University Of Pennsylvania

NIH Research Projects · FY 2025 · 2021-04

Project Abstract Live cell reporters of genetic changes in stiff vs soft surroundings – causes & consequences Solid tumors are often palpably stiff and more constrained in 3D growth than ‘liquid’ hematopoietic tumors. Extensive sequencing of dozens of cancer types further indicates that solid tumors within stiff tissues exhibit many more genetic changes than liquid and soft-tissue tumors [Pfeifer 2017]. Our first hypothesis is a mechano-genetics hypothesis, namely genetic changes are caused in part by the mechanics of the tumor or tissue micro-environment. A key limitation of current sequencing methods is that they require killing cells to isolate the DNA, which prevents tracking a cell before, during, and after a genetic change. A new method is needed to track genetic changes in living cells under diverse biophysical stresses. Our second hypothesis is that gene editing can be used to enable tracking some changes in the genetics of single cells in real-time. Preliminary results from a new approach already support both hypotheses. RFP (red fluorescent protein) is fused to a single allele of an abundant constitutive gene in cancer cells or normal cells. For appropriate genes, we find that RFP-neg cells have lost all or part of the edited chromosome, using methods that range from single cell DNA-seq to allele-specific PCR. For the one edited chromosome that has been studied most deeply (of three), the RFP-neg cells divide and pass on the genetic change, and they also exhibit a ‘go-and-grow’ phenotype consistent with partial loss of a key tumor suppressor. In solid tumor xenografts that start with freshly sorted RFP-pos cells, the fraction of RFP-neg cells scales strongly with the number of cell divisions, unlike 2D cultures, and 3D imaging further shows that (i) dividing cells are flattened in vivo, and (ii) interphase nuclei with high curvature tend to rupture and exhibit high DNA damage. In reductionist 3D culture studies, confinement and constriction likewise increase GFP-neg cell numbers. The preliminary results directly support our mechano-genetics hypothesis. We will replicate and extend our preliminary results both in vitro and in vivo with the ultimate goals of identifying mechanically modulated pathways of chromosome loss and consequences for phenotype. For relevance to patients, the in vivo studies will include liver cancer patient derived xenografts (PDX) that are gene edited and grown in liver as well as softer and stiffer sites.

NIH Research Projects · FY 2025 · 2021-04

Project Summary Adolescents account for a disproportionately high percentage of new HIV infections each year: in 2018, 30% of all new global infections were among 15-25 year-olds, and 21% of all new United States infections were among 13-24 years-olds 2-4. However, we know little about the effects of new infection and therapy on the developing brain in this critical time frame. Limited studies on HIV+ 18-24 year-olds on and off antiretroviral therapy (ART) demonstrate that up to 65% develop behavioral, cognitive and motor impairments meeting the criteria for HIV associated neurocognitive disorder (HAND) 5,6, a proportion higher than that seen in older HIV+ adult counterparts despite lower viremia, higher CD4+ T-cell counts, and shorter durations of infection in adolescents 7. A major gap in our knowledge is the mechanistic basis of this dysfunction in the developing central nervous system (CNS). The effect of virus-mediated and/or ART toxicities on normal myelination and synaptic pruning in the adolescent and young adult brain is unknown. It is well documented that functionally critical development of white matter (WM) and synaptic plasticity continues until the mid-twenties in humans 8. Interestingly, WM deficits, including myelin lesions, decreased myelin sheath thickness, and abnormal myelin protein expression, are among the persistent pathologic findings in HIV+ adults with HAND 1,9-11 Consistent with pathologic findings, transcriptome analyses of cortical gray matter (GM) and WM from HIV+ adults, both ART- naïve and ART-treated, have revealed decreased expression of genes associated with oligodendrocyte (OL) differentiation and myelination 12,13. We have shown HIV-associated neuroinflammation inhibits OL maturation through upregulation of the integrated stress response (a pathway shown to be dysregulated in the CNS of HIV+ patients) 14,15. Further, data from our laboratory also suggest that a subset of ARV drugs themselves can disrupt differentiation of OL precursor cells in vitro and remyelination in vivo 16-18. An independent effect of ARV drugs on WM pathology is clinically important not only in the care of HIV+ adolescents, but also in uninfected adolescents who use pre-exposure prophylaxis (PrEP), a combination of two nucleoside reverse transcriptase inhibitors, emtricitabine (FTC) and tenofovir disoproxil fumarate (TDF), to prevent HIV infection. Our preliminary data indicate that several ARV drugs, including FTC and TDF, inhibit the progression of OL maturation in vitro through lysosomal dysfunction suggesting a role for organellar stress. Thus, we hypothesize that HIV, ART and PrEP disrupt developmental myelination via organellar stress contributing to the multifaceted CNS deficits observed in adolescents and young adults. We propose to: 1) Determine the mechanisms by which HIV- induced neuroinflammation disrupts OL maturation in adolescents, 2) Determine the role of lysosome dysfunction in ART-induced changes in OL maturation in rodent models of adolescence and young adulthood, and 3) Compare OL maturation and myelination measures in Aims 1 and 2 to magnetic resonance imaging measures of WM volume and integrity in adolescent rats and a pre-existing cohort of adolescent humans.

NIH Research Projects · FY 2025 · 2021-04

PROJECT SUMMARY Oral wound healing is characterized by rapid resolution of inflammation and minimal scarring. As it is a prime example of ideal tissue regeneration, there is a growing interdisciplinary interest in studying the mechanisms of oral wound healing. Fibroblasts play an essential role in this process and are also implicated in oral diseases responsible for the global economic burden amounting to 442 billion dollars. Recent advances in connective tissue biology have elucidated the importance of fibroblast heterogeneity in the pathogenesis of dermal fibrosis and rheumatoid arthritis. However, the in vivo heterogeneity of oral fibroblasts and thereby a functional significance of select fibroblast population during oral wound healing is poorly understood. Here, we found that postnatal Prx1+ cells are found in mouse gingiva and express common markers of fibroblasts. Preliminary data demonstrate that wounds enriched in Prx1+ cells heal faster with minimal inflammation compared to wounds that lack these cells. Therefore we will test the overall hypothesis that Prx1+ cells represent distinct oral fibroblast progenitors and are responsible for rapid tissue regeneration through a mechanism that involves resolution of inflammation. Aim 1 will utilize an auto-transplantation approach and test the hypothesis that transplanted Prx1+ cells contribute to accelerated oral wound healing by functioning as mesenchymal progenitors in vivo. Aim 2 will investigate if lineage specific ablation of Prx1+ cells delays wound healing by causing the failure to quickly resolve inflammation in vivo, and explore mechanisms of immune cell modulation by Prx1+ fibroblasts in co- culture assays. In Aim 3, we will perform single cell RNA-sequencing to compare transcriptomic profiles of mesenchymal and leukocyte cell subtypes in Prx1+ enriched oral wounds to those in Prx1-poor wounds in mice. Moreover, we will test if Prx1-equivalent cells are found in human gingiva by single cell sequencing and in situ validation. Upon completion, the proposed studies are expected to reveal Prx1+ cells as pro-healing oral fibroblast subset and provide a significant translational value by implicating the clinical utilization of connective tissues or ex vivo stem cell therapy that are enriched with Prx1+ fibroblasts.

