University Of Pennsylvania

NIH Research Projects · FY 2026 · 2015-04

Project Summary Merkel cell polyomavirus (MCPyV), the most recently discovered tumor virus, can cause a highly aggressive form of skin cancer called Merkel cell carcinoma (MCC). While the incidence of MCC has tripled over the past twenty years, there is no effective therapy for metastatic MCCs, highlighting the need to better understand MCPyV oncogenic mechanism in order to develop more successful therapies. MCPyV asymptomatically infects most of the human population, but tends to cause MCC in the elderly and immunocompromised individuals. These observations suggest that host immunity plays a critical role in controlling MCPyV-induced tumorigenesis. However, very little is known about the innate immune response elicited by MCPyV. Neither is it clear how a dysregulated immune system contributes to MCC tumorigenesis. This is largely because MCPyV tropism was previously unknown and there was a lack of biologically relevant culture system for MCPyV. Recently, we discovered that human dermal fibroblasts (HDFs) support productive MCPyV infection and established the first in vitro as well as ex vivo infection models for MCPyV. Using these systems, we demonstrated that MCPyV infection activates STING-mediated innate immune responses, which in turn restrict viral amplification and spread. In addition, we discovered that STING is silenced in MCPyV(+) MCC tumors, revealing that loss of STING function is needed to drive MCC tumorigenesis. Our studies suggest that disruption of STING function may cause pathologic rampant replication of MCPyV to promote viral genome integration into the host genome, which is a key event in MCPyV- driven tumorigenesis. In addition, loss of STING function may allow MCPyV-induced pre-cancerous cells to circumvent its tumor suppressive effects, thus stimulating cell proliferation and tumorigenesis. Building on these observations, we hypothesize that STING functions not only as a key antiviral immune mediator for controlling MCPyV infection but also a prime tumor suppressor that blocks MCPyV-driven tumorigenesis. To test this hypothesis, we will combine the in vitro and ex vivo MCPyV infection models with 3D “artificial human skin” reconstructed in mice to examine the impact of STING innate immune sensing pathways on MCPyV infection (Aim 1) and to determine how disruption of STING signaling impacts MCPyV-driven MCC tumorigenesis (Aim 2). Through revealing the largely unknown interplay between MCPyV and the innate immune system, our ultimate goal is to understand how poorly controlled MCPyV infection leads to MCC development. Identification of immune effectors that normally restrict MCPyV propagation could also unveil novel strategies for preventing and treating the devastating MCC cancers.

NIH Research Projects · FY 2024 · 2015-04

CIRCUIT MECHANISMS OF SOUND PROCESSING AND DETECTION IN THE AUDITORY PATHWAY Auditory perception relies on predicting statistics of incoming signals, be it identifying the speech of a conversation partner in a crowded room or recognizing the sound of a bubbling brook in a forest. The human brain detects statistical regularities in sounds as a fundamental aspect of prediction, evidenced by reduced responses to repeated sound patterns and enhanced responses to unexpected sounds. Multiple studies demonstrate that the neuronal responses to regular signals are reduced through adaptation, which can contribute to prediction. However, adaptation alone is not sufficient to account for prediction and studies at cellular and neuronal population level in animals thus far lend onto partial support to existing theories of predictive coding. As such, the circuit level mechanisms for the prediction of statistical regularities beyond tone frequency in sounds, and their role in behavior, remain unknown. Our goal is to close this gap in knowledge and to determine the circuits that predict signals and detect statistical regularity and its violation in auditory behavior. To identify feedforward and feedback components of prediction of statistical regularities in sounds in the auditory system, we combine optogenetic selective perturbation and large-scale imaging and electrophysiology with behavioral methods in awake mice. First, we test whether and how excitatory-inhibitory interactions within the auditory cortex (AC) establish predictive code for sound patterns, detect statistical regularities, and contribute to enhanced responses for unexpected sounds. Second, we test whether and how detection of statistical regularities at the neuronal level contributes to behavioral detection of change in sound regularity. Third, we test whether and how feedback from higher cortical areas provides information about regularity and violation. Our results will identify the neuronal circuits for encoding statistical regularity and its violation in sound and establish their role in auditory behavior.

NIH Research Projects · FY 2025 · 2015-03

The accumulation of misfolded proteins represents a common pathological mechanism of most major neurodegenerative disorders. Neuronal inclusions comprised of aggregated α-Synuclein (aSyn), known as Lewy bodies (LBs) and Lewy-neurites (LNs), represent a key histopathological feature of Parkinson's disease (PD) and a family of related disorders known as synucleinopathies, most notably Dementia with LBs (DLB). LBs are also a prominent feature in nearly half of Alzheimer's disease subjects. Mutations and amplifications in the SNCA gene encoding aSyn also cause familial forms of PD. Although a large body of histological and genetic evidence firmly indicate a correlation between aSyn accumulation and disease, it remains unclear how aSyn pathology actually forms and subsequently contributes to disease. We and others recently demonstrated that minute quantities of recombinant or patient-derived aSyn aggregates can catalyze the formation of toxic LBs/LNs in cultured neurons and healthy non-transgenic mice. In both human PD and animal models, this “seeded” aSyn pathology progressively propagates and spreads to neuroanatomically connected regions, reminiscent of prion diseases. Importantly, animals with LBs/LNs recapitulate the cardinal features of PD, including progressive loss of dopamine-producing neurons and locomotor deficits. This R01 renewal addresses several key biological questions posed by our earlier findings and combines novel molecular, in vivo, and computational tools to further understand how LBs/LNs form, propagate, and ultimately contribute to neurodegeneration and neurological symptoms. Aim 1 will identify at the neuron subtypes that develop LBs/LNs following inoculation with misfolded aSyn. By combining traditional histological methods with FACS-assisted single-neuron RNAseq, we will determine the molecular signatures associated with subpopulations that are vulnerable or resistant to LBs/LNs formation. Aim 2 will examine how PD genetic risk factors reported in the literature intersect with aSyn pathobiology, by testing the effect of knock-down or knock- in of individual genes on the formation of seeded pathology and neuronal survival. Candidates that significantly alter either will be confirmed in vivo using knock-out/knock-in mouse lines. Lastly, Aim 3 will integrate our molecular, genetic, and in vivo experimental data together with publicly available connectivity and gene- expression atlases to interrogate the mechanisms of pathological spread. Using recently developed mathematical approaches to describe infectious agent spread, we will develop in silico models to understand aSyn pathology formation and spread. Completion of these studies should provide valuable insights into the potential mechanisms by which aSyn contribute to the progression of PD and related disorders. Increased understanding of the pathogenesis of this and related synucleinopathies should ultimately result in earlier detection and disease-modifying therapies for these currently incurable disorders.

