Yale University

NSF Awards · FY 2025 · 2025-08

Representation theory is concerned with the study of linear symmetries. These symmetries form algebras that often arise as quantizations or more general deformations of functions on classical spaces -- this is a mathematical counterpart of passing from Classical to Quantum Mechanics or Field theory in Physics. Individual representations form categories, and understanding these categories leads to understanding the representations themselves. Tools to study categories include understanding their own symmetries and showing that categories of different origin are, in fact, equivalent. The focus of this project is to study categories of representations of quantizations, the symmetries of these categories, and their equivalences. The project also involves training young mathematicians and writing books and survey articles to benefit undergraduate and graduate students. In more detail, the project consists of three parts. The first part proposes the study of categories of highest weight modules over affine quantum algebras. These categories should be viewed as categorical analogs of the polynomial representations of double affine Hecke algebras. They depend on parameters, and the task is to establish derived equivalences between the categories corresponding to different parameters and to relate their t-structures. The second part of the project seeks to relate several categorical versions of the elliptic Hall algebra, a close relative of the double affine Hecke algebra, proving derived equivalences between these versions. The third part seeks a conceptual geometric understanding of unitary representations of complex semisimple Lie 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.

NIH Research Projects · FY 2025 · 2025-07

ABSTRACT As part of canonical WNT signaling, beta-catenin forms activating transcriptional complexes with TCF7 factors to promote MYC-expression and proliferation in epithelial, neuronal, endothelial and mesenchymal cells. Despite its critical role in multiple organ systems, beta-catenin is dispensable for normal lymphopoiesis. While other cell types depend on beta-catenin to promote MYC-expression and proliferation, we discovered that B-lymphoid cells have evolved and critically depend on a previously unrecognized mechanism for high-efficiency beta-catenin protein degradation. beta-catenin mRNA levels in B-lymphoid cells were comparable to other cell types, however, beta- catenin protein levels were 80- to 200-fold lower and often undetectable. Lymphoid-specific high-efficiency beta-catenin protein degradation depends on concerted activity of the GSK3B and CK1a kinases, NEDD8-activating enzyme NAE1, and the immunoproteasome subunits PSMB8 and PSMB9. Inhibition or genetic haploinsufficiency of any of these components, reduced degradation efficiency, resulting in beta-catenin accumulation and acute cell death of B-lymphoid cells. In contrast to activating beta-catenin:TCF7 complexes that promote MYC-expression in other cell types, our studies in B-cells revealed repressive beta-catenin complexes with lymphoid Ikaros factors that induced transcriptional repression of MYC and acute cell death. We propose three Aims to (1) elucidate the mechanistic basis of high-efficiency beta-catenin protein degradation in B-lymphoid cells, (2) B-cell-specific composition and function of repressive beta-catenin complexes and (3) to develop concepts for therapeutic intervention at the level of GSK3B, CK1a, NAE1 and PSMB8 to disrupt beta- catenin protein degradation in B-cell autoimmune and lymphoproliferative conditions.

NIH Research Projects · FY 2025 · 2025-07

Project Summary Research into the molecules underlying synaptic exocytosis has revolutionized our understanding of synaptic transmission and connections to a variety of neurological and psychiatric disorders, but several fundamental challenges remain. In particular, decades of research have yet to resolve the precise function of a critical piece of the synaptic vesicle fusion apparatus: Complexin (CPX). CPX is a small cytoplasmic protein containing a highly conserved SNARE-binding motif known as the central helix (CH), that is surrounded by a poorly conserved accessory helix (AH) and a C-terminal amphipathic domain (CTD). Past studies suggest that CPX works in tandem with the vesicle-associated protein Synaptotagmin-1 (Syt1) to prepare and maintain synaptic vesicles (SVs) in a fusion-ready state, with all domains all playing crucial roles in CPX function. However, the precise mechanism remains unclear. Notably, perturbations of CPX function appear to have strikingly different impact on mammalian vs invertebrate model synapses, although few studies have directly compared CPX biochemical and functional properties together across widely divergent species. In this proposal, we describe a systematic and comprehensive approach to compare the proposed functions of worm and mouse CPX and its relationship to Syt1 using a combination of complementary in vitro, ex vivo and in vivo experimental systems, and computational modeling. Specifically, we aim to resolve whether AH domain function together with the CH and CTD domains or acts independently to determine the specificity and efficacy of the CPX inhibitory/facilitatory function. We compare the CTD-membrane interactions and curvature sensitivity to test the hypothesis that the CTD properly localizes CPX on vesicle membranes where it can efficiently bind assembling SNARE proteins. Additionally, we assess how variations in Syt1 inhibitory function influences CPX action across species. For in vitro analysis, we will deploy single-vesicle docking/fusion assay with high time resolution and precise control over protein identity/density. We will test worm/mouse CPX and Syt1 isoforms as well as variants/chimeras, with the species-specific SNARE proteins. These experiments will be complemented with physiological assays in both C. elegans and in cultured mouse neurons. We will utilize CRISPR/Cas9 gene editing and single-copy transgenics to explore the impact of the CPX/Syt1 variants on synaptic function in C. elegans. We will conduct correlative analysis in cultured mouse neurons by utilizing the fast fluorescent glutamate sensor iGluSnFR to image quantal glutamate release at individual presynaptic boutons, followed by post-hoc immunocytochemistry to correlate these release events with the expression levels of release machinery proteins. To close the loop, we will develop mechanistic models of synaptic transmission based on experimental data, incorporating the synergistic actions of CPX and Syt1, and test their feasibility through computational modelling. We expect this project will offer crucial insights into the molecular mechanisms underlying the regulation of neurotransmitter release and contribute to the development of a detailed mechanistic model.

