marcusmichelen.org/LakeMichiganWorkshop2025.php 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 2025 · 2025-04

As the U.S. tax law frequently changes, decision-support software plays a crucial role in helping taxpayers, professionals, and the Internal Revenue Service (IRS) navigate its complexities. The use of tax preparation software has witnessed a significant increase, with over 72 million people utilizing it in 2020. However, there has been limited independent research conducted to assess the accountability of tax software. This project takes on two main challenges: i) ensuring the software's compliance, accuracy, and fairness based on tax law and experts' perspectives, and ii) enhancing scalability and precision in testing, debugging, and patching tax software. The project specifically focuses on exemptions, credits, and deductions for low-income taxpayers, with the aim of ensuring that all taxpayers, including those from vulnerable communities, pay all and only the taxes that tax law prescribes. While it is expected that software with legal and social implications should be fair and compliant with the law, the absence of formal specifications regarding expected behaviors in legal-critical domains like tax software poses significant challenges in ensuring accountability. Since U.S. tax law adheres to the legal doctrine of precedent (stare decisis), this project proposes that these specifications naturally exist as metamorphic relationships between individuals who are considered similar within a given context. The project team plans to 1) explicate metamorphic relations from a large set of challenging requirements in U.S. tax law, 2) automate the extraction of such metamorphic relations by leveraging principles from the psychology of perception pertaining to relateness, 3) develop artifacts for assessing tax software that leverages those relations using formal verification techniques, and 4) experimentally compare the tax software's accuracy and perception of procedural justice to that of human tax experts. 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 2025 · 2025-04

Measurement of blood pressure (BP) is essential for early diagnosis and management of hypertension, a condition that 45% of US adults have and a risk factor for development of heart failure, the leading cause of death in the US. Worldwide, hypertension is one of the largest public health epidemics. Compared to ambulatory BP measurements, frequent out-of-clinic BP measurements are better predictors of cardiovascular events but, today, existing clinically-accurate technologies to measure BP require costly, uncomfortable, and cumbersome devices that prevent their extended use outside of the clinic. Given substantial healthcare and mortality burden of heart failure, rising healthcare costs, and the aging population, continued technological improvements to aid heart failure prevention, management, and surveillance are extremely important. The goal of this project is to address this need for an accurate, inexpensive, easy-to use device for continuously monitoring BP through the development of a novel wearable watch built for this purpose. This new technology will be a game-changer to protect at-risk individuals and effectively manage patients with hypertension proactively across the care continuum and reduce hospitalizations associated with hypertension. This study will also serve as fertile ground to support students in continuing their careers at the intersection of STEM and human oriented research. One tool that is well-suited for unobtrusive BP monitoring is bioimpedance (BioZ). In BioZ, an imperceptible electrical current is passed through the body to obtain insights into how blood flows through arteries and veins. Here, the Investigators propose to develop new measurement methods rooted with fluid and electricity principles to create a new BioZ sensing technology capable of enabling continuous, cuffless, and convenient BP monitoring. For this, a novel aspect of the approach taken will be the application of BioZ in conjunction with physiological, computational, and machine learning models to establish the underlying biological sources at the cellular level relating both signals. Once the models have been established and optimized to link BP to BioZ, the prediction accuracy will be evaluated in a cohort of individuals representative of a wide range of body indices and age groups. 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 2025 · 2025-03

This project aims to improve security and resilience of machine learning (ML) software. Machine learning has been deployed in many critical domains such as drug discovery, financial planning, autonomous driving, and malware detection. This makes it crucial for ML-based software solutions to function properly even when attacked by malicious actors, leading to a line of research focused on functional vulnerabilities, attacks that attempt to make ML systems produce incorrect results. Less studied, however, are other kinds of vulnerabilities that don't attack the core prediction functionality but still pose security risks. These "non-functional" vulnerabilities include denial of service attacks, which attempt to render the system unusable through overloading it; and side-channel attacks, which analyze features like response time to infer sensitive information about the models or data they are trained on. This project will develop methods for detecting and correcting these kinds of non-functional vulnerabilities and make those methods widely available, as well as disseminate educational materials to help security researchers and ML software developers be more aware of these risks. Despite a growing number of reported denial-of-service (DoS) and side channel (SC) vulnerabilities in core ML libraries such as NumPy and TensorFlow, a systematic approach to identifying and debugging them has not been explored due to multiple technical challenges: i) non-functional behaviors are not explicitly encoded in the syntax or semantics of ML code; ii) existing fault localization methods often fail to establish causal relationships; and iii) automatic DoS/SC mitigation is largely lacking for ML applications. This project will develop a novel methodology that combines evolutionary algorithms with a gradient-based guidance to detect DoS and quantify the strengths of SC vulnerabilities. For debugging, the project explores causally guided statistical methods to localize the root causes and guide an optimal mitigation policy. The project team will make a concerted effort to increase participation of women, Hispanic, and other underrepresented communities via special topic courses, research experiences for undergraduates, and summer camps for K-12 students. 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 · 2025-03

