University Of Rochester

NIH Research Projects · FY 2026 · 2026-03

PROJECT SUMMARY Pathogenic variants in tRNA modification enzymes are the cause of numerous diseases and disorders in the human population. However, the molecular basis of these pathologies are unknown due to major knowledge gaps that prevent our complete understanding of tRNA modification enzymes such as: How do modifications impact tRNA structure and function? What are the functions of vertebrate-specific tRNA modification enzymes? How do tRNA modification enzymes regulate cellular and developmental pathways? To resolve these knowledge gaps, our lab aims to elucidate the biological roles of tRNA modification enzymes. We will use an integrated approach combining biochemistry, molecular biology, and genetics with the development of new disease models and tools for detecting RNA modifications. We plan to decipher how modifications impact the global tRNA transcriptome to reveal conserved and novel roles for tRNA modification enzymes. Our studies will resolve the enigmatic functions of tRNA modifications and unravel the tissue- and cell-specific roles of tRNA modification enzymes linked to human disease. Importantly, elucidation of these mechanisms could reveal new modes of gene regulation that would inform strategies to understand and treat human pathologies linked to tRNA modification.

NIH Research Projects · FY 2026 · 2026-02

Abstract. The developing fetus is exceptionally vulnerable to chemicals in the environment. Prenatal exposure to environmental contaminants, such as heavy metals, PFAS compounds and pesticides, impose a substantial societal cost due to the intellectual disability burden to children exposed early in life. Adverse chemical exposures are unavoidable in many cases, due to contaminated environments or the co-exposure that come with foodstuffs and with contaminated drinking water. Therefore, understanding how maternal handling of toxicant exposure, and particularly how the pregnant state may enhance or compromise this function, are a top priority. Mercury (Hg) is among the top environmental contaminants that pose human health risks, ranking third on the U.S. Agency of Toxic Substances Disease Registry priority list of hazardous substances. Methylmercury (MeHg) is the most highly toxic form of mercury and is commonly consumed with fish where it ultimately poses its greatest health risk to the developing fetus. In this proposal we investigate the potential impact of pregnancy on moderating MeHg clearance kinetics in the mother and thus, toxicity for the fetus. We will expand upon exciting and unexpected preliminary evidence that as pregnancy progresses, maternal elimination of MeHg increases, potentially reducing the exposure to the fetus. By optimizing tools that we have previously developed to monitor MeHg metabolism and excretion in non-pregnant adults, we will now evaluate pregnant women, who choose to eat fish routinely, for changes in MeHg elimination over time. With prior knowledge that the gut microbiome is responsible for MeHg metabolism (demethylation) that promotes its faster excretion, we will evaluate the maternal gut microbiome for demethylation activity in parallel. In addition, we will perform metagenomic sequencing to resolve the entirety of species in the gut microbiome to attempt to identify the organisms responsible for faster elimination. Finally, we will compare the mother’s MeHg elimination rate to that the fetus in third trimester. We anticipate the outcomes of this study will determine whether or not: 1) increased MeHg elimination with the progression of pregnancy is generalizable to all mothers, 2) the gut microbiome is a potential mediator of pregnancy-induced MeHg elimination and 3) fetal elimination of MeHg is entirely dictated by the mother or is moderated in part by the fetus itself. We view this as a high-risk, high-reward study, with great potential to reveal generalizable traits of the maternal microbiome that can limit toxicant exposures and furthermore be accessible to modifications that will ultimately reduce toxicity risk to the fetus.

NIH Research Projects · FY 2026 · 2026-02

SUMMARY Tobacco/cigarette smoke (CS) including environmental tobacco smoke (ETS) exposure leads toxicological effects on the lungs associated with injury and inflammation in airway disorders, such as Chronic Obstructive Pulmonary Disease (COPD). COPD is the third leading cause of chronic morbidity and mortality, both in the United States and globally. Recently, my research has shown that ETS/tobacco smoke- mediated molecular clock disruption is associated with cellular senescence in lung cells. REV-ERBα is a critical component of the molecular clock, which regulates the expression of core clock genes, pro- inflammatory and pro-senescent mediators. We show that ETS-mediated cellular senescence is mediated by alterations in clock gene nuclear receptor REV-ERB in the lungs. I will leverage the ongoing program with my seminal contributions on ‘molecular clock senescence theme’, and continue the upward trajectory of the same high caliber science in the field of inhalation toxicology for improving the environmental human health. There is a gap in understanding the cellular characterization and interactions of senescence and molecular clock in human lungs over the lifespan, particularly in non-smokers, smokers, and COPD with and without smokers. Further, the role of molecular clock REV-ERBα dysfunction in chronic ETS-mediated toxicological lung effects remains unknown. In addition, there is a critical gap on restoration of molecular clock and cellular senescence by using targeted agonists (REV-ERBα) and/or senolytics/senomorphics (senescence inhibitors) in lung cells exposed to ETS. We hypothesize that ETS disrupts molecular clock function, specifically REV- ERBα abundance, resulting in cellular senescence via disruption of nuclear co-repressor complex (NCoR/Sin3A-HDACs) in pulmonary toxicity. Using a combination of cellular, molecular, and toxicological approaches, I propose the three overarching long-term goals on this R35 RIVER application to advance the field of inhalation toxicology and lung molecular clock-inflammaging in chronic environmental lung diseases. 1: Characterization of human molecular clock and lung cellular senescence over the lifespan in COPD (with and without smokers), 2: Determine the role of lung molecular clock REV-ERB in cellular senescence programming via nuclear corepressor complex and airway disease responses, and 3) Attenuation of REV- ERB and senescence and SASP/secretome by pharmacological agents/agonists in lung cells and EpiAirway 3D cells. This will characterize cellular molecular clock and senescent cells at an unprecedented spatial resolution in lungs. This transformative research with a compelling and broad vision will advance the field of environmental lung science, collaborations, and training. The outcome of this proposal will unravel the mechanisms, characterization, and programming of lung molecular clock and senescence based on cellular phenotypes and molecular signatures in the pathogenesis of airways disorder. In turn, this will have a great translational potential for the development of pharmacological therapies in environmental pulmonary diseases.