NIH Research Projects · FY 2025 · 2025-07

The unique characteristics of the human immune response in early life are critically important and yet remain poorly understood. Our overarching hypothesis is that the pediatric immune system is not just a naïve adult immune system but is fundamentally different. The challenges associated with pediatric studies, including small sample volumes and rare diseases, have been barriers to meaningful progress in the field, and there are numerous basic questions that remain unaddressed. By taking a synergistic multi-pronged approach, we aim to better understand the unique biology of pediatric immunity and its implications for normal immune function as well as a variety of disease states. The central hypothesis addressed in this program project is that genetics, developmental stage, and immune challenges shape the trajectories of antigen-specific and -agnostic homeostatic set points that determine future immune response quality and quantity. Our three projects, with support of our four cores, will synergize in addressing the following overarching and interconnected scientific aims. Aim 1: Uncover genetic and neonatal determinants of temporally ultra-stable, individualistic immune states established at infancy. Aim 2: Determine dynamic immune parameters remodeled throughout the pediatric age range by immune exposures, developmental variables, and genetics. Aim 3: Elucidate how baseline immune states predict and determine responses to immune challenges in an age-dependent manner in childhood. Our program will leverage multiple human subject cohorts that will offer important insights with broad relevance. Together, this work will enable us to construct a ‘growth chart’ of sorts for the pediatric immune system that will better enable identification and assessment of genetic, environmental, and developmental conditions that deviate immune trajectories into unhealthy ranges.

NIH Research Projects · FY 2025 · 2025-07

PROJECT SUMMARY Immune cells adopt distinct cell type identities and functional states to enable robust defense against diverse challenges. These distinct cell types and states are established by networks of interacting transcription factors, chromatin regulators and cis-regulatory elements. Many key molecular components of these gene regulatory networks are now identified; however, it remains unclear how they work together to orchestrate immune cell state transitions. This gap is in part due to the lack of strategies to concurrently turn on or off multiple components, and thereby probe their identities and modes of interaction. CRISPR/Cas9 technologies can facilitate recruitment of distinct transcription effectors to different loci, thus potentially enabling concurrent activation and repression of different genes in the same cell. However, current CRISPR activation (CRISPRa) or interference (CRISPRi) systems are challenging to implement in primary immune cells. Furthermore, current systems often still show weak and variable effects at target loci, precluding their systematic deployment in diverse immune contexts. These challenges will be overcome by developing a compact viral system for robust, concurrent CRISPR activation and interference (CRISPRa/i) in primary murine immune cells (Aim 1). This system will have the following innovations: (1) CRISPR RNA-scaffolds to recruit distinct transcriptional effectors to different loci in the same cell using a single Cas9 protein; (2) next-generation hypercompact effectors with high transcriptional efficacy; and (3) use of truncated (14-15 nt) scaffold RNAs that will render this system compatible with the widely- used Cas9 knock-in mouse strains. The system will be developed in primary mouse progenitors and optimized for system designs that show both high efficacy and reliability in the targeting of multiple genes. Next, this compact CRISPRa/i system will be used to map the landscape of interactions in the gene regulatory network controlling Bcl11b activation and T cell lineage commitment (Aim 2). The transcription factor Bcl11b is essential for T cell lineage identity; its irreversible all-or-none activation shuts down alternate fate options and commits progenitors to the T cell lineage. Here, a series of single and pairwise CRISPR activation and interference screens in multipotent progenitors will identify transcription factors, chromatin regulators and cis-regulatory elements controlling Bcl11b activation. These studies will identify the gene regulatory network components underlying Bcl11b activation and comprehensively map the genetic interactions between these components. More broadly, they will establish a widely-accessible viral system to concurrently turn on or off genes in primary mouse immune cells, with broad applications in a variety of basic and translational applications.

NIH Research Projects · FY 2025 · 2025-07

PROJECT SUMMARY Stimulant use and stimulant use disorder (StUD) are major contributors to morbidity and mortality in the U.S., disproportionately impacting racial and ethnic minoritized populations. As there is no U.S. Food and Drug Administration (FDA)-approved medication for StUD, development of medications is a high priority. However, medication development (and private sector investment) has been hampered by the lack of a practical, psychometrically sound, clinically significant, and broadly accepted indicator of treatment response, other than sustained abstinence. Recent FDA guidance for developing medications for treatment of StUD recommends the development of instruments for endpoints reflecting disease severity. In this project, we propose to advance development of the novel Stimulant Use Disorder Severity Scale (StUDSS) as a clinical outcome assessment (COA) qualified by FDA as a Drug Development Tool (DDT), which involves three sequential stages of submission and review outlined in FDA Center for Drug Evaluation and Research (CDER) guidance. This work will be conducted at geographically distinct sites in Connecticut and California to enhance validity across stimulant types and racial/ethnic diverse groups. Development will follow FDA Guidance for patient- reported outcome (PRO) measures. Preparation and submission of a Letter of Intent (LOI) to the CDER COA Qualification Program will initiate the qualification process (UG3 - AIM 1). The StUDSS will be administered to racially and ethnically diverse individuals with StUD (n=40) through 1:1 cognitive interviews to establish content validity and create a finalized instrument (UG3 - AIM 2). Following completion of milestones during the UG3 phase, and with input and recommendations from CDER, a qualification plan (QP) will be prepared and submitted to CDER COA Qualification Program (UH3 – AIM 1). The proposed observational study will involve repeated administration of the StUDSS over a 3-month period among n=300 individuals with StUD across sites at Yale and UCLA to establish reliability and validity (UH3 – AIM 2). This proposal is informed by rigorous prior research by our group and others demonstrating relationship between stimulant use outcome measures and functional outcomes; psychometric characteristics of StUD criteria in DSM-5; and value in measuring change in characteristics that define StUD. Our team brings together expertise in stimulant use research, scale development, substance use disorder diagnostic tools, outcome measurement, and the FDA qualification program. This project will produce: 1) a PRO measuring StUD symptom severity with accompanying content validity data, 2) a QP accepted in CDER COA Qualification Program, and 3) validity and reliability data from a racial and ethnic diverse sample. Preparation of a full qualification package (third and final submission stage) will be dependent on recommendations from QP determination letter and expected to occur after completion of the project period. A validated PRO measuring StUD symptom severity that becomes accepted by FDA as a DDT would be of high impact for advancing medication development, treatment research, and clinical care.