NIH Research Projects · FY 2025 · 2014-09

The organizational context in which nursing care is delivered plays a key role in health outcomes for patients. Through our NINR-sponsored program of research, continually funded since inception, we have produced vital information from large and representative samples of organizations (e.g., hospitals, nursing homes, primary care practices) on the impact of the context of nursing care on patient outcomes, quality of care, and nurse well-being. The modifiable features of interest include ensuring sufficient nurse staffing and resources, investing in nurse education, trusting nurses’ autonomy to make informed clinical decisions and act, fostering interprofessional teamwork, and involving frontline nurses in policy and decision-making. We conducted large-scale surveys of nurses in 1999, 2006, 2016, 2020, and 2021, aggregating their responses to produce organization-level nursing measures, as well as indicators of nurse outcomes (e.g., burnout) that we link with clinical outcomes data from patients in the same organizations. Most of the work was cross-sectional, and while suggestive, falls short of providing the confidence needed to translate evidence into policy and practice reforms. Our last renewal application enlarged the measurement and analytic frame to longitudinal analyses of organizational changes and outcomes at two points in time in 4 states. In this renewal, we will significantly extend and expand this work to enable replication of our data collection effort twice within the study period in 7 states (CA, FL, IL, NJ, NM, NY, PA), creating a unique panel dataset of organizations, the nurses working there, and the patients they care for, going as far back as 1999. We leverage a new partnership to substantially reduce the cost of data collection and add states that allow for new questions about the impact of modifying organizational features of nursing. The design emphasizes evaluation of factors inducing change in nursing practice, distinguishing the impact of the active and intentional, e.g., Magnet recognition, policies like staffing ratios, from the environmental and historical, e.g., COVID-19 pandemic, hospital consolidation trends, on outcomes for patients of all ages and clinical risk. Our aims are: 1) to determine whether there are sustainable effects of organizational change on nursing practice and associated patient outcomes and cost across a range of patient populations and settings; 2) to determine whether organizational nursing changes over time diminish outcome variance and if the changes and their effects are conditional on other organizational features; and 3) to examine if nursing-related policy interventions (e.g., nurse-to-patient ratios [CA], staffing committees [NY]) and organizational innovations (e.g., Magnet/Pathway) aimed at improving outcomes through work environment reform had a sustained impact over time and in the face of challenges like COVID-19. The overarching aim is to not just understand the benefits of organizational change for patient outcomes, but to understand how to target organizational change via interventions that can have a transformative impact on quality of care, nurse wellbeing, and patient outcomes.

NIH Research Projects · FY 2025 · 2014-09

Large prospective cohort studies with banked DNA have increasingly utilized next generation sequencing (NGS) to evaluate the effects of genes, the environment and lifestyle on health outcomes, but NGS can also identify actionable genetic variants that may significantly impact the future health of the research participant and/or their relatives. How best to educate participants about their options to decline or receive research results, how to honor preferences for receipt of results, and how to best communicate results, particularly in large cohorts remains unknown. In the RESPECT studies (R01 CA190871:Bradbury), we have developed and established the feasibility and favorable patient-reported outcomes with using an eHealth education and consent intervention as an alternative to traditional pre-disclosure genetic counseling. The goal of the proposed competitive renewal is to conduct a Hybrid Type 1 effectiveness-implementation study to evaluate eHealth delivery alternatives for pre-disclosure education and return of actionable genetic research results. Building upon the RESPECT studies (R01 CA190871: Bradbury), we will adapt our RESPECT eHealth pre- disclosure intervention to offer 1250 Penn Biobank participants (625 with actionable results and 625 controls) a chatbot enabled eHealth education intervention (eHealthED) that provides information about the benefits and limitations of receiving research results, how results will be returned and their options for declining receipt of results (Aim 1). In Aim 2, we will randomize participants with actionable research results to receive their results via telephone with a GC (usual care) or a stakeholder-informed and user-tested chat-bot enabled eHealth return of results intervention (eHealthROR). All participants randomized to eHealthROR (e.g. intervention arm) will be provided the option to speak with a GC as an alternative, before or after receiving results. Concurrently, we will conduct a CFIR (Consolidated Framework for Implementation Research)-informed process evaluation to understand moderators of eHealth intervention usage, patient outcomes, costs and facilitators and barriers to future implementation and sustainability of using eHealth interventions for return of actionable genetic research results in large and sociodemographically diverse research cohorts (Aim 3). We hypothesize that the majority of participants will access supplemental eHealth and chatbot enabled education and that disclosure of actionable research results by our eHealth intervention will result in non-inferior short-term and longitudinal patient cognitive, affective and behavioral outcomes and lower costs, providing a scalable model for returning actionable results to research participants in large biobanks. Thus, we expect this study to inform evidence- based practice guidelines for return of actionable genetic research results to participants.

NIH Research Projects · FY 2025 · 2014-07

PROJECT SUMMARY Cells and tissues are mechanosensitive. Many and tissues, including the liver, are subjected to mechanical stresses deformed over multiple time and length scales; these can both be altered in disease and drive disease.We have used in vitro experimentation and theory to show that tissue mechanics are an emergent property, arising from and requiring three components: the complex fibrous network of the extracellular matrix (ECM), the cells within that network, and the forces applied to the combined system. Our work in the three years of the past project period has specifically examined the microarchitecture and features of complex fibrous networks, the role of cytoplasmic inclusions and cytoskeletal networks on cell mechanics, and the impact of viscoelasticity on cell and tissue behavior. Collectively, this work has resulted in the development of a multi-axial model of a tissue. Notably, however, while significant strides have been made in understanding tissue elasticity, viscous dissipation and plasticity have been little studied, and the relationship between mechanics and structure – to the point that one can be predicted from the other – remains poorly understood. The overall goal in this competing renewal proposal is to demonstrate the in vivo applicability and predictive value of the concepts we have defined. Specifically, we propose to determine the contribution of the individual components of tissues to emergent tissue mechanics and the impact of these mechanics on cell behavior. Our model tissue in this proposal, as in previous project periods, is the normal, fibrotic, and cirrhotic liver. although our findings will be generally applicable to other organs in the body. We hypothesize that tissue mechanics including viscous dissipation can be described and predicted by integrating the features of the ECM fibrous network, the cells, and the applied forces. There are three specific aims: 1) to determine the relationships between matrix structure and viscous dissipation, elasticity, and plasticity in normal and diseased tissue; 2) to determine the impact of cell properties and cell-matrix organization on tissue mechanics, particularly viscosity; and 3) to measure tissue solid stress and interstitial fluid pressure in normal and diseased tissue and to define the impact of these forces on tissue mechanics, including dissipation. These specific aims will use experimentation and theory as well as machine learning approaches to predict the relationship between structure and mechanics, guide interventions, and generate a unified and therapeutically- targetable model of tissue mechanics in disease. We have previously identified many of the design principles underlying tissue mechanics. In the proposed work, we will further define the critical components of the three elements underlying tissue mechanics, asking whether we can predict mechanics (and their effects on cells and metabolism) from structure. This proposal thus has the potential to answer fundamental questions in tissue mechanics, and to suggest approaches to manipulating mechanics in clinically-relevant ways.

