University Of Pennsylvania

NIH Research Projects · FY 2025 · 2024-09

Project Summary Studying tumors in a spatial context will advance our understanding of intratumoral heterogeneity and how the complex interactions between cancer and surrounding non-cancer cells results in the growth of malignant subclones, which promises to address outstanding questions in cancer biology and improve the diagnosis and treatment of specific cancer subtypes. In both basic and translational cancer studies, the majority of biopsies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples, and a growing number of FFPE specimens are newly archived every year. Accordingly, spatial omics profiling in archived FFPE tissue can be invaluable for cancer research and potential novel biomarker or molecular regulators discovery. In this project, we propose to develop a first-of-its-kind technology for spatially resolved co-mapping of epigenome, transcriptome, and proteins in FFPE tissues at the cell level. Specifically, we will (Aim 1) develop spatial epigenome sequencing to measure not only gene expression but also epigenetic underpinning of cell type and state directly in FFPE tissues, (Aim 2) develop a novel deterministic barcoding strategy for joint profiling of accessible chromatin or histone modifications, mRNAs, and proteins in the same FFPE tissue section. This novel technology addresses the lack of capability for spatial multi-omics that can be integrated, scaled, and applied to FFPE tissue mapping. As FFPE samples are widely available and represent the most abundant format of archivable clinical tumor tissue samples, we envision that this work will open up new opportunities to revisit the huge resource of clinical tissue banks to study the mechanisms of pathophysiology and to discover new targets for diagnosis and treatment of human diseases.

NIH Research Projects · FY 2025 · 2024-09

ABSTRACT / SUMMARY While the number of lung transplantations performed worldwide is steadily growing every year, the number of viable donor lungs remains frustratingly small compared to the increasing demand. Indeed, the vast majority of potential donor lungs continue to be labeled as `marginal'—i.e., untransplantable—as a result of failing to meet current clinical organ procurement criteria: harvested from a donor 55 years old or younger, clear on x-ray, and adequately oxygenated under ventilation. However, because the measurements are based on an incomplete assessment of donor lung tissue status, they may also be unnecessarily restrictive. Developed as a technique for prolonging organ preservation prior to transplant while simultaneously offering a platform for evaluating and potentially reconditioning `marginal' donor lungs, ex vivo lung perfusion (EVLP) was first introduced in 2001 and has been employed clinically in hundreds of lung transplants since. To take full advantage of EVLP as a tool for expanding the pool of transplantable donor lungs, however, the development of non-invasive biomarkers capable of generating a more comprehensive assessment of donor lung health is needed in order to optimize the utilization of `marginal' donor organs. We propose to address this need by developing an imaging-compatible pre-clinical EVLP system capable of obtaining structural, functional and metabolic biomarkers in the donor lung, that can be used to optimize EVLP parameters in a rat lung transplant model. We will then utilize these biomarkers to non-invasively assess donor lungs with three commonly occurring defects in donor lungs that have been shown to lead to poor post-transplant outcomes: atelectasis, ventilator-induced lung injury (VILI), and reperfusion injury resulting from extended cold ischemia. Injury-specific treatment strategies will be applied during EVLP in order to recondition lungs prior to transplant, and surgical outcomes will be correlated post-transplant with imaging biomarkers obtained during EVLP. Finally, we will assess the full suite of developed markers to determine which justify translation, and will modify a clinical EVLP system to demonstrate that the same biomarkers can be obtained in human lungs rejected for transplant. Moving forward, the precise, quantitative, structural, functional, and metabolic information on donor lungs that this platform provides can be used to non-invasively assess the protective effects of established interventions aimed at rendering marginal lungs suitable for transplant—potentially unlocking EVLP's ability to meaningfully increase the donor pool.

NIH Research Projects · FY 2025 · 2024-09

Interstitial lung disease (ILD) is a highly morbid and potentially fatal complication of myositis. Current myositis phenotypes do not capture significant heterogeneity in ILD clinical behavior. Existing prediction models and biomarkers perform poorly in patients with myositis-ILD and require longitudinal validation in diverse patient populations. Because clinicians lack tools to prognosticate long-term myositis-ILD outcomes, many patients receive either inadequate or overly aggressive treatment. We have shown that the GAP-ILD Index performs poorly in myositis- ILD. Myositis-ILD specific prediction tools do not adequately model disease progression and do not generalize to populations outside of Asia. Previously, we demonstrated that specific human leukocyte antigen (HLA) alleles are myositis-ILD susceptibility factors. Our preliminary model of progression-free survival containing clinical data and HLA genotypes discriminated progression, suggesting that HLA haplotypes are also biomarkers of myositis-ILD disease activity and treatment responsiveness. As a next step, we plan to refine and validate our preliminary model. The goal of Specific Aim 1 is to utilize a large, diverse multicenter cohort of patients with myositis- ILD in North America to develop a prediction model of progression free survival using known and novel biomarkers. While increasingly recognized, there is no current strategy to confront the clinical and biological heterogeneity within myositis-ILD subgroups. Our preliminary data demonstrates two clusters of myositis-ILD. We hypothesize that these myositis-ILD clusters carry distinct pathobiology, treatment responsiveness, and outcomes. The goal of specific Aim 2 is to apply cluster analysis to clinical, genomic, and serological data from patients with myositis-ILD to identify novel subphenotypes. The data generated from this proposal will result in a novel classification of myositis-ILD subphenotypes and a superior tool for prognosticating important clinical outcomes. Our approach is feasible because we are building on existing clinical and biorepository data from five demographically diverse myositis-ILD referral centers in the United States. This contribution is significant because it will establish a validated clinical signature for precision therapy in patients with myositis-ILD and generate novel treatment approaches.

