Yale University

NIH Research Projects · FY 2026 · 2025-01

The list price of insulin has increased dramatically over the past two decades, hindering access to this essential medication, contributing to insulin rationing and ultimately worsening health outcomes for people living with type 1 (T1D) and type 2 diabetes (T2D). To address insulin affordability for Medicare beneficiaries, the Inflation Reduction Act (IRA) capped out-of-pocket (OOP) payments for one month’s supply of insulin to $35 for all Medicare beneficiaries enrolled in Medicare Part D plans effective 2023. Understanding the impact of IRA provisions on patients' OOP payments for insulin, diabetes management, and health outcomes in diabetes care is crucial to advancing effective solutions to barriers in diabetes care. Accordingly, we propose to evaluate the real-world implications of the IRA by leveraging rigorous quasi-experimental methods applied to data from OptumLabs Data Warehouse linked with Medicare fee-for-service (100% sample) claims from 2021-2022 (pre-IRA) and 2023-2024 (post-IRA). These data include both utilization and clinical information for beneficiaries in traditional Medicare and Medicare Advantage plans across the U.S., as well as those who are commercially insured (for comparison), with characteristics of each prescription plan (benefit design, including Senior Savings Model participation prior to IRA), OOP payments for each medication, and clinical data (diagnoses, procedures, clinical encounters, prescription medication fills, and even laboratory data such as hemoglobin A1c levels). Using this rich and comprehensive nationwide data asset, we will address the following aims: AIM 1: To examine the association between IRA implementation and patient OOP payments for insulin by comparing pre- and post-IRA trends among Medicare beneficiaries (separating those who participated in the Senior Savings Model vs. those who did not), then comparing them to corresponding trends among commercially insured patients 60-64 years. AIM 2: To examine the association of IRA implementation and clinical outcomes in the same patient subgroups, including rates of insulin use, type(s) of insulin used, insulin adherence, utilization of non-insulin guideline-recommended T2D diabetes medications (e.g., SGLT-2 inhibitors and GLP-1 receptor agonists for those with T2D), hemoglobin A1c levels, and rates of hospitalizations and emergency department visits for hypoglycemic and hyperglycemic emergencies. AIM 3: To examine whether IRA implementation is associated with changes in outcomes from Aims 1 and 2 across demographic, socioeconomic, and clinical patient subgroups. By evaluating the effectiveness of this landmark policy, we aim to inform future healthcare policy decisions about prescription drug affordability and contribute to improving the lives of individuals living with T1D and T2D in the United States.

NIH Research Projects · FY 2026 · 2025-01

Summary Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common potentially lethal genetic disorders, affecting ~1:1,000 people and producing end stage renal disease in 50% of affected individuals. The disease is characterized by the formation of nephron- derived fluid-filled cysts, whose initiation and expansion compromises the structure and function of the remaining renal parenchyma. ADPKD is caused by mutations in either of two genes, Pkd1 and Pkd2, which encode polycystin-1 (PC1) and polycystin-2 (PC2), respectively. PC1 is an extremely large membrane protein comprised of 4,302 amino acids that spans the bilayer 11 times. PC2 spans the membrane 6 times and is a member of the Trp family of non-selective cation channels. PC1 and PC2 interact with one another to form a complex that localizes to a number of subcellular compartments, including the primary cilium and the mitochondrion-associated membrane domains of the endoplasmic reticulum. More than two decades after their discovery, the principal physiological functions of these proteins and the processes through which their dysfunction leads to cystic disease remain largely unknown. PC1 undergoes cleavages within its N and C-terminal domains. C-terminal cleavage produces fragments that translocate to mitochondria and to nuclei. We have found that transgenic expression of a protein corresponding to the final 200 amino acid residues of PC1 (P200) in orthologous murine models of ADPKD suppresses the cystic phenotype and preserves renal function. This suppression depends upon an interaction between the C-terminal tail of PC1 and the mitochondrial enzyme Nicotinamide Nucleotide Transhydrogenase (NNT). The discovery that a short fragment of PC1 reduces disease severity in mouse models of ADPKD raises a number of exciting questions that will be pursued in our proposed studies. To explore these questions we will 1) determine whether P200 expression suppresses cyst formation and reverses established cystic disease in multiple mouse models of ADPKD; 2) determine how P200 affects mitochondrial function and cellular energy metabolism; and 3) determine how PC1 C terminal tail fragments are produced in vivo and how they affect metabolism and pathways involved in cyst formation. Addressing these questions will provide important insights into the normal physiological functions of PC1 and will suggest new potential targets for therapeutic development.

NIH Research Projects · FY 2026 · 2025-01

PROJECT SUMMARY/ABSTRACT This is a K23 award application for Dr. James Giles, a neurologist and young investigator pursuing patient- oriented clinical research on ischemic stroke caused by large vessel occlusion. A K23 award will provide him with the means to acquire critical skills in four key development areas: 1) computational biology for transcriptomic analysis of tissue and blood samples, 2) the biology of thrombosis in patients with acute ischemic stroke, 3) clinical translational project management and 4) research management and leadership. By acquiring these skills, Dr. Giles will develop as an independent investigator who can bridge the disciplines of computational biology and clinical research in vascular neurology. To pursue this goal, Dr Giles has assembled a mentoring team with expertise in translational transcriptomic analysis. Complementing them is an advisory team with expertise in computational biology and statistics, atherothrombosis and immunobiology. Acute ischemic stroke caused by thrombi occluding large cerebral vessels is associated with significant mortality and morbidity. Despite emergency revascularization, via intravenous thrombolysis and mechanical thrombectomy, poor neurologic outcomes remain common. Etiologies of thrombi include atherothrombosis and cardioembolism. A key challenge in stroke medicine is to identify the etiology of stroke thrombi, in order to more effectively prevent future strokes. Dr. Giles’s central hypothesis is that the cellular pathogenesis of stroke thrombi varies between clots of different etiologies, and that these differences can be identified via transcriptomic analysis of cells within acute thrombi and blood samples. We will test this hypothesis with transcriptomic analysis of cells comprising acute stroke thrombi and paired circulating blood cells. We will determine whether clots of different etiologies contain cells of different activation statuses and transcriptional programs (Aim 1). Further, we will test the hypothesis that blood cell gene activation within thrombi causing atheroembolic stroke are related to the clinical response to revascularization treatments in an assembled multi-center cohort of patients with stroke (Aim 2). The proposed research is significant because stroke due to large vessel occlusion causes substantial mortality and morbidity and requires new precision medicine approaches to improve the efficacy of revascularization therapies. Further, recurrent stroke continues to exert a significant burden, and new approaches are needed to diagnose stroke etiology. The proposed research is innovative because it combines advanced transcriptomic techniques to provide insight into mechanisms of different thrombus etiologies. Consistent with NINDS priorities to accelerate basic research findings towards patient use, this proposal will prepare Dr. Giles as an independent investigator who can develop new approaches for personalized, timely, and effective revascularization and preventive therapeutics to improve outcomes among patients with stroke.