NSF Awards · FY 2025 · 2025-07

With the support of the Chemical Synthesis (SYN) program in the Division of Chemistry, Professor Seth B. Herzon of Yale University develops novel synthetic routes toward bioactive complex molecules derived from living organisms known as natural products. The syntheses and structural analyses of natural products play an essential role in the chemical industries as well as in the development of new chemical methods. Moreover, natural products form the basis for a large proportion of pharmaceuticals. Access to natural products by synthetic chemistry allows for systematic evaluation of their molecular properties, including bioactivity, thereby providing the foundation for new medicines. Until now, the marine natural products known as chartellamides have remained relatively inaccessible, limiting our understanding of the properties of these molecules. During the last funding period, a synthesis of the related isolates known as securamines and securines was developed, and this will form the foundation of the approach to chartellamides. To access chartellamides, the development of novel synthetic transformations, which may be of general utility, will be required. To access chartellamide, a biomimetic strategy based upon direct introduction of the indolenine–imidazole bond, peripheral oxidative cyclization, and alkene bromoamination will be pursued. The total synthesis of chartellamide B will permit rigorous structural analysis and potential structural revision using computational, crystallographic, and spectroscopic techniques. The unknown cytotoxicity profile of chartellamide B will be assessed following completion of the proposed synthesis. The researchers involved in this project participate in the Pathways to Science Program through Yale University, focused on STEM education and mentorship for secondary school students in the New Haven area. Additionally, researchers on this project will serve as mentors in the Yale–GSK Scholars program, which provides summer research opportunities for undergraduate students. The researchers involved in this project are involved in the Yale Joint Safety Team, focused on chemical and biological safety education and career development for the broader Yale community. 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 · 2025-07

Opioid use disorder (OUD) and HIV, which affect 53 million and 40 million people respectively, exhibit a syndemic relationship due to structural social and health conditions that impact at least 20 million individuals globally. Both conditions contribute to central nervous system (CNS) dysfunction through distinct and synergistic pathways. Despite extensive research, the specific cellular mechanisms altered by OUD, HIV, and their interaction remain poorly understood. A comprehensive understanding of brain cell states and their localized responses is essential for developing targeted treatment strategies. The SCORCH initiative has facilitated unprecedented data generation through single-nucleus interrogation of brain tissue relevant to HIV and substance use disorders, providing an unparalleled opportunity to explore the molecular underpinnings of HIV, OUD, and their intersection. As the first data generation project supported by the SCORCH initiative, our Y-SCORCH program has significantly contributed to data generation and intellectual leadership. Y-SCORCH 2.0 aims to leverage our SCORCH experience and expertise to apply advanced tools to analyze transcriptomic and epigenetic data from the SCORCH consortium and novel spatial transcriptomic data to identify treatment targets. Y-SCORCH has already generated 346 single-nucleus transcriptomic and epigenetic datasets from the prefrontal cortex, insular cortex, and ventral striatum, across control, HIV, OUD, and HIV+OUD conditions. Through differential expression (DE) analysis, significant changes in immune activation and response have been identified, revealing widespread transcriptomic changes across cell types and elucidating cellular circuits involved in pathogenesis. The proposed research aims to mine SCORCH Consortium data to create a comprehensive catalog of DE genes in HIV and OUD across various brain regions and cell types. This will be achieved by applying standard protocols for DE analysis to ten brain regions and classifying DE genes in HIV versus controls, OUD versus controls, and HIV+OUD versus OUD cohorts. The team will also use neural network models to differentiate batch effects, intrinsic cell type representations, and disease-dependent variations. Additionally, the study aims to utilize neural networks and machine learning models to identify spatial signatures of HIV, OUD, and their interaction. Methods such as SIMVI (an unsupervised Variational Autoencoder) and SORBET (a supervised graph-neural network) will be used to analyze spatial transcriptomics data, identifying cell-cell interactions and expression gradients. The final aim is to leverage external datasets to further characterize the DE genes catalog and elucidate underlying mechanisms and etiology, using genome-wide association studies and other external resources. Y-SCORCH 2.0 will continue to advance the understanding of HIV, OUD, and their synergistic effects by employing cutting-edge methodologies, ultimately contributing to identification of therapeutic targets for these conditions.