NIH Research Projects · FY 2026 · 2014-05

Cryptosporidium is an important intestinal pathogen for which neither prophylaxis nor effective treatments are available. The parasite was first recognized as an AIDS-defining opportunistic infection, and immune suppression remains an important risk. However, immunocompetent individuals are also susceptible, and Cryptosporidium is responsible for frequent U.S. waterborne outbreaks. More recently, Cryptosporidium was identified as a leading global cause of disease and death in infants. Humans are susceptible to multiple Cryptosporidium species and strains, and the epidemiology of cryptosporidiosis is a complex web of human to human and zoonotic transmission. Population surveys suggest that genetic exchange between these lineages drives recent adaptation to new hosts and environments. Parasite sex offers an opportunity for recombination and virulence evolution, but this problem has been largely intractable. We developed new technology to harness the parasite lifecycle for forward genetics. We conduct genetic crosses between phenotypically distinct parasites and map quantitative trait loci associated with persistence and host specificity through bulk segregant analysis of selected progeny. Using reverse genetics and phenotypic assays we will validate association and explore specific gene function. We will define the molecular mechanisms that govern the ability to infect and persist in different hosts, understand how these mechanisms interact with host specificity, and establish to what extent they are modulated or breached by sexual recombination. Answers to these questions are not only critical to our understanding of Cryptosporidium epidemiology, but also of great concern to drug and vaccine development to gauge the potential of emerging resistance and evasion.

NIH Research Projects · FY 2025 · 2014-04

Summary Statement Primary open-angle glaucoma (POAG) represents a pressing public health problem in African Americans. This disease is the leading cause of irreversible blindness in these individuals. POAG affects African Americans more severely at earlier ages, contributing to younger generations with vision loss and adverse health and economic outcomes. Current pressure-lowering treatments for the disease have mixed success, with approximately 30% of patients still experiencing vision loss. POAG is a familial disease and there is a need for large genetic studies that elucidate disease mechanisms. This need is especially pronounced in African Americans, who, despite their increased burden of disease, remain seriously understudied. In its initial funding phase, the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study addressed this disparity by conducting the largest-ever POAG genetics study on African Americans recruited from a single city. For this renewal, we will study genetic data from a genome- wide association study of 7765 subjects and whole-exome sequencing of 8082 subjects, as well as rich phenotypic data on >90% of POAG cases. The proposed renewal will allow us to further investigate and identify variants of biologic importance to African American POAG. The aims of this study are: 1) to conduct post-GWAS analyses on genome-wide significant variants from the POAAGG study to elucidate their role in this disease, 2) to identify additional regions of interest for African American POAG through whole-exome and structural genomics analyses, and 3) to evaluate the functional impact of regions of interest in cellular model systems. Our findings will begin to define relevant biologic pathways for African American POAG, which can potentially provide targets for population screening and precision therapeutics.

NIH Research Projects · FY 2025 · 2013-09

Project Summary/Abstract Primary glomerular diseases, including minimal change disease (MCD), focal segmental glomerulosclerosis (FSGS), immunoglobulin A nephropathy (IgAN), and membranous nephropathy (MN), are associated with significant morbidity and mortality in both adults and children. The Cure Glomerulonephropathy (CureGN) study launched in 2013 to address critical knowledge gaps in the disease pathogenesis, natural history, and response to therapy of these heterogeneous disorders. It is a study of unprecedented size and remarkable depth, built by a unique collaborative interdisciplinary community. The international consortium includes researchers with diverse expertise, affected patients and advocacy groups, the biopharmaceutical industry, and federal funding agencies. CureGN has successfully recruited a diverse cohort of nearly 2800 adult and pediatric participants with MCD, FSGS, IgAN and MN from more than 60 clinical study sites into a prospective, longitudinal, observational cohort study. Biospecimens, clinical data, and patient reported outcomes are collected to enable high-quality clinical, mechanistic, and translational investigations. This foundational work is being conducted by a well-functioning collaborative group including the Data Coordinating Center (at the University of Michigan, Northwestern University and Cleveland Clinic) and four Participating Clinical Centers (managed at the University of Pennsylvania, Columbia University, University of North Carolina, and the Pediatric Nephrology Research Consortium). CureGN will pave the way for personalized care in glomerular disease by disentangling the heterogeneity of disorders that are etiologically diverse but currently grouped into only four diagnoses. In CureGN’s third study phase, we propose to maintain and enhance the CureGN Consortium infrastructure and ancillary study program to accelerate patient-relevant glomerular disease research. We will continue our core observational study, enrolling additional participants in a recruit-to-replace strategy to maintain an active cohort of 2000 participants with high quality clinical data and biomaterials. We will implement state of the art data collection tools including remote data and biospecimen collection, new biospecimen types, and use of mobile devices for patient facing engagement and medical record linkages. Mature scientific working groups, committees and ancillary infrastructure will continue to support a core and ancillary study program to achieve the scientific goals of CureGN. We will continue outreach to the scientific community by expanding CureGN’s role as an outstanding training vehicle for the next generation of glomerular disease researchers and attracting cutting-edge, established scientists to glomerular disease through opportunity pool grants, collaborations with patient advocacy groups and professional societies, training workshops and support of ancillary studies from academic and industry partners. Through this coordinated effort, CureGN is prepared to accelerate the improvement care of glomerular disease patients.