NIH Research Projects · FY 2026 · 2025-01

PROJECT SUMMARY The arginine methyltransferase PRMT5 has been identified as a potential target in cancers with loss of the metabolic enzyme MTAP, which occurs in ~15% of all malignancies including several (such as glioblastoma, pancreatic ductal adenocarcinoma, and esophageal cancer) that are refractory to standard therapies. MTAP loss partially impairs PRMT5 activity and sensitizes MTAP-deleted cancer cells to pharmacologic PRMT5 inhibition. As a result, the development of PRMT5 pathway inhibitors has accelerated, including two PRMT5 inhibitors recently reported to have clinical activity in patients with various MTAP-deleted solid tumor malignancies. While PRMT5 is a well-established regulator of multiple cellular pathways including transcription, RNA processing, and DNA repair, how it regulates these pathways and which processes are critical for maintaining cell viability is unclear. To address this knowledge gap, a genome-scale CRISPR activation platform has been leveraged to identify genes that modulate sensitivity to PRMT5 pathway inhibition in MTAP-deleted cancer cell models. Among the top-scoring gene products that reduce sensitivity of MTAP-deleted cells to PRMT5 pathway inhibition are previously unrecognized regulators of DNA damage response (DDR) and potential new PRMT5 substrates. The overall objective of this proposal is to define key components of the PRMT5 axis that impair cell viability upon PRMT5 inhibition and to define pathways that can restore viability. The central hypothesis is that the top- scoring gene products that reduce sensitivity to PRMT5 pathway inhibition represent previously unrecognized regulators of DDR, activate DDR pathways that protect cells from PRMT5 pathway inhibition, and may represent core PRMT5 pathway components. This hypothesis will be tested by pursuing 2 specific aims: 1) Determine how top-scoring proteins mediate responses to DNA damage and 2) Define mechanistic connections between top- scoring proteins and the PRMT5 pathway. The project will examine the impact of these gene products on generation of double-strand DNA breaks, R-loop formation, and homologous recombination (HR) pathways. Proteomic, biochemical, and genetic approaches will be leveraged to gain mechanistic insights about how these proteins intersect with the PRMT5 axis. The proposed work is significant because it will define genes and pathways capable of restoring viability of MTAP-deleted cells exposed to PRMT5 pathway inhibition and will inform a molecular and functional annotation of downstream effects of PRMT5 and compensatory pathways. The approach is innovative and distinct from prior studies because it builds on functional genomic insights to focus squarely on the therapeutically relevant functional roles of PRMT5. Successful completion of these aims will identify processes dysregulated by PRMT5 inhibition that impair cell viability, delineate molecular mediators of these processes, and provide fundamental insights about mechanisms of DDR regulation. The work may also identify additional therapeutic targets in the PRMT5 axis.

NIH Research Projects · FY 2026 · 2025-01

PROJECT SUMMARY Parkinson's Disease (PD) is characterized by the progressive loss of dopaminergic (DA) neurons within the substantia nigra (SN), resulting in debilitating motor impairments. To develop therapeutic interventions that can be administered prior to extensive DA neuron loss, early pathomechanisms at the DA synapse must be explored. Central to PD pathology is the dysregulation of dopamine neurotransmission, which is in part mediated by the dopamine transporter (DAT). Interestingly, DAT surface levels are controlled by the endolysosomal system, which includes several proteins mutated in familial and sporadic PD. For example, loss-of-function (LOF) mutations in the clathrin uncoating chaperone, auxilin, cause early-onset PD, whereas the D620N mutation in VPS35, a retromer protein, causes familial PD that is phenotypically similar to sporadic PD. My lab's study of auxilin knockout (KO) mice suggests that disruptions in DAT function and trafficking precede DA neurodegeneration, which is further supported by changes in DAT expression and function in VPS35 D620N knockin (KI) mice. Determining whether DAT dynamics are impaired across genetic etiologies of PD will be pivotal to the field's understanding of early PD pathology and DA vulnerability. This study will test the hypothesis that DAT recycling and trafficking defects occur in forms of PD involving endolysosomal mutations by using cutting-edge live and super-resolution imaging techniques and in vitro PD models. To measure DAT endo- and exocytosis with high temporal resolution in Aim 1, I developed a DAT-pHluorin that I will express in primary SN DA neurons from auxilin KO and VPS35 D620N KI mice. To account for species differences, I will also validate my results in induced pluripotent stem cell (iPSC)-derived DA neurons from PD patients with auxilin LOF and VPS35 D620N mutation. I hypothesize that auxilin PD models will display delayed DAT vesicle reacidification after endocytosis, and both auxilin and VPS35 PD models will exhibit reduced magnitudes and rates of DAT reinsertion following endocytosis, signifying impaired DAT recycling, due to distinct mechanisms. To further explore these mechanisms, Aim 2 will utilize DAT-PRIME imaging, which fluorescently labels surface DAT in live cells, to track DAT post-endocytic fate in the aforementioned models. Using stimulated emission depletion microscopy paired with immunofluorescence staining, I will assess the colocalization of DAT with various endolysosomal markers to understand the role of auxilin and VPS35 in controlling post-endocytic fate of DAT. I predict that loss of clathrin uncoating by auxilin will stall DAT trafficking at the early endosome stage, leading to reduced DAT trafficking to recycling endosomes and retromer compartments. On the other hand, VPS35 D620N neurons are likely to show enhanced lysosomal trafficking of DAT due to retromer LOF. This study will shed light on mechanisms underlying early DA dysfunction in PD and provides me with the opportunity to further my scientific training through mentorship by experts in synaptic biology, neuronal cell culture, and microscopy.

NIH Research Projects · FY 2026 · 2025-01

Type 1 diabetes (T1D) is an autoimmune disease with a metabolic outcome. A number of agents can change the course of the disease when given to patients with new onset (Stage 3 T1D) and teplizumab, the anti-CD3 mAb has been approved to delay the clinical diagnosis in patients at risk, prior to the clinical diagnosis. Two clear unmet needs have emerged from the clinical trial experience. First, the successful immunologic treatments do not last indefinitely and do not restore normal β cell function. Second not all patients respond to treatments. In this proposal, we plan to study the features of β cells between clinical cohorts that show different rates of progression to clinical T1D and in response to immune therapy (i.e. teplizumab) in the successful TN10 prevention trial. New York Stem Cell Foundation (NYSCF) Research Institute has developed robust, high- throughput robotic cell culture systems that have successfully been applied to induced pluripotent stem cells (iPSCs) reprogramming and differentiation into pancreatic organoids. Importantly, these procedures minimize technical variation, allowing the detection of complex, subtle disease phenotypes and responses to perturbation. Our overarching hypothesis is that there are β cell intrinsic features that determine the effects of immune mediators, progression of T1D and responses to therapies. Our overall goal is to identify the β cell intrinsic features that determine progression of T1D, their interactions with immune cells, and the responses to therapies. In the UG3, Phase 1 part of this program, we will characterize and analyze pancreatic organoids from 16 existing iPSCs (10 from patients with T1D and 6 healthy controls) and reprogram iPSCs and develop pancreatic organoids from 20 additional patients. We will also prepare autologous islet autoantigen reactive CD8+ T cell lines from the iPSC donors that will be used in responses with the organoids. We will validate our models for detection of β cell killing in vitro and in vivo and obtain preliminary data on the differences between the cohorts and with primary islets which we can determine our statistical power for studies in Phase 2. In the Phase 2 UH3 program, we will analyze and compare the responses of the islet organoids between cohorts and to primary islets including a detailed analysis of metabolic function. We will determine the changes in the islet organoids when they are exposed to inflammatory mediators and specifically analyze protein modifications and development of neoantigens that may be targeted by antigen reactive CD8+ T cells. We will test whether deletion of TET2 in the islet organoids, that we have shown is required for inflammatory responses of β cells, will prevent immune mediated killing of the organoids. Finally, we will use the NYSCF automated platform to screen molecules for their ability to prevent organoid damage and death from inflammatory mediators. Understanding mechanisms of β cell failures in this context will direct therapies to prolong efficacy of immune treatments to arrest autoimmunity, and permit restoration of metabolic function for individual patients.