NSF Awards · FY 2026 · 2026-02

With support from the Chemical Mechanism, Function, and Properties Program in the Division of Chemistry, a research team at the University of Illinois at Chicago are developing new reactions to rapidly assemble novel molecules through unconventional strategies using N-alkenylnitrones and N,O-dialkenylhydroxylamines as reactive intermediates. The rearrangement reactivity of these intermediates is being controlled to form more complex molecules with defined three-dimensional structure. Simple modular routes to generate N-alkenylnitrones and N,O-dialkenylhydroxylamines from readily available reagents are being used to facilitate these activities. This work is targeting improved synthetic efficiency to expand chemical space. Improvements in this area are necessary to support the discovery, accessibility, and study of biologically active molecules, as well as the development of new materials. These activities are also providing training for graduate and undergraduate students to become successful members of the chemical workforce and lowering barriers to students engaging in undergraduate research and considering chemistry career paths. Improving efficiency to enable rapid access to new molecular targets and expanding chemical space to include new molecular architectures remain two critical needs in organic synthesis to support demands for new compounds with novel properties for medicinal and material applications. The unique reactivity of N-alkenylnitrones and N,O-dialkenylhydroxylamines is being developed to address these goals by providing alternative solutions to synthetic challenges and improving the fundamental understanding of these versatile and unusual synthons to expand the synthetic toolbox of pericyclic and cascade reactions. More specifically, stereocontrol of the new C–C bond forming reactions that these synthetic intermediates undergo is being investigated through the development of: (i) catalytic asymmetric 4pi- and 6pi-electrocyclizations of N-alkenylnitrones for the synthesis of enantioenriched azetidine nitrones and oxazines, (ii) catalytic asymmetric sigmatropic rearrangements of N-alkenylisoxazolines for the synthesis of enantioenriched 1-pyrrolines, and (iii) stereoselective nitrone-templated sigmatropic rearrangements and C–H bond insertion reactions for the synthesis of 1,4-dicarbonyl compounds. These activities are training students in chemical experimentation and a series of events are engaging undergraduates in considering the merits of research experiences and opportunities available in chemistry career paths. 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 · 2026-02

Abstract Meiosis ordinarily ensures the fair segregation of alleles to gametes. Meiotic drivers are selfish genetic elements that subvert this normally fair process and bias their transmission to the next generation, violating the principles of Mendelian inheritance. Drivers are pervasive in sexually reproducing organisms and can spread in populations, even when they harm the host. We know little about the molecular mechanisms of drive but themes emerging from studies of sperm-killing male meiotic drivers implicate chromatin regulation and small RNAs as important factors. This project proposes to study the molecular mechanism of drive in a powerful model system: Segregation Distorter (SD), a sperm killer found in natural populations of Drosophila melanogaster. SD causes sperm dysfunction by inducing a chromatin defect in wild type spermatids containing a sensitive allele of its target—a large block of tandem satellite DNA repeats called Responder (Rsp)—through an unknown mechanism. This proposal studies the molecular basis of the SD- induced sperm chromatin defect and the role of the target in drive sensitivity. The project has two specific aims: 1) to determine the role of Rsp satellite-derived RNA in the mechanism of SD; and 2) to determine the timing and nature of the chromatin phenotype associated with sperm dysfunction. The proposal combines gene editing techniques to manipulate Rsp satellite-derived RNA, with genetic and cytological approaches to quantify the effects on drive strength and chromatin phenotypes. To study the chromatin defect in detail and pinpoint its timing, the proposal uses long-read-based epigenomic assays to study the dynamics of histone marks in driving testes and their controls. The fulfillment of these aims will shed light on mechanisms of drive, dynamic changes in chromatin states in testes, and how satellite DNAs are regulated in the male germline. These insights have broad implications for our understanding of factors influencing male fertility in general and how spermatogenesis is vulnerable to selfish genetic elements.

NIH Research Projects · FY 2026 · 2026-01

Abstract Since the medical breakthroughs of surfactant and synchronized mechanical ventilation in the 1990’s, there have been few new interventions that have substantially impacted morbidity and mortality of infants born at extremely low gestational ages (ELGANs), resulting in stalled even increased common morbidities. The most common ELGAN morbidities, including central white matter disease, necrotizing enterocolitis, bronchopulmonary dysplasia, retinopathy and sepsis share features of inflammation, suggesting immune-mediated damage may be a common causal pathway. However, there are major gaps in our understanding of normal human fetal and postnatal immune development in full-term infants, and even more so in preterm infants, which are born at a development stage of the immune system which was not meant to encounter the non-sterile extra-uterine environment. These gaps have limited our ability to discern, let alone treat harmful activated immune pathways. To make matters even more complicated in ELGANs, some age-associated immune pathways are necessary for sustained organ development, as evidenced by our previous work showing that ELGANs whose T cells do not follow an expected pattern of change over time are at higher risk for respiratory illnesses later in infancy. Thus, there is a critical need to understand both the molecular program that defines normal immune maturation, as well as the earliest timing during which abnormally developing immune pathways are likely to respond to intervention postnatally. The overall goal of the project is to identify key age-associated immune pathways in ELGANs T cells that can be targeted for treatments. We hypothesize that there is an underlying immune program that meets the unique demands of a developing fetus, but this program is vulnerable to disruption by common postnatal exposures, including antibiotics, during the first postnatal month. To address this hypothesis, we aim to 1) model typical and atypical longitudinal age-determined T cell subset trajectories in ELGANs, 2) frame a postnatal window during which immune trajectories are susceptible to modulation using discovery proteomics, 3) determine the gene regulatory program in ELGANs using single cell genomics, 4) Identify immune changes associated with a common exposure, antibiotics, and potential gene targets to mitigate their harmful effects. Successful completion of this study will provide the highest resolution immune trajectories during the most dynamic period of postnatal immune system development. These results will enable us to direct novel immunomodulatory therapies at the appropriate postnatal age in order to promote normal immune system development in ELGANs.