NIH Research Projects · FY 2026 · 2013-09

Targeting NAD Metabolism to Improve Glucose Homeostasis in Obesity and Aging We are testing the hypothesis that nicotinamide adenine dinucleotide (NAD+) metabolism can be targeted to improve physiology in aged and obese individuals. NAD+ is a ubiquitous molecule that is required as a redox cofactor or substrate for hundreds of enzymes within the cell. It can be derived from dietary tryptophan, niacin, nicotinamide, or administered synthetic intermediates. Prolonged deficiency of all of these precursors leads to pellagra (characterized by dermatitis, diarrhea, and dementia) and eventually death. In recent years, it has become appreciated that NAD+ concentration falls in many tissues with age or obesity, and that the pathogenesis of many diseases includes a component of NAD+ depletion within the target tissue. Multiple groups, including ours, have established that high doses of precursors have therapeutic effects in rodent models of disease. However, much remains to be learned about NAD+ metabolism, even as nutraceutical formulations containing precursors are being marketed to the general public. A substantial weakness of the current literature is that most of the published studies involve systemic treatment and measurement of only distal phenotypes, such as rudimentary blood biomarkers, general health, or disease outcomes. Because of this, the molecular mechanisms and sites of action for pre-clinical and clinical studies involving NAD+ often remain obscure, even for positive outcomes, while negative outcomes remain difficult to interpret. The major focus of our work during the prior award cycles has been to develop mass-spectrometry and genetics-based models to understand the metabolism of NAD+ precursors, their effects on cellular metabolism, and critical tissues and sites of action. Here we propose to extend these studies by: 1) Characterizing the effects of changes in NAD+ availability on subcellular distribution of the co-factor and on flux through NAD-dependent steps in glucose metabolism, 2) Mapping the distribution and metabolism of emerging alternative NAD+ precursors that might have more favorable uptake or stability profiles after oral delivery, and 3) Taking advantage of our recent discovery of the mammalian mitochondrial NAD+ carrier to study the consequences of selectively manipulating that NAD+ pool in vivo in liver and skeletal muscle. Together, the proposed studies will substantially advance our understanding of both the basic biology of NAD+ metabolism and how it might ultimately be targeted to improve health and alleviate conditions associated with aging and obesity.

NIH Research Projects · FY 2026 · 2013-09

Project Summary/Abstract Blindness is devasting condition that impacts millions of people across the world. In most cases of adult-onset blindness there is damage or dysfunction of the eye, retina, or optic nerve, but the visual cortex is left intact. Direct electrical stimulation of visual cortex, even in blind patients, produces perception of distinct spots of light known as phosphenes. It has long been recognized that this could form the basis for a visual cortical prosthesis (VCP), a device which could greatly improve the quality of life for blind patients by restoring some visual function. In recent years, there has been renewed interest in development of VCPs due to technical advances in computing, wireless data and power transmission, and electrode arrays. While these advances have greatly improved the interface with the cerebral cortex, substantial research is still required to determine how to use that interface to communicate visual information using electrical stimulation. VCPs have typically used electrical stimulation delivered in a way that provides an unnatural input to the visual cortex. This includes using a sequence of electrical stimulation pulses delivered at an arbitrary fixed frequency and delivered in a manner that is unrelated to ongoing cortical activity. Electrical stimulation delivered in this unnatural fashion has been one of the key limitations in the development of effective VCPs. This proposal focuses on multiple ways to deliver electrical stimulation in a more naturalistic fashion. Aim 1 examines the importance of stochastic variability in the timing and amplitude of electrical stimulation pulses in generation of visual percepts. Aim 2 evaluates the importance of coordinating electrical stimulation relative to patterns of ongoing cortical activity. If naturalistic stimulation is more effective in generating visual percepts, this should be accompanied by more effective activation of visual pathways, and this will be explicitly tested in Aim 3. This will be done by combining electrical stimulation of visual cortex with functional imaging. Naturalistic electrical stimulation protocols could lower the current requirements for future VCPs, and therefore improve device safety and longevity. More generally, the results from these experiments may reveal general principals of how to effectively and efficiently encode information into the cerebral cortex in other brain computer interface applications. Furthermore, determining the most effective ways to input information into the brain using electrical stimulation could improve scientific understanding of normal mechanisms of cortical information processing and the relationship between cortical activity and perception.

NIH Research Projects · FY 2026 · 2013-09

Title Understanding the pathogenic mechanisms of Rett syndrome Abstract Rett Syndrome (RTT) is an X-linked neurodevelopmental disorder caused by mutations in methyl-CpG binding protein 2 (MECP2) gene. It occurs primarily in heterozygous females and represents one of the leading causes of intellectual disability in women. Despite its seemingly simple genetic root and the significant research progress thus far, the molecular mechanisms underlying RTT pathogenesis, such as the delayed onset and progressive clinical course, remain poorly understood. This is partially because mechanistic studies in heterozygous females are confounded by random X-chromosome inactivation (XCI) and the resulting mosaic expression of X-linked genes at the cellular level. We addressed this challenge in the last funding cycle by developing an allelic series of knock-in mice where endogenous wild-type (WT) or mutant MeCP2 was tagged by Cre-dependent biotinylation, thus allowing the isolation of WT-expressing and mutant-expression nuclei from the same heterozygous female brain. This strategy effectively circumvents the X-linked cellular mosaicism in heterozygous females but also overcomes cell type heterogeneity in the brain. Using this strategy, we completed a series of transcriptome profiling longitudinally across different stages of disease progression in a RTT relevant heterozygous female mouse model. We found that beginning soon after the developmental increase in non-CG DNA methylation (mCA) in early life, MeCP2-mutant neurons gradually accumulate small- magnitude changes in gene expression over time. In contrast, neighboring wild-type neurons are not affected. These findings raise new outstanding questions about 1) the molecular trigger that elicit more changes in gene expression over time; 2) the changes to the abundance of mRNAs that localize to specific cellular compartments; and 3) the origin of synaptic deficits at the level of individual synapses. We propose to address these questions with new and innovative genetic and genomic tools, including spatial transcriptomics, in this application. Our goal is to uncover pathogenic mechanisms of RTT and gain insights into the molecular and cellular control of neuronal gene expression and neural development in general.

NIH Research Projects · FY 2024 · 2013-07

Project Summary This is an application for the renewal of a K24 mentoring award for patient-oriented research (POR) from Anne Cappola, MD, ScM, Professor of Medicine at the Perelman School of Medicine at the University of Pennsylvania (Penn). The candidate has had a strong record of mentorship, leadership, and research productivity during the initial award period. Her research program encompasses POR studies at the intersection of endocrinology and geriatrics. The scientific goals of this proposal are to investigate the age- specificity of the cardiovascular risks of mild subclinical hypothyroidism and to examine thyroid stimulating hormone (TSH) testing and levothyroxine prescribing patterns in older individuals. These studies are required to support a change in the upper limit of the TSH reference range for individuals aged 65 years and older. This change would improve the health and reduce health care costs for millions of older Americans through prevention of unnecessary prescription of thyroid hormone treatment, reduction in excessive TSH monitoring, and avoidance of iatrogenic thyrotoxicosis. The mentoring goals of this application are to support the candidate’s six current K-award mentees’ transition to R01 funded independence and to engage a new generation of Penn fellows and junior faculty to conduct POR in aging. The career development goal of this application is to support the candidate’s professional development and program building in clinical investigation. This will be achieved through focused learning about biomedical informatics, engagement in Penn’s CTSA to enhance lifespan research, and ongoing leadership to promote the visibility of aging research in the endocrine community. The institutional environment for clinical and translational science at Penn is outstanding, and the proposal integrates multiple programs from Penn’s CTSA. The Department of Medicine at Penn has made a substantial commitment, including protected time and dedicated space, toward the candidate’s sustained success as a patient-oriented researcher responsible for training a new generation of junior investigators who conduct POR in older participants. Renewal of this application will allow the candidate to cement the programmatic gains achieved during the initial award period and to assure their sustainability after the renewal has completed.