NIH Research Projects · FY 2025 · 2024-09

PROJECT SUMMARY The cohesin complex mediates the hierarchical organization of the genome into chromatin loops and topologically associating domains (TADs) through a proposed model of loop extrusion. Indeed, cohesin plays an important role in human health, since mutations in cohesin cause a developmental disorder known as Cornelia de Lange Syndrome (CdLS). However, mechanistically, it remains unclear how cohesin dysfunction contributes to the pathogenesis of CdLS. Interestingly, ~30% of CdLS patients do not harbor mutations in known cohesin components highlighting the gap in our understanding of cohesin regulation. Therefore, we reason that unknown factors are contributing to cohesin function, and that uncovering these factors may reveal mechanistic links between cohesin dysfunction and disease. To this end, we completed screening genome-wide for genes that can modulate chromatin interactions across TADs. We found that SMARCE1, which is a DNA-binding subunit of the ATP-dependent human chromatin remodeling complex SWI/SNF, promotes inter-TAD interactions, which cohesin also facilitates. We next determined that SMARCE1 genetically interacts with cohesin, suggesting SMARCE1 regulates cohesin-mediated chromatin looping. Strikingly, mutations in SWI/SNF cause Coffin-Siris Syndrome (CSS), a developmental disorder that shares overwhelming phenotypic overlap with CdLS. The goal of this proposal is to determine how SMARCE1 regulates cohesin and chromatin looping across the genome, and the extent to which a cohesin dysfunction may underlie a shared signature of gene misexpression in CdLS and CSS through two related, but independent aims. I will first determine the SWI/SNF dependency of SMARCE1 in promoting cohesin-mediated loop extrusion. Next, I will interrogate the consequences of SWI/SNF and SMARCE1 loss on global cohesin localization and chromatin organization. In parallel, I will intersect the changes in chromatin folding following SMARCE1 depletion with changes in SWI/SNF and cohesin localization. Taking advantage of publicly available genomic datasets, I will also intersect any detected differential looping or cohesin localization in the context of different chromatin states. Furthermore, the novel role of a CSS-associated gene in chromatin folding suggests that CdLS and CSS may converge on cohesin dysfunction. In addition to the overlapping clinical presentations of CdLS and CSS, I will define the extent to which CdLS and CSS share signatures of cohesin dysfunction in patient-derived cell lines. I will investigate whether chromatin is misfolded in CSS as in CdLS and how this chromatin misfolding correlates with comparative transcriptomics between CSS and CdLS. As is the case in CdLS, I will determine if any marker of cohesin dysfunction correlates with CSS disease severity. Completion of this proposal will define the role of SMARCE1 in regulating cohesin-mediated chromatin folding and highlight a potential shared molecular etiology at the intersection of CdLS and CSS providing the foundational knowledge upon which to further explore common therapeutic interventions in more complex in vivo models.

NIH Research Projects · FY 2025 · 2024-09

Project Summary Stillbirths and neonatal deaths are two adverse birth outcomes of critical global health relevance. In 2021, an estimated 1.9 million babies were stillborn, and 2.3 million liveborn babies died before reaching 28 days of age. Sub-Saharan Africa (SSA) stands out globally as the world region having the largest number of stillbirths and neonatal deaths (respectively 847,000 and 1,067,000 in 2021). These large numbers not only reflect large population sizes, but also high levels of stillbirth and neonatal mortality in the SSA region. Moreover, not only are neonatal mortality rates high in countries of the SSA region relative to other world regions, but in many SSA countries, they are high relative to the country’s own levels of postneonatal mortality. This indicates the existence in many SSA populations of a distorted age pattern of mortality at early ages with excess mortality at neonatal ages, impeding their ability to meet Sustainable Development Goals targets. In spite of the significance of these patterns, measurement and understanding of stillbirth rates and neonatal mortality in SSA countries are hindered by major gaps in data availability and quality. Undercount of stillbirths and neonatal deaths as well as misclassification of neonatal deaths vs. stillbirths in existing, mostly retrospective sources remain major concerns. Issues with availability and quality of information on preterm, low birthweight and small for gestational age – three major risk factors that can play a large role in both levels and age patterns of early-age mortality – are additional gaps that further impede proper monitoring of patterns of mortality during the late fetal and neonatal periods in the SSA region. The goal of this project is to improve our understanding of why many SSA populations stand out globally in terms of both their levels and age patterns of mortality during the late fetal and neonatal periods by collecting new prospective data in three surveillance sites located in three different SSA countries (Ethiopia, Gambia and Guinea-Bissau), covering a variety of contexts. While the focus of this project is on three SSA populations located in Ethiopia, Gambia and Guinea- Bissau, results will have methodological and substantive implications for other low-income countries, including other SSA countries, which are characterized by a high burden of stillbirths and neonatal mortality as well as large data gaps in their stillbirth and neonatal mortality information.

NIH Research Projects · FY 2025 · 2024-09

PROJECT SUMMARY/ABSTRACT Decades of treatment studies demonstrate that youth with significant behavioral health needs make more progress when their treatment planning is informed by ongoing quantitative data collection (e.g., by changing treatment strategies, increasing therapy hours, and adding services), however, aides often do not collect high quality data consistent with evidence-based practice. Measurement feedback systems (MFS), originally developed to support data collection and inform treatment decisions in outpatient therapy as part of measurement based care, may be an ideal starting point from which to improve aides' data collection; however, MFS have not been applied and tested in this setting. Our application, Footsteps, comprises a low-cost MFS and implementation strategy to support electronic data collection and target implementation mechanisms – aides' intentions, attitudes, norms, and self-efficacy – associated with data collection to optimize clinical care. Footsteps was developed in partnership with community behavioral health agencies, guided by behavioral economics principles, user-centered design, and a conceptual model that integrates the science of behavior change with organizational theory. Footsteps integrates digital data collection in a customizable, server-based, native app with tools for supervisors to review data and provide feedback, and behavioral-economics informed features, such as gamification, leaderboards, employee of the week emails, targeted reminders, celebratory/encouraging messages, and in-app data collection tutorials, to increase motivation to collect data. As part of our Penn ALACRITY Center (P50 MH127511), we conducted a pilot RCT in which we compared Footsteps with a data- collection-only app in a pilot trial. We found that Footsteps was acceptable to aides and feasible to use, and that it engaged our target mechanisms of attitudes, norms, self-efficacy, and motivation. We now are ready to test the app in a fully powered trial. Our formative work also raised three key questions: a) which behavioral strategies are most effective for increasing data collection; b) does Footsteps alter supervision processes; and c) does Footsteps ultimately improve youth outcomes? We propose a randomized, hybrid type 2 effectiveness- implementation pragmatic mixed-methods trial in which we enroll 150 aides and 30 supervisors. Specifically, we propose to: (Aim 1) examine whether Footsteps improves data collection quality and youth outcomes in an RCT on Footsteps vs. a “data collection only” application; (Aim 2) explore mediators of data collection quality, specifically changes in aides' intentions, norms, attitudes, and self-efficacy regarding data collection via biweekly surveys and interviews; (Aim 3) examine the impact of Footsteps on supervisory processes, team communication, and changes to child treatment plans via interviews and biweekly surveys with 30 supervisors and a subsample of 30 aides. The proposed study would be one of the first studies to examine the effect of theory-informed behavior change mechanisms on data collection in behavioral health care and will advance the science of digital health as a support to practitioners in implementing behavioral health programs.