NIH Research Projects · FY 2026 · 2026-01

PROJECT SUMMARY Alzheimer’s disease (AD) is a prevalent aging-related neurodegenerative disorder that causes severe cognitive decline, affecting memory and decision-making. While basic sensorimotor functions remain relatively preserved in its early stages, cognitive decline varies widely across individuals, suggesting that selective neural circuit dysfunction underlies this variability. The Frontal-Insular Network (FIN)—comprising the medial prefrontal cortex (mPFC) and anterior insular cortex (aIC)—plays a central role in integrating cognitive and affective processes essential for adaptive decision-making and behavioral flexibility. Hallmark AD pathologies, including beta- amyloid plaques and tau neurofibrillary tangles, accumulate preferentially in these higher-order association areas before spreading to primary sensorimotor regions. However, how this pathology interacts with the intrinsic features of the FIN, such as its dense dopaminergic (DA) innervation and low parvalbumin (PV) inhibitory neuron density, to drive age-dependent cognitive decline remains poorly understood. This project aims to investigate the selective vulnerability of the FIN in aging and AD by integrating in vivo structural, functional, and molecular analyses with behavioral assessments in mouse models. Aim 1 will determine age-related structural and functional changes in the FIN of wild-type mice by using two-photon imaging to track dendritic spine dynamics and DA terminal remodeling, along with fiber photometry to measure neural activity and DA release during cognitive flexibility tasks. Aim 2 will examine how AD-related genetic mutations (APP/PS1) accelerate FIN degeneration, using similar methodologies to compare APP/PS1 mice across disease progression stages with age-matched wild-type controls. Aim 3 will investigate cell-type-specific molecular dysregulation in the FIN using spatial transcriptomics and assess whether targeted neuromodulation (pharmacogenetics and optogenetics) can improve cognitive flexibility in APP/PS1 mice. This study is highly innovative, leveraging a multi-level approach to dissect the structural, functional, and molecular mechanisms of FIN vulnerability. Identifying circuit-specific deficits will provide critical insights into targeted interventions that could preserve cognitive function in AD, ultimately guiding therapeutic strategies for neurodegenerative diseases.

NIH Research Projects · FY 2026 · 2026-01

PROJECT SUMMARY AMPA receptors are critical components of excitatory synaptic transmission and play myriad roles in brain function. AMPA receptors are nearly always accompanied by one or more types of auxiliary proteins, principal among these being the transmembrane AMPA receptor regulatory proteins (TARPs). This family of four-pass transmembrane proteins contains prominent extracellular domains that interact with AMPA receptors to modulate channel gating. However, not all TARPs modulate AMPA receptors equally. For example, the TARP γ8 alters AMPA receptor kinetics to a greater extent than γ2 (a.k.a stargazin), even inducing a striking resensitization or superactivation response. Structural and functional studies implicate the large β1-2 extracellular loop of γ8 as critical for kinetic modulation. Consistent with this, swapping the larger β1-2 loop of γ8 with the smaller loop of γ2 can broadly exchange the modulatory phenotype. Because this β1-2 loop is flexible, it remains unresolved in cryo-EM structures. Thus, the precise contacts between the loop and the AMPA receptor, and the underlying mechanism of modulation, is unclear. Interestingly, focused refinement of the β1-2 loop indicates this segment may move between the resting, active, and desensitized states, potentially producing new contacts. Here we propose to identify contact sites between the γ2 or γ8 β1-2 loop and the AMPA receptor using a combination of non-canonical amino acid crosslinking and patch clamp fluorometry. In addition, we will use patch clamp FRET to discern if the β1-2 loops of γ2 or γ8 move during activation, desensitization, and superactivation. Taken together, these studies will advance our mechanistic understanding of AMPA receptor and TARP interactions and glutamate receptor gating. Furthermore, developing these techniques will allow us and others to interrogate the relative positions and ensemble movements of the many unresolved or intrinsically disordered regions of membrane proteins.

NSF Awards · FY 2025 · 2025-12

Enhancing memory safety in Graphics Processing Units (GPUs) is an essential requirement for secure Artificial Intelligence (AI) technologies. Scientific research increasingly depends on advanced AI technologies to drive breakthroughs, with GPUs serving as fundamental computational resources. Many scientific cyberinfrastructures (CIs) have made substantial investments in GPUs to support such efforts. While GPUs deliver considerable performance benefits, the security of GPU software, and memory safety in particular, has not received sufficient attention. Memory safety vulnerabilities such as buffer overflows can lead to serious consequences, including data corruption and unauthorized code execution. These vulnerabilities pose significant risks in shared scientific computing environments, where a single memory safety flaw can compromise the integrity of entire workflows and affect multiple researchers. This project addresses the urgent need to strengthen GPU software security against memory safety risks. The SecGPU4AI project enhances GPU memory safety through two complementary thrusts. The first thrust focuses on designing a fuzzing-based framework for detecting and repairing memory safety vulnerabilities in AI GPU toolkits commonly used in scientific computing. The second thrust focuses on developing lightweight, software-based run-time defenses (such as a secure GPU memory allocator) to detect and prevent common memory safety attacks. These defense mechanisms require no changes to GPU hardware or proprietary toolchains, and thus can be readily adopted in existing scientific computing environments. By improving GPU memory safety, this project considerably enhances the security and reliability of AI-driven research across a wide range of scientific domains. It also opens new research directions in GPU security methodologies that extend to other computing areas. The research team will open-source all developed tools and collaborate with CI providers to promote their adoption and real-world impact. 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 · 2025-10

Tendons connect muscles to bones and experience stretching forces when muscles contract. Many tendons also encounter compressive forces from physical contact with bone, a phenomenon known as “impingement.” While impingement is common in healthy tendons, tendon diseases often develop at sites of tendon impingement. Unfortunately, it is not known why impingement is typically benign yet sometimes harmful. Preliminary studies suggest that the speed of impingement could influence its effect on tendon. That is, while fast impingement produces large deformations in tendon cells and their surrounding structures, slow impingement produces smaller deformations and squeezes substantial amounts of water out of tendons. Importantly, this water loss could protect tendons from future episodes of impingement, much like a deflated balloon is harder to pop than a full one. Thus, the hypothesis for this research is that while fast impingement damages tendon health, slow impingement is not only less harmful but also protects tendon from later bouts of fast impingement. Since impingement has been linked to several painful tendon diseases, the findings of this study could one day impact clinical care for musculoskeletal disorders. In addition, this study will impact the greater Rochester community, as it will be carried out in tandem with the PI’s long-running summer research program for Rochester City School District high school students; and coursework that prepares graduate students to communicate science and engineering clearly to broad audiences. This project seeks to determine why a routine occurrence – physical contact between tendon and bone (i.e., “impingement”) – occasionally triggers a pathological response. To this end, the objectives of this research are to investigate whether the effects of impingement on tendon health are modulated by impingement speed and to test whether prior exposure to slow impingement protects tendon from rapid impingement. The experiments will be conducted using innovative multiscale experimental and computational methods that other biomechanics and mechanobiology researchers can adopt to advance their own work. Moreover, data will be acquired that could shed light on key unresolved questions, including why musculoskeletal pain is often worst in the morning before diminishing as the day progresses. Specifically, this work is expected to demonstrate that musculoskeletal tissues are especially vulnerable to impingement when they have not been recently loaded (e.g., in the morning). However, early joint movements expel water from the tendon, and this loss of fluid is protective against future impingement episodes (much like deflated balloons are difficult to pop). 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 · 2025-10