Herpes simplex virus type-1 (HSV-1) provides a valuable tool for identifying new cellular mechanisms that safeguard the cornea and innervating sensory nerves. HSV-1 infections in the cornea can lead to epithelial damage, chronic inflammation, and impairment of sensory nerve fibers, ultimately resulting in blindness. In recent research, we investigated the role of the optineurin (OPTN) gene in HSV-1 infection and unexpectedly found an inverse correlation between OPTN expression and the severity of herpes stromal keratitis (HSK) in experimental mice. Our published findings also demonstrated that OPTN dysfunction leads to accelerated loss of central nervous system (CNS) neurons after HSV-1 eye infection. OPTN-/- animals show issues with the development of adaptive immune responses and deficiencies in autophagic degradation of HSV-1 proteins. Notably, OPTN, an autophagy receptor, is known for regulating the transport of ubiquitinated proteins and damaged mitochondria to autophagosomes for degradation. Our preliminary findings using OPTN-/- animals indicate that the loss of OPTN directly correlates with the loss of corneal nerve functions, underscoring its unrecognized significance in herpes neurotrophic keratitis (HNK) and other sensory nerve complications, such as dry eye disease (DED). Additionally, our data suggest a unique role for OPTN in promoting optimal MHC class II levels in response to HSV-1 infection in antigen-presenting cells, such as Dendritic Cells (DCs), which has the potential to explain the issues with compromised immunity in OPTN-/- animals. Based on our recently published and preliminary data, we propose a stimulating hypothesis that OPTN plays a central yet poorly understood role in mitigating the severity of herpetic eye disease. To deepen our understanding, we plan to comprehensively investigate the impact of OPTN on herpetic disease in the cornea. Our research will pursue three independent Specific Aims, conducting extensive in vitro and in vivo studies to assess the molecular mechanisms regulated by OPTN, particularly regarding viral degradation and homeostasis in HSV-1-infected cells, as well as OPTN's role in antigen presentation and its influence on the innate-adaptive immune axis. Additionally, we will utilize wildtype and OPTN-/- murine models of corneal infection to investigate OPTN's involvement in corneal sensitivity loss, studying its effects on corneal neurons and sensory nerve fiber damage. Our findings will generate new knowledge of how OPTN contributes to reducing ocular infection severity and enhancing antiviral immunity while preventing the loss of sensory neurons during infection. Moreover, our findings will have broader clinical implications for ocular infections in general. Similar to our results in experimental mice, the analysis of publicly available human transcriptomic data showed significant downregulation of OPTN in bacterial keratitis patients. Furthermore, this research may uncover new information on autophagic control of corneal health, and novel therapeutic strategies for herpetic eye diseases, with implications for neurodegenerative diseases in general.

