Weill Medical Coll Of Cornell Univ

NIH Research Projects · FY 2026 · 2022-03

PROJECT SUMMARY/ABSTRACT This is a K01 Mentored Research Scientist Development Award submitted to the National Institute on Aging by Robert Tyler Braun, an Instructor in the Department of Population Health Sciences at Weill Cornell Medical College (WCMC). Dr. Braun's career goal is to become an independent researcher on improving end-of-life care for the elderly by assessing various policy interventions and delivery models of hospice care. This K01 application will provide Dr. Braun with the necessary training 1) to gain expertise in aging and hospice research; 2) to understand clinical care for hospice patients; and 3) to gain methodological skills to conduct qualitative studies related to hospice delivery and care. Dr. Braun has assembled a mentor team of accomplished researchers from WCMS and Vanderbilt University School of Medicine (VUSM): Dr. Lawrence Casalino (primary mentor) who is the Livingston Farrand Professor of Public Health at WCMC and an expert on health care organization and behavior, and qualitative methods; Dr. Holly Prigerson (co-mentor) who is the Irving Sherwood Wrights Professor of Geriatrics at WCMC and an expert on end-of-life care; Dr. David Stevenson (co-mentor) who is a professor and the holder of the Endowed Directorship in Health Policy Education at VUMC and an expert in the delivery of hospice care; and Dr. Mark Unruh (co-mentor) who is an Associate Professor in the Department of Population Health Sciences at WCMC with expertise in long-term care and Medicare claims data. Over the past couple of decades, the hospice industry has moved from largely a not-for-profit sector to predominately for-profit. Facilitated by relatively easy market entry and generous Medicare payments, PE firms and PTCs have been acquiring hospices (many of them non-profit), with the goal to deliver short-term, above market returns to their investors. Despite this emergence, little is known of its effect on hospice care. Building on his previous research and training on assessing this phenomenon in physician practices, Dr. Braun will identify the organizational, staffing, patient, and quality characteristics associated with PE and PTC acquisitions using publicly available hospice data from Center for Medicare and Medicaid Services (CMS) (Aim 1), use rigorous econometric methods to assess the effect PE and PTC acquisition on hospice care using patient-level Medicare claims (Aim 2), and use qualitative methods to assess organizational, cultural, and delivery aspects of hospices post-acquisition integration (Aim 3). This research will be a foundation for an R01 grant application and will incorporate the new skills acquired through his training, which inform opportunities for improvement in hospice delivery of care.

NIH Research Projects · FY 2026 · 2022-03

ABSTRACT Alzheimer’s disease (AD) and AD-related dementia (AD/ADRD) is the 6th leading cause of death in the United States (US) – is an aging-related neurodegenerative disease with complex pathogenic mechanism affecting an estimated 6.2 million Americans in 2021. Both the pathogenic mechanism and pathophysiology of AD/ADRD are complex, creating difficulties in finding effective new treatment or prevention strategies, despite significant investments in the last decade. On the other hand, the proliferation of large clinical research networks (CRNs) with real-world data (RWD), such as electronic health records (EHRs), claims, and billing data among others, offer unique opportunities to generate real-world evidence (RWE) that will have direct translational impacts on AD/ADRD. In the past, RWD such as EHRs have limited use for AD/ADRD drug repurposing and primarily used only for validating and evaluating the hypotheses generated by molecular level predictions of AD/ADRD repurposing agents, partially due to a number of key methodological gaps: (1) the lack of integration with existing rich biological and pathophysiological knowledge of AD/ADRD for hypothesis generation, (2) the lack of validated computable phenotyping (CP) and natural language processing (NLP) algorithms and tools that can accurately define the study populations, extract key relevant patient characteristics and meaningful outcomes (e.g., MMSE scores to determine severity), (3) the lack of consideration on the heterogeneity of the disease (i.e., AD/ADRD subtypes), and (4) the lack of recognition of the inherent biases in RWD and the need of applying causal inference principles. The goal of this project is to develop a comprehensive machine learning based causal inference framework for generating high-throughput and high-quality drug repurposing hypotheses for AD/ADRD by integrating heterogeneous information sources. There are three aims in this project. Aim 1 aims at developing computable phenotypes to extract key patient characteristics and outcomes relevant to AD/ADRD drug repurposing studies from RWD. Aim 2 aims at developing a learning-based causal inference framework for generating drug repurposing hypotheses from RWD, a deep knowledge embedding framework for generating drug repurposing hypotheses from biomedical knowledge bases (BKB); and a mutual information enhancement framework that combines the information from both RWD and BKB to further improve the quality of the generated hypotheses. Aim 3 aims at validating the generated hypotheses with diverse data sources and approaches. The project will leverage the patient data from two large clinical research networks (CRNs) contributing to the national Patient-Centered Clinical Research Network (PCORnet) – covering ~15 million Floridians and ~11 million New Yorkers. The developed algorithms and software will be open sourced and widely disseminated within the CRNs and the AD/ADRD research communities.

NIH Research Projects · FY 2026 · 2022-03

Project summary: The immune system faces the external world and encounters pathogens, including viruses in barrier tissues (e.g. skin, lung, and gut). There the immune system must detect and respond to pathogens, while simultaneously preventing autoimmunity and promoting tissue repair. Dendritic cells (DC) in tissue are the key cells which balance self-tolerance (preventing destruction of our bodies tissues) with pathogen surveillance. The goal of this application is to understand how DCs develop uniquely and are adapted in the tissue to perform and balance these functions. We have recently identified an important new mechanism, and a new molecular target that dictates how DC in tissues differentiate in ways that impact their function. The goal of this proposal is to gain a deeper understanding of DC biology along this regulatory axis, as a critical first step to intervene upon tissue DC to restore health, when dysregulated. This would advance better immunization strategies as tissue DCs are necessary for vaccine, viral, and cancer immunity. This application enables us to now test, for the first time, how our myeloid compartment is architected to balance immune tolerance and pathogen surveillance in barrier tissue sites. Upon completion of this project we will understand how DCs in tissue are locally conditioned to behave in a site- specific manner. We will gain an appreciation of how shared environmental sensing patterns are balanced against individual cell identities, and tailored to specific pathogenic contexts. We will understand how local cues modify the behavior of DCs, positioning us to test this in disease states. We will also identify DC behaviors that are modifiable by local cues, enabling improved intervention on DC during disease pathogenesis and a better model for successful DC development to improve adoptive cell therapy. The insights here are foundational, fill a critical knowledge gap, and represent basic science advances needed to advance human health.