The Noyce Track 3: Master Teaching Fellowship project aims to serve the national need of preparing and retaining highly-qualified STEM teachers to support K–12 education and workforce development in response to the rapid growth of domestic microelectronics and semiconductor industries. Additionally, this project plans to support 15 practicing STEM teachers in science, technology, engineering, and mathematics by offering leadership development, mentoring, and opportunities to co-design and implement locally relevant STEM initiatives. The proposed project components are positioned to enable high-achieving practicing teachers to become STEM teacher leaders with the capacity to engage students in innovative STEM learning experiences and to strengthen educational pathways that align with the evolving needs of regional microelectronics ecosystems in Idaho and New York. This project at Boise State University and the University of Rochester includes partnerships with rural and urban high-need school districts in Idaho and New York; the Industrial Associates Program at the University of Rochester; the Microelectronics Education and Research Center at Boise State University; and nonprofit organizations such as the Idaho STEM Action Center, the Idaho Rural Schools Association, and The Story Collider. Project goals include preparing and retaining 15 STEM teacher leaders over five years in science, technology, engineering, and mathematics to support the emerging microelectronics and semiconductor ecosystems in both states. These practicing teachers will have the opportunity to deepen their knowledge of microelectronics and semiconductors, enhance their leadership skills to promote educational innovation, and build communication competencies to support K–12 STEM initiatives tailored to local needs. Grounded in Social Cognitive Career Theory, the project emphasizes self-efficacy and outcome expectations to shape teachers’ professional trajectories and their students’ interest in STEM careers. This project is proposed to include an interactive evaluation component. Evaluation will be guided by the following questions: (a) In what ways do participants become integrated into the regional microelectronics and semiconductor ecosystems, and what is the relationship between these integrations and the project components? (b) To what degree did program participants advance their knowledge, skills, and dispositions in semiconductors and microelectronics based on program components? (c) In what ways did Noyce Fellows enact teacher leadership and how did program components contribute to these activities? (d) In what ways have Noyce Fellows advanced in communication skills to foster impactful engagement with students and community members? and (e) In what ways does a collaboration between institutions from different states benefit project participants, including project leaders? The results of this project will be disseminated to help enhance the field. This Track 3: Master Teaching Fellowships project is supported through the Robert Noyce Teacher Scholarship Program (Noyce). The Noyce program supports talented STEM undergraduate majors and professionals to become effective K–12 STEM teachers and experienced, exemplary K–12 teachers to become STEM master teachers in high-need school districts. It also supports research on the effectiveness and retention of K–12 STEM teachers in high-need school districts. This project is funded by the Robert Noyce Teacher Scholarship Program and is supported in part by funds from the Micron Technology, Inc. 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 · 2025-09

Abstract Recent publications have sparked a renewed interest towards the origin and functions of megakaryocytes localized to the lung. Our laboratory previously reported that lung and bone marrow megakaryocytes are morphologically and functionally distinct. Specifically, lung megakaryocytes are lower ploidy and more immune differentiated than bone marrow megakaryocytes. Despite these differences, however, we recently discovered that both megakaryocyte populations are derived from hematopoietic progenitors in the bone marrow. Consequently, we aim to determine the mechanistic determinants associated with differentiation of heterogenous megakaryocyte populations. My preliminary data identify the transcription factor Myb as a gene highly expressed in bone marrow, but not lung megakaryocytes. Using transgenic mouse models, I determined that Myb expressing megakaryocytes have decreased expression of immune markers. Furthermore, megakaryocyte specific deletion of Myb is associated with more immune differentiated megakaryocytes, representative of the subpopulation localized to the lung. We hypothesize that Myb limits megakaryocytes immune differentiation, and therefore regulates the function of lung versus bone marrow derived platelets. We seek to identify the mechanisms by which Myb regulates megakaryocyte immune differentiation to generate an expanded model of platelet function and phenotype. We seek to leverage this information to generate therapeutic strategies to target inflammation associated with cardiovascular disease pathologies.

NIH Research Projects · FY 2025 · 2025-09

ABSTRACT Human immunodeficiency virus (HIV-1) infection can lead to Acquired Immune Deficiency Syndrome (AIDS) and HIV-Associated Neurocognitive Disorder (HAND). In the life cycle of HIV-1, programmed ribosomal frameshifting (PRF) is a key event during translation of HIV-1 mRNA that allows the synthesis of viral enzymes. While the cis- acting RNA elements for HIV-1 PRF have been well defined, the trans-acting viral and cellular factors regulating HIV-1 PRF remain relatively unexplored, which constitutes a knowledge gap in HIV-1 research. We have performed a genome wide CRISPR knockout screen to identify host factors that regulate HIV-1 PRF. Our screen has revealed that m1acp3Ψ modification of rRNA, wybutosine (yW) modification of tRNAPhe, and diphthamide (DPH) modification of eEF2 are major trans-acting factors that repress ribosomal frameshifting on HIV-1 mRNA. These modifications (m1acp3Ψ, yW, and DPH) are of central importance to the accuracy of cellular protein synthesis. Individuals with deficiency of yW or DPH modification present with neurodevelopmental disorders and intellectual disability. We have also found that yW modification of tRNAPhe and DPH modification of eEF2 are blocked in HIV-1 infected cells. Our central hypothesis is that HIV-1 upregulates ribosomal frameshifting by depletion of yW and DPH to facilitate virus replication, while increased ribosomal frameshifting promotes HIV-1 inflammation and neurotoxicity. In this project, we will elucidate the mechanism by which HIV-1 downregulates yW and DPH modifications (Aim 1), determine the roles of yW, DPH, and m1acp3Ψ in HIV-1 PRF and replication (Aim 2), and determine the roles of yW and DPH in HIV-1 inflammation and neurotoxicity (Aim 3). Our proposed studies will significantly improve our understanding of the molecular mechanism of HIV-1 PRF and provide new insight into HIV-1 pathogenesis. In the long term, these studies will provide new targets and strategies for the treatment of HIV-1 infection.