NIH Research Projects · FY 2026 · 2025-03

Our overall goal of this project is to reveal the comprehensive mechanism of how metastatic breast cancer induces permeability of the blood-brain barrier (BBB), thereby facilitating breast cancer brain metastases (BCBM). BCBM is a leading cause of death in late-stage breast cancer patients. BCBM is particularly difficult to treat because drugs cannot easily cross the BBB, a protective barrier around the brain. Despite the critical role of the BBB in safeguarding the brain, it remains unclear how cancer cells can pass through it and metastasize to the brain. Based on our new findings, brain-metastatic breast cancer cells highly express and secret fetuin-A (FetA). Cancer-derived FetA transiently opened the endothelial barrier in vitro and the BBB in mice. Although FetA is known as a serum protein released from the liver, human serum FetA did not open the barrier in vitro and in vivo. These data clearly showed a significant biological difference between cancer-derived FetA and serum FetA. Furthermore, de-glycosylation of cancer-derived FetA abolished its activity on the endothelial barrier, suggesting glycosylation of cancer-derived FetA is critical for opening the endothelial barrier. The uptake of cancer-derived FetA by Annexin A2 (AnxA2) induced Ca2+ influx and activation of calmodulin-dependent protein kinase II (CaMKII) in the brain endothelial cells (ECs). The peptide inhibitor designed based on the docking model of FetA and AnxA2 inhibited cancer-derived FetA-induced brain endothelial permeability. Based on these solid supporting data, we hypothesize that brain-metastatic breast cancer cells secrete FetA to facilitate brain metastases by transiently opening the BBB. Thus, inhibition of FetA-induced BBB permeability helps develop a novel strategy to prevent BCBM. We will examine our hypothesis with two specific aims. AIM1: To elucidate a mechanism of how cancer-derived FetA induces BBB permeability. We will investigate glycosylation patterns of cancer-derived FetA by comparing them with human serum FetA. We will examine the roles of glycosylation of FetA in inducing brain endothelial permeability and the effects on each cell type of the BBB (brain ECs, pericytes, and astrocytes). AIM2: To examine how cancer-derived FetA facilitates breast cancer brain metastasis. We will determine the roles of cancer-derived FetA and its glycosylation by inducing knockout or glycosylation-defective mutant FetA in breast cancer cells and test their brain metastasis in mice. Further, we will employ peptide-based inhibitors for FetA uptake and test the effects on the FetA-induced BBB permeability and breast cancer brain metastasis in animal models. In summary, our project will reveal essential insights into how metastatic breast cancer opens the BBB to invade the brain to metastasize. Also, gaining a deeper understanding of the unique biological action involving FetA will contribute to developing a new concept for brain metastasis.

NSF Awards · FY 2025 · 2025-02

The IEEE International Microwave Biomedical Conference (IMBioC) provides a global platform for sharing latest innovations and developments in radio frequency (RF) and wireless technologies, antennas, and electromagnetic theory for biomedical and biological applications. The conference is financially sponsored by the IEEE Microwave Theory and Technology Society, with technical co-sponsorships from the IEEE Antennas and Propagation Society and the IEEE Engineering in Medicine and Biology Society. The 2025 IEEE IMBioC will be held in Kaohsiung, Taiwan on April 15-17, 2025. To support the training of the next-generation scientists and engineers working on RF and wireless technologies for biomedical applications, this NSF grant will provide travel support for 10 U.S. students to present their research papers at the conference and learn the state-of-the-art developments in this field. The travel grants will be awarded competitively to undergraduate and graduate students from U.S. universities who will present their accepted papers at the conference. The awardees will be selected by a review committee of the conference and the paper quality will be considered in the selection process. The proposed travel support will have long-term and broad impacts on the participating students' career developments and contribute to the U.S. STEM workforce development. The first IEEE IMBioC was formed in 2018 by merging two IEEE conferences: the IEEE BioWireless Conference and the IEEE International Microwave Workshop Series on RF and Wireless Technologies for Biomedical and Healthcare Applications. Since then, the conference has become an important forum for the international research communities in microwave technologies, antennas, wireless technologies, medicine, and biology to meet and discuss cutting-edge research results in this interdisciplinary field. The IEEE IMBioC in 2025 will have a diverse range of activities, including oral sessions, poster sessions, short courses, exhibitions, student paper competition, and invited talks by leading experts. Students attending the conference will learn about the latest state-of-the-art RF and wireless technologies for emerging biomedical applications. 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 · 2025-02

Our long-term goal is to advance the knowledge of the molecular and neurobiological mechanisms underlying chronic pain in sickle cell disease (SCD) and develop effective pharmacologic treatments. Pain is not only a life-long companion but also a predictor of mortality for the 100,000 Americans, millions more worldwide living with SCD.1-3 Pain and SCD are so intimately intertwined, that African tribal words for the disease, spoken hundreds of years before Herrick described SCD in the western literature, are onomatopoeic for pain. Nationwide epidemiological survey data indicate that annually only 39% of patients with SCD have no pain episodes, 55% have 1- 2 episodes, 5% have 3 to 10 painful episodes, and 1% of patients have more than 10 episodes.1 Though it is now appreciated that SCD pain is characterized by chronic pain with episodes of acute pain crisis,4-5 the neurobiology of chronic pain is poorly studied, not well characterized, and is often refractory to currently available therapies,6-8 a century after Herrick’s seminal paper.9 A great deal of research has been carried on the disease itself. Several transgenic models of SCD have been developed, including the humanized Berkeley (BERK) and Townes’ sickle cell transgenic mice (TOW), both representing SCD phenotypes that closely mimics many features of severe SCD in humans. We propose to employ these well- characterized sickle cell transgenic mouse models for studying epigenetic (microRNA), neurobiology (tyrosine hydroxylase), and gut microbiota mechanisms underlying chronic pain, which can hold much promise for a more thorough understanding of pain mechanisms in SCD and may guide the development of effective therapies. Our research applies the power of molecular and cellular biology, pharmacology, neurobiology, epigenetics, targeted drug delivery, and other cutting-edge tools, and we have ongoing research, existing expertise and research capacity for studying chronic sickle pain problems using the multipronged complementary approaches. Moreover, this R35 program is designed to have flexibility so that new research directions can be rapidly taken when new findings or emerging technologies become available. Our innovation has a high probability of success given our outstanding track record, vibrant ongoing research program, and the designed flexibility in pursuing new research directions. Having moved a drug candidate from bench to a Phase I study in patients with SCD, our team is uniquely suited to carry out future translation research to benefit the patients with SCD.