NIH Research Projects · FY 2026 · 2013-07

PROJECT SUMMARY/ABSTRACT The objective of this proposal is to understand how the first elements of olfactory circuitry are correctly wired together during embryonic development. Odorant sensing neurons project axons from the olfactory epithelium to the olfactory bulb in the brain. Each olfactory sensory neuron in the epithelium chooses a single odorant receptor to express from a very large gene repertoire. Remarkably, all the sensory neurons that have chosen the same odorant receptor to express extend axons that converge together in specific reproducible locations within the olfactory bulb. This research proposal addresses how olfactory sensory axons locate their specific targets in the brain. This project takes advantage of the relative simplicity of the zebrafish olfactory system and its developmental and experimental accessibility to study the guidance of sensory neurons between the olfactory epithelium and the bulb. In the first Aim, single cell RNA sequencing is used to identify cell surface or secreted proteins that are differentially expressed between groups of olfactory sensory neurons whose axons target different and distinct regions in the olfactory bulb. These are candidate genes involved in targeting, and their function will be assessed by knocking them down one at a time and testing whether OSN axons target their correct locations in the olfactory bulb. In the second Aim, we will examine the role an important family of axon guidance cues, the slits, play in directing olfactory sensory axons to their appropriate target regions in the bulb. These studies build towards a systems level understanding of how an important functional circuit is assembled during development. This knowledge will be essential in the formulation of therapies for the regeneration and repair of olfactory circuitry in aging or anosmic patients.

NIH Research Projects · FY 2026 · 2013-06

Overview Abstract/Summary The overarching theme of the Penn Mental Health AIDS Research Center (PMHARC) at the University of Pennsylvania (Penn), Children’s Hospital of Philadelphia (CHOP), and Wistar Institute (Wistar) is to transform how individuals with comorbid mental illness/AIDS are treated and managed by developing innovative, interdisciplinary, and integrative approaches to optimize psychiatric, behavioral, and medical outcomes and achieving a better understanding of the biological, psychological, and behavioral mechanisms underlying these combined illnesses and treatments. No other center in the U.S. is currently pursuing this explicit focus, making PMHARC unique in the NIMH ARC portfolio. A substantial body of work links psychiatric disorders to acquisition of HIV infection, accelerated immune dysfunction, poor access to HIV care, and poor adherence to antiretroviral treatment once in care. Yet, there remains a relative paucity of evidence-based interventions focused on the combined treatment of mental illness/HIV and related medical co-morbidities, and relatively little work in determining the relationships between mental health treatment and HIV disease and understanding the underlying biology. PMHARC will continue to stimulate novel approaches and strategies to address these problems by providing mentoring and resource support for both new and established investigators choosing to study comorbid mental illness/HIV, in part through innovative pilot studies. PMHARC's leadership has extensive expertise in contemporary pharmacotherapy of mental illness and HIV, cognitive behavioral treatments, and theory-based behavioral interventions. PMHARC will extend well-established collaborations at Penn, CHOP, and Wistar including those in the Department of Psychiatry and the CFAR, as well as with the CTSA/CTRC, the Delaney Collaboratory, and community partners in Philadelphia. A unique feature of PMHARC is the collaboration of well established mental health/HIV researchers, well-established mental health researchers who have not previously studied HIV, well-established substance use/HIV researchers who have not previously studied mental health, and HIV researchers not previously focused on mental health. PMHARC has an Administrative and Developmental Core, and four Shared Resource Cores.

NIH Research Projects · FY 2025 · 2013-06

Contact PD/PI: Greenberg, Roger A. Summary Evolutionary conserved DNA repair mechanisms cooperate throughout the cell cycle to faithfully maintain genome integrity. However, a minimal understanding exists for how damaged chromatin directs the series of events that dictate ensuing repair mechanism. This gap in knowledge is particularly relevant to a poorly understood homology directed repair mechanism that becomes active to maintain telomere length in approximately 15% of human cancers. Alternative lengthening of telomeres (ALT) occurs by noncanonical homology directed DNA repair mechanism in cancers of mesenchymal origin. The recombination mechanisms responsible for telomere maintenance represent a unique vulnerability in ALT reliant cancers. We have developed experimental systems that enable quantitative, real-time visualization of each step in the homology directed repair of damaged telomeres. Our published studies reveal that ALT is initiated by DNA damage dependent homology directed repair synthesis that proceeds unidirectionally to the end of the chromosome. We named this mechanism Break Induced Telomere Synthesis and showed that it is critical for telomere lengthening in cells that utilize ALT. Here, we examine the question of how DNA damage responses assemble on telomeric chromatin to direct long-tract homology directed repair telomere synthesis. We hypothesize that Break Induced Telomere Synthesis occurs by assembling elements of several different DNA repair mechanisms on telomeric chromatin to achieve homology directed repair synthesis. Our unpublished results definitively support this premise, showing extensive PCNA- ubiquitination and recruitment of the 5’-3’ nuclease SNM1A and 5’-3’ helicase FANCJ at damaged telomeres to promote DNA repair synthesis and telomere integrity. We will investigate the basis for their damage dependent association with telomeres and functions in recombination dependent repair synthesis at telomeres using a multifaceted approach that allows us to examine each step of the telomere damage response in cells and in vitro in highly purified systems that assemble the break induced replisome on defined substrates. These fundamental studies are designed to understand the critical elements of Break Induced Telomere Synthesis and how it allows telomere lengthening for sustained proliferation in cells that rely on ALT.

NIH Research Projects · FY 2026 · 2013-04

Contact PD/PI: Greenberg, Roger A. Summary Encounters between DNA replication proteins (replisome) and specific genomic lesions invoke requirements for BRCA1 and BRCA2 (BRCA) dependent repair by homologous recombination (HR). Replisome conflicts with endogenous DNA damage also elicit error prone homology directed repair (HDR) mechanisms and damage tolerance pathways that allow replication through persistent genomic lesions. Such noncanonical HDR pathways become prominent in BRCA mutated cells. They are also responsible for telomere maintenance in ~15% of human cancers that utilize the alternative lengthening of telomeres (ALT) mechanism. We have developed unique systems to investigate the endogenous lesions that provoke BRCA dependent and independent HDR and have used them to understand how each repair mechanism is initiated and resolved. In the current R01 funding period, we have demonstrated that (1) loss of the PAR dependent chromatin remodeler, ALC1, potentiates PARP inhibitor responses by several orders of magnitude specifically in HR deficient cells, (2) Break induced replication utilizes PCNA-Ub interaction with SNM1A for resection dependent template switch recombination bypass of polymerase blocking lesions, and (3) BLM helicase activity generates single-strand DNA at replicating telomeres to promote a damage response that executes ALT. The proposed research investigates the biochemical basis for these phenomena, and how they process specific endogenous DNA lesions to provoke either classical or alternative forms of recombination. We utilize approaches to identify the full spectrum of responses that occur at damaged telomeres and interrogate specific DNA replication associated structures that ALC1, SNM1A, and BLM act upon to affect repair mechanism. Overlapping genetic vulnerabilities in ALT and BRCA mutant cells suggest commonality in the repair processes that ensue in each scenario. Our overarching goals are to delineate molecular events necessary for each process and understand how classical and alternative mechanisms of homologous recombination intersect in the settings of (1) BRCA mutation, and (2) during ALT. These objectives will be performed in parallel and with equal emphasis. Our studies will yield fundamental advances to the understanding cancer genome integrity control.