NIH Research Projects · FY 2025 · 2021-04

Project Abstract In much of eastern and southern Africa, the incidence of HIV and other sexually transmitted infections (STIs) remains high despite the scale-up of promising biomedical and behavioral interventions. Recent studies have documented the crucial role of transactional sex – the exchange of money, material support or goods in age- disparate, sexual relationships – and heavy alcohol use in driving HIV/STI incidence and influencing men's and women's health outcomes. Existing policy responses to this challenge have largely focused on women, with various interventions to reduce women's engagement in transactional sex such as education subsidies, vocational training, and cash transfers for economic empowerment. However, the effectiveness of these interventions has been hindered by the relative lack of programs that target men's behavior. There is a vital need for interventions that can reduce men's engagement in risky behaviors that increase HIV/STI risk. This project will test an innovative, theoretically-motivated economic intervention to reduce men's engagement in transactional sex and other risky behaviors. Leveraging innovations in mobile financial services and research on savings behavior in low-income countries, our intervention will motivate high-risk, income-earning men in Kenya to reduce their spending on risky behaviors and instead save their disposable income in local bank accounts. These bank accounts will include (a) additional incentives to save in the form of lottery-based rewards linked to amounts saved, (b) opportunities to develop savings goals, and (c) periodic reminders about the incentives and goals. Through a direct economic mechanism (incentives to shift expenditures from the present to the future) and a psychological mechanism (increasing future orientation), this intervention can generate significant behavior change and improve health outcomes. We will conduct a randomized controlled trial among high-risk men to determine effects of the savings intervention on their health and economic outcomes. Specific aims of the project are as follows. Aim 1: Determine the impact of the savings intervention on incidence of HIV and other STIs. Aim 2: Determine intervention impacts on savings and expenditures as well as risky health behaviors. Aim 3: Quantitatively and qualitatively assess mechanisms of behavior change among participants and among a sample of female partners. By testing an intervention to promote forward- looking behavior and reduce the risk of acquiring HIV and other STIs in a high HIV/STI burden setting, this project has high potential for scientific and public health impact.

NIH Research Projects · FY 2025 · 2021-04

PROJECT SUMMARY Chronic disability due to traumatic brain injury (TBI) affects 2% of the total population, and neuronal loss is generally considered permanent, owing to limited capacity for neuroregeneration in the adult mammalian brain. There are currently no approved treatments for improving recovery after TBI, and innovative approaches to enhance neuroregeneration are desperately needed. Intriguingly, new neurons are generated in the subventricular zone (SVZ) and then guided to the olfactory bulb/tract (and possibly striatum) via the rostral migratory stream (RMS) for integration into existing circuitry. Recent publications have demonstrated that SVZ neuroblasts can be redirected into lesions, differentiate into region-specific neuronal cell types, integrate into circuitry, and improve functional recovery in adult rodents, but a translational strategy to direct and enhance neuroblast migration into lesions has yet to be established. To address this challenge, we have assembled a multi-disciplinary team of stem cell specialists, neurobiologists, clinicians, and tissue engineers to develop the first anatomically-inspired microtissue designed to structurally and functionally emulate the glial tube of the RMS. In an exciting breakthrough, our team developed novel microtissue engineering techniques that promote the self-assembly of astrocytes into longitudinally aligned bundles that recapitulate the organization of the glial tube of the RMS. To date, we have biofabricated this Tissue Engineered Rostral Migratory Stream (TE-RMS) using rodent derived astrocytes as well as human stem cell derived astrocytes and, importantly, we have shown that the TE-RMS directly facilitates the alignment and migration of immature neurons in vitro and in vivo. In the current proposal, we will first validate the TE-RMS as an in vitro test bed to elucidate mechanisms of neuronal progenitor migration and cell fate determination (Aim 1). We will then test the ability of the TE-RMS to divert endogenous neuronal progenitors in vivo and repair damaged cerebral cortex following experimental TBI in rats (Aim 2). In this Aim, the TE-RMS will be stereotaxically microinjected after the acute injury period to span from the SVZ into lesioned tissue, and the redirection of migrating neurons to repopulate cortical areas, functional integration with residual circuitry, and facilitation of behavioral recovery will be assessed. Finally, as a first step towards clinical translation, we will perform in vitro and in vivo studies to validate the TE-RMS built using astrocytes derived from stem cells harvested from adult human gingiva to develop methods for the eventual creation of autologous, patient-derived implants from an easily accessible cell source (Aim 3). The TE-RMS recapitulates the brain's own method for delivery and integration of new neurons. Thus, the execution of these Aims will significantly advance a translational bioengineering approach capable of providing targeted and sustained cell replacement following neurotrauma and/or degeneration. Our team is uniquely positioned to provide a feasible, yet highly innovative neuroregenerative approach that can have a significant impact on patients suffering from the otherwise intractable consequences of TBI.

NIH Research Projects · FY 2025 · 2021-04

ABSTRACT This application responds to PAR-16-454: International Bioethics Research Training Program (D43) with a focus on bioethics research training in Tanzania. The need for doctoral-trained bioethics scholars and bioethics scholarship in low and middle-income countries (LMIC) is urgent. With the recent emergence of the coronavirus public health pandemic and concerns about the allocation of finite resources, LMICs face daunting challenges when making ethical decisions that affect their citizens. They also face other day-to- day ethical issues in clinical care and clinical research, including informed consent from vulnerable patients, HIV incidence and prevalence, cultural views about decision-making roles, truth-telling to patients and families, and many others. All these areas require educating and developing bioethicists in Tanzania (ENGAGE). We capitalize on nine years of successful interdisciplinary collaboration between Muhimbili University of Health and Allied Services (MUHAS), Dartmouth and the University of Pennsylvania to prepare a cadre of doctoral prepared bioethics scholars in Tanzania. The collaboration has facilitated the creation, staffing, and demonstrated sustainability and successes of the Department of Bioethics and Health Professionalism in the School of Public Health and Social Sciences. The Department offers the Masters of Bioethics and teaches bioethics across the broad spectrum of degree programs offered at MUHAS. The purpose of this application is to build on this accomplishment and address the need to develop bioethics scholars who can integrate theory, research, and public-health policy and become intellectual and academic leaders in the field of bioethics relevant to the country. To achieve this aim, we propose to: (1) recruit and train six individuals at the doctoral level; (2) prepare the next generation of bioethics scholars who will be at the forefront of scientific inquiry and advancement of the public's health in Tanzania, and (3) develop a sustainable research capacity for bioethics in the region. There is no institution in Tanzania that offers formal bioethics training at the doctoral level. Thus, the country and the region will benefit from doctoral prepared bioethicists who have the skills to address the country's most pressing bioethics and public health-related problems.