NIH Research Projects · FY 2025 · 2022-02

SUMMARY Genomic analyses of thousands of MDS patients has established that mutations in RNA splicing factors are the most common class of genetic alterations in patients with MDS. In parallel, functional studies have revealed that several of these genetic lesions appear to drive aberrant hematopoietic self-renewal and differentiation that is characteristic of MDS. Specifically, mutations in splicing factor 3b subunit 1(SF3B1), a core spliceosome component, are among the most common in patients with MDS and lead to incorrect intronic branch point recognition. Despite these advances, our knowledge of the effects of this genetic alteration on downstream gene expression programs within actual disease initiating cells has been hampered by the coexistence of normal wildtype hematopoiesis together with the aberrant clone harboring somatic driver mutations. While some of these limitations are now beginning to be addressed with single cell genomics, performing a layered genomic analysis to simultaneously capture somatic mutations, gene expression, RNA splicing, and chromatin state in single cells has never been performed. Expression of RNA-binding proteins is in turn cell type dependent, necessitating the simultaneously profiling of gene expression, full-length cDNA and SF3B1 mutational status at the single cell level, allowing splicing to be examined in the proper cellular context. To address this challenge, we developed an array of multi-omic single-cell technologies that are capable of capturing multiple layers of information (e.g., genotypes, transcriptomes, methylomes, protein expression) from the same single cells. Moreover, we addressed the specific challenge of genotyping in scRNA-seq in single cells at high throughput by developing Genotyping of Transcriptomes (GoT). Importantly, GoT turns the admixture of mutant and wildtype hematopoiesis from a limitation to an advantage, enabling the direct comparison of mutant and wildtype cells within the same individual. Capitalizing on a unique cohort of bone marrow samples from individuals with MDS and CH, we now aim to apply and extend the multi-omics single-cell toolkit to test define how SF3B1 somatic mutations lead to clonal growth advantage. First, we will perform GoT across MDS and CH samples with canonical SF3B1 driver mutations. We will integrate GoT with Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE- seq) (GoT-CITE), to add the critical layer of cell surface markers to single-cell whole transcriptomes. Second, mutations in splicing factors are specifically associated with greater risk of transformation in CH. Therefore, we will develop and implement GoT-Splice, where long-read sequencing will be used to define splicing variation as a function of cell identity. Third, given the high importance of epigenetic patterning to hematopoietic stem cell identity, we will develop and apply targeted single-cell genotyping in the context of chromatin accessibility (GoT-ChA). This will allow us to unravel the regulatory underpinnings of SF3B1-driven CH and MDS.

NIH Research Projects · FY 2025 · 2022-02

PROJECT SUMMARY/ABSTRACT Radical prostatectomy (RP) is a standard treatment for localized prostate cancer with 60,000 procedures per year in the U.S. Commonly recognized long-term adverse events of RP include persistent urinary incontinence (~20%) and erectile dysfunction (~65%). Less commonly known risks include penile shortening (~50%), penile deformity/curvature (~15%), and inguinal hernia (~15%). These adverse events lower health- related quality of life, cause decision regret and require additional treatment. A new surgical technique, pelvic fascia-sparing RP (PFS-RP), preserves fascial support structures, arterial supply to the penis, and nerves that are severed and resected during conventional RP. Several retrospective series have shown significaly reduced urinary and erectile dysfunction after PFS-RP. However, these studies have been small and had limited follow- up for oncologic endpoints. A multi-center, randomized controlled trial (RCT) with longer follow-up is clearly indicated. However, adequately powered surgical RCTs face significant challenges: 1) a traditional RCT of this new technique would cost ~$10 million; and 2) typically, such RCTs accrue only about six patients per center per year and often close prematurely due to low accrual. Indeed, there is almost a complete absence of sufficiently powered RCTs in oncologic surgery. After considering these challenges, we developed two innovative methodological approaches that have strong published, preliminary data. The first is to use a two-stage RCT consent that lowers information overload, decisional burden, and anxiety. Making consent easier for patients also reduces the burden on surgeon investigators making them more willing to accrue. Preliminary data suggest that two-stage consent dramatically improves accrual – in one recent study, 98% of eligible patients were accrued - while maintaining patient understanding of consent as assessed by a standard questionnaire. The second innovation employs a web-based portal to incentivize self-entry of patient-reported outcomes by giving patients feedback and advice in response to their answers. This portal has already been used by ~15,000 patients and captured the endpoint for two RCTs. We propose a RCT using these two novel methodologic approaches. This will randomized 600 patients to PFS-RP or traditional RP conducted at four centers that receive NCI SPORE awards for prostate cancer. We will test whether PFS-RP is able to reduce urinary and erectile function, as well as immediate surgical complications, while being non-inferior for cancer control. The study will include a rigorous surgeon quality assurance approach, involving surgical videos uploaded to a central site and quantitative scoring of discrete surgical steps. Successful completion of the study would not only provide evidence on the best practice for one of the most common cancer operations but provide a novel methodological approach that could facilitate future studies in surgical oncology.

NIH Research Projects · FY 2026 · 2022-02

ABSTRACT The goal of this project is to refine and test WellPATH-PREVENT, a novel, mobile, principally stand-alone psychosocial intervention designed to improve cognitive reappraisal ability (target) and reduce suicide risk (outcome) in middle-aged and older adults (50-90 years old) who have been discharged after a suicide-related hospitalization (i.e. for suicidal ideation or suicide attempt). Suicide rates in this group are alarmingly high, and reducing suicide rates in at-risk populations is a major NIMH priority. Our conceptual framework views suicidal ideation and behavior as failed attempts to regulate negative emotions, and by improving cognitive reappraisal, an effective emotion regulation strategy, we expect to reduce suicide risk. WellPATH-PREVENT focuses on the training, coaching, and use of WellPATH app, a tablet-app that incorporates triggers, negative emotions, and personalized easy-to-use cognitive reappraisal techniques. The patient uses the tablet during emotionally charged situations and scheduled training sessions. The R61 phase is a proof-of-concept phase and its goals are to test WellPATH-PREVENT’s target engagement and optimization (6 vs. 12 weeks duration). Interventionists will administer WellPATH-PREVENT to 40 middle-aged and older adults (50-90 years old) after a suicide-related hospitalization. Research assistants, unaware of the study aims, will conduct assessments at study entry (admission/during hospitalization), discharge, 6 and 12 weeks post-discharge. Target engagement will be assessed with electrocortical measures (i.e. late positive potential, LPP), self-reported affect during an emotion regulation task, and Emotion Regulation Questionnaire (ERQ), an interviewer-administered instrument of cognitive reappraisal. The R33 phase aims to provide further evidence of target engagement of the optimized WellPATH- PREVENT in a larger sample, evaluate the relationship of cognitive reappraisal with suicide risk as measured with Columbia Suicide Severity Rating Scale (C-SSRS), examine preliminary signal of efficacy, and obtain implementation parameters for a large-scale clinical trial. A unique sample of 75 middle-aged and older adults (using the same inclusion/exclusion criteria as for the R61 phase) will be randomized (2 to 1) to WellPATH- PREVENT (N=50) or to Attention Control Usual Care (AC-UC) (a control condition with parallel delivery and a tablet that doesn’t include WellPATH) (N=25). Assessments will be conducted at study entry (admission/during hospitalization), discharge, 6, 12 and 24 weeks post-discharge. Primary aims are: 1) WellPATH-PREVENT participants will show improvement in cognitive reappraisal from discharge to end of treatment; 2) improvement in cognitive reappraisal in WellPATH-PREVENT participants will be associated with suicide risk over 24 weeks; and 3) examination of preliminary signal of efficacy of WellPATH-PREVENT vs. AC-UC on cognitive reappraisal and on suicide risk over 24 weeks.