NIH Research Projects · FY 2025 · 2024-09

Project Summary Parental acceptance after youth come out as gay or bisexual is a protective factor for the health of this youth group; however, parents lack support in initiating and sustaining sexuality discussions inclusive of their teens’ attractions, behaviors and identities. Thus, in the absence of skills and supports, adolescents’ and parents’ mental health, health behaviors and overall family functioning tend to be negatively impacted after sons come out as gay or bisexual. The overall objective of this application is to test the efficacy of Parents ASSIST (Advancing Supportive and Sexuality Inclusive Sex Talks), a sexuality communication intervention for parents, after youth disclose gay or bisexual identities. We will conduct a randomized controlled trial with parent and gay or bisexual youth dyads (N=476) to establish the efficacy of Parents ASSIST as a hybrid 5-session online intervention that educates parents about germane sexuality-specific topics and provide communication skills for family discussions. Our Specific Aims are to (1) determine whether Parents ASSIST enhances parent-adolescent sexuality communication quality (e.g. parent- and child-reported comfort) and quantity (e.g. frequency and range of topics discussed) compared to the control group, (2) establish whether Parents ASSIST results in decreases in mental health symptomology (e.g. depressive and anxiety symptoms) among parents and gay or bisexual youth, increases dyadic health behavior (e.g. accessing preventive health services, health screening behaviors), and improves family functioning (e.g. affective response, communication, general functioning) over 12 months of follow-up, and (3) examine how theory-based variables (e.g. attitudes and norms, self-efficacy and intentions to discuss sexuality with gay or bisexual child) mediate the intervention effects on adolescent and parent mental health, parent-adolescent health behavior and family functioning over time. This proposal is innovative because it is one of few studies that investigate the role of parent-adolescent sexuality communication with gay or bisexual youth and examines both individual and dyadic health outcomes. Ultimately, fortifying the capacity of parents to initiate and broach sexuality-sensitive communication with gay or bisexual sons offers new opportunities for families to be protective of all youth.

NIH Research Projects · FY 2025 · 2024-09

Project Summary Sexual well-being (SW), the cognitive and emotional evaluation of an individual's sexuality, is an important aspect of overall health and quality of life, yet it is often overlooked in research and clinical practice. Issues around sexuality may have wide-ranging repercussions, from mental health problems to damaged interpersonal relationships, psychological distress, risky behaviors, to violence. Despite this, we still know little about which factors determine SW, and how to measure it. Existing self-report scales are either designed to be brief, only suitable for certain groups, and/or focus mostly on sexual functioning and the absence of negative factors such as coercion or sexually-transmitted infections. While this is important, it is not sufficient for optimal sexual health, which is “a state of physical, emotional, mental and social well-being related to sexuality;[...]not merely the absence of disease, dysfunction or infirmity” (WHO, 2006). Optimal SW may also encompass positive factors, such as feeling loved by one's partner, the ability to enjoy pleasurable experiences, and self- acceptance. Challenges in measuring SW hinders the research process, making informed decisions on sexuality education, and the development of impactful interventions. Here we address these gaps by developing a comprehensive model and in-depth scale of SW which includes positive, strength-based aspects of sexuality. Our team includes experts in sexuality, public health, psychology, and measurement scale development. We will use a proven, highly rigorous three-phase methodology over a five year project timeline. In phase one, we will identify all potential dimensions of SW by applying surveys, analyzing focus groups, conducting interviews, literature review, and more. Phase two focuses on validation of the identified dimensions and development of a robust SW measurement scale. We will first generate a pool of questionnaire items that cover all candidate dimensions and then use interviews, expert feedback, and pilot studies to refine them. Subsequently, we will conduct large-scale studies with thousands of participants to establish the scale's dimensionality using factor analysis, and will test scale validity across different subgroups of our samples. In the final phase, we will assess the value of the resulting SW scale for research and public health by administering it to 3000 participants in a U.S. nationally representative probability sample. We will examine how SW dimensions vary with age, gender, and other demographic variables, as well as associations with health and well-being. Participants will also rate the importance of each dimension, as individuals differ vastly in what they care about in sexuality. We will test whether incorporating importance ratings into scale item weights improve its ability to predict health outcomes. Ultimately, our research will deliver a robust SW scale with demonstrable value for predicting health outcomes, thereby laying a robust foundation for future investigations, clinical applications, and interventions.