NIH Research Projects · FY 2025 · 2021-04

Finding a cure for Alzheimer's disease (AD) is one the greatest scientific challenges of our time. There is a growing realization that experimental treatments should target the earliest, presymptomatic stages of disease. But the cost of conducting clinical trials in participants who may not develop symptoms of AD for years can be prohibitive. There is a growing need for more effective biomarkers of AD, particularly biomarkers of therapeutic efficacy that can detect slowing or reversal of AD-related changes due to treatment as early in the clinical trial as possible. These biomarkers must be as sensitive as possible to disease progression and also account for AD heterogeneity, i.e., the fact that the majority of individuals who have AD pathology also have one or more concomitant pathologies that may affect their ability to respond to experimental treatments for AD. This proposal focuses on deriving effective presymptomatic and early symptomatic AD biomarkers from magnetic resonance imaging (MRI), the imaging modality that provides the most direct evidence of neuritic and neuronal loss in neurodegenerative disease. Rather than propose new MRI acquisition protocols, we focus on the most commonly collected type of MRI scan in AD research (T1-weighted 3D gradient echo scans with approximately 1x1x1mm3 resolution) and use advanced computational analysis to quantify changes in the subregions of the medial temporal lobe (MTL), the brain region that associated with early stages of AD pathology as well as with early stages of multiple concomitant non-AD pathologies. Aim 1 will develop and validate advanced algorithms that combine conventional multi-atlas segmentation with deep learning to reliably extract small subregions of the MTL, such as Brodmann area 35, explicitly accounting for anatomical variability in the MTL. Aim 2 will correlate quantitative digital pathology measures derived at autopsy with antemortem MRI to discover distinct patterns of change that we hypothesize are associated with concomitant pathologies in AD, including TDP-43 pathology, alpha-synucleinopathy, non-AD tauopathies, and cerebrovascular disease. Aim 3 will apply deep learning to improve the sensitivity of measures of change in longitudinal MRI, hypothetically leading to a more sensitive early marker of treatment effectiveness in trials targeting preclinical AD than existing cognitive and imaging-based measures. Taken together, improved precision of segmentation (Aim 1), determination of spatial patterns of AD and concomitant non-AD pathology (Aim 2), and advanced longitudinal measurement methodology (Aim 3) will optimize MTL subregional sensitivity and specificity for the earliest neurodegenerative changes of AD, providing a potentially critical therapeutic efficacy measure to accelerate clinical trials of disease modifying treatments in early AD.

NIH Research Projects · FY 2026 · 2021-04

PROJECT SUMMARY Mid-substance Achilles tendinopathy is a painful, debilitating, and chronic tendon pathology. Rehabilitation exercises are the first treatment option for patients, but clinical studies have reported 20-60% of patients continue to experience pain and symptoms 5-years later. Even when patients experience symptom relief, only one-quarter of these patients fully recover muscle-tendon function. Current clinical guidelines recommend patients perform heel-rise exercises to eccentrically load the pathologic tendon and promote healing. However, Achilles tendon loading during daily-living often exceeds these structured rehabilitation loads, and the biomechanical properties of pathologic tendon varies amongst patients. Identifying patient subgroups based on similarities in tendon loading and biomechanics is a critical next step towards improving patient outcomes and tendon healing. Our long-term goal is to develop personalized rehabilitation protocols that maximize tendon recovery following acute and chronic Achilles tendon injuries. The overall objective of this study is to determine similarities in tendon loading and biomechanics in patients with mid-substance Achilles tendinopathy and how these similarities affect tendon healing, pain, and functional outcomes. This study leverages innovative techniques to 1) continuously monitor Achilles tendon loading during rehabilitation and daily-living and 2) quantify tendon status using ultrasound stress-imaging. Aim 1 will identify groups of patients with Achilles tendinopathy based on loading patterns and stress-imaging profiles. Aim 2 will determine if tendon healing and outcomes change over time. Aim 3 will explore the impact of sex on tendon healing and outcomes. This study will be the first to identify Achilles tendon loading profiles that are associated with tendon healing and outcomes based on patient-specific factors including tendon biomechanical properties and sex. By measuring circulating levels of sex hormones, this study will determine if specific levels of estrogen and progesterone – which can be modified using hormonal contraceptive pills – impact tendon health. Finally, with the recent shift towards telemedicine, this study will remotely monitor Achilles tendon loading, which has the potential to expand clinical care beyond patient visits to the clinic.

NIH Research Projects · FY 2025 · 2021-04

SUMMARY Revealing the key events that specify the first differentiated cell lineages during mammalian development is key to understand how the early embryo is organized to implant in the uterus and establish a pregnancy. The first mammalian cell lineages comprise the pluripotent inner cell mass (ICM) that will form the fetus, and the outer trophectoderm that will form the placenta. Yet, the mechanisms explaining how these lineages differentiate are unclear. In many non-mammalian embryos, asymmetrically inherited cell-fate determinants specify lineage fate, yet similar mechanisms are thought to be absent during early mammalian development. We have established live-imaging approaches to study cell and molecular dynamics during early mouse development. Recently, we identified a new role for intermediate filaments assembled by keratins in lineage specification. Our studies reveal that keratin filaments are asymmetrically inherited precisely during the cell divisions that physically segregate the future ICM and trophectoderm. Moreover, the inheritance of these filaments by the outer daughter cells helps to specify their trophectoderm identity and promote their maturation. Thus, our main hypothesis is that keratin filaments function as a new form of asymmetrically inherited factor specifying the first trophectoderm cells during development. To test this, we will reveal the mechanisms by which keratins become asymmetrically inherited (Aim 1) and can bias cell fate (Aim 2). We will first test how interactions with proteins present at the apical cell cortex, and the dynamics of the filaments inside the cell, control their asymmetric inheritance by outer cells during cell division. We will then determine how keratins can regulate key aspects of cell mechanics and polarity to control the distribution of the key transcription factors that specify trophectoderm fate. In summary, in this proposal we will address a fundamental open question about the specification of the first differentiated cell lineages during mammalian development, and unveil some of the first functions of keratin intermediated filaments during early mammalian development, which unlike those of other cytoskeletal elements like microtubules and actin, remain largely unknown.