NIH Research Projects · FY 2026 · 2024-12

ABSTRACT The utilization of genetically engineered T-cells containing Chimeric Antigen Receptors (CARs) has demonstrated remarkable efficacy in treating hematologic malignancies. Despite this success, CAR-T cell therapies have encountered challenges in specificity and off-target toxicity when confronting solid tumors. To address these challenges, we propose an innovative approach that harnesses mechanical forces, which is overlooked in current therapeutic strategies. Mechanical forces are pivotal in immune signaling because they impact the activation of key receptors, such as the T cell receptor, chimeric antigen receptor (CAR), and co- receptor PD1. We recently developed force sensitive coiled-coils that can be genetically encoded and inserted into any protein of interest. These coiled-coils change conformation under force and expose reactive residues that can be harnessed for force detection or enzyme recruitment. This project aims to build on our experience to engineer a mechano-transduction platform that will be implemented to enhance CAR T-cell therapies. In aim 1, we will use our force sensors to measure the forces along key immune receptors. In aim 2, we will engineer force transduction modules by combining our force sensors to releasable transcription activators able to induce the expression of any protein of choice, and insert these tools into CARs to enhance CAR T-cell specificity and safety. The successful realization of this project will demonstrate the feasibility and utility of new capabilities to improve the efficacy of CAR-T therapies, extend their application and speed up their development, with high potential impact in cancer immuno-therapies. It will also lay the foundations for new immuno-therapies using different receptors and modes of action.

NSF Awards · FY 2024 · 2024-12

Predicting the motion of small micron-size particles known as colloids in porous media is relevant to many technological, environmental, and biomedical applications, from microplastic spreading in the soil to drug delivery to tumors. The colloidal particles are often suspended in flow through a porous medium in these applications. These flows also produce variations in the concentration of a solute such as a salinity gradient in coastal zones or a contaminant gradient in soil near a discharge. This project will use a combination of experiments, numerical simulations, and theoretical modeling to determine the effects of chemical gradients on the motion of colloids in porous media. The project will integrate research with education and outreach activities, involving high-school and undergraduate students in museum demonstrations of experimental modules related to microplastic spreading in soil, synthetic trees, and extraction of energy from salinity gradients. Predicting and controlling the transport of colloids in porous media is essential in a broad range of problems from filtration and wastewater treatment to contaminant spreading and remediation in subsurface flows. Colloids in these environments are often exposed to chemical gradients, which can lead to their diffusiophoretic migration. This project will use experiments, simulations, and modeling to systematically probe the role of flow velocity disorder, solute gradients, and the 2D/3D nature of the problem on the dispersion and transport of colloids through porous media. This is a multiscale problem, from the nanometric Debye layer next to solid surfaces, where surface charge and zeta potential impacts the diffusioosmotic flows, to the macroscopic dispersion of colloids over the scale of the porous medium. The combination of experiments and simulations probe a wide range of length and timescales, isolating and highlighting the role of key physicochemical ingredients such as surface properties at the nanoscale on the dispersion of colloids at macroscopic scales. Results will advance our fundamental understanding of colloid transport in porous media and lead to predictive models that describe, control, and guide colloids in the presence of flow and solute gradients. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-12

This doctoral dissertation project investigates relationships between early human diet and the population dynamics of extinct human ancestors (hominins). Could different dietary strategies explain why some hominin species lived for hundreds of thousands of years while others lived for briefer periods? Contemporary research does not provide evidence for an "optimal human diet," but there is still much to learn about how diet influences human behavior, biology, and evolution. Archaeology is well-positioned to uncover complex interactions between diet and human evolution. Specifically, studying animal bones in areas of past hominin activities allows archaeologists to track hominin resource use through time and space. Previous research on ancient human diets reveals close linkages between broad dietary strategies and species’ resilience, suggesting that diet played a key role in the survival of some early human ancestors and, ultimately, the evolutionary success of modern humans. However, few of these studies focus on aquatic animals, like fish and turtles, despite important nutrients in aquatic fauna and evidence that ancient hominins lived close to water sources. Further, aquatic resources often leave behind small traces when compared to the bones of megafauna, resulting in fossil collections that are dominated by large mammals. Considering the wide range of modern human diets, and the importance of diet to human health, examining the dietary strategies of ancient hominins is a worthwhile endeavor. This project provides research opportunities for underrepresented populations in science to study human evolution, including female undergraduates at US-based institutions. The research is conducted in a region with extensive hominin fossils, stone tools, and butchered animal bones. The researchers plan to collect and examine aquatic fossils at sites that span over ~1.25 million years, a timeframe which associated with hominin activity and sites that are natural death assemblages. By combining targeted aquatic fauna fossil collections with thorough sampling methods designed to recover small remains, this project generates a comprehensive fossil dataset that enables nuanced interpretations of the faunal fossil record and human diet. With the newly collected aquatic fossils, the researchers identify skeletal elements, bone completeness, taxonomic group, and bone surface modifications, a potential marker of hominin activity. Comparisons are made between hominin-activity sites and natural sites. This information helps answer the questions: (1) which aquatic taxa, and how many of each, were available at each site, (2) did taxonomic groups or abundances change through time, and (3) did hominin exploitation of aquatic fauna change in tandem with aquatic taxa and associated abundances? This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-12

Quantum computers have the potential to create a revolutionary form of information processing, however current hardware is very prone to errors. A grand challenge is to learn how to correct these errors so that one can build large-scale fault-tolerant quantum computers. This ERASE project will address this challenge by developing an innovative quantum computing platform based on ‘erasure flag’ qubits that herald when and where errors occur. Erasure flag information will make it easier to correct the errors and achieve fault tolerance. Researchers will have access to advanced tools for developing new algorithms and improving software systems, as well as the opportunity to experiment with quantum error correction and create new quantum algorithms that use mid-circuit measurements and program branching (decision making) based on the measurement results. ERASE is a collaboration between academia and an industrial hardware partner, Quantum Circuits, Inc. (QCI), to drive research towards practical quantum information technologies. ERASE will promote educational initiatives to cultivate a skilled quantum workforce, in partnership with historically black colleges and universities. The aim is to build a vibrant national ecosystem for quantum research, paving the way toward achieving quantum advantage in computation and simulation. Our goal is to deploy novel high performance superconducting hardware whose logical qubit states are defined by a single microwave photon shared between two long-lived resonators. This dual-resonator (‘dual-rail’) logical encoding can detect the dominant error (photon loss) converting leakage out of the code space into a flagged erasure error. Concatenating this dual-rail error detection code into a larger code will allow efficient correction of the dominant errors since their locations are flagged. Because our proposed architecture has unique hardware characteristics, it will enable new types of algorithms and require a rethinking of the systems software toolflow. The ERASE team will form a national community of researchers in applications/algorithms, software, and systems architecture to develop a National Quantum Virtual Laboratory in collaboration with our hardware partner, QCI. QCI will provide researchers with access to this new computational paradigm through an Application Programming Interface (API) into multiple levels of the system stack to: (1) develop and execute new algorithms designed for the error-detecting and error-correcting capabilities of our novel superconducting quantum computing testbed; (2) contribute to improved middleware design (e.g., error-aware compilers; efficient control flow for mid-circuit measurements and feedforward) ); (3) co-design of improvements in error correction protocols. This project advances the objectives of Quantum Information Science and Engineering at NSF in response to the National Quantum Initiative Act for the continued leadership of the United States in QIS and its technology applications. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2026 · 2024-12