NIH Research Projects · FY 2025 · 2022-01

PROJECT SUMMARY Obesity afflicts 42% of the adults in the United States and is associated with significant deleterious health effects. Acute respiratory distress syndrome (ARDS) represents a final pathway of acute lung injury (ALI) arising from infectious, such as pneumonia, or sterile, such as ventilator induced lung injury, etiologies, and is associated with high mortality. Obese patients are at increased risk of developing ARDS. This proposal addresses the critical need to better understand the mechanisms that underlie the increased susceptibility of obese patients to ARDS. We have shown in a murine model of high fat diet that obesity results in more severe ALI in sterile and infectious models of ARDS. Obesity is characterized by increased fatty acid (FA) release that exceeds metabolic demands. Although FA are important for the physiologic regulation of a number of processes, high levels are deleterious. We have found increased free FA in the lung of obese mice after infectious and sterile ALI. FA are broken down by means of oxidation for energy generation inside the mitochondria, whereas endogenous FA are synthesized de novo from acetyl coenzyme A. High fat diet was associated with increased lung expression of carnitine palmitoyltransferase 1a (CPT1a), an essential rate limiting enzyme for oxidation, and decreased expression of fatty acid synthase (FASN), the enzyme catalyzing de novo FA synthesis, and of the mitochondrial fusion protein mitofusin 2 (MFN2) after ALI. Mitochondria alter size and shape via fission and fusion to meet cellular metabolic demands. Mitochondrial alterations in the alveolar epithelium have been implicated in ALI pathogenesis. We demonstrated that depletion of FASN in alveolar epithelial type 2 cells was associated with more severe ALI and impaired mitochondrial bioenergetics. In this proposal, we hypothesize high fat diet induced downregulation of mitochondrial fusion and lipid synthesis lead to impaired mitochondrial metabolisml after injury. Mitochondrial overload through excessive oxidation further exacerbates mitochondrial dysfunction. Aim 1 will investigate the role of FA utilization in the pathogenesis of experimental obesity induced ALI by using genetic and pharmacologic approaches to inhibit and enhance oxidation. Aim 2 will delineate the association between FASN regulation, mitochondrial dynamics and alveolar epithelial cell type 2 dysfunction in ALI with high fat diet using genetic approaches to inhibit FASN and MFN1/2 in a sterile and infectious model of ALI. Aim 3 will characterize dysregulated metabolic pathways based on body mass index (BMI) in patients with ARDS using plasma metabolomic profiling. These studies will provide insight into the interplay between obesity and ARDS and may uncover an unappreciated role for lipid metabolism in ALI. This proposal plays a central role in a career development plan for becoming a successful independent investigator focused on lung biology and lipid metabolism. Weill Cornell Medicine is an ideal environment in which to execute this training plan not only because of its excellent physical resources, but also because of its intellectual community of researchers with a track record of strong mentorship of early stage investigators.

NIH Research Projects · FY 2026 · 2022-01

Project Summary/Abstract Despite highly effective pharmacologic and non-pharmacologic interventions to lower blood pressure, elevated blood pressure remains the leading global risk factor for early mortality. In Tanzanian communities, 28% of adults aged 35 and above have hypertension, yet only 2% are aware of their diagnosis and less than 1% are on anti-hypertensive treatment. Our long-term goal is to improve hypertension-related health outcomes in Tanzanian communities. The overall objective of this proposal is to adapt our established model of promoting community health interventions in partnership with highly respected religious leaders in order to bridge gaps in rural communities’ awareness, prevention, and control of high blood pressure. Our central hypothesis is that empowering religious leaders to engage their communities about high blood pressure will improve health behavior and reduce the average blood pressure among adults both with and without hypertension in the community. The rationale for our proposal is that even small reductions in community-wide blood pressure can sharply decrease the risk of premature cardiovascular death in that community. To test this hypothesis, we will pursue three specific aims: 1) Adapt and pilot-test our prior Religious Engagement in Health Intervention to address blood pressure in religious contexts; 2) Determine the effectiveness of this intervention on reducing mean community systolic blood pressure in a cluster randomized trial; and 3) Assess reach, effectiveness, adoption, implementation, and maintenance of this intervention for 24 months. In the first aim, we will use data from previously conducted interviews with religious leaders and community members to adapt, refine, and pilot-test our Religious Engagement in Health Intervention to address the problem of high blood pressure using the sequential ADAPT-ITT model. In the second aim, we will conduct a hybrid type I effectiveness- implementation cluster randomized trial to test the hypothesis that the intervention communities will achieve at least a 3 mmHg greater reduction in mean community systolic blood pressure than control communities. In the third aim, we will use convergent mixed methods guided by the RE-AIM framework to measure reach to religious leaders and community members, effect on community blood pressure and linkage to care, adoption by religious leaders, fidelity to the planned intervention, and maintenance of the benefit at 24 months. We will refine the intervention for dissemination and implementation in partnership with biomedical and religious leaders. The proposed research is innovative because it uses a novel approach to impact community health, it offers contextual flexibility to be adapted by religious leaders or other trusted community messengers for their own contexts, and it may be a creative way to engage men. The proposed research is significant because a community systolic blood pressure reduction of 3 mmHg is estimated to decrease premature cardiovascular mortality by 13% in that community. If successful, this approach could prevent many thousands of deaths in Tanzania and could be adapted for use in U.S. communities in which hypertension outcomes are poor.

NIH Research Projects · FY 2026 · 2021-12

PROJECT SUMMARY The long-term goal of this proposal is to understand the molecular and cellular mechanisms in the tumor microenvironment that govern hepatocellular carcinoma (HCC) development, with a special focus on the role of hepatic stellate cells (HSCs) as central players in this process. While it is clear that activation of non-parenchymal cells is a key contributor to liver tumorigenesis, unfortunately, our knowledge of the molecular mechanisms whereby key stromal and immune cell populations regulated HCC initiation and progression still is fragmentary. Activated HSCs are key contributors to liver fibrosis and inflammation. The present proposal is based on our previously published results demonstrating that the autophagy and signaling adaptor p62 is reduced in HSCs from HCC patients and that its inactivation in mice, either globally or HSC-specific, promoted HCC due to the hyperactivation of the inflammatory and fibrotic activities of HSCs. Our new unpublished preliminary results demonstrate that the genetic ablation of NBR1, either globally or selectively in HSCs, completely reverts the pro- tumorigenic role of p62 deficiency in HSCs. However, this unexpected effect of NBR1 deficiency does not revert the pro-fibrotic, TGFb-driven effect of p62 loss and did not affect autophagy but resulted in the hyperactivation of the interferon (IFN) cascade that renders CD8+ T cells more active, increasing anti-tumor immunosurveillance. Our preliminary data also suggest that this hyperactivation of the IFN pathways is due to impaired chaperone- mediated autophagy (CMA). Therefore, in this proposal we intend to unravel the mechanisms whereby NBR1 promotes CMA to restrain IFN activation. We will also establish how reduced CMA due to the inactivation of NBR1 in HSCs results in the reprograming of the tumor microenvironment to repress tumorigenesis. To that end, we will build on our preliminary data to address the following critical questions: (Aim 1) Establish the molecular mechanisms whereby NBR1 regulates the IFN response in HSCs by (Aim 1.1) determining the effect of NBR1 and p62 inactivation on CMA activity in HSCs; (Aim 1.2) determining the functional contribution of CMA to NBR1- mediated IFN regulation in HSCs; and (Aim 1.3) determining the molecular mechanisms whereby NBR1 regulates CMA. We will also (Aim 2) establish the contribution of NBR1 to HSC activation and the creation of a tumor-suppressive microenvironment by (Aim 2.1) determining the impact that NBR1 deletion in HSCs has in the tumor microenvironment of HCC; (Aim 2.2) determining the functional contribution of the CMA-STING-IFN axis in NBR1-deficient HSCs to HCC progression in vivo; and (Aim 2.3) determining the impact of NBR1 loss in HSCs in therapy response and its relevance in human HCC. Results from these studies will serve to identify new biomarkers as well as non-parenchymal new therapeutic targets for the prevention and treatment of HCC.