NIH Research Projects · FY 2025 · 2025-09

Bronchiolitis obliterans (BO) is a devastating lung disease of the small airways that is becoming more frequently associated with certain environmental inhalation exposures. Two chemicals commonly associated with BO after inhalation exposures are 2,3-butanedione (diacetyl; DA) and 2,3-pentanedione (PD). Both chemicals are highly reactive diketones ubiquitous to the environment and frequently added as a flavoring additive to foods and drink. While preclinical models demonstrate a clear dose-response of inhalation exposures to these chemicals and BO, the mechanisms contributory to disease induction remain poorly understood. We have shown previously chemical exposure to DA in both primary human airway epithelial cells and rats injures not only the airway epithelia but, more importantly, airway basal cells – the primary progenitor cells of the airway epithelia – via damage to cytoskeletal keratins. With repeated exposures, damaged keratins aggregate in airway basal cells, activating the integrated stress response (ISR) and downregulating two proteins, plectin and integrin beta 4 (ITGβ4), that connect airway basal cells to the basement membrane. We hypothesize that airway basal cell stress through damaged keratins, ISR activation and decreased ITGβ4 expression is a common mechanism to environmentally induced BO after inhalation exposures to structurally similar chemicals. In support of this hypothesis, airway basal cells isolated from rats exposed to DA at occupationally relevant concentrations who develop BO show impaired regenerative capacity with decreased epithelial proliferation and differentiation. Second, human airway epithelial cells exposed to PD develop similar damage to keratins and decreased ITGβ4 protein expression, supportive of a common mechanism across structurally similar chemicals. Third, ITGβ4 overexpression in exposed cells promotes epithelial repair with reduced ISR activation. Fourth, a ‘stressed’ airway basal cell phenotype with high ISR and low ITGβ4 expression is identified in human lung tissue affected by BO from prior environmental exposures. Aim I of this proposal will assess the number and function of airway basal cells using a rat model for establishing a dose-response of chemical inhalation exposures to basal cell stress and BO induction. Next, exposed rats will be treated with an ISR inhibitor as a novel therapy for preventing BO. Aim II will assess the interaction between ISR activation and hemidesmosomes after chemical exposures to DA or PD using a combination of viral transfections and chemical inhibition studies for delineating the mechanisms contributory to airway basal cell stress. In Aim III, multiplex immunofluorescence and spatial transcriptomics will be used to semi-quantitate and spatially localize the previously identified ‘stressed’ airway basal cell phenotype in human BO lesions from different environmental insults. At project completion, a common mechanism of airway basal cell stress will be identified across structurally similar chemicals as well as in human lungs tissue affected by BO from different environmental insults. Future therapies targeting this new mechanism of airway basal cell stress may benefit a devastating lung disease with no FDA-approved therapies.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY Daily activities, such as driving a car, require selective processing of external information that is present in the environment (i.e., during selective attention) and internal information that is stored within the mind (i.e., during working memory). Previous research has shown that the sampling of external information and the maintenance and sampling of internal information are associated with shared neural resources in frontal, parietal, and sensory cortices. Shared neural resources might lead to competitive interactions between these processes during tasks that require both external and internal sampling. Here, we will investigate the neural mechanisms through which the brain coordinates the sampling of external and internal information to avoid competitive interference. There are two specific aims. In Aim 1, we will test whether the same neurons or different neurons represent and sample external and internal information under different task conditions. We will intracranially record from macaque frontal, parietal, and sensory cortices while the animals complete a task that requires (i) only external sampling, (ii) only internal sampling, or (iii) both external and internal sampling. We predict that during trials that require both external and internal sampling (i.e., during dual-task trials), there will be a shift toward functional segregation, with neurons (and perhaps brain regions) specializing for external or internal sampling. In Aim 2, we will use the same data to test whether the competition between external and internal sampling—for shared neural resources—leads to the separation of functionally specific neural activity over time. That is, we will test whether external and internal sampling are temporally coordinated on a sub-second timescale, consistent with previous evidence that competing neural processes can be coordinated by theta- rhythmic neural activity (3–8 Hz). Our findings will provide critical insight into how the brain flexibly accomplishes selective processing during tasks that require both environmental information and internally stored information. It will also provide cross-species translation between humans and macaques, given that we are building on a human EEG project that used the same behavioral task. Finally, the proposed experiments will address several ongoing debates in cognitive neuroscience, including (i) the extent to which selective attention and working memory utilize a shared sampling process, (ii) whether higher order (i.e., frontal and parietal) cortices engage visual cortex to help represent to-be-remembered information (i.e., during working memory), and (iii) whether the theta-rhythmic coordination of neural activity provides a general mechanism for avoiding functional conflicts during cognitive processes. Dysfunctions of attention and working memory are markers of common disorders, such as attention-deficit/hyperactivity disorder (ADHD). By investigating how the brain typically balances the sampling of information from the environment and internal memory stores, we will provide important insights to help the development of effective treatments for these disorders.

NIH Research Projects · FY 2025 · 2025-09

Project Summary The University of Rochester Medical Center (URMC) is committed to advancing research excellence by providing state-of-the-art facilities and cutting-edge technologies for biomedical and biological research. Spatial ‘omics is transformative new technology that seeks to harness the power of ‘omics (eg. genomics, proteomics, metabolomics, lipidomics) to provide a deep molecular profile of individual cells in a way that maintains the spatial relationships that exist between cells and their surroundings in intact tissues. The URMC proposes the establishment of the Western New York Spatial Biology Research Center (SBRC). This pioneering initiative will integrate tissue processing, histology, genomics, and bioinformatics/data analytics into a unified organizational entity, closely integrated with tissue and biobanking efforts. The 5,700 square feet of wet- and dry-lab space is centrally located to researchers where the SBRC will serve as a comprehensive hub for spatial omics research, enabling validation and discovery at an unprecedented scale. By centralizing URs expertise in histology, genomics, and bioinformatics and positioning the SBRC near the Wilmot biobank, we will foster innovative collaborations, enhance accessibility, and streamline research to accelerate scientific discovery. We will develop data analytics excellence by establishing a modernized data analytics collaborative space, equipped with advanced IT infrastructure, to enable the analysis of large-scale spatial ‘omics datasets and to develop novel analytical techniques integrating multilevel ‘omics data. Additionally, the creation of this new collaborative dry-lab space will catalyze interdisciplinary partnerships and the development of novel research methodologies. Through dynamic collaborations with our regional and national partners, the SBRC will serve as a central hub for transformative cross-disciplinary science. Our commitment to training the next generation of researchers will ensure that scientists are equipped with cutting-edge skills in spatial omics, empowering them to tackle urgent scientific challenges and discover life-changing cures. The SBRC is strategically positioned to elevate translational research in key areas such as musculoskeletal diseases, cancer biology, autoimmunity, and neuroscience. By providing researchers with access to cutting-edge methodologies, SBRC will empower new scientific breakthroughs. Moreover, it aligns with the University of Rochester's educational mission by offering advanced training in bioinformatics and data analysis, thereby broadening the adoption of spatial omics across diverse research domains. This initiative represents a transformative step forward in promoting research excellence at the University of Rochester and beyond. By fostering critical advancements in health-related research and serving as a regional resource for translational discovery and education, SBRC will solidify URMC's position as a leader in biomedical innovation.