ABSTRACT This is a career mentoring award to support Dr. Matthews with protected time to create and deploy a sustainable, structured approach to mentoring and to increase the number of trainees mentored. The PI, Lynn Matthews, MD, MPH is an infectious disease trained clinician-scientist with research expertise developing andtesting HIV prevention strategies for men and women in the context of sexual health and reproductive goals. Her mentoring portfolio focuses on groups who face barriers to becoming independent investigators in science and medicine. Mentees will work alongside Dr. Matthews on newly proposed research in this K24 and ongoing studies. Dr. Matthews proposes mentoring aims to (1) Provide mentorship in HIV prevention research to an estimated 15 investigators in the U.S. and abroad. Dr. Matthews seeks training in skills and tools to effectively mentor and optimize mentorship and support for trainees conducting patient-oriented research. (2) Establish a structured mentoring program to support mentees (phase 1) and mentors (phase 2) to be delivered within the UAB CFAR and Yale CIRA and adapted for collaborative partners. Dr. Matthews proposes novel research aims using new skills gleaned through training aims. The research will (1) explore preliminary implementation strategies for novel PrEP agents for planning for, with, or post pregnancy in Alabama and Uganda. She proposes a rapid analysis approach to analyze in-depth interviews and focus group discussions conducted with key stakeholders and end-users (people of reproductive potential with potential for HIV exposure) across the two sites. Surveys with providers, administrators, and other key stakeholders will assess feasibility and acceptability of the implementation strategies raised in the qualitative work to inform a future implementation trial. She will then select preliminary implementation strategies for a future adaptive trial through a modified Delphi process. Dr. Matthews and the team will use these data and information from the literature to design an adaptive trial for evaluating implementation strategies for novel PrEP for women planning for, with, or post-pregnancy in rural Uganda and Alabama. This award will contribute to the growth of talented researchers, while advancing the science of HIV prevention implementation in the U.S. and abroad.

NIH Research Projects · FY 2025 · 2024-12

SUMMARY This proposed Mentored Patient-Oriented Research Career Development Award (K23) will provide Samuel Gentle, MD, with the mentorship, training, and research experience needed in his transition towards an independent clinician scientist and leader in the field of bronchopulmonary associated pulmonary hypertension (BPD-PH). Over the course of his career, Dr. Gentle aims to reduce morbidity and mortality in children with BPD-PH, a disease in which 50% of children die by 2 years of age and nearly half of survivors have continuation of disease into adulthood. This commitment therefore directly aligns with the mission of the National Heart, Lung, and Blood Institute to prevent and treat heart and lung disorders so that individuals live longer and more fulfilling lives. Dr. Gentle will accomplish this career goal through novel translational and interventional investigations and future multi-center clinical trials of therapeutic strategies that reduce adverse outcomes in infants with BPD-PH. In order to further facilitate these accomplishments, Dr. Gentle’s complimentary and comprehensive mentorship and advisory team provides a group of investigators with a rich history of NIH funded investigations and prior mentorship; formal training inclusive of a (1) Master of Science in Public Health in Biostatistics, (2) completion of a graduate certificate in Medical Signal and Image Analysis, and (3) echocardiographic assessment of BPD-PH; and a research strategy that is an intentional extension of his ongoing research in infants with BPD-PH. Dr. Gentle has recently produced multiple high impact publications in AJRCCM including an investigation of intermittent hypoxemia characteristics related to BPD-PH thereby providing a surrogate metric to evaluate therapeutic responses to BPD-PH interventions including those in the current proposal’s SA2 and SA3. These characteristics, in addition to demographic and clinical characteristics detailed in Dr. Gentle’s additional publication in AJRCCM, provide the framework for BPD-PH risk estimation as detailed in SA1. In summary, the current proposal addresses the minimal evidence for (1) prediction of BPD-PH in extremely preterm infants (SA1), (2) characterizing subphenotypes of infants with BPD-PH using group trajectory modeling (SA2), and (3) oxygen saturation targets that reduce echocardiographic BPD-PH by performing a randomized, crossover trial in infants with established BPD-PH randomized to oxygen saturations of 92-95% and 95-98% (SA3). Insights from these investigations will strengthen the currently expert consensus-based recommendations from the American Thoracic Society and American Heart Association in the optimal oxygen saturation targets and pulmonary hypertension specific pharmacotherapies used to treat children with BP-PH. Subsequent R01 funded multi-center clinical trials will provide consequential evidence that will influence standards of care in children with this disease.

NIH Research Projects · FY 2026 · 2024-12

PROJECT SUMMARY Phenotypic plasticity and epigenetic reprogramming stand as two noteworthy cancer hallmarks. Lineage plasticity, in particular, has been recognized as a key mechanism that enables cancer cells to evade targeted therapies. Prostate cancer (PCa), especially its most aggressive form, metastatic castration-resistant prostate cancer (mCRPC), exemplifies lineage plasticity-based resistance to Androgen Receptor (AR) targeted therapies. This resistance significantly constrains patient clinical outcomes, rendering mCRPC incurable, underscoring the critical demand for elucidating the mechanisms of resistance and identifying actionable therapeutic targets to overcome resistance. We identified ZNF397 as a pivotal coactivator for AR expression, essential for the transcriptional program governing AR-driven luminal lineage in various cancers. ZNF397 deficiency, a prevalent event observed in 25-40% of PCa patients, enables the transition of cancer cells from an AR-driven luminal lineage to a TET2-driven lineage plastic state, consequently leading to AR therapy resistance. Preliminary results also suggest that both genetic and pharmaceutical inactivation of TET2 eradicates AR targeted therapy resistance, highlighting TET2 as a potential therapeutic target to combat AR targeted therapy resistance in advanced PCa, including mCRPC. Therefore, the Overall Objective of this study is to comprehensively decipher the molecular mechanism of ZNF397-deficiency in promoting lineage plasticity and AR-targeted therapy resistance, with a goal to develop innovative therapeutic approaches to overcome resistance and benefit patients suffering from this devastating disease. We proposed three aims to test the hypothesis that the frequently observed ZNF397-deficiency is a molecular driver that promotes the transition of cancer cells from an AR-driven luminal lineage state to a TET2-driven lineage plastic state, which subsequently becomes non-responsive to AR- targeted therapy. In Aim 1, we will comprehensively assess the effect of ZNF397-deficiency in PCa tumorigenesis, therapy responsiveness and lineage plasticity, using our uniquely generated GEMM with ZNF397-KO, as well as single cell RNA-seq and spatial transcriptomics. In Aim 2, we will elucidate the molecular mechanism of TET2-driven epigenetic rewiring and lineage plasticity in ZNF397-deficient PCa. In Aim 3, we will assess the predictive potency of ZNF397 expression as a biomarker for AR targeted therapy response and examine the efficacy of two novel strategies to overcome resistance in ZNF397-deficient tumors: TET2 inhibitors and ZNF397-DUBTACs. The proposed aims will capitalize on our laboratory's expertise and that of our collaborators to comprehensively define the molecular function of ZNF397. Completion of this project will not only refine our understanding of the mechanisms propelling AR-targeted therapy resistance but also lead to a new predictive biomarker and two innovative therapeutic strategies to combat this lethal complication of modern targeted therapies, thereby improving the clinical outcomes for patients.