NIH Research Projects · FY 2026 · 2024-09

PROJECT SUMMARY Psychiatric disorders remain a leading cause of disability in the US and are associated with increased morbidity and mortality. Early detection and treatment is essential to improving long-term outcomes, yet a substantial proportion of patients with psychiatric complaints experience long diagnostic odysseys before receiving an appropriate diagnosis and initiating effective treatment. “Learning health care systems” aim to short-circuit this slow process by leveraging the diagnostic, treatment, and utilization patterns left behind in “big data” (e.g., clinical, genomic, and social determinants of health) to more efficiently and accurately match the right patient with the right diagnosis/treatment, at the right time. Furthermore, over the past several years, a new paradigm–precision medicine–has moved to the forefront of biomedical research and clinical practice. Precision medicine has been defined as “an approach to disease treatment and prevention that seeks to maximize effectiveness by taking into account individual variability in genes, environment, and lifestyle.” Since its inception in 2018, the mission of the PsycheMERGE network has been to advance precision psychiatry in a learning health care system framework. This application, which was developed collaboratively by PsycheMERGE Network members, represents an opportunity for profound advancement of both basic and translational research in precision psychiatry. We propose extending our foundational efforts to now address barriers to scalability, utility of genomic data, clinical application, and translation to clinical practice in a precision psychiatry paradigm. Specifically, Aim 1 creates a nation-wide federated transfer-learning platform for the development of generalizable and bias-aware algorithms. Aim 2 integrates state-of-the-art methods to perform trans-ancestry genomic analysis of biobank samples and further innovates by leveraging the breadth and depth of medical record data to discover novel biology that can further inform precision psychiatry paradigms. Aim 3 addresses the application of algorithms by focusing on two use cases including (a) differential diagnosis between bipolar disorder 1 and other mood disorders, as well as (b) probabilistic treatment response to antidepressants for acute depressive episodes. Lastly, Aim 4 uses mixed methods to assess the feasibility, utility, and attitudes towards precision psychiatry tools. Our combined sample of clinical EHR data exceeds 29 million individuals and of those, nearly 2 million also have genetic data already available for analysis across the twelve sites included in this application. A cross-cutting theme throughout the application is the intentional focus on generalizable performance of algorithms, and trans-ancestry genomic analyses. The sites included are also representative of the United States including the East and West Coasts, the South, and the Midwest. This application represents a major step towards precision psychiatry and brings the field closer to the goals outlined in the updated NIMH Strategic plan.

NIH Research Projects · FY 2024 · 2024-09

Contact PD/PI: Powell, David ABSTRACT Improving naloxone access is a central pillar of the policy landscape to curb rising overdose deaths rates in the United States. In particular, improving access among “laypersons” is considered one of the most cost-effective naloxone distribution options, but there is surprisingly little evidence about the share of people who carry naloxone, where and how those who carry naloxone obtained the medication, barriers and perceived barriers to purchasing or otherwise obtaining naloxone, optimal price points, and so on. Although two over-the-counter (OTC) naloxone products were recently approved, there is little research about how this policy decision will change behavior. This project will provide some of the first evidence on the state of naloxone carrying in the United States, including near real-time monitoring of knowledge of and purchase behavior related to the OTC products as they become more widely available. This project will also track new and evolving barriers to the purchasing of OTC naloxone. We will use vignettes to study optimal price points for naloxone at the pharmacy and, separately, for the OTC naloxone products, providing especially timely evidence as policymakers wrestle with how to keep the OTC products affordable when many sources of insurance may not cover them. We will field a survey in each year of the project about naloxone access and use in (1) a nationally- representative online sample and (2) a sample of individuals self-reporting “opioid dependence.” These samples provide an opportunity to gather and publish timely evidence as the naloxone market experiences a major shift, potentially encountering new and unforeseen barriers further hindering access and use of naloxone. This project will ask specifically about barriers such as stigma, price, and other factors to understand the scope for improving naloxone purchasing and possession. We will report time-sensitive evidence about the importance of several factors with policy recommendations to address those barriers. Given policymakers' specific concerns with price, we will field vignettes to determine the willingness-to-pay distribution for naloxone (both at the pharmacy and OTC). We will report how naloxone purchasing would change if prices were reduced to different levels. As overdose death rates continue to rise to unprecedented levels in the United States, improving naloxone access has become an increasingly necessary policy objective. Yet, we do not have access to even basic metrics to understand how naloxone carrying rates are evolving. This project will represent a major step forward in our goal to increase naloxone use. Project Summary/Abstract Page 6

NIH Research Projects · FY 2024 · 2024-09

PROJECT SUMMARY Age-related diseases are together the leading causes of death in the United States, and drugs targeting basic mechanisms of aging have recently entered clinical trials. Single cell sequencing has enabled unprecedented resolution in the study of cell types implicated during aging, contributing to our study of age-related diseases. Yet, critical deficiencies remain in our experimental and computational toolbox, limiting our ability to study cellular aging in two fundamental ways: (1) A hallmark of cellular aging is stochastic epigenetic drift, where cells gradually accumulate errors in their cytosine methylation and histone modification profiles, leading to cell-type specific aging phenotypes, such as loss of plasticity in stem cell populations. It is unclear how errors accumulated at the chromatin level propagate to RNA transcription and splicing and how these errors impact observed aging-related phenomenon, such as cellular senescence. This gap in knowledge is due, in part, to the lack of formal definitions and actionable models for measuring epigenetic and transcriptomic dysregulation. (2) The accumulation of senescent cells, i.e. cells that have entered irreversible cell cycle arrest, in our tissues as we age has been widely appreciated as a driver of aging. Yet, there are few studies of the relationship between epigenetic and transcriptomic noise and cellular senescence, partly because of the aforementioned lack of analysis tools, and partly because senescent cells, which are usually present at small proportions even in aging tissue, are difficult to isolate and characterize. In this project, we will develop methods to estimate intrinsic noise, as it was classically defined by Elowitz, Levine, Siggia, and Swain (2022), from single cell sequencing data. Across tissues and cell types, our preliminary studies show that intrinsic noise measures the accumulation of error at the per-cell and per-gene level. We will develop computational methods for the measurement of intrinsic biological noise at the levels of chromatin accessibility, gene expression, and transcript splicing. Synergistically, we will perform experiments on which the new methods will be applied to investigate the relationship between intrinsic cellular noise and cellular senescence, and address essential questions in cellular aging, senescence, and anti-aging drug therapy. Our central hypothesis is that epigenetic, transcriptional, and splicing noise provides both a quantitative profile of cellular aging and a critical new perspective for understanding gene (dys)regulation, senescence, and tissue aging in a cell type specific manner. Preliminary results support this hypothesis and suggest that our methods will be of interest to the broader research community with the potential for wide adoption.