NIH Research Projects · FY 2025 · 2025-07

Project Summary This proposal seeks support for a dedicated research PET/MR system for the Yale School of Medicine, featuring a TOF PET instrument integrated with a high-resolution MR system. This system is the first of its kind in the State of Connecticut and will enhance multiple research projects and training grants. Benefits include improved protocol workflow, multinuclear spectroscopic imaging, MRI-enhanced PET images (motion and partial volume correction), increased lesion detection sensitivity, and radiation dose reduction. Advances in MR and PET imaging have spurred significant research in modeling, image reconstruction, and clinical applications, enabling extraction of crucial physiological information. Together the two modalities are even more powerful. MRI can offer additional functional and anatomical information beyond PET, such as diffusion-weighted imaging (DWI), perfusion-weighted imaging (PWI), functional MRI (fMRI), and magnetic resonance spectroscopy imaging (MRSI). Integrating these modalities with PET can provide a more comprehensive understanding of biological processes under investigation. The simultaneous acquisition enables better spatial and temporal alignment between the modalities and improves image fusion accuracy and reduces motion artifacts, which is particularly useful in dynamic imaging studies or applications requiring precise localization, as is true of many of the projects at Yale. Combining the two modalities also reduces the number of scans needed for a subject, increasing their comfort and decreasing overall costs and scheduling complications. The essential administrative and technical leadership is already in place at Yale to ensure efficient utilization of this instrumentation. The Yale School of Medicine has agreed to provide funding to cover the balance of the cost of the scanner along with renovation costs and seed funding for pilot studies. The proposed PET/MR system with its unique capabilities will be a major asset to a community of NIH-funded investigators and likely lead to major innovations in PET/MR imaging research.

NSF Awards · FY 2025 · 2025-07

Mathematical systems underlie today’s data encryption, navigation, and imaging technologies. Yet many of their most important behaviors occur in “infinite‐volume” settings that current theory cannot explain. This project develops new mathematical tools to understand the long-term dynamics and inherent rigidity of such systems, with an emphasis on groups that model negatively curved-space symmetries. By advancing the frontier of pure mathematics, the work directly fulfills the National Science Foundation’s mission “to promote the progress of science.” The results will be presented widely, including in a plenary lecture at the International Congress of Mathematicians (ICM 2026)—the world’s largest mathematics meeting—taking place July 23–30 2026 in Philadelphia, Pennsylvania, USA (https://www.mathunion.org/icm/icm-2026.) Sharing these results on a global stage accelerates discovery in the mathematical sciences and inspires the next generation of STEM talent. The project also incorporates research opportunities for graduate students and postdoctoral scholars. The project investigates dynamics on infinite-volume homogeneous spaces which are quotients of semisimple Lie groups by their discrete subgroups, with a focus on Kleinian groups and higher-rank Anosov subgroups.Goals are to (1) establish ergodicity, quantitative mixing, and orbit-closure criteria for diagonal and unipotent flows, (2) classify invariant measures in settings where finite-volume methods fail, and (3) derive sharp orbit-counting and equidistribution theorems via thermodynamic formalism. Methods blend homogeneous dynamics, Riemannian geometry, geometric group theory, Lie-theoretic representation theory, and spectral/transfer-operator techniques. Expected outcomes include new measure-rigidity theorems, effective counting asymptotics, and a unified framework connecting Kleinian, Anosov, and arithmetic lattice dynamics, laying groundwork for applications in geometry and number theory. 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 · 2025-07

PROJECT SUMMARY The gut-brain axis is emerging as a central mediator of health and disease. Multiple studies have associated gut microbiota composition with neuroinflammatory and neurodegenerative diseases, and several recent studies suggest trafficking of immune cells from the gut to the brain. However, mechanistic understanding of how gut- educated T-cells get to the brain and why this axis exists at all are unclear. We recently discovered that CD4 T- cells are present in mouse and human brain and anatomically localize to the subfornical organ in the brain at steady state. In humans and mice, we performed deep transcriptional and functional profiling of CNS CD4 T- cells and found that they are Th1-like. Using mouse models, we found that CNS CD4-T-cell-derived IFN is required for CNS homeostasis by signaling to astrocytes. We found that CNS T-cells are derived from both the gut and also, surprisingly, the white adipose tissue, and can be phenotypically shaped by the states of both the gut microbiota composition and the state of the fat. Transcriptional and functional profiling across brain, white fat, and gut in mouse and humans identified potential mechanisms of how CD4 T-cells get from the gut to the brain. In this proposal, we will identify the mechanisms by which gut microbiota and the white fat control the CD4 T-cell compartment.

NIH Research Projects · FY 2025 · 2025-07

Abstract Mycobacterium tuberculosis (Mtb) infects nearly 10 million people yearly and kills almost 1.5 million. Treating even drug-susceptible tuberculosis (TB) is difficult because subpopulations of bacteria, while not genetically resistant, can evade killing by antibiotics. To discover small molecule inhibitors for these tolerant subpopulations, we need to understand where they are located and what is their physiology. Directly identifying tolerant bacteria is impossible with conventional methods that rely on measurements from millions or billions of cells. Here, to overcome these limitations we have assembled a team with expertise in single-cell measurements, live-cell microscopy, and TB pathogenesis and metabolism. Leveraging these skills, we have succeeded in quantifying the growth and metabolism of individual mycobacteria in different subcellular environments. We propose to build upon these results and establish which subcellular environment is most associated with drug tolerance, and what carbon source is used by drug-tolerant M. tuberculosis. Then, we will design in vitro culture conditions mimicking this environment. These culture conditions will be used in future drug screening efforts designed to find small molecule inhibitors of drug tolerant mycobacteria.