NIH Research Projects · FY 2025 · 2021-12

PROJECT SUMMARY More than 500,000 patients with end-stage kidney disease (ESKD) receive chronic hemodialysis (HD) in the U.S. each year. The prevalence of ESKD/HD is increasing, particularly among racial/ethnic minorities. There is a compelling need to address the many clinical concerns that ESKD/HD patients routinely face. One of the most pressing concerns is poorly managed pain. Pain affects up to 90% of ESKD/HD patients; compromising mood, functioning, and overall quality of life (QoL). Pharmacotherapy remains the most common approach to managing pain and substantial numbers of ESKD/HD patients continue to receive long-term opioid treatment. This approach to managing pain is limited by substantial risks of adverse outcomes, including falls, fractures, and hospitalization. Novel non-drug therapies are needed to reduce pain and lessen reliance on opioid therapy in the patient population. Given the increasing prevalence of ESKD/HD in persons of color, it is essential that studies evaluate rigorously the safety and efficacy of new treatments in minority populations. Transcranial direct current stimulation (tDCS) is a non-invasive neuromodulatory therapy, designated as having minimal risk that can reduce pain and analgesic consumption in patients with diverse types of chronic pain. Previous randomized controlled trials (RCTs) have been limited by small sample sizes and stimulation protocols that are brief (≤10 sessions), have not employed at-home stimulation capability, and have only assessed for short-term effects, i.e., mostly employed post-intervention follow-ups of 4 weeks or less. To the best of our knowledge, no tDCS analgesic trial has evaluated longer-term treatment outcomes or determined whether treatment effects vary as a function of race/ethnicity status. Our highly experienced multidisciplinary research team from Weill Cornell Medicine/Cornell University, NY, the Rogosin Institute, NY, and the Metropolitan Jewish Healthcare System (MJHS) Institute for Innovation in Palliative Care, NY has pioneered an at-home, remotely supervised tDCS-telehealth approach that enables long-term stimulation protocols suitable for populations with serious chronic illness such as ESKD/HD. We propose to conduct an adequately powered RCT (N=100) that ensures enrollment of approximately equal numbers of Hispanics, non-Hispanic Blacks, and non-Hispanic whites, with the following aims: 1) determine the short-term (at 2 weeks and upon conclusion of the 40-session 8-week tDCS protocol) and longer-term (12, 16 and 26 weeks after baseline) effects of at-home tDCS, versus sham stimulation, on pain (primary outcome) and on analgesic consumption, pain interference, depressed mood, and quality of life (secondary outcomes); 2) evaluate whether tDCS effects on outcomes vary by race/ethnicity; and 3) ascertain the tolerability of tDCS in terms of side effects and assess patient satisfaction with device use and study procedures. At-home tDCS is a highly promising nonpharmacologic treatment for pain in ESKD/HD. Establishing its longer-term effects could transform the way pain is managed in this ethnically diverse growing population of patients.

NIH Research Projects · FY 2025 · 2021-10

Project Summary/Abstract Tissue stem cells stem cells of the epidermis protect us from external insults, grow hair, and repair wounds. Extensive characterization of epidermal stem cells (IFE-SCs) and hair follicle stem cells (HFSCs) has uncovered how their transcriptional and signaling pathways regulate regeneration. Far less is known about how stem cells incorporate metabolic inputs, which can profoundly affect the balance between proliferation and differentiation. When regeneration is slowed in wound repair, it can be detrimental and lead to hyperproliferative states associated with inflammation and malignancy. Therefore, a knowledge of how metabolism impacts the regenerative capabilities of stem cells will fill a critical knowledge gap and an unmet and pressing need for new ways to promote tissue regeneration and wound repair. Furthermore, it may provide novel avenues to curb inflammation and metastatic cutaneous squamous cell carcinomas (SCCs). Serine is an attractive candidate for therapeutic intervention, as we know that SCC cells become addicted to serine uptake to avoid serine biosynthesis and production of the metabolite a-ketoglutarate (aKG). To be able to clinically translate these findings, we must understand how serine impacts normal HFSCs and their two regenerative processes: 1) HF regeneration, which involves lineage specification, and 2) wound healing, where HFSCs re-epithelialize epidermis and undergo a fate switch to the IFE-SC lineage. These two processes entail different stem cell fate decisions and demonstrate different responses to histone modifications. Given the importance of aKG in regulating histone modifications and its accumulation upon exogenous restriction of serine, I hypothesize that serine metabolism controls stem cell fate decisions in both wound healing and hair regeneration via aKG-dependent histone demethylase enzymes (KDMs). My preliminary data demonstrated a striking acceleration in wound repair upon dietary serine/glycine restriction, which results in increased de novo serine biosynthesis. I also observed a marked reduction in the histone mark H3K27me3, implicating activation of aKG-dependent KDMs. Thus, in Aim 1, I will first test whether dietary serine and glycine restriction controls HF regeneration. In Aim 2, I will test whether the effects of serine and glycine restriction on HF regeneration and wound repair are HFSC-autonomous. In Aim 3, I will test whether dietary ser/gly restriction alters the histone modification and chromatin accessibility landscape and dissect the underlying mechanism behind it. I expect these studies to 1) provide the first direct evidence of whether serine metabolism controls endogenous stem cells during tissue regeneration, 2) inform novel therapies to promote wound repair, and 3) enable dietary or metabolic interventions in the prevention and treatment of SCC in ways that do not harm normal regenerative processes.

NIH Research Projects · FY 2025 · 2021-09

Opioid driven exacerbations of neuropathological events and alterations in HIV transcription contributing to HIV associated CNS dysfunction are well-reported. Despite years of continuous suppressive antiretroviral therapy (ART), latent HIV persists and finds sanctuary in many of the same brain regions involved in opioid use disorder (OUD) suggesting interactions between HIV and opioids in brain cells. However, there is a sizeable gap in our knowledge on how OUD impacts cellular responses and viral persistence in HIV-infected brain on ART in humans or relevant model organsims. This proposal seeks to generate topographical data sets and evidence at single cell resolution across the hippocampus and prefrontal cortex (PFC), two brain regions known for predilection for HIV persistence and OUD in non-human primate (NHP) and in post-mortem human brain. These data will provide an unprecedented cellular landscape of multiple modalities that can be harnessed to develop strategies to limit viral persistence and restore and retain optimal brain health in people living with HIV. In our published and preliminary work we have developed innovative single-cell approaches: (A) Single-cell isoform RNA sequencing (ScISOr-Seq), which enables single-cell long-read RNA sequencing of polyadenylated RNAs across thousands of single cells; (B) Slide-isoform sequencing (Sl-ISO-Seq) to spatially locate isoforms in brain slices and (C) a single-cell platform that identifies HIV sequences at single cell level (ScHIV-Seq). In concert these novel sequencing and computational methods, along with scATAC-Seq for chromatin accessibility, will permit the mapping of cellular gene expression, open chromatin regions, isoforms and the detection of HIV across single- cells of hippocampus and PFC. Recent literature supports the presence of HIV in the brain and more specifically in microglia and astrocytes present within the hippocampus and PFC. Importantly, these brain regions are also involved in associative learning processes for OUD. Moreover, our prior studies in rodent hippocampus have laid the groundwork for the proposed studies by establishing the regional and cell-specific distributions of opioid peptides and receptors as well as related signaling molecules, and how these distributions are impacted by sex, stress and opioid-associated learning. In further preliminary studies, we conduct opioid receptor mapping, brain spatial transcriptomics, NHP cognitive behavioral assessment and pharmacological profiling of current ART regimens in tissues. These approaches will provide a comprehensive regional landscape to support our single cell specific phenotypes. We propose an overarching hypothesis that: (i) our new integrated single-cell methods will map single-cell and cell-type specific human and NHP transcriptome and epigenome signatures in the hippocampus and PFC of S/HIV in NHPs and post-mortem human brain; (ii) chronic opioid exposure adds a distinguishable signature to S/HIV infection with long-term ART and defines cell subtypes in which these signatures are rooted; and (iii) these signatures are different from chronic opioid exposure on uninfected brain. These studies further an understanding of molecular mechanisms in HIV and OUD in brain.