NIH Research Projects · FY 2025 · 2025-09

(PLEASE KEEP IN WORD, DO NOT PDF) Clonal hematopoiesis (CH) is driven by mutated hematopoietic stem cells (HSCs) that expand in the bone marrow. Inflammation has been shown to drive CH progression; however, despite the presence of systemic inflammation, we showed that HSCs exclusively expanded in the marrow cavities with bone resorptive activities. These results raised questions of whether CH clonal development also depends on physiological bone turnover (a process initiated by bone resorption) and emphasizes the importance of establishing a robust methodology to track the CH clones along with the skeletal dynamics in live animals. To address the knowledge gap, we recently developed an intravital imaging protocol to visualize engraftment of non-malignant clones in a functional microenvironment that only received ultralow-dose (0.5 - 2 Gy) irradiation. Leveraging this model, we propose to determine the causality of bone turnover, local inflammatory profiles, and expansion of CH clones via longitudinal imaging, and further assess and optimize its applicability for tracking CH progression to clonal cytopenia or advanced clonal disorders. In Aim1, we will perform longitudinal imaging and functional assays to determine immune cell phenotypes altered by physiological bone remodeling within a marrow cavity. Imaging will be performed at a two-day interval to follow changes induced by a bone resorption cycle. The experiments will be performed at the steady state and in animals transplanted with CH clones to further delineate contributions from the mutant cells. In Aim2, niche occupancy and lineage contribution of the mutant clones will be characterized in the ultralow-dose irradiated model over the course of one year. Additionally, microenvironment cells surrounding the CH clones will be harvested at distinct disease stages for transcriptomic assays to delineate overlapping and differential microenvironment factors over disease evolution. Taken together, currently, the dynamic niches in the marrow microenvironment responsible for expansion of CH clones are not well defined, and the experimental tools to pinpoint the niches remain to be tested. The proposed work will address these knowledge gaps and provide the field with validated technology for therapeutic discovery leveraging the bone marrow microenvironment.

NIH Research Projects · FY 2026 · 2025-09

Suicide rates among adults in the U.S. are a significant public health problem. Suicide rates increase with age, yet mechanisms that account for elevated rates among adults in middle to later-life are not well-understood. The Interpersonal Theory of Suicide proposes that life stressors increase suicide risk by impacting two specific forms of social disconnection – low belonging and perceived burden on others and that changes in these states are the most proximal determinants of suicidal behavior. However, the role daily, and even hourly, changes in social connection have in promoting belonging or alleviating perceived burden for adults in mid- to late-life, over and above changes in daily stress levels and mood, has not been comprehensively examined. This study builds on our team’s descriptive and interventional work on social connection in suicide prevention, which indicates that social engagement is a unique predictor of a sense of mattering to one another and a group. In line with institute priorities to identify mechanisms leading to interventions to promote health, our objective is to examine the role that social engagement (i.e., behaviors throughout the day that are social/relational) has in promoting belonging or alleviating perceived burden, and thereby decreasing suicide risk in adults. We propose an observational study of n = 200 adults in mid-to later life (age 40+) who report elevated suicide risk (past year suicide ideation or lifetime suicide attempt) in which subjects complete baseline interviews (to obtain histories of suicide ideation and behavior), 14 days of smartphone-based ecological momentary assessment and passive sensing of social behavior (including social engagement and suicide risk) at baseline and 3-months, and a qualitative interview with a subset (n=50) of subjects to contextualize findings. Aim 1 is to examine whether daily social engagement predicts daily fluctuations in social connection (mattering, loneliness, belonging, and perceived burden) while controlling for daily stressors and mood. We hypothesize that days with greater social engagement will be associated with clinically meaningful increases in social connection even when controlling for stressor frequency and intensity (i.e., stress buffering effect of social connection), and that greater social engagement during the day will predict evening and next morning increases in social connection. Aim 2 examines whether social engagement predicts daily variations in suicide risk (suicide ideation, depression severity) via social connection. We hypothesize that lower social engagement during the day will predict evening and next morning suicide risk via changes in social connection. Aim 3 is to identify what aspects of social engagement (e.g., group, one-on-one) are most helpful in reducing suicide risk via qualitative interviews to inform translation to intervention. Understanding mechanisms whereby social factors alleviate suicide risk can inform optimization of suicide prevention interventions targeting social connection for adults in middle to later life.

NIH Research Projects · FY 2025 · 2025-09

The University of Rochester (UR) Clinical and Translational Science Institute (CTSI) T32 Pre-Doctoral Training Program aims to cultivate the next generation of leaders in translational science research (TSR). It encompasses a comprehensive mentored research experience, transdisciplinary educational opportunities, career development planning, and a supportive environment conducive to growth and achievement. Our training encompasses competencies across eight fundamental domains of a translational scientist (e.g. rigorous researcher, team player, boundary crosser, and population health champion), equipping trainees with the knowledge and skills needed to improve the health of patients and populations, and supporting the overall UR CTSI goals of advancing translational science by fostering Research Without Walls. Our specific aims are: Aim 1: Contribute to a well-trained clinical and translational science workforce by recruiting, mentoring, and immersing students into focused training opportunities across the translational science spectrum. We will form a coordinated learning community through structured collaborative coursework, research experience, translational science and regulatory science competitions, innovative academic challenges, and participation in professional development opportunities. Formal T32 training addresses TSR, population health, and bioinformatics and health analytics. Aim 2: Develop a heterogeneous Trainee pathway and stimulate interest in clinical research training and career paths. Integral components are targeted recruitment efforts, including summer research programs for undergraduates, tailored mentorship programs, and integration with UR CTSI undergraduate and Master’s programs. Aim 3: Ensure a safe and supportive research training environment through evidence-based mentor training and evaluation. T32 trainees will be mentored by a tailored structure consisting of multi-disciplinary faculty teams. We prioritize formal mentor training through our Ever Better Mentoring course, and we will implement a responsive evaluation approach that includes data-driven assessments and regular review of Trainee outcomes. Aim 4: Promote exploration of translational training and careers by leveraging institutional and CTSA Consortium resources and engaging with alumni. We will intentionally engage University faculty, former faculty, alumni, current and previous CTSI TL1/T32 and KL2/K12 Trainees, student organizations, and students and researchers across the CTSA Consortium to facilitate scientific and professional networking. The UR CTSI T32 Pre-Doctoral Training Program is the foundation of a research education ecosystem that reaches beyond the UR CTSI to leverage resources and faculty expertise across the institution, facilitating Trainee transformation from student to translational scientist. It is closely integrated with the K12 program and UM1 Workforce Development Element D through shared and integrated governance structures, CTSI services and a shared mentor base.