NIH Research Projects · FY 2026 · 2024-12

Project Summary Motor learning is a critical function of the vertebrate nervous system. Foundational theoretical work has described how motor learning may proceed at the algorithmic level, where an internal model predicts the sensory outcome of descending motor commands and adapts future movements to reduce prediction errors. At present, the internal model framework does not specify the necessary and sufficient neural signals that are required for error-based motor learning. This project is designed to fill this gap. In our framing, motor learning is made possible by two signals – a motor plan and a subsequent sensory prediction error. In light of this hypothesis, we predict that motor learning can proceed even in the absence of movement. Here, we test this hypothesis in two distinct domains – upper-limb and speech adaptation. This project thus proposes a unique hypothesis concerning multiple forms of motor learning and is poised to increase our understanding of this critical function of the human motor system. The research plan centers on two Specific Aims. In Aim 1 we use behavioral studies, electromyography, and functional neuroimaging (fMRI) to ask if motor planning and error processing are necessary and sufficient for upper limb motor learning, even in the absence of movement execution. We test the idea that motor plans need not reach the muscles to act as effective input to the brain’s internal models for movement. We also posit several constraints on motor learning without movement, where motor errors must be spatially localized near the goal of preceding motor plans to induce learning, and that the two signals must also occur close in time. Finally, using a novel fMRI experimental design, we attempt to map the neural correlates of the planning and error signals that constitute the key ingredients of motor learning. Aim 2 takes a parallel tack, but in the domain of speech motor learning. Thus, Aim 2 provides a stringent generalization test of our framework, asking whether predictive processing is a fundamental and universal computation of the motor system. Moreover, our novel behavioral design helps us to, for the first time, directly test competing theories of speech adaptation. Aim 2 also utilizes a novel fMRI protocol for mapping neural circuits underlying planning and prediction error processes in speech adaptation. It is critical to better understand how motor learning works at a basic algorithmic level – the knowledge gleaned by this proposal will support the development of unique mechanistic and clinical insights into future rehabilitation strategies, the underlying nature of BCI learning, and the power of human predictive processing.

NSF Awards · FY 2024 · 2024-12

This project will assess the effect of floods and landslides caused by Hurricane Helene on spatial genetic and phenotypic variation of freshwater fish populations in the southern Appalachian Mountains. Extreme events provide a rare opportunity to investigate the role of disturbance on evolutionary processes. The record-breaking river flows and the transport and deposition of sediment associated with Hurricane Helene is likely to have profound impacts on freshwater fish. Flooding may influence population diversity by causing mortality, physically moving individual organisms across the landscape, or restructuring suitable habitat and dispersal pathways. The project will resample approximately 20 sites across the upper Tennessee River, the Savannah River, and the Santee River in western North Carolina and Tennessee that were previously sampled from 2021-2024, prior to Hurricane Helene. This research will contribute to the essential effort to understand how biodiversity will be affected by a changing planet. The research is of particular importance in the southern Appalachian Mountains, which is located within a temperate freshwater biodiversity hotspot and hosts an exceptional number of freshwater fish species. Results from the proposed work will be communicated to conservation practitioners at the annual Southeastern Fishes Council meeting. Evolution may be contingent on stochastic and impactful events like mutations or extreme abiotic disturbance, and it has been proposed that historical contingency can reduce the degree to which evolution is predictable. Alternatively, natural selection may determine the outcomes of stochastic events, yielding predictable evolutionary trajectories. We will rely on our pre-storm collections of genomic datasets or tissues, targeting seven species that vary in body size, reproductive strategies, and microhabitat preference: Nothonotus chlorobranchius (Greenfin Darter), Etheostoma blenniodes (Greenside Darter), Hypentelium nigricans (Northern Hogsucker), Luxilus coccogenis (Warpaint Shiner), Nocomis leptocephalus (Bluehead Chub), Notropis rubricoceus (Saffron Shiner), and Notropis spectrunculus (Mirror Shiner). The project will use doubledigest restriction site associated DNA sequencing to assess changes in spatial genetic variation before and after the storm, and compare morphological and meristic traits in pre- and post-storm specimens. The project will assess whether the effect on evolutionary processes can be predicted by the degree of abiotic disturbance by using geomorphic observations to estimate discharge and shear stress at maximum flood stage and will assess the influence of landslides and debris flows through analysis of remotely sensed topographic and satellite datasets. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2026 · 2024-12

PROJECT SUMMARY Over the last 10 years, the lysosome-mediated degradation pathway macroautophagy has gained prominence in the study of aging-related disorders and extension of lifespan. Macroautophagy is an essential cellular pathway responsible for the elimination of cytosolic proteins, lipids, and organelles, and as such, the field has focused upon the role of macroautophagy in clearing protein aggregates or dysfunctional organelles (such as mitochondria) that specifically accumulate in the cytoplasm. Increasingly however, protein and toxic lipid accumulation and organelle dysfunction are observed to occur within the nucleus, apparently shielded from cytoplasmic processes by the double-membraned nuclear envelope. Furthermore, links between aging and nuclear envelope structural defects are emerging, including nuclear envelopathies caused by mutations in the envelope scaffolding lamins and associated integral inner nuclear membrane proteins. Recent work has also established that the nuclear envelope is a hotspot for lipid metabolism, raising the specter that the buildup of toxic lipid species may impact nuclear envelope function if they are not effectively cleared. There is compelling evidence that components of the nuclear envelope and the nucleus are subject to macroautophagy-dependent turnover (termed nucleophagy) but the molecular mechanisms remain unknown. Here, we leverage the S. cerevisiae model to define the molecular and ultrastructural steps that define a model nucleophagy pathway. In our published and preliminary data, we establish a kinetic and ultrastructural timeline of nucleophagy. We will use these data to integrate molecular machineries that we have already discovered into this timeline to understand the mechanisms that underpin each step. These experiments will be supported by in vitro reconstitution to provide a deep insight into how these factors remodel the nuclear membranes. Lastly, we test the innovative hypothesis that nucleophagy clears toxic lipid species in order to rejuvenate the nuclear membranes and ensure robust chronological lifespan. The latter will employ leading-edge lipidomics platforms to provide much needed insight into how the nuclear envelope lipidome is altered during aging.