NIH Research Projects · FY 2025 · 2021-09

Project Summary/Abstract: Cirrhosis and its complications including hepatocellular carcinoma (HCC) are increasingly common causes of morbidity and mortality in the United States. The central hypotheses of this application are that (1) the creation of a prospective cohort study of patients with compensated cirrhosis will facilitate the generation of novel prediction models based on the clinical, behavioral, metabolic, and biomarker data we collect to predict clinical decompensation, (2) this cohort can validate and then be supplemented by a larger electronic health record (EHR)-based virtual cohort, the latter of which will enable validation of electronic cirrhosis phenotypes and subsequent analysis of real-world data on the safety and effectiveness of individual lipid-lowering agents on multiple outcomes among patients with cirrhosis and (3) long-term statin therapy will provide clinical benefits in preventing hepatic decompensation and HCC independent of its lipid lowering effect. To investigate these hypotheses, we propose unique approaches to both the cohort study and statin-based clinical trial for the Liver Cirrhosis Network (LCN). In Aim 1a, we will create a prospective cohort of highly phenotyped patients with compensated NASH, ALD, cholestatic and cryptogenic cirrhosis, in order to facilitate the interrogation of biospecimens, patient reported behaviors and outcomes, and clinical data for novel predictors of disease progression, and to understand through serum lipoproteins measurement the complex interaction between cirrhosis and lipid metabolism. In Aim 1b, we will create a large LCN-wide EHR-based virtual cohort of patients with compensated cirrhosis, prospectively validate electronic phenotypes for cirrhosis and its clinical complications with our in-person cohort, and evaluate the use, safety and effectiveness of different classes of lipid lowering medications upon outcomes in this large real-world virtual cohort. In Aim 2, we propose to study the safety and efficacy of statins in preventing clinical decompensation among patients with NAFLD or ALD cirrhosis while exploring the potential pleiotropic mechanisms of statins. In this trial, patients with and without an established non-hepatic indication for lipid lowering will be randomized to pravastatin v. alirocumab (stratum 1) or placebo (stratum 2), respectively. This innovative approach to the statin-based clinical trial will acknowledge the patient's baseline indication for lipid-lowering therapy, and offer an alternative lipid lowering pathway in PCSK9 inhibition, which has similar or greater LDL-lowering potency but lacks the pleotropic effects of statins, to allow for novel insights into mechanisms by which statins might impact outcomes independent of its effects on lipids. Throughout the cohort and interventional trials, we will study lipoprotein metabolism, inflammatory markers, and collect microbiome and biospecimens for future translational research to better understand the mechanisms behind disease progression in cirrhosis and for any potential impact of pravastatin and alirocumab on clinical outcomes. These innovative strategies therefore leverage both cohort and clinical trial designs to maximize the knowledge gained and improve clinical outcomes among patients with cirrhosis.

NIH Research Projects · FY 2025 · 2021-09

Project Summary/Abstract Plasmodium falciparum is the causative agent responsible for the most severe form of human malaria, a disease that kills more than 400,000 people a year, mostly young children in Africa. These protozoan parasites invade and ultimately destroy circulating red blood cells (RBCs) of their host, leading to severe anemia and the frequently lethal syndromes of cerebral malaria and pregnancy associated malaria. Over the course of an infection, small sub-populations of parasites arise that have an altered antigenic phenotype, thus avoiding the antibody response of the host. This process is referred to as antigenic variation and is responsible for the persistent nature of the disease as well as the waves of parasitemia frequently observed in P. falciparum infections. Antigenic variation of P. falciparum infected RBCs results from switches in expression between individual members of the multi-copy var gene family. Each var gene encodes a different form of a protein called PfEMP1. This protein is placed on the infected RBC surface and mediates adhesion to specific receptors found on the endothelial surfaces of the blood vessel walls of the infected individual. This adhesion is responsible for many of the disease manifestations of infection with P. falciparum, including both cerebral malaria and pregnancy associated malaria. Only a single var gene is expressed at a time by any given parasite, thus determining both the antigenic phenotype of the infected cells as well as their adhesive properties. Therefore var gene expression is at the heart of both antigenic variation and virulence of malaria infections. The long-term objectives of this project are to understand the molecular mechanisms that regulate var gene expression and antigenic variation by malaria parasites. Significant work in recent years has defined many molecular aspects that maintain a gene in the active or silent state, however the mechanisms governing switching between transcriptionally active genes remain entirely undefined. Moreover, given that an infection can include billions of individual parasites, how they seemingly coordinate switching events to limit activation to a single or small number of genes at a time is completely unexplored. In contrast, uncoordinated, random switching would rapidly exhaust the entire var repertoire. There is no evidence of communication between parasites, and there does not appear to be a strict switching order within the var gene family, therefore how this is accomplished remains completely mysterious. The specific aims of the project are designed to decipher the mechanistic basis of this phenomenon. Aim 1 investigates the role of an unusual, highly conserved var gene that appears to function as central organizing gene that coordinates switching events. Aim 2 will determine how parasites sense the presence of a placenta and alter var gene expression to take advantage of this unusual niche. This project will contribute to the ongoing effort to disrupt the process of antigenic variation and thereby shorten the length of an infection and reduce its severity.

NIH Research Projects · FY 2024 · 2021-09

The DEPTH trial represents an innovative approach to slowing the progression of emphysema in people living with HIV (PLWH), a population that has accelerated disease progression for which there is no targeted therapy. We propose a phase II, multi-center, randomized, double-blind, placebo-controlled trial of doxycycline 100 mg po BID to slow the progression of emphysema as assessed by change in diffusing capacity (DLCO) among PLWH who are current or former smokers. Eligible participants with emphysema and well-controlled HIV will be randomized 1:1 to doxycycline or placebo, stratified by smoking status (current vs former smoker) and clinical site, utilizing dynamic randomization. The primary endpoint of the study is the rate of decline (slope) of percent predicted DLCO over the 72-week treatment period. We have assembled a team of experienced clinical sites that has the patient population and expertise to efficiently enroll and conduct this trial. In our previous studies, we observed that HIV+ individuals with early emphysema have increased matrix metalloproteinases (MMP-2, -7, -9, -12; each implicated in emphysema pathogenesis) in bronchoalveolar lavage (BAL) fluid samples. MMPs are therefore potential targets for intervention aimed at modifying progression of emphysema specifically in people with HIV. We successfully demonstrated the feasibility of this approach in our NHLBI-funded single-center randomized, double-blind, placebo-controlled pilot study to test the safety and tolerability of doxycycline (FDA-approved as an MMP inhibitor to prevent tissue breakdown in gum disease) over 24 weeks (NCT 01744093). We studied 27 individuals with HIV and COPD/emphysema randomized 2:1 to doxycycline 100 mg po BID or placebo. In addition to acceptable safety and tolerability, there were trends toward stabilization of the diffusing capacity (DLCO) and a reduction of BAL fluid MMP-9 activity in participants assigned to the doxycycline arm. The DEPTH trial will extend these promising pilot data to a formal Phase II clinical trial. We anticipate that upon completion of this proposed study, our data will support repurposing the inexpensive antibiotic doxycycline, to slow emphysema progression in PLWH. Specifically we expect to show: 1. Doxycycline slows the progression of emphysema in PLWH, as assessed primarily by DLCO and secondarily by HRCT. 2. Doxycycline is safe and tolerable when taken orally for 72 weeks in PLWH who have emphysema. 3. Doxycycline improves respiratory quality of life and functional status in PLWH who have emphysema.