NSF Awards · FY 2024 · 2024-09

This project investigates the implications of climatic and environmental hazards for children’s development. These implications are holistic – affecting learning, health and nutrition, security and relationships. They are embedded in a complex ecological framework with possible interactions across ages as children develop from conception through adolescence. Actions to mitigate and adapt to these hazards require understanding of children’s development and the needs of local communities for children from different socio-demographic, economic, and cultural backgrounds. Advancement of scientific understanding of environmental impacts on the world’s children, and development of research-informed strategies for prevention, mitigation, and short- and long-term resilience, requires collaborations among social scientists with expertise from different disciplines – sociology on entrenched childhood inequalities, demography on health and population displacement, economics on human-capital development, and developmental psychology on behavioral development and psychosocial well-being. Significant advancements also require engagement beyond the social sciences, with public-policy experts, geographers and geoscientists, educational planners, engineers and designers, and medical and public-health experts. Such collaborations are rare and challenging to implement. The goal of this planning project is to develop plans for a multi-university Center Consortium on Global Climate Risks and Resilient Childhoods (CC-GCRRC) to a) investigate the complex implications of climatic and environmental hazards for child development and welfare and b) identify and evaluate promising sources of short- and long-term climatic and environmental adaptation and mitigation in the lives of children. Child development is negatively impacted by numerous climate and environmental hazards, and this project develops a research infrastructure to address those challenges. The project team investigates how to identify children at risk to reduce the impacts of extreme-climatic/environmental shocks on the most vulnerable in society, how to develop programs to build resilience into human-capital infrastructures to safeguard human-capital development and growth and ameliorate ill effects when they occur, and how to provide communities with tools to improve future conditions for child development. The objectives of the project are 1) to identify and test a series of new metrics for assessing childhood vulnerability to, resilience to, and impacts of various climatic and environmental risks, 2) develop an agenda for identifying adaptive and mitigation strategies to promote continuity of housing, health, and educational services in the context of various climatic and environmental hazards and disasters, including those that could cause large-scale population displacements, and 3) plan a research agenda for investigating effective educational strategies for developing and promoting climate-resilient curricular and pedagogical tools for sharing with educational systems. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2025 · 2024-09

OVERALL ABSTRACT/SUMMARY The mission of this Penn PO1 Center on “Mechanisms underlying heterogeneity of cognitive outcome in synucleinopathy” is to understand why the same underlying core pathology – inclusions of alpha-synuclein (aSyn) – varies so widely in the pace and pattern of spread within the brain, resulting in dramatically divergent clinical trajectories. The Lewy body disorders (LBD) – namely, dementia with Lewy bodies (DLB), Parkinson’s disease (PD), and Alzheimer’s disease with Lewy bodies (LBD+AD) – share the core feature of neuronal aSyn inclusions. However, patients manifest very differently from one another, with differences in cognition playing a vital role with respect to patient quality of life and cost to the healthcare system. Because the LBD affect so many, with no FDA-approved disease-modifying therapies, they constitute one of the most important Alzheimer’s Disease Related Dementias (ADRD) affecting the world today. This PO1 Center hypothesizes that several key features play fundamental roles in determining whether a given LBD individual might develop dementia from the outset, after a few years, after many decades, or not at all. These features are: (1) the interplay of aSyn with - amyloid plaques and tau neurofibrillary tangles, (2) the conformation of aSyn, (3) host genomics and proteomics, and (4) the locus/entry point of early pathology. We test this hypothesis in four synergistic Research Projects. Project I investigates the role of concomitant -amyloid and tau pathology in governing patterns of aSyn spread in human postmortem brain. Project II characterizes human brain-derived aSyn strains with cryo-ET and cell biological techniques. Project III leverages genomic and biomarker data to derive candidate molecular players, then manipulates these genes/proteins in neurons to understand their role in the uptake of fibrillar aSyn, development of aSyn pathology, and cell-to-cell transmission of aSyn pathology. Project IV extends our investigations of host factors to mouse models, testing the role of genetic background, route of aSyn exposure, and type of aSyn strain in modulating in vivo pathological aSyn spread. All four research projects focus on mechanisms, grounded in human data, and they are supported by four Cores that (1) serve Administrative functions, (2) recruit Clinical patients, (3) provide biosample Resources to Research Projects and to external investigators, and (4) manage Data for Research Projects and sharing to external investigators. Thus, the Penn PO1 Center seeks to discover and develop new therapeutic strategies to delay or prevent dementia in the LBD.