NIH Research Projects · FY 2025 · 2021-04

PROJECT SUMMARY/ABSTRACT: The development of an effective HIV vaccine has proven to be a daunting challenge. Previous strategies for HIV vaccine design aimed to elicit protective T cell responses, non-neutralizing antibodies, broadly neutralizing antibodies (bnAbs), or some combination of the three. All three approaches have thus far failed to consistently protect nonhuman primates (NHPs) or humans from infection. This grant aims to elicit bnAbs by means of a novel strategy that combines – for the first time – germline-targeting, immunofocusing and molecularly guided affinity maturation. This study design evolves from a growing consensus that critical elements to a successful bnAb-based vaccine will be its ability to efficiently bind and activate rare naïve B cell germline precursors of bnAbs; to immunofocus these B cell responses to canonical, conserved bnAb epitopes on the HIV Env trimer and away from off-target strain specific or trimer base epitopes; and to mature or “polish” this bnAb lineage response by a process of molecularly guided Env-Ab coevolution. The study design proposed in this application addresses each of these three essential requirements as it aims to elicit bnAbs targeting the highly conserved HIV-1 V2-apex site. The principal investigators (Andrabi and Shaw) have assembled a talented collaborating research team with a strong track record of scientific discovery, bioengineering and molecular tool development, including the discovery of V2-apex bnAbs (Burton), development of germline targeted V2 apex immunogens (Andrabi), bioengineering of phosphoserine-linked alum nanoparticle antigen displays (Irvine), discovery of V2- apex immunofocusing chimpanzee simian immunodeficiency viruses (Hahn), creation of CRISPRCas9 knock-in mice (Batista), development of next-generation “designer” SHIVs (Shaw) and preclinical-clinical translation (Dey). The project consists of four aims: Aim #1 will isolate HIV envelope V2-apex targeted bnAbs from SHIV infected rhesus macaques, identify their UCA’s, and generate UCA-expressing knock-in mouse models for vaccine evaluation. Aim #2 will design novel V2-apex germline-targeted and immunofocused SOSIP Env trimer immunogens and by mammalian display saturation mutagenesis and structure-guided design present them as soluble proteins or alum-based nanoparticles for enhanced B cell responses. Aim #3 will optimize germline- targeting and B cell immunofocusing boost strategies in V2-apex bnAb UCA-expressing KI-mice and outbred RMs, and will identify in SOSIP Env primed and SHIV infected RMs, Env “immunotypes” that can drive neutralization breadth. Aim #4 will design and test, first in KI mice and then in a pivotal preclinical trial in RMs, an all-SOSIP Env vaccination regimen designed to prime, boost and affinity-mature bnAb responses in a majority of animals. If successful, this would be the first example of a vaccine regimen that consistently elicits bnAbs in an outbred animal model, and it would represent an important beachhead in HIV-1 vaccine science, one that could be transitioned rapidly by our translational partner into human testing.

NIH Research Projects · FY 2025 · 2021-03

Abstract: Poly (ADP-ribose) polymerase (PARP) inhibitor drugs (PARPi's) have emerged as important new therapeutic agents targeting a broadening class of gene mutations present in breast, ovarian, prostate and a host of other cancers. Identification of patients who might benefit from PARPi's has relied on assays for defects in homologous recombination (HRD), such as BRCA1/2 mutations, but these assays have been imperfect predictors of response to PARPi's. Drug binding to PARP1 present in tumor cells is a common and necessary factor for effective PARPi therapy. [18F]fluorthanatrace (FTT) is a PET-labeled analog of the PARPi rucaparib, and early clinical data in ovarian and breast cancer trials support [18F]FTT tumor uptake as an in-vivo measure of regional PARP1 drug binding, and indicate the potential of [18F]FTT PET as a PARPi predictive imaging biomarker. [18F]FTT could therefore provide benefits for patients with breast and other cancers by identifying those most likely to respond to PARPi therapy, while sparing those who will not respond from toxicity, unnecessary expense, and wasted time. To further the development, clinical translation, and commercialization of [18F]FTT, we propose an Academic Industrial Partnership (AIP) comprised of The University of Pennsylvania ((Penn), lead academic partner), MD Anderson Cancer Center(MDACC), and Washington University (WU) with Trevarx Biomedical, Inc (Trevarx). Trevarx, a radiopharmaceutical corporation with the exclusive license for [18F]FTT, is developing [18F]FTT as an imaging biomarker to guide PARPi treatment, with a first indication in breast cancer. Based on discussions with the FDA and advisors, [18F]FTT approval will require a Phase 3 study of the accuracy of [18F]FTT PET/CT for diagnosing PARP1 expressing cancer. The aims of this AIP proposal focus on critical components necessary for a Phase 3 trial for [18F]FTT FDA approval: (1) a Trevarx-held IND with standardized tracer production methodology and product specification; (2) validation of an immunohistochemistry (IHC) assay of PARP1 expression in formalin-fixed paraffin embedded (FFPE) tissue as a reference standard for [18F]FTT PET diagnostic accuracy; and (3) a Phase 2 multi-center trial to test and validate methods in a multi-center setting and provide preliminary data to design the pivotal Phase 3 trial. Completion of the these aims will enable a Phase 3 trial to support [18F]FTT FDA approval, commercial supply of [18F]FTT, and ongoing research by the academic partners to document the value of [18F]FTT PET/CT for guiding PARPi treatment, including prospective multi- center biomarker-focused studies.

NIH Research Projects · FY 2025 · 2021-03

Alzheimer's disease (AD) is the most prevalent neurodegenerative disorder. Interventions at the preclinical and prodromal stages are appealing targets for slowing or halting disease progression. It is desired to achieve accurate prognosis of AD dementia and cognitive decline for people with mild cognitive impairment who have increased risk to develop AD. In order to achieve fast and accurate prognosis of AD dementia based on neuroimaging data, we will develop and validate novel deep learning techniques. Particularly, we will develop unsupervised deep learning methods for segmenting brain images and reconstructing cortical surfaces from structural magnetic resonance imaging data. These fast and accurate image processing methods will be used in conjunction with advanced deep learning methods to build prognosis models of AD dementia and cognitive decline in a time-to-event analysis framework using large-scale imaging datasets. Finally, we will develop and disseminate a user friendly, open source, modular, and extensible software package to improve prognosis of AD dementia. Source code, standalone programs, and web-application interfaces of all the algorithms will be made available on GitHub and NITRC. Our tools will enable real-time neuroimaging data analysis and can find applications in diverse fields, including quantifying brain changes associated with aging and development.