NIH Research Projects · FY 2024 · 2013-04

Periodontal disease is a chronic inflammatory disorder driven by polymicrobial infection. The pathogenesis of this disorder involves activation, and possibly perturbation, of both innate and adaptive immune responses. Over the course of our investigation we have demonstrated that Aggregatibacter actinomycetemcomitans (Aa), a putative pathogen implicated in the pathogenesis of localized aggressive periodontitis (LAP), produces an immunotoxin, the cytolethal distending toxin (Cdt). Cdt is a heterotrimeric holotoxin which functions as an AB2 toxin: the cell binding (B) units are comprised of the CdtA and CdtC subunits and the active (A) subunit, CdtB. We have demonstrated that CdtB functions as a 5'-phosphatidylinositol (PI) triphosphate phosphatase as it degrades the PI-3K signaling lipid, PI-3,4,5-triphosphate (PIP3) to PI-3,4P2; this action leads to blockade of the signaling pathway. Blockade of PI-3K signaling in human macrophages leads to a pro-inflammatory cytokine response involving both canonical and noncanonical inflammasome activation. Cdt also induces production of inflammatory mediators derived from arachidonic acid including PGE2 and thromboxanes. Most recently, we have observed phagocytic defects in Cdt-treated macrophages consistent with altered phago-lysosome maturation. We propose that Cdt perturbs macrophage function thereby contributing to both inflammation and sustained infection. Our overarching hypothesis is that the Aa Cdt contributes to altered local host defense which facilitate Aa survival and enables other microbes to evade host defense. The goal of our study is to extend our investigation and advance our knowledge of the molecular events that link PI-3K signaling blockade to downstream pro- inflammatory responses and altered vesicular trafficking and fusion. Specifically, we propose that CdtB induces GSK3â-dependent HSP90 activation and further that HSP90, via its effects on NLRP3, Cox-2 and possibly ESCRT proteins is a critical intermediary in events leading to release of mature cytokines and eicosanoids (specific aim 1). We plan to advance our understanding of the role that Cdt plays activating the noncanonical inflammasome which involve gasdermin D (GSDMD) pore formation and pyroptosis. Our focus will be to determine how CdtB activates caspase-4 and contributes to GSDMD pore formation; the latter studies will focus on PI-3,4P2 and pore repair via the ESCRT system (specific aim2). In specific aim 3 we will focus on perturbation of vesicular transport and phago-lysosome formation. We propose that altered PI distribution due in part to CdtB-mediated production of PI3,4P2 facilitates CdtB retrograde transport and modulates the formation of phago-lysosomes. The long-term goals of our study are to translate our understanding of the molecular events that govern Cdt toxicity and, in turn, the pathogenicity of Cdt-producing organisms. These studies are of particular significance as Cdt is produced not only by Aa but many other pathogens that contribute to chronic infectious and inflammatory disorders. Insight gained through this investigation will advance our understanding of the molecular events underlying LAP and other diseases caused by Cdt-producing organisms and identify new avenues for therapeutic intervention. .

NIH Research Projects · FY 2024 · 2013-01

Project summary. Our research objective is to define the mechanistic underpinnings of the protein disaggregases, Hsp104, and its partial human homolog, Skd3 (human ClpB), which are poorly understood. In non-metazoan eukaryotes, Hsp104 couples ATP hydrolysis to the disaggregation of diverse proteins trapped in disordered aggregates, preamyloid oligomers, and amyloids. Hsp104 is the only factor known to dissociate α- synuclein (α-syn) oligomers and amyloids linked to Parkinson's Disease (PD) and rescue neurodegeneration in a rat PD model. However, Hsp104 activity is limited against α-syn and high Hsp104 concentrations are required for optimal effects. Thus, we engineered potentiated Hsp104 variants, which dissolve fibrils formed by ?-syn as well as TDP-43 and FUS (which are linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), an Alzheimer's Disease-Related Dementia (ADRD), which mitigate neurodegeneration in the metazoan nervous system more effectively than Hsp104. Though potent disaggregases, these potentiated Hsp104 variants lack substrate specificity and are prone to toxic off-target effects. To address this issue, we engineered new potentiated Hsp104 variants with minimal off-target effects and α-syn-specific Hsp104 variants, which exhibited enhanced therapeutic utility. These engineered disaggregases could provide a disruptive technology to combat neurodegenerative disease and enable purification of aggregation-prone proteins for basic or pharmaceutical purposes. Curiously, Hsp104 does not have an exact metazoan ortholog. Remarkably, we have found that a partial homolog of Hsp104 found in human mitochondria, an AAA+ protein called Skd3 (human ClpB), has powerful protein disaggregase activity comparable to potentiated Hsp104 variants. Despite these important advances, our mechanistic understanding of Hsp104 and Skd3 is limited by three critical barriers. First, we do not understand how Hsp104 selects substrates for disaggregation. Thus, we have not yet developed TDP-43- or FUS-specific variants for ALS/FTD. Second, we do not understand how Hsp104 is regulated. Thus, the mechanism by which specific mutations in nucleotide-binding domain 2 (NBD2) potentiate Hsp104 remain unclear. Third, Skd3 is poorly characterized in terms of its disaggregase capabilities, structure, and mechanism. Based on our preliminary data, we hypothesize that: (1) potentiated Hsp104 variants can be engineered to be more selective for ALS/FTD-linked TDP-43 and FUS; (2) specific NBD2 mutations potentiate Hsp104 via a novel mechanism; and (3) Skd3 is a powerful human protein disaggregase with broad capabilities and mechanistic similarities to Hsp104. Thus, we will meet three aims: (1) Define Hsp104 variants with enhanced TDP-43 and FUS selectivity; (2) Define how specific NBD2 mutations potentiate Hsp104 activity; (3) Define the capabilities, mechanism, and structure of the human Skd3 AAA+ disaggregase. In this way, we will secure an enhanced mechanistic understanding of Hsp104 and Skd3, which will empower their development for important applications in biotechnology and medicine.