NIH Research Projects · FY 2026 · 2024-12

ABSTRACT. Limited selective social attention represents one of the best-replicated biomarkers in ASD. The mechanisms underlying differences in social attention in ASD remain to be identified. One of the mechanisms that contributes to attentional selection in neurotypical individuals is value learning. Value learning represents an implicit (i.e., occurring outside conscious awareness) process through which initially neutral stimuli (e.g., a face) when paired with a reinforcer (e.g., the face smiling) gains enhanced capacity to attract attention, or value-based salience. Our group has demonstrated that compared to typically developing and developmentally delayed children, preschoolers with ASD exhibit attenuated value learning when both stimuli and reinforcers are social (face, smiling face) and enhanced value learning when both stimuli and reinforcers are nonsocial (fractal, evolving fractal). If present early in life, this type of imbalance in propensity to learn about social and nonsocial stimuli may alter the experience-dependent development of neural circuitry supporting salience detection and learning and contribute to atypical development in ASD. Despite their potential importance for development of selective attention and cognition, the factors contributing to differences in value learning in ASD are not fully understood. Specifically, it is not clear if altered value learning results from children having trouble making associations between stimuli and reinforcers (value learning) whenever the stimuli are social (or nonsocial) in nature (stimulus effect) or whenever the reinforcers are social (or nonsocial) in nature (reinforcer effect) or when the stimulus and reinforcer type conspire together to give rise to specific patterns of value-based attentional biases. In the present proposal we plan to carefully manipulate the type of stimuli and reinforcers and consider key cognitive, affective, and biological covariates, to elucidate the processes through which initially neutral social and nonsocial stimuli gain privileged status in the attentional system in toddlers with and without autism. We also plan to investigate how individual differences in this value learning associate with core attentional and behavioral features of autism. The project will examine value learning in 18- to 30-month-old toddlers with ASD (n=100), typical development (TD) (n=50), and developmental delays (DD) (n=50) matched for chronological age and sex using a gaze-contingent eye- tracking implicit value learning task developed in our lab. To test our predictions, in Aim 1, effects of stimulus (social versus nonsocial) and reinforcer (social versus nonsocial) on indices of value learning will be examined in ASD, TD, and DD groups. In Aim 2, we will examine the associations between value learning indices and selective social attention measured using both a validated free-viewing screen-based (2a) and a novel live eye- tracking (2b-exploratory) task. In Aim 3, we will examine concurrent (18-30 months) and prospective (36 months) associations between indices of value learning (Aim 1) and selective social attention (Aim 2) and measures of severity of autism symptoms in the social and repetitive behavior domains.

NIH Research Projects · FY 2026 · 2024-12

ABSTRACT Individuals with neuropsychiatric manifestations of post-acute sequelae of SARS-CoV-2 infection (neuro-PASC) report cognitive impairment, new or worsening anxiety and/or depression, altered sleep, autonomic dysfunction, headache, dizziness, post-exertional malaise, and/or neuropathy, among other symptoms. Currently, an estimated 10% of individuals who contract SARS-CoV-2 go onto develop PASC, which represents an enormous disability as well as clinical, social, and economic burden worldwide. Yet, there is a large gap in our understanding of how neuro-PASC alters the function of the brain leading to persistent symptoms and deficits. In response to RFA-NS-23-021, this proposal is aimed at merging two powerful lines of investigation here at Yale to provide a biological basis for the clinical symptoms observed. The first strength is the NeuroCOVID Clinic at Yale, which has seen over 600 patients with neuro-PASC. We then created The COVID Mind Study at Yale under the leadership of Dr. Spudich and have enrolled over 90 participants with neuro-PASC and 60 controls with no PASC. The clinic and study will serve as key sources of subject recruitment. The second strength is the robust and innovative neuroscience and neuroimaging group at Yale under the leadership of Dr. Constable. His group has leveraged the NIH interest in the human connectome and developed methods that link circuit-level (dys)function in the brain to cognitive profiles measured through standardized testing and clinical symptoms. This framework uses a powerful predictive modeling approach and machine learning strategies to localize circuit (dys)function and quantify the contributions of different networks to clinical symptoms and behavior. With both of these strengths, we are ideally positioned to investigate this critical public health issue. Our preliminary data from The COVID Mind Study demonstrates significant cognitive deficits in individuals with neuro-PASC, particularly in language, working memory, declarative memory, non-dominant motor function, and perception compared to COVID negative controls. They also demonstrate greater negative valence issues, including depression, rumination, apathy, anxiety, and perceived stress. We also demonstrated the neuro-PASC group had significantly lower cerebral blood flow in the left superior parietal lobule compared to PASC negative controls using MRI perfusion imaging. To date, there have been no comprehensive assessments of the impact of neuro-PASC on brain function. Using novel methodology developed for this project centered on predictive models for generating reliable associations, we will identify the circuit level brain changes, potential compensatory mechanisms in each cognitive domain, and understand the distinct role of mood alterations in neuro-PASC. We will generate targets for the development of future treatment strategies in neuro-PASC. Our overarching hypothesis is that there are distinct changes in the brain-behavior circuits in individuals with neuro- PASC that will provide key insight into the pathophysiology of this disorder and guide future treatments. The outcome of these studies will have a major impact in how such patients are perceived and managed.

NIH Research Projects · FY 2026 · 2024-12

Co-transcriptional processing of precursor messenger RNA (pre-mRNA) through 5’ capping, splicing, and 3’ end formation regulates gene expression by controlling transcript diversity and stability. Aspects of these processes are sensitive to environmental stress. In mammals and plants, alternative isoforms are generated under stress conditions through alternative splicing (AS) and alternative polyadenylation (APA). A variety of genes in human tissue culture cells also exhibit repression of 3’ end cleavage under stress, leading to the production of downstream-of-gene (DoG) RNAs. Human activity contributes to abiotic stresses in aquatic environments, such as changes in water temperature and purity, with the introduction of toxic heavy metals like arsenic. These factors threaten water quality and expose aquatic organisms to more frequent stress events. How environmental stressors, such as heat and water pollution, affect pre-mRNA processing in aquatic organisms like algae is unknown. To address this gap in knowledge, I propose the use of the freshwater green alga Chlamydomonas reinhardtii as a model organism due to its ease of laboratory cultivation and its fully-sequenced, intron-rich genome. I hypothesize that environmental stressors – changes in temperature and exposure to arsenite – induce specific changes in pre-mRNA processing in C. reinhardtii that can be quantified and evaluated for biological significance. To address this hypothesis, I propose three aims. In Aim 1, I will determine the effects of environmental stress on global pre-mRNA processing by identifying changes in AS and APA using next generation sequencing (NGS) and long-read sequencing (LRS) of mature RNA. LRS is a relatively recent sequencing strategy that identifies all of the sequence in single transcripts. This associates all possible changes, such as alternative exons and alternative polyadenylation sites, enabling me to predict the protein isoforms produced in every case. This can critically impact the interpretation regarding function. My preliminary results have identified over 300 cases of alternative cassette exon usage induced by high temperature; this includes an exon skipping event that is predicted to introduce a premature termination codon within the sequence coding for the kinase domain of a serine-threonine protein kinase. In Aim 2, I will characterize transcriptional defects induced by environmental stress by quantifying DoG induction using NGS and LRS of nascent RNA, a specialty of the Neugebauer lab that has previously led to mechanistic insights. For both Aims 1 and 2, I will validate the biological significance of these RNA processing events by generating mutant strains with CRISPR and by assessing their performance in a stress survival assay. Finally, in Aim 3, I will analyze the conservation of gene sequences and RNA processing changes among freshwater algae using comparative genomics and reverse transcription polymerase chain reaction (RT-PCR). Together, these results will provide valuable insights into the ways aquatic organisms cope with environmental stress at a molecular level. These results will also enable the development of bioassays and/or bioindicators that relate molecular phenotypes, such as changes in AS, APA, or DoG induction, with water quality.