NIH Research Projects · FY 2025 · 2021-03

Escherichia coli and related bacteria employ multi-step phosphorelays to sense intra- and extra-cellular environmental signals and to modulate diverse cellular processes. However, the significance of the multiple phosphoryl transfer steps that characterize these systems remains poorly understood. As part of our long- term goal to understand the interplay between the various signal transduction systems that bacteria employ to adapt to diverse environmental conditions, this proposal will explore several of these systems that are particularly tractable, due to well-established inputs and/or outputs, and that play critically important roles in E. coli physiology. The primary focus will be on two phosphorelays that are important for the transition to anaerobiosis, Arc and Tor, as well as a phosphohistidine phosphatase that modulates the nitrogen-related phosphotransferase system. Progress in understanding these networks will provide new insights into both the mechanisms enabling infections by pathogens and the maintenance of a healthy microbiota in host niches. The results may ultimately lead to the development of novel antibiotics or treatment regimens, as well as strategies for manipulating the microbiomes to maintain the health of the host.

NIH Research Projects · FY 2025 · 2021-03

Project Summary The healthy skeleton continuously renews itself throughout the lifespan via closely coupled bone resorption and remodeling-based bone formation. In contrast, modeling-based bone formation, i.e., de novo bone formation without prior activation of bone resorption, is less commonly found in the adult skeleton, but has been identified as an important mechanism by which anabolic agents for osteoporosis, e.g., intermittent parathyroid hormone (PTH) and PTH related peptide (PTHrP), and sclerostin antibody (Scl-Ab), rapidly elicit new bone formation. By developing a novel imaging platform that enables reliable identification of MBF and RBF and subsequent tissue-level mechanical testing in adult rat bone, we discovered that MBF responds faster than RBF to anabolic treatments. Moreover, bone tissue resulting from MBF has a greater resistance to anabolic treatment withdrawal-induced bone loss and increased heterogeneity of elastic modulus compared to pre-existing bone and bone tissue resulting from RBF. These exciting preliminary data provide a strong scientific premise to support our central hypothesis that MBF is a highly efficient regenerative mechanism that leads to sustainable therapeutic benefits on bone tissue quantity and quality, and whole bone strength. Furthermore, our data suggest that, upon early withdrawal from anabolic treatment, ongoing bone formation continues at MBF sites, forming an “anabolic window” that retains the treatment effect; In contrast, the majority of bone tissue formed at RBF sites were resorbed following treatment withdrawal. Therefore, we propose that a cyclic and sequential treatment regimen with alternating anabolic and anti-resorptive treatments will lead to increased mineral deposition and number of MBF, improved retention of bone tissue at RBF and quiescent bone surface, and improved tissue heterogeneity and whole bone strength. The overall objective of this study is to elucidate the cellular mechanisms (Aim 1a) and mechanical consequences (Aim 2a) of MBF and RBF, and to evaluate the new treatment regimen which leverages MBF to improve and extend treatment efficacy (Aim 2a and 2b) using a rat model. By combining our innovative imaging and image analyses with tissue-level mechanical testing approaches, this proposed research project will fill the critical knowledge gap of long-term mechanical consequences of bone tissue formed through MBF and RBF, and provide important insight for the clinical design and optimization of treatment strategies that modulate MBF, a highly efficient but often overlooked regenerative mechanism.

NIH Research Projects · FY 2025 · 2021-03

Despite recent advances in neuroimaging, approximately 2/3 of intractable epilepsy patients that undergo surgical evaluation continue to require intracranial EEG (IEEG), arguably the most invasive diagnostic test in medicine. We currently lack methods to quantitatively map noninvasive imaging measures of structure and function to IEEG. Specifically, there is a critical need to validate whole-brain noninvasive neuroimaging network- based biomarkers to guide precise placement of electrodes and translate noninvasive network neuroimaging to change the paradigms of clinical care. The long-term goal of this proposal is to predict IEEG functional dynamics and surgical outcomes using noninvasive MRI-based measures of structure and function. Our overall objective, which is the next step toward attaining our long-term goal, is to develop open-source noninvasive imaging tools that map epileptic networks by integrating MRI and IEEG data. Our central hypothesis is that noninvasive measures of structure and function relate to and can predict the intricate functional dynamics captured on IEEG. The central hypothesis will be tested in patients undergoing IEEG targeting the temporal lobe network by pursuing three specific aims: 1) To map the patient specific structural connectome to IEEG seizure onset and propagation, 2) To correlate seizure onset and propagation on IEEG with network measures derived from resting state functional MRI (rsfMRI), and 3) To integrate the structural (Aim 1) and functional (Aim 2) connectome with standard qualitative clinical data to predict IEEG network dynamics and surgical outcomes. Under the first aim patients will undergo diffusion tensor imaging (DTI) prior to stereotactic IEEG, an IEEG method that inherently samples long range networks. The functional IEEG network will be mapped to DTI thus defining how seizures are constrained by the underlying structural connectome as they propagate. Under the second aim patients with temporal lobe epilepsy will undergo rsfMRI on 7T MRI prior to stereotactic IEEG. Functional network measures from rsfMRI and IEEG will be coregistered and rsfMRI will be used to predict functional EEG ictal and interictal networks. In the third aim two models predicting IEEG network dynamics and epilepsy surgical outcomes will be created building off of methods developed in Aims 1 and 2. The proposed research is innovative because it represents a substantive departure from the status quo by directly connecting noninvasive multimodal imaging with measures of functional network dynamics in IEEG. The proposed research is significant because it is expected that successful completion of these aims will yield personalized strategies for IEEG targeting based on noninvasive neuroimaging.

NIH Research Projects · FY 2026 · 2021-02

Alzheimer's disease (AD) is the 6th leading cause of death in the USA and there are no effective treatments. Moreover, the prevalence of this age-related neurodegenerative disease is likely to increase as the US population ages. Therefore, there is a great need to understand AD and develop therapeutics. ApoE is an appealing target because this lipid transporter is one of the strongest genetic risk factors for AD. ApoE3 is the most common isoform and is considered neutral. Carriers of ApoE4 are up to 15-fold more likely to develop AD, while ApoE2 appears to be protective against AD. Subsequent experiments have confirmed that ApoE4 plays a causal role in AD. However, the mechanism coupling ApoE and AD remains unclear. Strikingly, ApoE4 and ApoE2 each differ from ApoE3 by a single substitution (C112R in ApoE4 and R158C in ApoE2). Neither substitution occurs in a functional site, suggesting they indirectly impact function by altering the protein's conformational preferences. However, characterizing these structural differences remains challenging. Partial crystal structures of the different isoforms are essentially identical and the rest of the protein has largely defied structural characterization because ApoE's role in lipid transport requires it to be partially disordered and prone to oligomerization. This proposal aims to uncover the structural determinants of ApoE-induced neurotoxicity by building and analyzing atomically-detailed Markov state models (MSMs) of neurotoxic and non-toxic variants. The primary focus will be on monomeric, lipid-free ApoE as it is the relevant species for many functional processes, lipid-free ApoE is believed to be the neurotoxic species, and the fluctuations of the monomer are expected to reveal structures whose populations are enhanced/suppressed by binding partners. In Aim 1, new adaptive sampling algorithms will be developed to address the extreme conformational heterogeneity of disordered regions. Then these algorithms will be applied to understand the gross structural properties of representative ApoE variants, such as the extent of domain opening. Computational predictions will be tested with single molecule Förster resonance energy transfer (smFRET) experiments performed with our collaborators. In Aim 2, the allosteric mechanism that couples distant regions of ApoE will be dissected, employing tools once again designed to account for disorder. Resulting insight into the structural differences between neurotoxic and non-toxic isoforms will provide a foundation for the design of new variants to test our models. We will also design `structure correctors' that stabilize non-toxic conformations, providing leads for the future design of drugs that combat AD.