NIH Research Projects · FY 2025 · 2025-09

Project Summary/Abstract People with fetal alcohol spectrum disorders (FASD) experience barriers to care and a lower quality of life (QOL). FASD- informed services and supports are lacking, especially during the transition to adulthood – a critical developmental period for QOL. The proposed project will develop and initiate testing of a scalable person-centered planning (PCP) intervention to support QOL for adolescents and adults with FASD. PCP is an evidence-based intervention for people with disabilities. Research suggests PCP is a good fit FASD; however, it has yet to be adapted or tested with this population. In this project, we will use rigorous implementation science frameworks to systematically adapt and test a PCP intervention for adolescents and adults with FASD. Given the importance of social support networks in PCP, we will also draw upon the growing literature and team expertise on social network interventions to inform the development and evaluation of the intervention. Consistent with other interventions in our lab, we expect the proposed intervention to leverage technology to offer scalable solutions to overcome current barriers to care. During the R61 phase of the project, we will use the implementation science framework “Intervention Mapping – Adapt” to carefully adapt the core principles and methods of PCP and social network interventions for FASD. This 6-step process involves a planning team of people with FASD and other stakeholders and careful attention to theory and logic models to guide adaptation decisions. Based on our preliminary logic models, self-determination theory is a strong fit with the proposed intervention that we are currently calling “Thrive.” Additional research activities in Aim 1 will also inform the planning group’s decision making as they refine logic models, determine intervention structure and components, develop materials, and finalize evaluation procedures. Specifically in Aim 1a, we will conduct individual and group interviews with adolescents and adults with FASD and members of their social networks to characterize key features of their support networks that may be amenable to intervention. Following initial production of intervention materials, we will complete two rounds of usability testing (5 participants per round) in Aim 1b to aid in refining intervention materials and evaluation procedures for the pilot randomized controlled trial (RCT) in the R33 phase. Following successful attainment of R61 milestones, we will conduct a type 1 hybrid effectiveness-implementation pilot RCT of the developed Thrive intervention (R33). This trial design involves gathering data on both effectiveness and implementation outcomes, which will help us optimize the intervention for future larger-scale trials and more rapid translation into community settings. We will recruit 60 adolescents and adults (ages 15-30) with FASD to participate in the pilot RCT, with random assignment to the 1) Thrive PCP intervention or 2) comparison group receiving social network and strengths assessments only. Although significance testing and effect sizes will be calculated, a larger emphasis will be placed on feasibility to guide the design of a fully powered larger-scale RCT R01 application. For example, in addition to the feasibility of the intervention itself, we will assess feasibility of recruitment and trial procedures, sensitivity of measures to intervention change, and intervention process. Our proposed PCP intervention has high potential to improve QOL of people with FASD at the critical transition to adulthood.

NIH Research Projects · FY 2025 · 2025-09

Project Summary: The University of Rochester’s Golisano IDDRC fosters innovative and collaborative research efforts among multidisciplinary investigators. The center's primary goals include advancing basic and translational science to understand the causes and consequences of intellectual and developmental disabilities (IDDs), sustaining essential research infrastructure, building interactive research teams, attracting and training new investigators, fostering communication and collaboration, and promoting community outreach and education. The Golisano IDDRC operates through four scientific cores: Human Phenotyping and Recruitment (HPR), Translational Neuroimaging & Neurophysiology (TNN), Cell and Molecular Imaging (CMI), and Animal Behavior and Neurophysiology (ABN). The center also focuses on specific research clusters, including rare neurodevelopmental diseases, parental stress and early life exposure, neuroinflammatory mechanisms, autism spectrum disorder, and multisensory integration. The center's efforts are supported by an annual fund for IDD pilot projects and a commitment to evaluating progress and maximizing impact. Our objective is to leverage institutional resources and areas of expertise to optimize the efficiency, innovation, and quality of research to improve the lives of patients and families with IDD.

NIH Research Projects · FY 2025 · 2025-09

Psoriatic arthritis (PsA) is a chronic inflammatory disease characterized by involvement of the skin, peripheral joints, axial skeleton, and entheses. The heterogeneity in clinical presentation and diverse tissue resident cells suggests that inflammation in different tissue compartments arises from distinct yet overlapping cellular and molecular mechanisms. However, the immune endotypes driving pathology across tissue domains remain poorly defined. Consequently, personalized treatment strategies are lacking, and despite multiple FDA-approved therapies, remission is rare, and frequent medication adjustments are needed to manage tissue-specific flares. A major barrier to targeted therapy is the absence of biomarkers that identify tissue-specific immune pathways. To address this challenge, we developed a humanized mouse model of PsA by injecting sera and PBMCs from PsA patients into immunodeficient NSG-SGM3 mice. These mice recapitulated key clinical features—arthritis, enthesitis, psoriasis, axial involvement, and dactylitis. In contrast, mice receiving samples from healthy donors did not develop disease. Spatial transcriptomics of joint tissues revealed enrichment of IL-32 and CXCL14-expressing CD8+ T cells. Strong expression of IL-17 was noted in axial tissues and dorsal root ganglia. Notably, disease development required human serum antibodies, and we identified hornerin, a defensin protein, as a candidate autoantigen. Importantly, mice humanized with blood from PsA patients unresponsive to TNF inhibitors developed skin and joint inflammation that did not respond to TNF blockade but improved with other biologics, mirroring patient treatment responses. This proposal aims to: (1) identify cellular and molecular signatures across PsA tissue domains; (2) define shared and distinct CD8+ T cell clonotypes to uncover candidate autoantigens; (3) test whether hornerin-specific autoantibodies promote inflammation via antigen presentation; (4) elucidate plasmablast-driven autoantibody production; and (5) evaluate IL-32 blockade in humanized mice derived from biologic-refractory PsA patients. These studies will provide mechanistic insights into PsA pathogenesis and enable the development of precision therapies*