NIH Research Projects · FY 2025 · 2024-11

ABSTRACT The Resuscitation Science Symposium (ReSS) is an annual specialty conference of the American Heart Association, Council on Cardiopulmonary, Critical Care, Perioperative and Resuscitation (3CPR). The first meeting was held as a pre-conference in 2003, bringing together leading scientists and investigators dedicated to improving outcomes from cardiac arrest. Today, the symposium is a 2-day event with approximately 50 multidisciplinary conference faculty presenting innovative and novel science to an international audience. ReSS has evolved over the years, with a focus on advancing the careers of early scientists, building a diverse and inclusive community for inquiry, and expanding into scientific realms that encompass all aspects of the cardiac arrest “Chain of Survival.” Since it's inception, ReSS has included events to promote early-career scientists by hosting a Young Investigator Networking Event the night prior to the start of official scientific proceedings, as well as an annual Women in Resuscitation Event that varies in content from open forum discussion to career coaching. ReSS also boasts a phenomenal track record of being the forum for presentation of ground-breaking research, including topics such as targeted temperature management and dual sequential defibrillation. It is a meeting where thought-leaders debate outcomes, create collaborations, and plot a pathway forward to improve outcomes from cardiac arrest. In light of this opportunity, the programming committee for ReSS recognizes the strength in diverse, collaborative teams. We are firmly committed to growing the pipeline of future investigators in cardiac arrest research. To that end, we recognize the importance of a diverse and inclusive team that sponsors and grows investigators for all demographic, region, and specialty. This proposal to the NIH is requesting support to provide resources to individuals who are young investigators, members of underrepresented groups, attendees what might have hardship travelling due to caregiving needs, financial hardship or disability. The ReSS programming committee is invested in growing our community as a means of creating novel inquiry that will undoubtedly improve outcomes from cardiac arrest.

NIH Research Projects · FY 2024 · 2024-11

Project Summary/Abstract Differential local adaptations in human populations during our evolutionary history have contributed to the variation in phenotypes and disease risks observed in modern humans. While statistical genomic signatures of local adaptation can be detected across ancestries, the variants and genes underlying these adaptive traits, as well as their function, remain nearly entirely unknown. The signature of high linkage disequilibrium (LD) that enables detection of adaptive loci also hinders our statistical fine-mapping ability at these loci. Moreover, these variants are often in non-coding, cis-regulatory elements (CREs) of the genome, in which it is difficult to predict the impact of genotype on function. Additionally, current GWAS and quantitative trait studies commonly used to interpret regulatory variation, are European-biased, rendering them underpowered in diverse ancestries. Discovering the evolutionary trends, mechanisms, and phenotypes of adaptive variation therefore requires LD-independent, ancestry-agnostic tools that can characterize putatively adaptive variation at scale. During my dissertation I will generate a catalog of well-characterized putatively-causal adaptive CRE variants by pairing previously-designed machine-learning detectors of adaptation with scalable functional genomics technologies. DeepSweep, a machine-learning algorithm developed by the Reilly Lab, drastically reduces the number of putatively causal variants per causal loci to the point that they can be experimentally tested. I will functionally fine-map DeepSweep-identified putatively adaptive variants from non-admixed 1000 Genome Project populations using the Massively Parallel Reporter Assay to identify expression-modulating variants (emVars). I will next identify the gene targets of functional adaptive variants using single-cell CRISPR-interference screens. Knowing these gene regulatory targets will enable an understanding of the biological processes, pathways and higher-order phenotypes impacted by adaptation. This catalog of functionally fine-mapped adaptive CRE variants linked to target genes will resolve phenotype impacting variation at high-LD loci, and for the first time, provide enough instances of characterized adaptation to discover trends of adaptation shared across ancestral histories. I will Interrogate the medical utility of this catalog by intersecting emVars with phylogenetic constraint scores and emVar regulatory targets with genome-wide association catalogs and gene ontologies. The prevalence of recurrent adaptation in human evolution will be investigated by intersecting emVars with transcription factor motif databases and pathway analysis of emVar regulatory targets. Furthermore this catalog of global adaptive variation will be increasingly useful in resolving causal trait-associated variants at high-LD adaptive loci as association studies become more global and diversified.

NIH Research Projects · FY 2024 · 2024-09

Project Summary/Abstract Healthy vision depends on multiple levels of processing in the retina, the neural tissue that lines the back of the eye. Photoreceptors respond to light and drive signals in retinal interneurons. Interneurons converge onto the retinal ganglion cells (RGCs), the retina's output neurons that project axons through the optic nerve to multiple targets in the brain. All of our visual processing depends on signals generated by the RGCs. The RGCs become injured and die in glaucoma, the leading cause of preventable and irreversible vision loss in humans. A leading risk factor for the development of glaucoma is increased intraocular pressure (IOP). With increased IOP, RGC axons become compromised as they exit the eye to form the optic nerve. Subsequent axon degeneration and RGC death permanently impairs vision. We understand that RGC electrical activity can influence RGC health, and it is known that RGC activity is compromised in mouse models of glaucoma, following either elevations in IOP or direct injury to the optic nerve. Here, we will use two mouse models of optic nerve injury (increased IOP and optic nerve crush) to investigate how these injuries impact RGC activity and identify cellular and synaptic mechanisms underlying the changes in activity. Furthermore, we will consider different categories of RGC types, which have dramatically different responses to glaucomatous injury. Resilient RGCs survive glaucomatous insults well, while susceptible RGCs die quickly after injury. We will test methods for controlling RGC activity in vivo and evaluate the impact of these manipulations on survival for specific RGC types. The experiments will use patch clamp recording in an in vitro preparation of the mouse retina at specific time points following RGC injury and will characterize specific RGC types that are either resilient or susceptible to injuries. Specific Aims will (1) determine underlying cellular and synaptic mechanisms that explain changes in RGC activity following each type of injury; and (2) validate methods for controlling activity in injured RGCs and test their impact on RGC survival. The results will improve our understanding of activity changes in specific RGC types following injury and will facilitate the development of future studies aimed at modulating activity in vivo and improving the survival and regeneration of RGC signaling in human glaucoma.