NIH Research Projects · FY 2024 · 2024-09

ABSTRACT Poverty long has been recognized as an important social determinant of health. Despite many years of progress, in 2018 nearly 10% of the world's population lived in extreme poverty — below $1.90 per day. The Covid-19 pandemic has further increased poverty, leading to a 12% increase in extreme poverty in 2020, with ongoing increases in low-income countries in 2021. Large-scale, government-led cash transfer programs that provide money to individuals or households (with or without conditions) have been a vital part of poverty reduction strategies in many countries during the past two decades. Unlike multi-country evaluations of major health aid programs like PEPFAR, the vast majority of studies of cash transfer programs have focused on individual countries and impacts on beneficiaries in those countries, generally using datasets that are not large enough to precisely estimate effects on mortality rates and many other important health outcomes. In recent work, we used data from 37 low- and middle-income countries (LMICs) and numerous Demographic and Health Survey (DHS) surveys to generate longitudinal mortality datasets for about 7 million adults and children. Using a difference-in- differences approach, we found that government-led cash transfer programs resulted in large and statistically significant reductions in mortality among adult females (adjusted risk ratio 0.80) and children <5 years of age (adjusted risk ratio 0.90), but not among adult males or older children. This work raises an important question about the possible pathways that explain these findings, including behavioral pathways (such as increased engagement in health-promoting behaviors like antenatal care or childhood vaccination) as well as health and nutrition pathways (such as improved child nutrition). The proposed project will address this question by combining DHS data with our newly constructed database of cash transfer programs, using difference-in- differences analyses to examine the association between cash transfer programs and outcomes among adult females and children <5 years of age. Aim 1 of the project will assess the association between cash transfer programs and key behavioral outcomes that might affect mortality rates and other health outcomes, and Aim 2 will assess the associations between these programs and key health and nutrition outcomes that are of considerable interest themselves and might also mediate effects of cash programs on mortality rates. Regression models will include country and year fixed effects and time-varying confounders at the individual- and country- levels. We will conduct secondary and sensitivity analyses like temporal analyses and alternative modeling approaches to assess the robustness of our results, including use of alternative estimators to address bias that can be introduced in difference-in-differences analyses with variation in intervention timing. At a time when many countries are considering scaling-back or expanding cash transfer programs, this project has the potential to have timely public-health and policy impact by producing a comprehensive, global assessment of the causal effects of cash transfer programs on key child- and maternal-health outcomes.

NIH Research Projects · FY 2025 · 2024-09

PROJECT SUMMARY / ABSTRACT Advances in genetics and genomics have raised hopes for the development of gene-based treatments for inherited retinal diseases (IRDs) which are single-gene defects that cause vision loss. Some of the greatest successes for gene-based treatments has occurred in the most severe subset of IRDs that fall into the rubric of Leber congenital amaurosis (LCA) with vision loss often occurring congenitally. LCA success stories from human clinical trials include those caused by deleterious variants in the genes RPE65, LRAT, CEP290, GUCY2D, and AIPL1. Although these disorders present with severe vision loss in early childhood, the great majority of trials have not included young pediatric patients, where efficacy measures are very challenging. Our overarching long-term goal is to evaluate treatments for congenital blinding conditions in younger pediatric patients who stand to gain the most before the window of cortical plasticity closes. Recently we initiated gene augmentation therapy for adults with LCA5, which is a retinal ciliopathy resulting in particularly severe early onset vision loss. Improving vision for the adult population with LCA5 would immensely impact quality of life. Initial results in this adult trial using an AAV8 vector with a subretinal injection appear very promising with evidence of safety and efficacy. We propose to perform a clinical trial of LCA5 gene augmentation therapy in the older pediatric population (i.e. adolescents) and prepare for future clinical trials by developing novel outcome measures in, and for, the very young pediatric population. We will leverage the existing IND, regulatory support, and OPGx-001 clinical vector provided by our industry partner (Opus Genetics), to accomplish two Aims. Aim 1: Perform a clinical trial of OPGx-001 for LCA5 in pediatric patients aged 13 to 18 years. Re-defined outcome measures (including the addition of innovative measures tested in a `seamless' clinical trial design) will be used to determine the safety and efficacy of uniocular subretinal gene delivery of OPGx-001 in a Phase I/II dose escalation (1.0x1010, 3.0x1010 and 1.0x1011 vg/eye) clinical trial. Three eligible patients ages >13 to 18 will enter each dose group and will be followed for 3 years as an extension of the current gene therapy trial in the adult population. Aim 2: Develop novel ocular outcome measures for pediatric patients aged >1 to ≤13 years with LCA5 and other forms of LCA for future interventional trials. We will develop subjective and objective measures of vision, and validate their performance in patients ages ≥8 before deploying them in a younger (<8) group of patients with LCA that are the target population in this and future trials. At completion, the project will provide safety and efficacy data for OPGx-001 in adolescent patients, and a specific path for treating very young patients with vision loss due to LCA5 or other gene defects.

NIH Research Projects · FY 2025 · 2024-09

Project Summary While pulmonary arterial hypertension (PAH) is a progressive disease of the pulmonary vasculature associated with high morbidity and mortality, it also has multiple systemic manifestations affecting many organs. There is a growing body of evidence suggesting respiratory and skeletal muscle dysfunction in patients with PAH; however, loss of muscle mass has not been adequately studied in PAH. Loss of lean mass is increasingly recognized in individuals with chronic conditions and when present, is associated with decreased physical activity and worse outcomes. Our preliminary data shows that almost 42% of patients with PAH enrolled in a prospective observational cohort had low lean mass and obese individuals had a higher prevalence of low lean mass as compared to individuals with normal weight. Fat depots are metabolically active and produce an array of inflammatory cytokines and adipokines that likely contribute to the muscle loss. We are proposing a comprehensive evaluation of lean mass in patients with PAH. First, in a prospective cohort of patients with PAH, we will characterize the endophenotype of PAH patients with low lean mass and identify the metabolomic signature of low lean mass which will provide us with insight into novel putative pathways. We also aim to understand the role of epicardial adipose tissue in the pathogenesis of low lean mass. We will assess the impact of low lean mass on patient-centered outcomes including quality of life, physical activity, and hospitalizations. Second, we will identify radiographic features of muscles on thoracic non-contrast chest CTs to allow for earlier and easier screening for low lean mass in patients with PAH. Finally, we will conduct a small pilot study to explore the response of adiponectin and muscle oxygenation to a low- resistance exercise intervention in patients with PAH. The results of this study will lay the foundation for “personalized” interventions trial targeting low lean mass in PAH.