NIH Research Projects · FY 2024 · 2021-09

Older people living with HIV (PLWH) disparately experience an increased risk of cardiovascular disease (CVD) and develop exacerbated age-related cardiometabolic comorbidities compared to uninfected individuals. Multiple risk factors in older people living with HIV including aging, HIV alone, antiretroviral therapy, microbial translocation, traditional CVD risk factors, lifestyle, opportunistic infections, and substance abuse create the "perfect storm" for increased immune activation, systemic inflammation, atherosclerosis, and CVD. Indeed, studies suggest the features driving an elevated risk of CVD include both HIV-specific, and traditional and non- traditional CVD risk factors. Yet, therapeutically targetable biological mechanisms driving an exacerbated HIV- related CVD burden remain unclear. Our previous work identified immunometabolism dysfunction as a mechanism linked to age-related comorbidities in PLWH. Targetable immunometabolic features and immune cell types differentially dysregulated in older PLWH linked to increased CVD risk remain undefined. With a multidisciplinary team including expertise in immunometabolism, cardiology, radiology, and infectious disease, we are uniquely positioned to uncover immunometabolic changes as a key mechanism linking HIV-mediated immune activation and inflammation to CVD comorbidity burden. We will leverage an established cohort of older PLWH at WCM and enroll 100 HIV+ participants (age > 50 years) all on suppressive ART with undetectable plasma HIV RNA in a longitudinal study with three study visits to assess inter- and intraindividual variability in immunometabolic study measures. We will apply a state-of-the-art single cell immunometabolism assay of fresh immune cells obtained from participants in real-time at three time points to overcome artifacts of cryopreservation, profile validated inflammation and cardiac injury biomarkers, and acquire longitudinal advanced cardiovascular and vascular bed CT imaging at baseline and a 36 month follow up time point. Our central hypothesis is that the synergistic effects of HIV and long term ART on CVD comorbidity burden is driven by an exacerbated metabolic reprogramming of monocytes and T cells towards glycolysis in older PLWH on ART. The specific aims are Aim 1: To longitudinally assess the immunometabolic state of monocytes and T cells at single cell resolution, peripheral inflammation, and cardiac injury markers in 100 PLWH > 50 years on stable ART. Aim 2: To quantify the change over time in the degree of subclinical plaque burden across the vasculature in 100 PLWH > 50 years on stable ART and evaluate associations with immunometabolic states of monocyte and T cell subpopulations. The results of this longitudinal study will enhance our understanding of inter- and intraindividual immunometabolism dysfunction in older PLWH linked to subclinical atherosclerosis, provide a roadmap for early detection of CVD based on the individual level and type of risk, and lead to the development of new therapeutics based on exploiting the specific metabolic programs of distinct immune cell populations to mitigate CVD risk in older PLWH.

NIH Research Projects · FY 2025 · 2021-09

ABSTRACT: The incidence of cardiovascular disease (CVD) in people with HIV (PWH) is ~2.5-fold higher than among HIV-uninfected adults of similar age. HIV-attributable CVD risk is highest in Africa. Ambulatory blood pressure (ABP) monitoring with a portable cuff worn for 24 hours provides mean daytime and nighttime blood pressures and detects abnormalities in the diurnal variation of blood pressure such as nocturnal non-dipping, which is defined by the absence of the 10% usual fall (dip) in blood pressure at night. ABP more accurately predicts CVD events than office blood pressure. Elevated nighttime blood pressure and non-dipping may contribute to the excess CVD risk in PWH. Small, cross-sectional studies suggest that non- dipping is more common in PWH and may be associated with CVD. The long-term goal is to reduce CVD morbidity and mortality in PWH. The study objectives are to 1) compare the time course of non-dipping and resulting preclinical CVD in PWH vs. HIV-uninfected adults and 2) to identify potential pathophysiologic pathways that could be targets for future intervention. We propose a comparative cohort study of PWH and HIV-uninfected adults with repeated measures of ABP, sleep, SNS activity and preclinical CVD to be conducted in an established cohort of 500 PWH and 500 HIV-uninfected adults in Tanzania. Aim 1: To determine the prevalence of confirmed non-dipping and its association with incident preclinical CVD after 36 months in a cohort of 500 PWH on stable ART and 500 matched HIV-uninfected adults (age >30 years) in Tanzania. ABP will be performed at baseline and then repeated at 1 month. Preclinical CVD will be quantified at baseline and after 18 and 36 months. Incidence of CVD events will also be monitored. We will also examine other ABP abnormalities in relationship to preclinical CVD. Aim 2: To determine the temporal relationship between sleep disorders, SNS activity and non-dipping and whether this differs by HIV status or gender. We will quantify sleep and SNS activity at baseline and after 18 and 36 months on all participants. We will also investigate the renin-angiotensin system, insulin resistance and chronic inflammation as potential pathways leading to non-dipping. We will also compare temporal trends in sleep and SNS activity between PWH and HIV-uninfected adults. The proposed research will be the first longitudinal study of ABP and sleep disorders in Africa and will directly inform HIV-specific and general guidelines. We will also lay groundwork for a mechanistic clinical trial to test a novel, low-cost strategy targeting ABP abnormalities to prevent CVD in PWH.

NIH Research Projects · FY 2025 · 2021-09

Abstract As of March 2021, SARS-CoV-2 has caused more than 50 million infections and 2 million deaths, constituting an unprecedented pandemic in the modern world. While infected individuals rapidly develop IgG responses against the viral Spike after infection, some studies have indicated that individuals with mild infection generate weaker neutralizing Ab responses compared to those with severe disease. The durability of the immune response following natural infection and its afforded protection against subsequent infections and emerging related variants remain unclear. Interestingly, unlike other respiratory viruses, children are rarely develop severe disease following SARS CoV-2 infection. Antibody responses in hospitalized children and those who developed the multisystem inflammatory syndrome (MIS-C) have been characterized, but, there is a gap in knowledge of the magnitude, quality, durability, and breadth of antibody responses in asymptomatic or mildly symptomatic children, responses that may contribute to making children less susceptible to severe infection compared to adults. Moreover, the possibiltiy of reinfection or infection with a novel variant in previously-infected children is not known, making the possibility of restarting congregate settings for children without a childhood vaccine quite challenging. Our overarching goal is to characterize the kinetics, function, breadth, and durability of humoral immune responses elicited by SARS-CoV-2 infection across the pediatric age spectrum in comparison to that of adults. We hypothesize that pediatric immune responses to SARS-CoV-2 infection is distinct from that of adults, and associates with protection against symptomatic disease and durability of immunity. Using samples from two unique ongoing community studies of SARS-CoV-2 infections in adults and children, we will test our hypothesis through the following aims: 1) Define the similarities and differences in the kinetics, magnitude, specificity, function and durability of SARS-CoV-2-specific Ab responses in children and adults; 2) Investigate the breadth and potency of antibody responses in SARS- CoV-2-infected children against established and predicted variants of SARS-CoV-2; and 3) Define the SARS-CoV-2-specific B cell repertoire and characterize the potency of pediatric SARS CoV-2-specific monoclonal antibodies. These evaluations will identify immune correlates of protection against severe disease and provide insights for immunization strategies towards the long term control of SARS CoV-2 which will likely become an endemic pathogen.

NIH Research Projects · FY 2025 · 2021-09

The Weill Cornell Medicine-New York Genome Center (WCM-NYGC) Center for Functional and Clinical Interpretation of Tumor Profiles is submitted in response to RFA-CA-20-053. Continuing our involvement in the Genome Data Analysis Network (GDAN) over the past five years and leveraging novel algorithms and methods developed by our group, the Center will perform integrative analyses of coding and non-coding variants to unravel the function of specific classes of mutations and assess their clinical potential. As specified in the RFA, we have chosen to focus on two Core Competencies: (1) DNA Mutations (in coding and non-coding regions, somatic and/or germline) and (2) Copy Number / Purity Analysis ,with a focus on complex structural variants.Our team has developed novel algorithms and pipelines for the analysis of DNA mutations in coding and non-coding regions, characterization of complex structural variants, tumor evolution and linked-read sequencing. We have developed three Specific Aims. In Aim 1, we will perform systematic clinical and functional annotation of coding and non- coding mutations. This includes (1) clinical annotation of coding variants, (2) prioritization and functional annotation of non-coding variants (3) integration of transcriptomic analyses, such as cell type deconvolution of impure tumor samples to provide stromal context to somatic variants (4) correlation of variants with clinical phenotypes, including response to therapy. In Aim 2, we will analyze clinically relevant signatures of genome-wide somatic alteration patterns. We will utilize our state-of-the-art analytic tools for complex structural variant characterization and mutational topography to link (1) mutational processes and (2) cell-of-origin footprints to cancer outcome and drug response. We will also (3) adapt our cutting-edge genome graph visualization tools to build interactive data portals for browsing complex structural variation patterns in impure samples. In Aim 3, we will dentify and characterize variants that drive tumor evolution using multi-samples analysis. We will apply our state- of-the-art computational tools to study structural variant evolution across multiple tumor samples to (1) identify drivers of drug resistance and relapse in matched primary and recurrence/metastasis samples and (2) assess genomic divergence between primary tumors and matched tumor organoids.