NIH Research Projects · FY 2025 · 2025-02

Abstract This R01 application responds to PAR-23-062: Innovations to Optimize HIV Prevention and Care Continuum Outcomes. In Indonesia, an estimated 33% of people with HIV (PWH) are undiagnosed. Interventions are needed to increase timely HIV testing and diagnosis among people who have come into contact with the virus. Assisted partner notification (APN) is a voluntary process that utilizes health workers to encourage and assist people diagnosed with HIV to inform their former sex and drug use partners about possible shared exposure to HIV. When carried out in community care settings, APN increases partner notification and HIV testing with safety and effectiveness. Our research will demonstrate APN”s benefits among people in prison care settings, who face additional barriers to informing their numerous at-risk and mostly female partners in the community. A hybrid type I effectiveness-implementation design will be used to evaluate Impart, a prison-based APN model that we developed and successfully pilot-tested in Indonesia to encourage and assist IPWH to inform their former sex and drug-injecting partners in the community about possible exposure to HIV. With Impart, community health workers are trained to work in prisons as APN Counselors to coach inmates to self-notify partners, or, if inmates prefer, APN Notifiers will notify partners anonymously (without identifying the index) and offer them HIV testing and treatment referrals. In our pilot study, APN was preferred by inmate participants to notify partners and also proved the more successful in generating new HIV testing and in identifying and referring partners with previously undiagnosed HIV. The proposed research will introduce Impart at 8 Indonesia correctional facilities to evaluate its effectiveness to increase partner notification and HIV testing (Aim 1), while also evaluating Impart's reach and organizational sustainability across a range of prison contexts (Aim 2). A randomized trial with 216 incarcerated PWH and up to 450 sex and drug-injecting partners will compare our Impart model (choice of APN or self-tell for each partner) with a self-tell notification only condition that is aligned with international guidelines. As outcomes, we will compare the number of partners who are HIV tested, newly diagnosed, and linked to HIV care within 6 weeks. We will train and mentor 12 community health workers as APN Counselors and Notifiers to deliver Impart during the study's randomized trial phase. As indicators of implementation success, we will examine Impart's reach, fidelity, and sustained implementation by Impart service providers and clinic staff at each prison facility for one year after the randomized trial phase ends. Qualitative interviews and other data collected at each implementation phase will be used to evaluate prison-based contextual factors associated with varying levels of implementation success. This study will yield a prison-based APN model for adoption in prison settings in Indonesia and possibly elsewhere to increase HIV testing and earlier diagnosis among at-risk partners of inmates. The study addresses priority areas within the NIH Office of AIDS Research and the NIMH Strategic Plans for HIV-related Research and also the trans-NIH plan to Advance Science for the Health of Women (2019-2023).