NIH Research Projects · FY 2026 · 2024-09

During sleep, the mammalian brain alternates between two major brain states, rapid eye movement (REM) and non-REM (NREM) sleep. Recent work showed that the electroencephalogram (EEG) during NREM sleep in both humans and mice exhibits a pronounced infraslow (~50s) modulation in the sigma (10-15 Hz) power range Transitions from NREM to REM sleep and spontaneous awakenings are synchronized with this infraslow o power (ISP) rhythm, suggesting that it plays a crucial role in shaping sleep architecture and influencing sleep quality. Yet, the mechanisms underlying the generation of infraslow rhythms remain largely unknown. Importantly, the ISP rhythm also strongly modulates the activity of neurons in REM sleep-regulatory brain areas including the locus coeruleus (LC), dorsomedial medulla (dmM), periaqueductal gray (PAG), and dorsal raphe (DR). However, current models of sleep regulation lack this prominent infraslow rhythm, and a functional understanding of its impacts on sleep architecture therefore remains elusive. The central hypothesis of this proposal is that the dmM controls the ISP rhythm through its interactions with the LC and that infraslow fluctuations in the activity of DR/PAG neurons control the stability of NREM sleep and consequently gate transitions to REM sleep. The specific aims combine experimental studies and biophysical computational modeling to determine mechanisms governing the ISP rhythm, and to understand the consequences of this rhythm on sleep architecture, particularly NREM--+REM transitions. In AIM 1, we will perform Neuropixels recordings along with optogenetic manipulation to identify how network interactions between dmM and LC neurons regulate the ISP rhythm In parallel, we will develop computational models informed by recorded data to identify underlying mechanisms of infraslow rhythm generation in the dmM-LC circuit In AIM 2 we will conduct Neuropixels recordings to identify the functional connectivity among different subclasses of DR/PAG neurons. By optogenetically blocking external infraslow inputs to the DR/PAG and conducting behavioral REM sleep deprivation, we will probe how the infraslow rhythmicity and REM sleep pressure affect the dynamics in the DR/PAG network and state transitions. In parallel, we will construct computational models informed by the recorded data to identify the dynamic interactions among different DR/PAG neuron subclasses and to analyze the effects of infraslow activity and REM sleep pressure on simulated sleep architecture. Our studies will bridge a fundamental gap in our understanding of how the mammalian brain generates infraslow rhythms. Furthermore, results will identify targets for enhancing the ISP rhythm to test its impact on sleep quality, and will lay the groundwork to develop complementary and integrative health approaches to leverage infraslow brain dynamics to promote healthy sleep and thus physiological and emotional well-being.

NIH Research Projects · FY 2025 · 2024-09

SUMMARY Hyperpolarized 129Xe MRI of the lung with polarized gases is capable of providing valuable regional information about ventilation and gas exchange that is unobtainable using other imaging modalities. However, current HP 129Xe MRI is limited by the fact that imaging takes place during a non-physiological breath-hold. In this project, we propose to develop a technique to dynamically image the lung using 129Xe MRI during free-breathing; in addition to enabling a more physiologically relevant assessment of lung function, this method will be feasible in patient populations that have thus far been inaccessible to 129Xe MR imaging due to poor breath-hold tolerance: young children, end-stage lung disease, etc. To enable the repeatable lung function measurements during free-breathing, we will construct and optimize a system to automatically deliver a small fixed volume (~50 ml, proportionally delivered based on inhaled gas flow) of 129Xe at a constant rate with each breath, via a small tube connected to a sealed facemask worn by the subject. This set-up will allow us to implement a breathing / imaging protocol that requires no subject effort or training, and is therefore more compatible with widespread clinical implementation. Using a novel 3D spiral acquisition designed to optimize signal, navigator fidelity, and resolution of spectral components, we will acquire a number of novel imaging parameters capable of assessing specific lung regions' dynamical behavior over the course of a breathing cycle. Finally, we will establish the reproducibility and sensitivity of these markers to early smoking- induced changes in lung function via imaging in both healthy subjects and at-risk smokers. While the studies proposed in this project focus on assessing functional alterations indicative of early COPD, the dynamic imaging technique we propose to develop has several other potential clinical applications. Most notably, these include conditions (e.g., unexplained dyspnea, long COVID) in which the aspect of lung function limiting gas exchange is unknown, and clinical syndromes (like COPD) in which disparate pathophysiology requires an assessment tool with broad sensitivity to identify and classify functional change in early disease.

NIH Research Projects · FY 2025 · 2024-09

PROJECT SUMMARY Although lifestyle factors have been investigated for their potential to modify risk of adverse pregnancy outcomes, initiating interventions during pregnancy may not have the greatest impact. Therefore, it is crucial to focus on preconception interventions to support healthy placental development and reduce the risk of metabolic conditions. However, there is a lack of data regarding the optimal timing and strategies for preconception health to improve pregnancy outcomes. Physical activity, diet, and sleep play pivotal roles in preconception care as they influence metabolic health and body weight regulation, which can impact the subsequent risk of pregnancy complications. Existing preconception care often emphasizes weight loss, but there is limited evidence on the most effective amounts and strategies for improving later pregnancy health. Moreover, using body mass index as the primary measure for obesity classification may misidentify individuals who would benefit the most from weight loss, as it fails to distinguish between lean mass, fat mass, and fat distribution. Methodological challenges in studying preconception exposures have hindered the establishment of a robust evidence base for optimizing pregnancy health. To address these gaps, we propose an innovative approach utilizing the linkage between the National Health and Nutrition Survey (NHANES) and Medicaid data. With this data examine pregnancy outcomes among low-income reproductive-aged women who become pregnant and utilize Medicaid services following their NHANES assessment. Medicaid covers a substantial portion of U.S. births, making studies of Medicaid-covered pregnancies highly generalizable. Leveraging the NHANES-Medicaid data as a "preconception cohort," we will investigate the impact of preconception exposures on pregnancy outcomes. Employing advanced epidemiological methods to minimize selection bias and improve generalizability, we will apply a target trial framework to assess preconception strategies for optimizing pregnancy outcomes. The comprehensive phenotyping data available in NHANES will enable robust assessment of confounding variables, reducing the impact of unmeasured confounders and mimicking randomized trials of lifestyle factors. Using NHANES-assessed exposures, we will evaluate the influence of preconception dietary patterns, physical activity, sleep, body composition, and weight loss attempts and strategies on adverse pregnancy outcomes. This analysis will provide the most extensive and generalizable evidence to date on preconception health and its impact on adverse pregnancy outcomes, ultimately informing the development of evidence-based preconception care guidelines.