NIH Research Projects · FY 2025 · 2021-09

Project Summary Brain microvascular endothelial cells (BMECs) which line the vascular network of the central nervous system (CNS) in conjunction with perivascular cells form a specialized barrier termed the blood-brain barrier (BBB) that regulates the dynamic traffic of select molecules into and out of the CNS. Studies of BBB dysfunction have been hampered by an inability to perform direct testing in patients and a lack of in vitro models. Analysis of available putative BMECs from pluripotent stem cell sources reveals that they do not harbor bona fide brain EC molecular signatures. Using a transcription factor-based reprogramming strategy, we demonstrate that durable and functional true endothelial cells with BBB traits may be derived. We will use these verified BMECs in the development of isogenic BBB/on-a-chip devices. Cortical brain organoids derived from patient specific induced pluripotent cells (IPSC) will be vascularized by matched IPSC derived bona fide BMECs in a microfluidic device. To explore the potential of this new technology we will investigate the pathobiology of cerebral malaria a severe disease syndrome that causes neurodisability in 20% of survivors. Red blood cells infected with the Plasmodium falciparum parasite adhere to the brain microvasculature causing dysfunction. We hypothesize that the parasite primes the brain endothelial cells for adherence through their “education” by small extracellular vesicles termed exosomes. This is an established paradigm in cancer biology in which malignant cells educate metastatic “microniches” to prime for and enhance tumor survival. The exosomes mediate local and systemic intercellular communication through the horizontal transfer of information in their proteomes. We recently were able to identify a critical prognosis biomarker for brain metastasis in breast cancer through studies of exosomal cellular uptake and proteomic analysis. We will analyze the proteomes of exosomes from children with cerebral malaria and infuse them into our innovative microfluidic-based BBB model. We will monitor in real time how exosomes trigger BBB dysfunction and subsequently affect IPS-derived brain organoids from patients affected by CM. These studies will provide new insights into disease pathogenesis and potentially identify new prognosis biomarkers.

NIH Research Projects · FY 2025 · 2021-09

Post-transcriptional mechanisms control gene expression in virtually every cell. A major mediator of post-transcriptional gene regulation is the translating ribosome, which comprises three different types of RNAs: rRNA, tRNA and mRNA. These RNAs, along with ribosomal and mRNA-binding proteins, form a multi-RNA/multi-protein complex that can markedly influence mRNA stability and translation. Importantly, this complex is not constitutive. Instead, rRNA-tRNA, rRNA-mRNA, and tRNA-mRNA interactions are highly regulated, although the mechanisms of its regulation are poorly understood. A potential mechanism may involve chemical modification of their nucleotides. Indeed, rRNA, tRNA and mRNA are subjected to diverse chemical modifications whose stoichiometry is highly regulated in different tissues or disease states. Our underlying hypothesis is that the regulated nucleotide modifications in rRNA, tRNA, and mRNA act as a “code” that controls these RNAs and their mutual interactions, thus encoding unique patterns of gene expression. Although rRNA, tRNA, and mRNA nucleotide modifications are poised to be critical regulators of gene expression, studying how these modifications influence each other to control gene expression has been difficult to explore. In part this reflects the lack of scalable methods to quantify and profile nucleotide modifications in rRNA, tRNA, and mRNA. Another problem is that understanding the interactions of rRNA, tRNA, and mRNA requires specialized expertise in each of these three major areas of RNA biology. It is therefore critical for experts in rRNA, tRNA, and mRNA to work together to decipher the mutual interactions of these RNAs. The Center will bring together a team of experts in these diverse types of RNAs who will work together to develop novel techniques to probe nucleotide modifications and how they interact to orchestrate unique patterns of gene expression. The Center will develop novel technologies for mapping and quantifying rRNA, tRNA, and mRNA modifications, identify the dynamic modification sites in tissues and disease, and determine the function of these dynamic modifications. The methods and datasets that will be developed in the Center will provide the foundational knowledge needed to accelerate new areas of epitranscriptomics research in rRNA, tRNA, and mRNA biology. The Center has a major outreach and educational mission. The outreach/educational opportunities will include sponsored undergraduate research, breakout project funding, funding for training visiting outside investigators, and funding for an annual symposium. We will also develop a website that curates the epitranscriptomic mapping data generated by the Center to ensure rapid and easy access to the new data we generate. Overall, the Center’s mission is to serve as a hub for training researchers in epitranscriptomics, as well as to develop new enabling technologies, develop foundational datasets, and reveal fundamental principles of modified nucleotide function in rRNA, tRNA, and mRNA that are needed to open up new areas of epitranscriptomics research.

NIH Research Projects · FY 2024 · 2021-09

Project Summary Hearing loss is the most common sensory pathology in the United States, with one in five adults experiencing unilateral or bilateral hearing loss. In the inner ear, hearing is mediated at the level of the hair cells: when a sound deflects the hair bundle, ion channels atop the stereocilia open, allowing for the mechanotransduction of sound. The identity of the gating spring, the element that controls the opening of these channels, and thus the precision and sensitivity with which we hear, is unknown. Connecting adjacent stereocilia is the filamentous tip link complex, which comprises a dimer of protocadherin 15 (PCDH15) and a dimer of cadherin 23. Previous work in the laboratory showed that the monomer of PCDH15 is softer under physiological forces than predicted based on its structure alone, suggesting that it has the appropriate properties to serve as a component of the gating spring of hearing. Using a high-speed optical trap, I have obtained preliminary evidence that the dimer of PCDH15 is stiffer than the monomer. In Aim 1, I will examine the behavior of the PCDH15 dimer in response to force at different critical Ca2+ concentrations. I will perform force-ramp experiments on the PCDH15 dimer, in which force is increased at a constant rate, in order to delineate its response to physiological levels of force. There are multiple Ca2+ binding sites in the linker regions between extracellular cadherin (EC) domains in PCDH15, and previous work has shown Ca2+-dependent structural changes in the monomer of PCDH15. I therefore hypothesize that the dimer will exhibit a similar Ca2+ dependence and will perform experiments at three Ca2+ levels to probe this. In Aim 2, I will investigate how EC domain unfolding contributes to the overall response of the PCDH15 monomer to force. Previous work on the monomer of PCDH15 revealed a class of unfolding events corresponding to the unfolding of an entire EC domain. I therefore hypothesize that EC domain unfolding is a critical mediator of tip-link tension. I will probe this by performing force-ramp experiments on a PCDH15 construct in which each EC domain is prevented from unfolding. In Aim 3, I will study how a mutation that results in non-syndromic deafness affects the mechanics of the PCDH15 monomer. Approximately 50 % of all congenital hearing loss stems from genetic causes. There are many mutations in PCDH15, such as the V507D mutation in EC5, that result in non-syndromic deafness. In order to study how the mechanics of PCDH15 are affected in patients with this mutation, I will perform force-ramp experiments on the monomer of this construct. I hypothesize that PCDH15 V507D will depend critically on Ca2+ concentration and will undergo more unfolding events than does the wildtype monomer. Taken together, these studies will yield insight into the role of PCDH15 in normal and aberrant hearing and elucidate its ability to serve as a portion of the gating spring of hearing. These studies will be carried out with the direct mentorship of Dr. A. J. Hudspeth in the group’s laboratory at The Rockefeller University, situated within the richly supportive environment of the Tri-Institutional MD-PhD Program. This proposal will greatly support my goal of becoming a physician-scientist.