NIH Research Projects · FY 2025 · 2025-07

Pseudomonas aeruginosa is an opportunistic pathogen that is intrinsically resistant to many antibiotics, metabolically plastic and capable of secreting molecules that manipulate prokaryotic and eukaryotic competitors and predators. When it establishes prolonged chronic infections in human hosts, it further evolves to survive antimicrobial treatment and evade host defenses. Many such adaptive changes occur on the P. aeruginosa cell surface, but our technologies for directly identifying such adaptations are limited. To address this unmet need, we have combined phage display of VHH recognition domains derived from camelid heavy chain-only immunoglobulins (“nanobodies”) with high-throughput DNA sequencing (HTS) to create a high throughput, highly multiplexed technology for surveying bacterial cell surfaces that we call “Phage-seq”. We performed phage display panning on hundreds of pairs of bacterial genotypes and used sequencing data to analyze the dynamics of the phage display selection process. Our published data demonstrate that these datasets capture important biological information about the surfaces of the cells under study. Phage-seq has also enabled the discovery of dozens of nanobodies to date that recognize key P. aeruginosa virulence factors, including determinants of antimicrobial resistance, in their native conformations on live cells. These recombinantly expressed nanobodies have numerous potential applications in diagnostics and therapeutics. We propose that “Phage-seq” enables a new paradigm for studying the bacterial cell surface by identifying and profiling many surface features in parallel. Importantly, Phage-seq does not require antigens to be known in advance and decouples profiling from antigen identification. In this application we extend the reach of Phage- seq to a broad range of genetically diverse P. aeruginosa isolates. The Phage-seq datasets that result will be compared to both genomic data and phenotypes measured via other experimental approaches, allowing us to assess how this method contributes to understanding of bacterial cell surface biology.

NIH Research Projects · FY 2025 · 2025-07

Project Summary / Abstract: Neutrophils are the most abundant leukocytes in the circulation. They are the first to be recruited to the sites of inflammation and abundantly present in many inflammatory diseases. Neutrophils are important for host defense against microbial infections, but also responsible for tissue injuries during acute and chronic inflammation responses. Thus, they are generally considered as being detrimental to tissue well-being in sterile inflammation-related diseases such as acute lung injury and myocardial, renal, and cerebral ischemia-reperfusion injuries as well as some of the autoimmune diseases (inflammatory bowel disease and Type I diabetes). Neutrophils possess great plasticity, heterogenicity, and functional ambivalency. They can be beneficial or detrimental to host well-being depending on contexts. In our investigation of WNT5A and WNT5B, we found that the lack of these proteins protected colitis as the result of increased suppression of colon cytotoxic CD8 T cells by CD101-high neutrophils. These CD101 high neutrophils are produced from splenic extramedullar hematopoiesis, which is stimulated by WNT5-deficiency. In this application, we plan to examine the role of CD101 in immune suppression, characterize functional responses of CD101-high neutrophils, investigate the mechanisms for WNT5 to regulate splenic EMH, and determine the transcription factors that control molecular and hyper-immunosuppressive characteristics of CD101H neutrophils.

NIH Research Projects · FY 2025 · 2025-07

PROJECT SUMMARY/ABSTRACT Nanoparticle (NP) drug delivery systems enable the protection of therapeutic cargoes with tunable target specificity. Polymeric NPs exhibit phagocytic tropism, accumulating in the reticuloendothelial system of the liver and spleen. This property is a barrier to non-phagocyte drug delivery but a boon for the development of phagocyte-mediated disease therapies. We have developed a highly tunable, biodegradable NP platform composed of poly(amine-co-ester) (PACE) polymers that has been successfully utilized to deliver nucleic acids to various tissues. We have demonstrated that NP design and administration variables dictate the organ and cellular biodistribution of PACE NPs. How these variables dictate biodistribution to specific phagocyte subpopulations and how these principles are modulated in the presence of phagocyte-mediated disease are unknown. This proposal outlines a four-year training program for Dr. Thomas C. Binns, MD – enabling his development into an independent investigator with expertise in understanding NP-phagocyte interactions with the goal of developing novel drug delivery approaches for the treatment of phagocyte-mediated diseases. Dr. Binns will study how PACE NP design/administration principles influence uptake in hepatic and splenic phagocyte subpopulations during health and disease. The most important NP design variables – size, charge, stiffness, surface hydrophobicity, and dose – will be evaluated, as we have previously demonstrated that these variables influence biodistribution on the organ and cellular scales. Dr. Binns will carry out these investigations in established murine models of health (Aim 1) and antibody-mediated erythrophagocytosis (AME; Aim 2). This work addresses an area of unmet medical need: AME defines several diseases including warm autoimmune hemolytic anemia, a disease with an estimated 40,000 patient US prevalence, 50% relapse rate, and 10% mortality. A novel treatment option with a long duration of activity and/or a lower drug-mediated morbidity profile could significantly change the therapeutic paradigm for patients with relapsed/refractory disease. Findings will be leveraged to develop a preclinical nucleic acid therapeutic for AME facilitated by PACE NP delivery (Aim 3). Dr. Binns has assembled a team of experts in polymer synthesis, NP formulation, nucleic acid therapeutic design, antibody-erythrocyte interactions, and phagocyte biology/phenotyping who will provide experimental insights, technique advisement, and career mentorship. He will gain training in polymer synthesis, sophisticated data acquisition and analysis (e.g., highly-multiplexed flow cytometry), drug development/translation, and laboratory management in an environment conducive to training physician- scientists. These skills will enable Dr. Binns to successfully transition to an independent position with the goal of developing drug delivery approaches for the immunomodulation of phagocytes.