NIH Research Projects · FY 2024 · 2024-09

PROJECT SUMMARY Alzheimer's disease (AD) is a neurodegenerative disease resulting in dementia and ultimately, death. No cure exists for the disease and treatments start only after symptoms are presented. Thus, early AD detection is crucial to start the treatment to slow down the progress of the disease. Olfactory dysfunction is shown to be present as a disturbed sense of smell, proposed as an early sign of neurodegenerative diseases, but also including AD. The mechanisms underlying olfactory deficits in AD remain largely unknown. Olfactory bulb (OB) and its associated piriform cortex (PCX), a region that is involved in olfactory learning, can be a key candidate for investigating early functional changes in the brain induced by AD pathology. In addition, functional and structural changes in entorhinal cortex (EC) and hippocampus (HC) can be detected years before significant clinical symptoms, and therefore, suggested as potential biomarkers for AD diagnosis. There are a close anatomical and functional associations between olfaction (OB-PCX) and memory (EC-HC) systems. OB-PCX circuit is closely connected with the EC-HC circuit and is suggested as one of the earliest regions affected by AD. Therefore, we hypothesize that progressive neurodegeneration in AD disrupts the connectivity of the olfactory circuit to the memory circuit, leading to early deficits in olfaction followed by memory impairment. Detection of structural, functional and behavioral changes related to olfactory and memory function may result in early AD detection. Our recent work to study AD progression in a rodent model and its response to therapeutic intervention serves as the basis, as well as our recent innovation in a novel functional MRI (fMRI) method which enables simultaneous imaging of the rat cerebral cortex and the olfactory bulb. The overall goal of this project is to develop neuroimaging methodologies that enable early detection of AD and olfactory function via biomarker imaging. To achieve this goal, we will longitudinally perform imaging/spectroscopic and behavioral studies on transgenic TgF344-AD and wildtype (WT) rats from early to more advanced stages of the disease (3-12 months) (Aim 1) and assess mitochondrial energy metabolism (Aim 2). We will use in vivo multi-modal MRI/MRS (at 11.7T) in conjunction with behavioral testing to characterize AD development and progression. We will specifically examine the (a) functional connectivity alterations in the olfactory networks using resting fMRI and bulbar/cortical responses by task fMRI, (b) mitochondrial energy metabolism by 31P-MRS and (c) memory and smell abilities using behavioral measurements (novel object recognition, spatial memory and olfactory tests). The characterization of AD pathology in this rat model using highly translational MRI techniques highlights the potential of this model to be used in valuable future preclinical AD research as well as its use for potential treatment evaluation.

NIH Research Projects · FY 2025 · 2024-09

Cannabis (CB) is frequently used by people with HIV (PWH) for its claimed benefits alongside antiretroviral therapy. However, the immunomodulatory impact of CB in the context of the chronic inflammation experienced among PWH is unclear. The interaction between HIV and CB in the host genome remains poorly understood. Previous studies on the epigenetic effects of HIV and CB have been limited and most studies conducted in bulk peripheral blood mononuclear cells (PBMCs), which only provides an average view of DNA methylation (DNAm) changes across various cell types. Our recent research of DNAm in CD4+ T cells isolated from PWH identified DNAm CpG sites that were linked to HIV-1 latent reservoir and a set of druggable genes, including the target for Ibalizumab, a medication for treatment resistant of HIV infection. The result underscores the value of cell specific DNAm analysis in uncovering mechanisms of HIV pathogenesis and potential therapeutic targets. Nonetheless, the combined effects of HIV infection and CB use on DNAm, particularly considering genetic variants that influence DNAm (methylation quantitative trait loci, meQTL), have yet to be fully explored. To address these gaps, we hypothesize that CB use alters DNAm in a cell type-specific manner within the HIV-infected host, with these changes potentially modulated by meQTL specific to each cell type. Our study aims to dissect the epigenomic landscape of CB and HIV interaction by conducting cell-type based genome-wide DNAm and meQTL analyses in two large cohorts of PWH, assessing their potential for druggable targets. This will involve comprehensive profiling of DNAm across five different cell types isolated from PBMCs, alongside functional validation studies both in vivo and in vitro. The functional validation involves transcriptome-wide association analyses, single-nucleus RNA and ATAC sequencing to elucidate the functional impact of specific epigenetic modifications and their relevance to drug development. In preliminary work, we employed a computational algorithm to deconvolve DNAm data to specific cell types and validated these findings through direct sequencing. This has revealed a more nuanced understanding of HIV's impact at the cellular level, identifying cell type specific DNAm sites and highlighting the unique genetic landscapes influenced by HIV across different cell populations. Furthermore, we have developed a novel algorithm, Hierarchical Bayesian Interaction model, to uncover genetically influenced DNAm at cell type level. These preliminary findings provide the framework for this proposed project. Our team's established expertise in epigenomics among PWH, positions us uniquely to achieve our goal. Successful completion of this study promises to deliver unprecedented insights into the mechanisms of CB's immunomodulatory effects in HIV, paving the way for novel therapeutic strategies through targeted drug repositioning.

NIH Research Projects · FY 2025 · 2024-09

This K01 seeks support for formal coursework, seminars, interdisciplinary mentorship, and research in Eastern Europe to expand the skills of a sociologist who has been academically productive in examining the social production of HIV risk in prisons but now aims to shift their career toward tailoring implementation strategies for HIV prevention among people who use drugs. Dr. Azbel seeks to broaden their training to emerge as an independent researcher who can leverage newly acquired skills in ethnography, implementation science (both theory and real-world experience), and mixed methods research and apply them to a new setting, probation, which aligns with decarceration goals. They aim to shift their research trajectory from retrospectively unpacking why an intervention did not work as expected (using qualitative interviews) to prospectively refining strategies to improve interventions (using quantitative and ethnography). The training will support Dr. Azbel's two proposed research projects, which use the EPIS framework to understand the influence of the inner and outer contexts on the successful implementation of a screening-engagement-treatment (SET) strategy for opioid agonist therapy (OAT) scale-up. The projects will occur in probation in Georgia and Moldova, two distinct epidemiological, social, and geopolitical contexts. The conflicting roles of upholding public health and public safety strain the complex and understudied officer-client relationship, which research has shown to be crucial for the successful implementation of evidence-based practices. The core of these projects will be to refine strategies to align probation officers’ primary focus (public safety by reducing crime) with their evolution toward public health mandates (to reduce transmission of HIV through facilitating clients receiving OAT). Project 1.1, guided by the socioecological model, will examine the barriers and facilitators within the inner context (officers and clients) to implementing SET procedures to promote OAT scale-up using mixed methods, including structured surveys and nominal group technique (NGT). Project 1.2 will use ethnographic methods to explore the dynamic interrelations of the inner (client, officer) and outer (probation leadership, OAT clinics) contexts as SET is implemented and process changes are introduced via NIATx (a bundle of implementation tools). The candidate will test the hypothesis that NIATx improves collaboration and trust between probation staff, leadership, and clients, particularly as their goals align as OAT improves individual health and reduces crime. These research aims will be enhanced through the candidate getting certified as a NIATx coach where they will coach change teams in probation in Kyrgyzstan. As probation services expand, including in the U.S., such analysis can be leveraged to expand OAT as HIV prevention in ways that promote decarceration and are responsive to local needs and contextual differences. The candidate’s long-term career goal is to become an independent global health investigator focused on implementing culturally attuned HIV prevention interventions that target criminal justice populations, especially where decarceration efforts are involved.