NIH Research Projects · FY 2025 · 2021-09

Project Summary Late-onset Alzheimer's Disease (AD) is a slowly progressing, untreatable neurodegenerative disorder that affects a substantial fraction of the aging population today. Hundreds of clinical trials and massive investments into drug development efforts have so far not resulted in a single disease-modifying therapy that showed a significant beneficial effect on the disease. Drug repositioning, the application of approved drugs in a novel disease context, has gained increasing attention as a promising alternative to identify treatment options for AD. For successful pharmaceutical intervention in AD, a drug or drug combination needs to target the complex molecular changes observed in AD in a specific manner. To identify drugs exerting these desired effects a detailed understanding of the molecular networks across regulatory layers that underly the biological system is required. However, these networks are not readily available and are scattered across hundreds of studies and complex databases. To address this challenge, we propose TargetAD, a network-based framework that builds this molecular network from genetic associations, co-expression/correlation networks, metabolic pathways, gene regulation data, protein-protein interactions, and tissue-specific gene and protein expression data augmented with AD multi-omics associations, as well as drug-drug target data and molecular drug signatures. We will achieve this by leveraging the power of large-scale, multi-omics association results generated within NIH's large “Accelerating Medicines Partnership - Alzheimer's Disease” initiative and other large-scale population-based studies. The collective evidence will be stored in a publicly accessible graph database, which we then use for the identification of candidate drugs or drug combinations (“candidates”). Through the development of a novel network-based machine-learning method, we will rank candidates in the database by their probability to affect AD networks in a beneficial way. High-ranking candidates will be subjected to a comprehensive prioritization pipeline. To this end, we will retrospectively investigate whether longitudinal AD-related biomarker profiles of individuals who took a repositioning candidate show evidence for healthier aging in large studies of AD. These analyses will be complemented by examining whether the post-mortem neuropathological burden supports a beneficial effect of the candidate. To increase power and coverage of candidates, we will further analyze electronic health records from the UK Biobank for additional evidence. The three most promising candidates will be selected in discussion with a panel of experts. These will be evaluated by preclinical validation studies in animal models of AD. In summary, the unique combination of multidisciplinary expertise, access to high-profile datasets and advanced computational integration pipelines will allow us to identify molecular pathways disturbed in AD that are targetable by drug repositioning candidates, which thus are prime candidates for testing in clinical trials.

NIH Research Projects · FY 2024 · 2021-09

Abstract Over 150,000 HIV-1 infants are infected via mother to child transmission (MTCT) each year, accounting for nearly 10% of the global annual HIV-1 infections. Even implementation of highly effective antiretroviral therapy (ART) cannot prevent up to 5% of HIV-1 infected women from transmitting the virus to their infants. Thus, approaches that synergize with ART will be needed to eliminate MTCT. The most promising interventions in under clinical development to prevent HIV infection includes passive administration or active induction of broadly-neutralizing antibodies (bnAbs). Yet, paradoxically, broad neutralization activity in maternal plasma has been associated with risk of infant transmission, raising concerns about the safety of these approaches in pregnancy. Thus, a better understanding of the role of maternal neutralizing activity and MTCT risk is needed to develop effective bnAb-based interventions, which together with ART can more effectively block MTCT. HIV MTCT is a unique transmission route that occurs in the setting of preexisting antibody raised against autologous viruses. We previously found that transmitted/founder (T/F) viruses in infants were more resistant to neutralization by paired maternal plasma than non-transmitted maternal viruses. Moreover, we established that bnAb activity in maternal plasma can drive the development of circulating viral escape variants that become infant T/F viruses. We hypothesize that multispecificity of maternal plasma bnAb activity is associated with reduced risk of MTCT and autologous virus escape from these functional responses by infant T/F viruses is a risk factor for transmission. Moreover, identifying bnAb escape variants that are fit for transmission is important to designing combination bnAb approaches that can effectively prevent virus transmission. We will use the following three Specific Aims to test our hypotheses: (1) Compare the specificity and polyfunctionality of plasma bnAb activity from transmitting and non-transmitting mothers to assess the role of maternal bnAb activity in vertical virus transmission risk. (2) Determine if infant T/F viruses and circulating viruses of transmitting mothers are more resistant to plasma neutralizing activity compared to that of non-transmitted maternal variants from transmitting and non-transmitting mothers. (3) Define genetic signatures responsible for escape from the maternal Env-specific B cell repertoire among transmitted infant Env variants using a panel of native Env trimer-specific mAbs isolated from transmitting mothers. Defining the specificity and function of pre-existing maternal neutralizing antibodies that can reduce virus escape and impede transmission will be critical to design novel passive and active vaccine approaches that can eliminate HIV transmission from mothers to infants, and is a tool to define the population impact of the future use of bnAb- based prophylaxis on HIV transmission dynamics.

NIH Research Projects · FY 2024 · 2021-09

The NaV1.5 voltage-gated Na+ channel encoded by SCN5A is the fundamental component of macromolecular protein complexes that initiate the cardiac action potential. Abnormal NaV1.5 function is a prominent substrate for inherited and acquired forms of cardiac arrhythmias, reflected by a staggering array of identified NaV1.5 mutations. A small subset of these are associated with dilated cardiomyopathy but the underlying mechanisms are not known. A leading hypothesis, that the arrhythmias drive the cardiomyopathy, cannot explain why most arrhythmogenic NaV1.5 mutations do not cause cardiomyopathy nor why knockout of the NaV1.5 interacting protein FGF13 leads to arrhythmias yet is protective for pressure overload-induced heart failure (HF) despite associated NaV1.5 dysfunction. Moreover, HF from other causes leads to pathological remodeling that disrupts regulation of the VGSC macromolecular complex and increases arrhythmia risk through mechanisms that are poorly understood. Complicating mechanistic insight is that there are different NaV1.5 pools defined by distinct subcellular localizations with the cardiomyocyte, each hypothesized to have protein partners that uniquely define the distinct pools and confer specific channel properties and functions. However, the critical partners remain poorly understood because of challenges of low throughput “favorite” candidate approaches. We propose an unbiased multilevel discovery strategy, employing newly developed second generation proximity labeling tools, novel mouse models, coupled with carefully calibrated cross comparisons designed to increase the specificity of our findings. Exploiting the expertise from two labs with individual and collaborative track records applying a large tool set to dissect complex physiologic mechanisms and define perturbations in pathological states, we propose adaptable candidate validation approaches to establish a comprehensive picture of NaV1.5 interactomes under physiological states and when perturbed by disease. With these innovative approaches we propose to: 1) Define the static and dynamic NaV1.5 channel interactomes and “neighborhoods” within distinct subcellular pools; 2) Elucidate how HF alters the NaV1.5 microenvironment; and 3) Determine the HF-protective effects for ablation of the NaV1.5 interactor, FGF13. With these aims, our goals are to define the contributions of the NaV1.5 macromolecular to development and progression of HF and its associated arrhythmias and to unravel how HF perturbs the NaV1.5 complex to increase arrhythmia risk and exacerbate HF in a vicious cycle.