NIH Research Projects · FY 2025 · 2021-02

Abstract A remarkable feature of the nervous system is its ability to adjust stereotyped behavioral responses in a context dependent manner. In vertebrates, sudden and intense acoustic stimuli evoke an evolutionarily conserved startle response. While the execution of the acoustic startle response is extremely stereotyped, response probability is modulated in a context-dependent manner. For example, repeated presentation of a startling stimulus suppresses a behavioral response, representing a simple form of learning known as habituation. In humans, modulation of startle behavior is impaired in several neuropsychiatric disorders, including in Attention Deficit- Hyperactivity Disorder and autism spectrum disorders. Despite its importance, the molecular mechanisms underlying startle modulation not well understood. Zebrafish show a remarkable behavioral plasticity, and we have previously shown that larvae exhibit modulation of the acoustic startle response- including prepulse inhibition and habituation- with behavioral and pharmacological characteristics similar to those in mammals. We previously conducted the first forward genetic screen in vertebrates to isolate mutants defective in startle modulation, and identified 14 mutants with defects in habituation behavior. None of these 14 mutants exhibit morphological defects or overt defects in startle performance. Importantly, five of the six mutants we cloned so far encode genes previously not implicated in vertebrate habituation. Here we propose to build on our success in using a molecular genetics, phenotype based strategy to decipher the molecular and circuits mechanisms that drive vertebrate habituation behavior. Specifically, rather than focusing on a single habituation gene, our strategy is to continue to use whole genome sequencing to clone six additional mutants from our screen. Combined with the six mutants we have already cloned, this provides an unparalleled toolbox critical to attain a comprehensive model of the molecular-genetic and circuit mechanisms underlying habituation. Simultaneously, we focus on select genes as entry points to further link genetic mutants to behavioral phenotypes and to decipher the molecular and circuit mechanisms that regulate behavior. The experiments in this proposal will: (1) use a molecular genetic approach including transgenic behavioral rescue to identify the neuronal populations in which three genes critical for habituation function; (2) to use molecular and pharmacogenetic approaches in conjunction with a behavioral assay to determine the signaling pathways through which the adaptor protein-2 sigma subunit (AP2s1) critical for receptor endocytosis and the huntingtin interacting gene hip14 promote habituation; and 3) to use an established whole genome sequencing/bioinformatics pipeline to identify the causative gene mutations for six additional habituation mutants isolated from our genetic screen, generate CRISPR/Cas9 alleles to confirm their identity and determine their expression in the brain. Combined this will provide both breadth and depth both at the molecular and at the circuit level critical to comprehensively address fundamental molecular genetic questions in vertebrate startle modulation, also relevant to human disease conditions.

NIH Research Projects · FY 2025 · 2021-02

Project Summary Hospitalized patients receiving antibiotic treatment experience a disruption in the intestinal microbiome enabling opportunistic pathogens, such as Clostridioides difficile to colonize the intestinal tract. Complications resulting from C. difficile associated disease are a major burden on the health care system costing an estimated one billion dollars and resulting in 12,000-20,000 deaths per year (11, 13). Current antibiotic treatment options have a high recurrence rate highlighting the need to develop alternative treatment strategies. Fecal microbiome transplantation (FMT) has proven to be a remarkable effective strategy for treatment of recurrent C. difficile infection (21). However, the host and microbial factors that contribute to FMT success remain poorly defined. The murine model of C. difficile infection offers insights into the mechanism of action of FMT. Data presented in this proposal demonstrates an important role for the host’s immune system, specifically CD4+ T-regulatory (TReg) cells, in supporting FMT efficacy. In aim 1 of this proposal we will investigate the immunoregulatory mechanisms through which TReg cells shape the intestinal environment to promote FMT engraftment and C. difficile resolution. Conversely, aim 2, will assess the innate immune inflammatory mediators that shape the intestinal environment to inhibit FMT engraftment and C. difficile resolution. In parallel to murine studies, we will conduct longitudinal profiling of human immune cell populations in severe C. difficile infected patients before and after FMT. These aims will identify immune mechanisms that support successful FMT therapy in C. difficile infection and potentially identify novel therapeutic targets in treating C. difficile associated disease. 1

NIH Research Projects · FY 2025 · 2021-02

PROJECT SUMMARY As polypharmacy becomes increasingly common in patients with kidney disease, drug-drug interactions (DDIs), the phenomenon of one drug altering the effect of another drug, grow as potential sources of preventable harm in this vulnerable population. The clinical impacts of DDIs are poorly understood, particularly in the hospital setting, where up to half of patients have acute or chronic kidney disease. Further, the potential for bidirectional relationships between kidney disease and DDIs—with kidney disease functioning as both an outcome of DDIs and a baseline factor that alters DDI severity—complicates epidemiologic study and necessitates novel methodologic approaches. This proposal aims to improve the safety of pharmacotherapy in patients with kidney disease through the following broad objectives: 1) examine whether commonly used antibiotics in the hospital setting interact to increase the risk of acute kidney injury (AKI) and subsequent chronic kidney disease (CKD); 2) examine whether changes in kidney function in turn produce variability in DDI severity; 3) train the applicant in renal pharmacoepidemiology, prospective research design and analysis, and pharmacokinetic simulation methods, which will enable a novel translational approach to DDI research; and 4) provide the preliminary data and mechanistic insights for future R01 funded studies that quantify the health impacts of DDIs in the kidney disease population and develop preventive interventions. The applicant will integrate the results from large scale pharmacoepidemiologic studies, prospective cohort studies, and simulation models to achieve the stated objectives. The applicant will first determine the impact of a potential DDI between two common antibiotics on inpatient AKI risk and subsequent CKD using a large-scale health system database and prospective cohort study (Aim 1). The applicant will then examine the effect of kidney disease on the magnitude of a DDI mediated by hepatic CYP450 inhibition using two distinct, yet complementary approaches: developing a pharmacokinetic simulation model of the interaction, followed by a retrospective cohort study of the same interaction (Aim 2). Integration of methods will provide insights into the effects of kidney disease on CYP inhibition that wouldn't be possible with either method in isolation. This proposal will train the candidate in renal pharmacoepidemiology, advanced statistical modeling, and pharmacokinetic simulation, and have important implications for drug safety in the 35 million hospital admissions each year. This research will generate new knowledge extending beyond the specific drugs under study and foster the candidate's progression towards becoming an independent investigator in renal pharmacoepidemiology.