NIH Research Projects · FY 2025 · 2025-07

HIV-1 Fusion on Native Membranes Captured by Cryo-Electron Tomography Summary Human immunodeficiency virus 1 (HIV-1) infection is initiated by binding to host cells through interactions of the viral envelope glycoprotein (Env) with the cellular receptor CD4 and co-receptors CCR5 or CXCR4. While structures of Env in complex with soluble domains of these receptors have been determined in vitro, the understanding of how these proteins interact on membranes to mediate fusion remains incomplete. Specifically, it is poorly understood how Env, CD4, CCR5/CXCR4 and membranes interact in a higher-order manner at membrane-membrane interfaces, and how the conformational changes of Env, triggered by the engagement of receptors, lead to membrane fusion. These molecular events need to be investigated in their native environment on membranes, where virus fusion occurs. Using a virus-like particle (VLP) system and cryo-electron tomography (cryoET), we have recently reconstituted prefusion membrane-membrane interfaces and revealed unprecedented intermediates of HIV-1 Env bound to one, two, and three CD4 molecules. At these interfaces, Env–CD4 complexes organized into clusters and rings, bringing the opposing membranes closer. Although adopted to an open conformation, the Env trimer bound to three CD4 molecules did not engage the membrane-embedded co-receptor, likely due to steric constraints imposed by membrane-associated CD4 molecules. Consequently, key structures such as HIV-1 Env bound to co-receptors and Env intermediates during refolding that drive membrane fusion are still missing. Here, we propose to extend our research into the dynamics of HIV-1 fusion using cryoET and integrate molecular dynamics (MD) simulations to understand how these components orchestrate the fusion process, to determine the structural intermediates during HIV-1 Env refolding that drive fusion, and to investigate the mechanisms by which fusion inhibitors block HIV-1 infection. Specifically, we will 1) determine if HIV-1 Env-CD4 receptor clustering is necessary or advantageous for HIV-1 Env fusion, 2) determine how Env binds to coreceptor followed by the refolding of gp41 that drives membrane fusion, and 3) investigate the timeline of action for various HIV-1 fusion inhibitors and their effects on the conformational transitions of Env during fusion.

NIH Research Projects · FY 2025 · 2025-07

Project Summary/Abstract In this proposal we hope to build on our efforts showing innate and adaptive immune cell infiltration of labyrinthine tissue in Meniere’s disease. These findings have led us to propose an autoimmune basis for the disease. Our efforts will be directed at confirming our preliminary data that specific pathways including druggable TNF alpha and mTOR pathways are upregulated in Meniere’s disease and establishing that labyrinth infiltrating B cells are autoreactive. We hope that our work will lead to better understanding and rational therapeutics of this poorly understood disease.

NIH Research Projects · FY 2025 · 2025-07

ABSTRACT The Clinical High-Risk Syndrome for Psychosis (CHR-P) is a DSM-5-recognized condition affecting youth and young adults who experience attenuated delusions, hallucinations, and thought disturbances that, while subthreshold for full psychosis, are distressing and impair daily functioning. Attenuated Psychosis Syndrome (APS), listed under "Conditions for Further Study" in DSM-5, affects approximately 1.7% of the general youth population and nearly 20% of youth presenting to psychiatric services, yet remains under-recognized and poorly served by qualified assessment tools. Current clinical outcome assessments (COAs) for APS include the Structured Interview for Psychosis-Risk Syndromes (SIPS) and the Comprehensive Assessment of At-Risk Mental States (CAARMS). Differences between these instruments have historically hindered harmonization across research and clinical trials. In response, the National Institute of Mental Health led a harmonization effort that resulted in the Positive SYmptoms and Diagnostic Criteria for the CAARMS Harmonized with the SIPS (PSYCHS), a semi-structured ClinRO instrument designed to assess 15 distinct attenuated positive symptoms organized into three general concepts: attenuated delusions, hallucinations, and thought disorder. There are currently no FDA-qualified COAs for measuring APS severity in CHR-P clinical trials, presenting a major obstacle to drug development. The PSYCHS is now implemented in the FNIH-funded AMP SCZ observational study and will be further evaluated in the upcoming ProCAN randomized controlled trial, which includes PSYCHS assessments, blinded raters, and ecological momentary assessment. These data provide a unique opportunity to establish the PSYCHS as a reliable and valid ClinRO for use in regulatory trials. The objective of this project is to develop a comprehensive Full Qualification Package (FQP) for the PSYCHS. We aim to: (a) engage the FDA to refine our Qualification Plan through ongoing consultation; (b) systematically evaluate content validity using input from clinicians, researchers, patients, and trainers; and (c) conduct preliminary qualitative and quantitative studies to assess test–retest reliability, recall periods, clinically meaningful change, and within-patient thresholds. The FQP will integrate data from previous studies, ongoing observational research, and a forthcoming clinical trial to support regulatory qualification of the PSYCHS instrument.