NIH Research Projects · FY 2026 · 2025-01

PROJECT SUMMARY / ABSTRACT Acute Respiratory Distress Syndrome (ARDS) is a life-threatening lung injury caused by various factors such as infection and trauma, currently lacking a cure. Annually, approximately 190,000 Americans are diagnosed with ARDS, a number further amplified by the COVID-19 pandemic. The primary pathology involves damage to the alveolar epithelium, necessitating innovative approaches to accelerate alveolar epithelial regeneration for treating ARDS. Alveoli, surrounded by abundant capillaries for gas exchange, remain poorly understood in their regulatory role within this intensive capillary niche. Our focus is on aerocytes, a recently identified capillary endothelial population specialized in the lungs and positioned on the outer surface of the alveolar epithelium. Given this unique location, we propose that aerocytes play a pivotal role in alveolar epithelial regeneration. Preliminary data indicate that aerocytes express the angiocrine factor R-spondin3, a Wnt signaling activator, and stem cell factor. Loss of angiocrine R-spondin3 impedes regenerative epithelial remodeling and lung repair following injury, suggesting a crucial role for aerocyte-derived signaling in lung alveolar regeneration. Our research proposal aims to establish the central role of aerocytes in regulating alveolar regeneration post lung injury, with a specific focus on the signaling molecule R-spondin3. We hypothesize that aerocytes guide regenerative alveolar remodeling through R-spondin3, enhancing Wnt signaling in alveolar epithelium, and orchestrating interstitial macrophage plasticity for the necessary regenerative niche. To rigorously test this hypothesis, we outline the following specific aims: Aim 1: Investigate the role of aerocyte-derived R-spondin3 in lung growth and recovery using loss-of- function and gain-of-function animal studies within disease-related lung injury models. Aim 2: Define the mechanisms of regenerative alveolar remodeling guided by aerocyte-derived signaling, focusing on AT2 cell renewal, transition into TSCs, and differentiation into AT1 cells using advanced techniques such as alveolar organoids. Aim 3: Examine the impact of aerocytes on interstitial macrophage plasticity in establishing a regenerative alveolar niche. By unveiling the role and mechanisms of aerocytes in alveolar epithelial regeneration, this research potentially leads to innovative therapeutic strategies for treating ARDS by targeting aerocyte-derived signaling to regenerate the alveoli, ultimately improving the health and quality of life for individuals affected by severe respiratory complications associated with COVID-19 and ARDS.

NIH Research Projects · FY 2026 · 2025-01

Project summary DNA topoisomerases carry out changes in DNA structure needed for transcription, replication, and maintenance of DNA structure. Topoisomerases introduce transient breaks in DNA with a protein/DNA covalent intermediate termed the cleavage complex. This cleavage mechanism allows cells to carry out changes in DNA conformation such as relaxation of DNA supercoiling without the dangers of frank DNA double strand breaks. Nonetheless, topoisomerase-induced breaks can persist due to small molecules that interfere with the topoisomerase reaction, due to alternate DNA structures, or due to mutations within the topoisomerase protein. Our recent work led to the identification of mutations in eukaryotic Top2 that generate high levels of Top2 cleavage complexes in the absence of small molecule inhibitors (hcTop2). Importantly, we found that expression of hcTop2 mutants in yeast is mutagenic and causes de novo duplications of 2-5 nucleotides. This pattern of duplications is very similar to ID17, a mutational signature found in some cancer cells. Cells with the ID17 pattern carry a point mutation in human Top2, Top2K743N. We constructed the yeast ortholog yTopK720N and showed that the purified protein gives rise to elevated levels of Top2 cleavage and that expression of the mutant protein in yeast cells leads to a pattern of mutations that was similar to ID17. These hcTop2 proteins can be applied to address fundamental questions concerning how topoisomerases regulate cleavage reactions, and how they impact genome stability. A major question that we plan to address in this work is to determine how the biochemical properties of a topoisomerases dictate where genome instability occurs. We hypothesize that a combination of the biochemical properties of topoisomerases, along with other factors such as chromatin structure and DNA repair pathways are likely to determine important aspects of genome instability induced by the enzymes. We developed an assay to assess sites of DNA cleavage using reactions with hcTop2 mutant proteins in vitro followed by detection of cleavage sites by next generation sequencing. Since we have identified many mutations induced in yeast by hcTop2 expression, we can address whether hotspots of mutation induced by Top2 correlate with strong Top2 cleavage sites in vitro. Notably, not all hcTop2 mutants give rise to the same mutation spectrum, implying that the Top2 enzyme plays a direct role in the sites of induced mutations. Since we identified mutations in human Top2 andTop2 that are hyper cleavage, we can use these mutants to address whether human Top2 proteins give rise to the same pattern of mutations as seen with yeast Top2. Finally, the hcTop2 mutants can be applied as a tool to identify pathways to repair Top2-induced DNA damage. Since hcTop2 mutants in both Top2 and Top2 are present in cancer genome database, we hypothesize that these hcTop2 mutants can be drivers of genome instability and carcinogenesis in mammalian cells. These Top2 mutants may reveal new vulnerabilities of cancer cells that express mutant DNA metabolic enzymes.