NIH Research Projects · FY 2025 · 2025-09

Project Summary/Abstract Cigarette smoking is the main cause of occurrence of Chronic Obstructive Pulmonary disease (COPD). Studies show that cigarette smoke (CS)-mediated increase in cellular senescence causes premature ageing in the lung, thereby leading to the development of COPD. However, the exact mechanism of disease development via alterations in cellular senescence over a prolonged period in CS-induced COPD is not known. In this respect, various inter-individual variations are observed amongst regular smokers, thus indicating potential involvement of epigenetic regulations in modulating the downstream signaling. Considering this I hypothesize that the epigenetic regulation of cellular phenotypes and gene expression of cellular senescence- associated genes (p16, p21 and p53) drives disease-fate towards emphysema upon chronic CS exposure. To test this hypothesis, I propose to: (1) determine the time (1, 3, and 6 months(mo)) and age-dependent (2mo versus 18 mo) effects of CS-exposure on the lung cellular senescence and associated epigenetic regulation in vivo using SNARE-sequencing (K99 phase), and (2) study the determinants of cellular senescence and associated epigenetic mediators in primary human small airway epithelial cells (SAECs) from healthy and diseased (COPD) individuals (R00 phase). My postdoctoral work has shown that clearance of senescent cells results in reduction of CS-induced neutrophilic inflammation and reversal of alveolar wall damage in mouse model (p16-3MR). Thus, studying the CS-induced changes in the lung neutrophil and epithelial cell population is the focus of this project. Upon completion of these aims, I will be able to identify gene targets and associated chromatin sites that are altered on cigarette smoking and associate them with disease development in COPD. Use of two mouse models (C57BL/6J and p16-3MR) will help in understanding the role of p16-dependent senescence in CS-mediated alterations in the lung. Additionally, use of Multiome (SNARE-seq) technology in Aim1 will provide a chance to identify unique cell phenotypes based on differentially expressed genes and correlate them to the epigenetic signatures within the cell upon CS exposure. These results would lead to future publications, collaborations, and grant proposals, thus helping to launch my career as an independent researcher in the field of lung biology.

NSF Awards · FY 2025 · 2025-09

With support from the Chemical Structure and Dynamics (CSD) program in the Division of Chemistry, Professor Daniel Mittleman of Brown University and Professor Michael Ruggiero of the University of Rochester are investigating guest-host molecule interactions in porous materials using a combination of vibrational spectroscopies and computational methods. This project aims to uncover the atomic-level mechanisms that drive the adsorption of gases in porous materials such as metal-organic frameworks (MOFs) and clathrates. A key challenge is that the intermolecular forces are often weak, requiring probes in the terahertz range. The team will apply low-frequency infrared and Raman spectroscopies, exploiting a unique capability to obtain such measurements in a custom-designed pressure cell, to reveal how gas loading alters the vibrational dynamics in real time. Quantum mechanical simulations will help to interpret these spectral changes, linking them to structural information. The combination of computational and experimental results will clarify important open questions in the field, such as the impact of structural disorder on adsorption dynamics. These new insights will inform the rational design of materials optimized for particular applications such as hydrogen storage or toxic chemical remediation. These efforts are linked to a hands-on week-long summer course developed for high school students in Rochester and Providence, which will further the pedagogical training of the graduate students participating in the project. This project integrates state-of-the-art experimental and theoretical techniques to study the vibrational dynamics of porous media under gas-loading conditions. Vibrational spectroscopy, including terahertz time-domain and Raman measurements, will be used to monitor subtle structural changes, through changes in the low-frequency modes, which reflect shifts in the intermolecular forces during gas adsorption. A gas-dosing manifold with stoichiometric control will enable precise quantification of guest molecule uptake and its impact on vibrational spectra. These data will be compared to solid-state density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations to interpret experimental results and uncover structure–dynamics relationships. The results will reveal the role of host framework flexibility, host/guest molecule disorder, and cooperative phase transformations on the gas loading mechanisms and associated kinetics. The ultimate goal of this project is the development of predictive models that link spectroscopic signatures to molecular-scale mechanisms. This project will establish a new paradigm for characterizing and designing functional porous materials using laboratory-based spectroscopic methods. 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 · 2025-09

ABSTRACT Endothelial cells are vital for maintaining homeostasis and facilitating repair following vascular injury or disease. Vascular regeneration is increasingly recognized as critical for treating vascular diseases, with recent evidence highlighting the role of resident angioblasts. Despite their importance, the cellular characteristics and regulatory mechanisms governing angioblasts remain poorly understood. This project seeks to bridge this gap by leveraging existing scRNA-seq data to explore the trajectory of pulmonary angioblasts (PACs), their derived cells, and the molecular markers and signaling pathways that drive their differentiation and function. As such, this proposal aligns perfectly with the NIH PAR-23-036 funding opportunity, which supports the reanalysis of existing data to address critical gaps in knowledge. By reanalyzing these datasets, we will uncover novel insights into PAC identity, fate, and the regulatory mechanisms driving their function. This approach allows us to address important questions in pulmonary vascular biology with minimal experimental burden, maximizing the utility of existing data while advancing our understanding of vascular development. Our preliminary analyses of available scRNA-seq datasets have identified PACs with significant self-renewal capacity in mouse lungs, peaking between embryonic day 12.5 (E12.5) and postnatal day 7 (P7). Intriguingly, trajectory analysis reveals that PACs do not directly differentiate into mature endothelial cells (ECs) such as arterial ECs (aECs), venous ECs (vECs), or capillary ECs (C2-ECs). Instead, PACs differentiate into an intermediary population of CD34high cells (C1-ECs), subsequently generating other EC subtypes. Underscoring their importance, PACs and their progeny were significantly reduced in hyperoxia-induced bronchopulmonary dysplasia (BPD) mice, which have arrested pulmonary vascular development and alveolarization. We have identified several major knowledge gaps in our understanding of pulmonary vascular development. a) How vasculogenesis, intussusceptive and sprouting angiogenesis are coordinated with lung development remains unclear. b) The spatial-temporal lineages of EC- related cells during lung development and regeneration are unexplored. c) The functional roles of different lineages in lung development and homeostasis are not well defined. d) The specificity of the PACs vs angioblasts from blood island during the embryo stage in mice. e) The regulatory mechanisms guiding PAC cell fate and localization are largely unknown. The previous findings about pulmonary vascular development and our preliminary data lead us to hypothesize that PACs are crucial for pulmonary vasculature development by residing in specific niches that facilitate lung development. PACs have the most robust self-renew ability. In proximal regions, PACs localize along arterial and venous vessel walls to contribute to intussusceptive angiogenesis. In distal regions, PACs differentiate into CD34high cells and lead the protruding into secondary septa, which form neovasculature and promote the alveolar-capillary structure. (Fig. 1). To test this hypothesis, we propose two specific aims. Aim 1: Define PAC cell identity, cell fates, and regulatory mechanisms in mice and humans. Aim 2: Visualize PAC and PAC-derived cell lineages during development and vessel injury.