NIH Research Projects · FY 2025 · 2025-07

There is a compelling national need to train a new generation of scientists who are well prepared to advance translational biology. At the same time, the growing desire among a robust cohort of our most talented students to obtain a sophisticated understanding of human disease and to utilize their training to create novel solutions and expedite application to humans presents tremendous opportunity. To capitalize on this aspiration, we are excited to propose this Medical Research Scholars Program (MRSP), a Certificate-based interdisciplinary training program designed for highly motivated predoctoral students to apply their curiosity, creativity and drive to problems arising from the pathogenesis of human diseases. This new interdisciplinary program is career enriching and will facilitate the long-term engagement of Scholars with mentors and peers during and after the predoctoral period to foster collaboration and expand the network of translational science. The MRSP is designed to be complementary and concurrent with the programs within the aegis of Yale’s Combined Program in Biological and Biomedical Sciences (BBS), allowing scholars to pursue in depth their individualized research and dissertation goals while acquiring the breadth of skills, background, and emotional intelligence needed to contribute productively to future careers that leverage translational science. The major elements of the formal curriculum are: 1. Core Courses providing a foundation in biomedical sciences using contemporary, active learning pedagogical techniques in interactive classrooms; 2. the Mentored Clinical Experience (MCE), the lynchpin of the MRSP, which exposes students to four dimensions of a human disease: 1) clinical manifestations and pathogenesis; 2) contemporary diagnostics & therapeutics; 3) direct interaction with patients in a mentored setting; and 4) cutting edge research & unaddressed scientific challenges. As important as the formal curriculum, 3. Career Development Activities to promote expression of the unique interests of each Scholar through an extended relationship with a clinician mentor, critical thinking exercises with peer teams, sharing of respective research, and community building through supplemental components, such as “beyond the bench” and “lunches with leaders”, engagement with other predoctoral students pursuing translational research at Yale, and an Annual Symposium. The primary objective of the MRSP is to attract and prepare our Scholars to be leaders with sustained careers in academia, industry, and other research-related paths. Outcomes will be measured using self-assessment and reflection, regular surveys of current and alumni scholars, and long-term tracking of career choices and endeavors. This translational research training program enjoys the commitment from our institution manifest by stipend support for the first year of pre-doctoral training, the administrative infrastructure for the MRSP, and the Career Development components. Furthermore, the MRSP will take advantage of the deep biomedical sciences applicant pool at Yale as well as the extraordinary research strengths of the faculty in the basic and translational sciences.

NIH Research Projects · FY 2025 · 2025-07

Project Summary Not required for this submission

NIH Research Projects · FY 2025 · 2025-07

ABSTRACT Early in the development of the brain, the Kv3.4 voltage-dependent potassium channel is highly expressed in all major fiber tracts as they elongate towards their final destination. In most of these tracts, expression of Kv3.4 disappears as synapses form. The canonical function of Kv channels is to generate K+ flux during action potential firing in order to repolarize the plasma membrane, modulating the influx of Na+ and Ca2+ ions. In contrast, recent findings indicate that Kv3.4 triggers the formation of filopodia and promotes neurite outgrowth even in the absence of ion flux through the channel. Kv3.4 also differs from other closely related channels in that it directly binds the cell adhesion molecule Protocadherin 9 (PCDH9). Binding to PCDH9 is absolutely required for Kv3.4 to be retained and function as a K+ channel in the plasma membrane. The experiments in this proposal will test the hypothesis that the binding of Kv3.4 to PCDH9 allows the latter protein to activate the WAVE complex, triggering the extension of filopodia and neurite outgrowth by nucleation of actin filaments. Biochemical, imaging and patch clamp studies will determine how the ability of Kv3.4 to trigger the formation of filopodia in mammalian cells and the extension of neurites in cerebellar granule neurons is affected by membrane potential and by voltage-dependent inactivation of the channel. Experiments will determine the regions of the cytoplasmic C-termini of Kv3.4 and PCDH9 that are required for the protection of the channel from degradation and for coupling the Kv3.4/PCDH9 complex to the actin-nucleating WAVE complex. Finally, experiments in the intact nervous system will determine how loss of Kv3.4 affects the cellular organization of the cerebellum, and whether this can be rescued by early re-expression of wild-type Kv3.4 or of channel mutants that do not conduct K+ ions or interact with PCDH9. Because marked increases in Kv3.4 levels occur in adults during several disease states, including spinal cord injury, Alzheimer’s Disease and Huntington’s Disease, our findings will provide novel insights into plastic changes in neurite growth associated with these conditions and provide potential therapeutics targeted at the Kv3.4-PCDH9 complex.

NIH Research Projects · FY 2025 · 2025-07

PROJECT SUMMARY / ABSTRACT The overdose crisis in the United States (US) has contributed substantially to mortality, decreased life expectancy, and increased healthcare costs. Xylazine, a veterinary tranquilizer not approved for use in humans, has emerged as an adulterant to the unregulated opioid supply. This has created a rising concern amongst public health practitioners, healthcare providers, and harm reductionists alike, as there is evidence that xylazine (a) may be contributing to the rise in opioid overdoses through increased respiratory depression and decreased heart rate and (b) can induce painful skin ulcers that can have extensive necrosis and are vulnerable to infection. However, due to the novelty of this adulterant in the US, people who use drugs (PWUD) and those that provide services to PWUD have very little information about this substance and its related sequelae. Thus, in this proposal I will pursue two multi-methods studies to characterize the impact of xylazine on PWUD. The first study, based in North Carolina, aims to describe the perceptions of and experiences with xylazine and its related complications (i.e., wounds and overdoses) among PWUD. I will collaborate with North Carolina Survivors Union to recruit participants and use both survey and interview methodologies to ascertain how xylazine is impacting PWUD’s drug use behavior, health outcomes, and healthcare seeking/access. My second study is based in Maine and aims to both (a) elucidate the feasibility and acceptability of a community-based drug checking program that allows PWUD to test their drugs for xylazine and (b) qualitatively and quantitatively describe drug supply changes over time. To assess feasibility and acceptability of a drug checking intervention, we will conduct focus groups amongst PWUD, staff of syringe service programs implementing drug checking, and medical care providers. To describe drug supply changes over time, we will analyze chemical analysis samples of drugs provided to three syringe service programs in Maine. Drug checking, from both Fourier-transform infrared (FTIR) spectroscopy tests in the field and confirmatory gas chromatography–mass spectrometry (GC-MS) conducted in an academic laboratory, will help improve epidemiological surveillance of the volatile drug supply in Maine. Through rigorous scientific evidence, our study is designed to identify key strategies for reducing the harms associated with xylazine among PWUD. This multi-methods proposal ultimately hopes to inform both medical care and harm reduction best practices.