NIH Research Projects · FY 2024 · 2012-09

The Testicular Cancer Consortium (TECAC) is the only international collaborative group whose goal is to understand the genetic susceptibility to testicular germ cell tumors (TGCT). The incidence of TGCT is highest among men of European ancestry, and the most common cancer affecting men aged 15-45. TECAC and its members have conducted successful genome-wide association studies (GWAS) of TGCT; our latest analysis has identified 22 novel susceptibility alleles bringing the total validated risk markers to 68, accounting for 43% of heritability. Our studies have revealed the critical role of variation affecting essential pathways of male germ cell development and maturation, sex determination, chromosomal segregation, and DNA maintenance in TGCT susceptibility. We propose three complementary aims to deepen our discovery of inherited variation of susceptibility to TGCT, results of which will refine our understanding of the biology of TGCT and male germ cell development, provide insights into inherited variation predisposing to genomic instability, and improve our ability to identify patients at highest risk of disease. In Aim 1, we will identify rare and common variants (individual and gene burden) using whole exome (WES) approaches followed by independent validation. We will conduct de novo WES on extant biosamples from 1000 and 1000 men with and without TGCT, respectively, and assemble existing WES data from 2066 men with TGCT from TECAC members for comparison to genomically matched (1:4) unaffected men from the Penn Medicine and UK Biobanks. To address data heterogeneity, WES data from all sources will be called together using a common pipeline. Fifty genes and 500 SNPs will be selected for validation in an independent set of extant biosamples from 5000 and 5000 men with and without TGCT, respectively, all with existing genome-wide genotyping. In Aim 2, we will conduct a transcriptome-wide association study (TWAS), preceded by the largest GWAS study to date in 15,847 men with TGCT and 27,178 (230,610 with deCODE) men without TGCT. We will use a customized version of FUSION to perform the TWAS, annotated with expression data derived from TGCT cell lines, fetal and adult germ cells, GTEx, and single cell sequencing of germ cells. In Aim 3, after in silico assessment and prioritization, 20 top loci/genes will be evaluated in TGCT in vitro models using siRNA and CRISPR to assess over-expression and knockdown effects on morphology, proliferation, chromosomal abnormalities, and cisplatin sensitivity. We will select candidate genes from our past genetic association efforts (11 preliminarily prioritized) and from novel loci/genes found in our WES (Aim 1), GWAS and TWAS (Aim 2) efforts. Our renewal builds upon our accomplishments and paves the way to identify novel susceptibility loci through three highly cohesive aims. Our findings will lead to further ground-breaking insights into the biology and genetic etiology of TGCT and will provide data needed to identify men at greatest need for surveillance, the optimal way to decrease serious TGCT treatment-related morbidity.

NIH Research Projects · FY 2026 · 2012-07

Despite effective viral control by Antiretroviral therapy (ART), HIV associated neurocognitive disorder (HAND)persists in 30-50% of people with HIV (PWH). The pathology of HAND includes white matter (WM) changes such as decreased myelin sheath thickness, myelin lesions, and abnormal myelin protein expression. We have found that both HIV infection and a subset of antiretroviral drugs disrupt oligodendrocyte (OL) maturation and myelination. These data support our overarching hypothesis that HIV infection and select ART compounds attenuate OL differentiation and myelin formation, contributing to CNS dysfunction in persons with HIV (PWH) on ART. Our in vitro data on the effects of HIV and ART drugs on OL differentiation align with in vivo evidence for a prominent role of the integrated stress response (ISR) and lipid metabolism in ART drug- and HIV-induced changes in WM. Transcriptome studies reported significant induction of transcripts indicative of activation of the ISR and unfolded protein response coincident with significant decrease in transcripts encoding regulators of lipid metabolism and specific myelin proteins in WM from PWH on ART. We have reported that a subset of ART drugs and a model of HIV infection induce the ISR, particularly the Protein kinase R-Endoplasmic Reticulum Kinase (PERK), in OLs. Our preliminary data demonstrate altered levels of lipid metabolism enzymes and lipids in response to ART drugs. Both processes correlate with inhibition of OL differentiation. Numerous studies have demonstrated that ISR kinase PERK regulates lipid metabolism; however, the role of ISR/PERK-induced stress granule (SG) formation, which are membraneless organelles containing mRNAs that protect a subset of transcripts during ISR activation, has not been investigated. Our preliminary data demonstrate the presence of SGs in OLs in WM of PWH with HAND and in OLs exposed to ART drugs in vitro. These findings have led us to hypothesize that HIV infection and a subset of ART compounds induce the ISR leading to stress granule formation and disruption of lipid metabolism in OL, causing defects in differentiation and myelin formation in PWH, contributing to CNS dysfunction. To address this hypothesis: aim 1 will determine whether HIV or select ART drugs cause the ISR-induced formation of SGs, which mRNAs critical for myelination are sequestered in SGs, and whether SGs are toxic to the cell. These goals will be pursued in our well-tested in vitro model of oligodendrocyte differentiation, in a small animal model and in samples from PWH. In aim 2, we will determine how both HIV and select ART drugs alter lipid composition and lipid regulation in OLs, also employing our in vitro model, a small animal model and samples from PWH. We will also determine the impact of ISR on lipid regulation and composition in this system. Finally, in specific aim 3, we will determine if neuroimaging-based measures of WM health associates with genetic variants of PERK and lipid metabolism in the context of functional subdomains of cognitive and mental health changes in PWH.