NIH Research Projects · FY 2025 · 2021-02

Project Summary The ability to navigate from one place to another is essential for a flourishing and autonomous human life. Cognitive scientists have long believed that navigation in humans and animals is guided by mental representations of the spatial structure of the world, which are referred to as “cognitive maps” because they play a functional role that is similar to physical maps. Consistent with this idea, electrophysiologists have identified neurons in rodent brains that fire as a function of spatial variables that are essential elements of a cognitive map, such as location, distance, and heading direction, while cognitive neuroscientists have investigated possible neural correlates of cognitive maps in several regions of the human brain, including the hippocampal formation (HF) and the retrosplenial complex (RSC). Notably, these brain regions are also known to be essential for several important cognitive functions besides spatial navigation, including memory, imagination, and thinking about the future. However, despite this previous work, there remain two crucial gaps in our knowledge. First, we have an incomplete understanding of how cognitive maps are represented in the human brain. Behavioral studies indicate that our spatial knowledge is often fragmented, hierarchically organized, and distorted in multiple ways compared to metric truth, and we do not yet understand how these “real” cognitive maps are represented in brain structures such as HF and RSC. Most notably, we do not understand how the brain divides environments into spatial parts (such as rooms within a building, or neighborhoods in a city), and how it then combines these parts into a larger whole. Second, we do not yet have a good theory of how spatial cognitive maps can be applied to non-spatial domains, thus allowing brain structures such as HF and RSC to mediate both spatial and nonspatial functions. The current project will address these issues by using advanced neuroimaging techniques, such as multivoxel pattern analysis and individual difference analyses to: (i) identify the neural mechanisms that allow the brain to encode subspaces within a larger space; (ii) delineate the neural processes by which subspaces representations are combined into a larger cognitive map, and (iii) understand how the principles underlying spatial cognitive maps can be applied to nonspatial domains. This project has the potential to make a major and sustained advance in the field by resolving longstanding questions about the cognitive and neural systems underlying spatial navigation, and by providing fundamental knowledge about how the brain mediates a wide range of basic cognitive functions, including not just navigation, but also semantic and episodic memory, prospective thinking, and reasoning.

NIH Research Projects · FY 2025 · 2021-02

Abstract Low back pain is the leading cause of disability in the United States, with an estimated socioeconomic cost exceeding $100 billion each year. Intervertebral disc degeneration, a cascade of cellular, compositional, structural and compositional changes, is strongly implicated as a cause of low back pain. Current clinical approaches for treating low back pain associated with disc degeneration have limited long term efficacy as they seek only to manage symptoms without restoring native disc structure and mechanical function. There is an overwhelming clinical need for new treatment options, which target not only the symptoms of low back pain, but also the underlying causes. Mesenchymal stem cells (MSCs) are an attractive option for cell- based disc regeneration due to their safety, ease of isolation and ability to adopt phenotypes similar to those of disc nucleus pulposus cells. A major challenge to successful MSC-based disc regeneration, however, is the local cellular microenvironment, which presents conditions of limited nutrition, low oxygen, low pH, and persistent inflammation that predispose therapeutic interventions to failure. The objective of this proposal is to develop a novel biological therapy that maximizes the survival and anabolic potential of therapeutic stem cells by simultaneously neutralizing the degenerate disc microenvironment via the sustained delivery of nutrients, anti-inflammatory drugs and buffering agents. To accomplish this goal, we will leverage our newly established goat model of disc degeneration that mimics clinically relevant structural, composition and biomechanical characteristics, including tissue-level inflammation, and novel drug delivery methods to enable controlled and sustained release of biofactors that neutralize the degenerative microenvironment. In Aim 1 we will leverage our goat model define the in vivo cellular microenvironment of the disc as a function of degeneration severity, using cutting edge in situ physiological monitoring and ex vivo biomolecular assays. In Aim 2 we will optimize our novel microcapsule drug delivery system to neutralize the degenerate disc microenvironment through sustained delivery of glucose, anti- inflammatory drugs and buffering agents. In Aim 3 we will carry out short and long term in vivo studies to establish therapeutic efficacy in our goat model, including clinically-relevant pain assessments. At the conclusion of these studies we will have developed a rapidly translatable therapy that maximizes the regenerative potential of MSCs in the disc microenvironment, and established long term preclinical efficacy, thus placing us in a strong position to move towards human clinical trials.

NIH Research Projects · FY 2025 · 2021-01

Alzheimer's Disease (AD) affects over 5 million Americans posing a significant burden to the community and health care system, Machine learning (ML) methods have been crucial in detecting the disease and characterizing its progression, Due to the lack of an in vivo "ground truth" diagnosis, ML approaches have typically relied on clinically derived labels and a casecontrol design in their search for a single imaging pattern that optimally distinguishes between the two groups in the case-control design, However, heterogeneity within clinical labels may degrade performance and interpretability, The goal of this project is to address this limitation and accurately characterize heterogeneity in preclinical and symptomatic AD, Given that age is a major risk factor for developing dementia, we will characterize healthy aging using multimodal neuroimaging data and ML in Aim 1, To this end, we propose to develop a novel unsupervised multi-view machine learning tool that can integrate information from multiple imaging modalities (Le,, structural Magnetic Resonance Imaging, and amyloid and tau sensitive Positron Emission Tomography) in a principled way, This will enable us to define the normal trajectory of agerelated changes across all modalities, providing the necessary context to understand AD pathology, We will characterize AD pathology using multimodal neuroimaging data and ML in Aim 2, To this end, we propose to develop a novel semi-supervised ML framework that integrates multimodal information and derives data-driven disease dimensions, This is achieved by identifying and quantifying at the individual level imaging patterns that capture neuroanatomical and neuropathological alterations, Our approach builds on our extensive prior work on using an advanced, unsupervised multivariate pattern analysis technique, termed orthonormal projective non-negative matrix factorization, for analyzing neuroimaging data, Importantly, our project leverages two large multimodal datasets, the Knight AD Research Center (ADRC) cohort and AD Neuroimaging Initiative (ADNI), which sample participants across the continuum of AD making them ideal for investigating heterogeneity of AD pathology using advanced ML techniques, If successful, our approaches could be used for studying any brain disorder and could be readily integrated into personalized medicine strategies in the future when rich, multimodal imaging data collection will become a routine diagnostic procedure in hospitals,