NIH Research Projects · FY 2026 · 2025-07

Tissue injury requires the proper establishment of a dynamic inflammatory niche to clear invading pathogens and damaged cells, and then to promote tissue repair. Clinical cases of poor wound healing are marked by prolonged inflammation, often associated with immune dysfunction, which leads to tissue damage and a spectrum of pathological outcomes. Inflammation immediately after injury is largely driven by early-stage monocyte-derived macrophages and neutrophils, and so understanding the mechanisms that control inflammation in these cell types will provide new therapeutic treatment options. There is increasing interest in how changes in metabolism control the phenotypes of macrophages and other immune cells by regulating signaling and gene expression that are central to activation, including inflammation. Recently, our laboratories uncovered an unexpected and intriguing role for glutamine metabolism in regulating macrophage function in skin wound healing. In particular, we found that mice fed glutamine-deficient diets have prolonged inflammation and defective wound repair. Our data further reveal that glutamine regulates specific subsets of inflammatory genes and epigenetic changes in macrophages. Therefore, the overall objective of this proposal is to define the contributions of metabolic regulation of macrophages to skin wound healing. Our central hypothesis is that glutamine metabolism controls the inflammatory niche during tissue repair in the skin and macrophages are the primary mediators of this response. This hypothesis is based on our findings that: 1) macrophages display altered metabolic profiles during early and mid-stage repair; 2) the inflammatory niche is altered in mouse wounds that lack glutamine metabolism in monocyte-derived cells; 3) glutamine metabolism alters the inflammatory gene expression of macrophages. Through three focused and complementary Specific Aims, we will (1) identify the role of glutamine metabolism after injury in vivo and in human macrophages in vitro, (2) define how glutamine metabolism impacts epigenetic regulation and redox signaling in skin wounds, and (3) examine the impact of diabetes on glutamine metabolism during skin repair. The work proposed in this application is innovative because it will take advantage of multiple genetic mouse models that allow specific depletion of glutamine metabolism, and state-of-the-art genomics and systems analysis of mouse and human wound data. The proposed research is significant because it will provide information about the precise function of glutamine in skin repair in vivo, which is currently poorly understood. The rationale for this research is that amino acid enriched dietary supplementation can improve chronic diabetic wounds, which impacts over 4 million patients in the US and over 7 million worldwide, but more information about the mechanisms is needed to optimize therapeutic applications. Our proposed studies will identify specific mechanisms that can be utilized to promote healing in human patients with defective wound healing or inflammatory disorders.

NSF Awards · FY 2025 · 2025-07

Although current physics theories successfully explain nearly all laboratory experiments carried out to date, they cannot account for key properties of the universe as determined from astrophysics. For instance, the observed structure of the universe can only be explained through the existence of dark matter—a form of matter that is fundamentally different from atoms, and which has never been detected on Earth because it interacts only extremely weakly with regular matter. In addition, although gravity has been studied for hundreds of years, gravitational forces between microscopic particles that obey the laws of quantum mechanics have never been measured, and theories of gravity may need to be modified in the quantum realm. In this work, the research team will develop new types of force sensors that may allow detection of the tiny forces imparted by dark matter, or from gravity between microscopic particles. Students and postdocs participating in this work will be trained in advanced quantum sensing techniques and will work with the PI to teach a hands-on summer program for local high school students about physics in their everyday lives and connections to state-of-the-art research. This research program will employ arrays of micro- and nano-particles trapped in ultra-high vacuum as sensitive force sensors for searches for physics beyond the Standard Model of Particle Physics. The research team will use these particle arrays to search for dark matter that primarily interacts coherently with nano- or micro-sized particles (rather than single nuclei or electrons), with several orders-of-magnitude improved sensitivity over previous searches for such dark matter models. In addition, the research team will develop techniques to trap solid noble gas particles, such as solid xenon, in a cryogenic optical trap. Solid noble gas particles may provide significant advantages over existing techniques (that primarily employ silica particles) due to their extremely high purity and ability to construct large particle arrays. 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 · 2025-07

While modern developments in large-scale sensing and imaging modalities bring great premise in discovering novel scientific phenomena and improving the quality-of-life, making sense of the sensed data in an efficient and accurate manner require transformative designs of scalable and effective optimization methods for solving inverse problems that go beyond classical linear models. There is a significant need to advance the theory, algorithms, and applications of nonlinear inverse problems, where the collected data exhibit a nonlinear relationship with respect to the unknowns being sought after. Focused on taming nonlinear inverse problems, this project will be tightly integrated with education, outreach and dissemination activities including mentoring both graduate and undergraduate students with diverse backgrounds, developing courses and monographs on nonlinear inverse problems in data science, and organizing special sessions at suitable conference venues. The intellectual goal of this project is to develop theoretical and algorithmic foundations for solving nonlinear inverse problems, including the design and analysis of efficient algorithms with provable guarantees, characterization of fundamental trade-offs between resources (sample, computational and memory complexities, signal-to-noise ratio, etc.) and performance (statistical error rates, resolution, etc.), and validations on real data whenever applicable. The project seeks to leverage the diversity of multiple measurements and the invariance of data representation in the algorithm designs to minimize complexity and improve performance. The tools and techniques developed in this project will lead to further cross fertilization among the fields of signal processing, inverse problems, optimization theory, and machine learning. 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.