NIH Research Projects · FY 2025 · 2012-07

This application is for the continuation of a T32 Institutional Training Grant in Environmental Health Sciences (EHS) entitled: “Translational Research Training Program in EHS” (T32-ES019851) at the University of Pennsylvania (Penn). This training grant is the only dedicated mechanism to support formalized EHS research training at the pre- and post-doctoral level at Penn and meets a significant need based on trainee interest in the environment and its health impact and biomedical work force need. The mission of the T32 Training Program is to train the next generation of environmental health scientists to identify the mechanisms by which environmental exposures cause disease and to translate these findings into effective prevention and treatment and improvements in public health. The research training reflects the translational research themes of Penn’s P30 Environmental Health Sciences Core Center, the Center of Excellence in Environmental Toxicology (CEET). These themes include Air Pollution & Lung Health, Environmental Exposures & Cancer, Windows-of-Susceptibility, and Environmental Neuroscience. These themes are underpinned by exposure assessment, adverse outcomes, and translation to human subjects, communities, and policy. Training is provided through coursework from the Certificate Program in Environmental Health Sciences, which includes a mandatory Community Environmental Health Rotation, and by conducting a full-time translational research project co-mentored, where possible, by a basic scientist and clinician-scientist to generate new knowledge in EHS. The 48 distinguished Training Grant (TG) faculty come from Penn and Children’s Hospital of Philadelphia, 21 are clinician-scientists. The TG supports common experiences, including a research club, a dedicated seminar series, an annual symposium dedicated to a translational research theme, and optional externships at the US EPA, the Silent Spring Institute, the Research Institute for Fragrance Materials, and a Science Policy Institute, so that trainees are exposed to alternative career options. The T32 award currently supports three predoctoral fellows to conduct dissertation research on an EHS topic and four postdoctoral fellows to perform mentored EHS research. Predoctoral trainees are supported for a total of three years (2nd year completion of the Certificate Program in EHS and two years dissertation research) and postdoctoral trainees are supported for two to three years. Trainees are prepared for a suite of careers in the employment sector e.g., academia (in EHS, Pharmacology and Toxicology), government agencies (e.g. US-EPA, CDC, FDA, NTP, NIEHS); and industry (drug, food, cosmetic and nanotechnology). In the last two cycles, the Training Grant has supported 29 trainees, who have published 108 papers, and alumni have continued with scientific careers in academia and industry.

NIH Research Projects · FY 2026 · 2012-04

Project Summary NIA has established the National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS) as a national genetics data repository in order to facilitate access by qualified investigators to genotypic data for the study of the genetics of late-onset Alzheimer's Disease (AD). It is the policy of the NIA that all Genetic Data derived from NIA funded studies for the genetics of late-onset Alzheimer's disease be deposited at NIAGADS or another NIA approved site or both whenever possible. NIAGADS is also the Data Coordinating Center for Alzheimer's Disease Sequencing Project (ADSP), a National Institute on Aging initiative to identify new genetic variants by sequencing genomes/exomes of more than 30,000 AD patients and cognitively normal controls. In the third funding period, NIAGADS will continue our primary mission as the national repository for AD genetics and genomics, support ADSP data coordination, and collaborate with NIA- funded and other relevant ADRD research initiatives. The growing data will evolve into a long-lasting resource and a major legacy of ADSP. NIAGADS will: (1) Curate, update, and disseminate a high-quality, lasting data collection with 80,000 or more genomes for ADRD genetics/genomics research; (2) Support ADSP data production and analysis activities; (3) Develop informatics infrastructure for cloud-based data analysis, management and dissemination; (4) Expand computational tools for genetic and genomic data annotation, report and visualization; (5) Collaborate with other research resources and initiatives, and expand the outreach program.

NIH Research Projects · FY 2025 · 2011-09

SUMMARY Crosstalk between immune cells and the epithelium protects the intestinal barrier from infectious and non- infectious threats. Elucidating the signals that mediate this cellular crosstalk is necessary to improve our understanding of diseases associated with barrier dysfunction, such as Crohn's disease (CD), a major type of inflammatory bowel diseases (IBD). We previously established a model to investigate how a commensal and otherwise beneficial virus induces immune-mediated damage in a genetically susceptibility host. Infection of Atg16L1 mutant mice with murine norovirus (MNV) inhibits the function and viability of Paneth cells, antimicrobial epithelial cells in the gut. Tissue sections and intestinal organoids derived from CD patients harboring the ATG16L1 risk variant display similar Paneth cell defects. Thus, we have been using the MNV infection model to examine how environmental factors cause epithelial defects associated with intestinal disease. In preliminary data, we found that MNV inhibits secretion of a unique anti-inflammatory effector by T cells that we identified as apoptosis inhibitor 5 (API5). Our data further suggest that API5 prevents inflammatory cell death (necroptosis) of Paneth cells that are defective in the cell biological process of autophagy due to Atg16L1 mutation. The objective of this proposal is to investigate the epithelial-intrinsic and -extrinsic mechanisms that underlie these observations. We will determine how: (1) ATG16L1 and autophagy prevent necroptosis in the intestinal epithelium, (2) API5 secretion by T cells is regulated in response to viral infection, and (3) extracellular API5 exerts protective functions. By investigating this virus-host susceptibility gene interaction, we anticipate identifying new mechanisms involved in intercellular communication and epithelial resilience to injury, thereby improving our understanding of immune-epithelial crosstalk during health and disease.

NIH Research Projects · FY 2025 · 2011-08

Project Summary/Abstract In this application, we present the unique strengths of the University of Pennsylvania clinical site that have allowed us to make significant academic, clinical, and administrative contributions to the Pelvic Floor Disorders Network (PFDN) in our two cycles of participation. Our core team of five academic investigators is part of a team of twenty pelvic floor specialists and includes three fellowship-trained urogynecologists, one fellowship- trained urologist and a behavioral nurse practitioner who provide diverse and complementary expertise in multi-center trials of pelvic floor disorders. Our investigators have contributed to all areas of clinical trial design and development, recruitment and retention and scientific reporting in the Network. Specifically, Penn investigators are leading several active research protocols including 1) surgical trial of mixed urinary incontinence (Harvie) 2) gut microbiome and metabolome in fecal incontinence (Arya) 3) behavioral interventions for urinary and fecal incontinence (Newman) 4) cost-effectiveness analyses for all seven trials (Harvie) and 5) use of Penn Clinical and Translational Science Award (CTSA) to validate a fecal transplant protocol for potential application in the PFDN (Andy). Our recruitment and retention in multi-center trials is outstanding and the result of an exceptional research infrastructure and culture of research that permeates all our clinical activities. Our unique geographical location allows us to recruit a large and ethnically diverse patient population from three states (Pennsylvania, New Jersey and Delaware). We consistently rank in top half of recruiting sites for all seven randomized trials conducted in our two cycles of participation and 32% of our enrolled subjects are minorities (highest recruitment of Black/African-American subjects from all sites). Additional unique strengths of the Penn site include 1) strong collaboration with Urology co-investigator (Smith) that placed us in top three recruiting sites for two trials 2) a dedicated clinical research unit in the Department of OB/GYN that provides direct financial, logistical and personnel support beyond the PFDN budget 3) the Penn CTSA funded Institute for Translational Medicine and Therapeutics (ITMAT) that provides PFDN investigators low cost access to all state-of-the art technologies specified in the RFA including fecal transplant 4) a Health Care Innovation Center that is supporting a patient-centered texting platform for urinary incontinence in our concept proposal and 5) Administratively, Penn holds the IND for botulinum toxin A (mixed urinary incontinence) and fecal transplant (fecal incontinence). Ultimately, the team of investigators, available population, our cost-effective and efficient approach to recruitment and outstanding university resources make the University of Pennsylvania an ideal site to advance the productivity of the Pelvic Floor Disorders Network.