NIH Research Projects · FY 2025 · 2021-01

PROJECT SUMMARY Over 1.1 million patients admitted annually to skilled nursing facilities (SNFs) for post-acute care after a hospitalization have Alzheimer’s Disease or Related Dementias (ADRD), and their outcomes are poor and variable. Given the high clinical complexity and care coordination needs of patients with ADRD, one potential solution to improving the outcomes of patients with ADRD receiving SNF care is through physicians who specialize in SNF-based care. “SNFists” (i.e., physicians for whom SNF patients comprise the majority of their practice) are becoming increasingly common. Our prior work found a 37% increase in the prevalence of SNFists from 2012 to 2015, with a high degree of variability across markets. In this study, we will examine whether physicians specializing in SNF-based care improve functional outcomes and reduce potentially avoidable healthcare utilization (such as hospital readmissions) of patients with ADRD receiving post-acute care in SNFs. To accomplish these goals, we will expand an existing dataset of Medicare claims and SNF clinical assessment data for Medicare fee-for-service beneficiaries discharged from an acute care hospital to a SNF from 2012 through 2019. Using this database, we will examine the trends in physician specialization in SNF care in the context of market, facility, and physician characteristics. Next, we will measure the impact of physician specialization in SNF care on the outcomes and healthcare utilization of patients with ADRD using difference-in-differences cross-temporal matching. Lastly, we will conduct semi-structured interviews with key SNF personnel (e.g., director of nursing, medical director) to quantitatively identify practice strategies and care processes that differ between physicians in high- vs. low-performing SNFs based on the outcomes of patients with ADRD. When complete, these studies will inform practice and policy to optimize (increase or reduce) post- acute care patients’ access to physicians who specialize in SNF-based care. The findings will be used to develop interventions to improve the value of SNF-based post-acute care for patients with ADRD.

NIH Research Projects · FY 2025 · 2021-01

Project Summary/Abstract Respiratory failure commonly occurs in amyotrophic lateral sclerosis (ALS) and leads to significant morbidity and mortality. The onset of respiratory weakness heralds an increased risk of aspiration related to bulbar muscle weakness and ineffective cough, hypercapnic respiratory failure due to chronic hypoventilation, and pulmonary infections, ultimately leading to death. Despite the key role of respiratory failure in the morbidity and mortality associated with ALS, there remains uncertainty concerning optimum initiation and maintenance of respiratory care for this disease. ALS has a very heterogeneous clinical presentation and symptom progression, which causes variable evolution of respiratory involvement. Given the significance of respiratory morbidity with this disease combined with the unclear timing, identifying high-risk subgroups may facilitate studying outcomes of early respiratory interventions. Our group has published a clinical prediction tool which can predict a high risk of respiratory failure within six months in ALS. We have also published a latent class analysis to identify subphenotypes of ALS patients by their differing trajectories of forced vital capacity over time. Applying our clinical prediction tool and knowledge of phenotypes to a sample of ALS patients would identify a subgroup suitable for future clinical trials. However, given the emotional burden of ALS, patient perspectives on respiratory interventions are critical to successful implementation. To our knowledge, a prospective investigation on a cohort of ALS patients at high risk of respiratory failure has yet to be performed. The goals of this study are to use our clinical prediction tool to identify the prevalence of newly-diagnosed ALS patients at high risk of respiratory failure, to elucidate patient perspectives on early respiratory care, and to implement a pilot trial of lung volume recruitment in high-risk patients. This proposal will involve a multicenter study at three academic centers in Philadelphia. We will perform a prospective cohort study of patients with ALS, apply our clinical prediction tool, and monitor them for respiratory failure over one year. We will use semi- structured interviews to gather patient perspectives regarding circumstances under which they would accept early respiratory care in ALS. Third, we will perform a single-arm pilot intervention of lung volume recruitment in newly-diagnosed ALS patients at high risk of respiratory failure within six months. This project will provide essential preliminary data for a Research Project Grant application that will (1) conduct a randomized controlled trial of early respiratory therapy in high-risk ALS patients (2) elucidate physician and caregiver perspectives regarding respiratory care in ALS, and (3) identify which characteristics are associated with different trajectories of respiratory function, thus allowing for personalized medicine.

NIH Research Projects · FY 2025 · 2021-01

Project Summary / Abstract This is an application for a K24 mentoring award for patient-oriented research (POR) from Julio Chirinos, MD, PhD, Associate Professor of Medicine at the Perelman School of Medicine at the University of Pennsylvania (Penn). Dr. Chirinos‘ long-term goals are to: (1) Substantially contribute to our understanding and approaches to the prevention and treatment of aortic aging and its associated disease burden, and; (2) to mentor the next generation of investigators interested in the epidemiology of aortic aging and its consequences in human health. This mid-career development award will be critical to help him achieve these goals via dedicated/protected time for mentoring activities, research and development of new skills that are anticipated to greatly enhance the applicant’s impact in this field throughout the rest of his career, as well as the impact and success of his trainees. The candidate has a strong record of mentorship, leadership, and research productivity. His research program encompasses epidemiologic, translational and POR studies of arterial aging and its role in Heart Failure with Preserved Ejection Fraction (HFpEF) and other conditions that afflict our aging population. The scientific goal of this proposal is to investigate the genetic determinants of age-related thoracic aortic stiffening and elongation using large available biobanks with associated genomic and aortic imaging data. These include the UK Biobank and the Penn Medicine Biobank. The projects will include the application of a novel method for quantification of aortic pulse wave velocity that can, for the first time, be applied retrospectively in widely available clinical imaging studies. Deep learning for high-throughput aortic phenotyping will play an important role in this research. The mentoring goals of this application are to engage and support the training of Penn fellows and junior faculty to conduct POR in arterial aging. The career development goal of this application is to support the candidate’s professional development and acquisition of new skills for POR research in aging, specifically: (1) genomics (genome-wide association studies, next generation sequencing, and Mendelian Randomization); (2) Applied deep learning to leverage large banks of imaging data in order to accomplish accurate high-throughput phenotyping of aortic aging. This will be achieved through formal training courses and engaging in sustained collaboration experiences with experts in these topics. The candidate will also engage in career development and promotion of arterial aging research through convening scientific meetings on aortic aging research and improving the national network of POR research in arterial aging through existing professional societies. The institutional environment for clinical and translational science at Penn is outstanding. 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 research in older participants.