NIH Research Projects · FY 2025 · 2024-09

PROJECT SUMMARY The maternal mortality rate in the United States (US) is the highest among high-income countries and has been steadily rising in recent years. Near misses for maternal mortality, including both physical health indicators captured by severe maternal morbidity (SMM) and mental health near misses such as suicidality and overdose (hereafter, SMM+), are also increasing among birthing individuals. Racial and other disparities in maternal mortality and SMM+ are widening. Telehealth utilization increased dramatically in response to the COVID-19 pandemic and has great potential to reduce SMM+ and SMM+ disparities through increasing healthcare access and utilization, patient experience, and quality of care. However, there is little data on maternal safety outcomes like SMM+, whether telehealth could reduce or exacerbate disparities in SMM+, and how telehealth can be optimized with the goal of reducing SMM+ and SMM+ disparities. This project will determine the impact of telehealth on SMM+ and SMM+ disparities and develop multidisciplinary clinical and community consensus guidelines for how telehealth can be implemented to address equity issues and reduce disparities in SMM+. We will apply a mixed-methods approach, conducting novel causal inference analyses of a national Medicaid claims database, the largest US health insurance provider during pregnancy (>40% of births; 65% of births to Black individuals), and qualitative work centered in Philadelphia, a city with a high maternal mortality rate and one of the country's only local maternal mortality review committees. We will form a community advisory board (CAB) that includes multidisciplinary stakeholders and lived experience experts to provide substantial input on all aspects of the proposal. Specifically, we will estimate effects of hybrid telehealth versus in-person only prenatal and postpartum care strategies and state policies expanding coverage for telehealth modalities on SMM+ and SMM+ disparities using a novel trial emulation framework (Aim 1); identify barriers and facilitators to implementing telehealth care with the goal of reducing SMM+ and SMM+ disparities (Aim 2); and develop and disseminate best practice recommendations for using telehealth to detect early warning signs of SMM+ (Aim 3). Successful completion of this work will fill critical gaps in knowledge about the safety, effectiveness and equitableness of maternity telehealth care and how telehealth can be leveraged to reduce maternal health disparities. Through sustained partnership with a CAB and dissemination of best practice recommendations, our methodologically innovative project will inform care, guidelines, and policy in Philadelphia and nationally. By sharing our project's key findings, methods and software code, we will generate a community-driven research agenda and cultivate collaborators for future research using our database and CAB.

NIH Research Projects · FY 2024 · 2024-09

The female reproductive system, the uterus, fallopian tubes and the ovaries, is a complex interrelated set of organs that is physiologically dynamic and not only important for fertility but critically interrelated with general health. Single cell studies of the human female reproductive system and related tissues have been previously studied, but, as of yet, a comprehensive program, aligned with the goals of the HuBMAP, to define a molecular map of the entire system, integrating multi-modal assays, spatial diversity, and individual variations has not been established. The Penn Department of Obstetrics and Gynecology performs approximately 3,500 surgical procedures annually, of which many procedures allow sampling of multiple organs and locations from the same subject under normal conditions. Here, we propose to leverage the sampling opportunities afforded by the Penn ObGyn group and the single cell biology expertise of Penn investigators to establish a Penn Center for Multi-scale Molecular Map of the Female Reproductive System. We will obtain a comprehensive molecular characterization of the female reproductive system using six different molecular assays for at least ~700 tissue samples in anatomically indexed samples, creating a key resource for both basic science and women’s health. The molecular assays include single cell RNAseq, clampFISH spatial transcriptomics, simultaneous single cell open chromatin and RNA assays, and spatial open chromatin assay, among others. We will also generate a 3D anatomical model to provide spatial coordinate for our molecular characterization. All assay data will be registered to our 3D anatomical map that will be integrated with the HIVE Common Coordinate Framework. All metadata from subject records, clinical procedures, molecular procedures, and informatics pipelines will be collected, curated, and deposited as structured data. All data, including an extensive set of metadata, will be made available as a public resource. The completion of this resource will impact reproductive medicine for women’s health and also inform basic biology of human cell communities.

NIH Research Projects · FY 2025 · 2024-09

Project Summary Decades of genetic and experimental evidence has placed α-synuclein (αS) as a central player in the pathogenesis of several neurodegenerative diseases including Parkinson’s Disease (PD), Alzheimer’s Disease (AD) and related dementias (ADRD). αS protein levels closely correlate with PD and ADRD risk, and reduction has been shown to be protective in multiple disease models, making lowering αS levels a target for therapeutic intervention. Despite that, there is very poor understanding of how the abundance and turnover of endogenous αS protein is regulated. We recently found, using unbiased CRISPR screens in human cell lines and iPSC- derived neurons, that disruption of the NatB complex resulted in a stark reduction in endogenous protein levels and is well tolerated in human iPSC derived neurons. NatB installs N-terminal acetylation (AcN) of αS. While AcN is a prevalent post-translational modification, its functional consequences are not well understood. AcN has been implicated in several processes specific to αS, such as membrane binding, cell uptake, and aggregation. Indeed, our own preliminary data support the importance of these effects and more. These results led us to hypothesize that lack of αS AcN compromises interactions that are fundamental to its molecular function and that pharmacological targeting of AcN represents a novel therapeutic strategy for αS’s involvement in PD and ADRDs. We propose three aims that will rigorously investigate the implications of these findings on αS biology and therapeutics. In Aim 1, we will identify the molecular interactions that are lost when αS lacks AcN. We believe that this will provide critical insight into its biological function. We will also investigate the mechanisms responsible for the rapid degradation of non-AcN αS compared to AcN αS. This may provide additional tools for therapeutic reduction of pathological αS in disease and insight into αS turnover mechanisms. In Aim 2, we will focus on understanding the outcome of NatB inhibition on the proteome and N-terminal acetylome of human cells and neurons using quantitative proteomics approaches. Such understanding will be essential for the development of NatB as a therapeutic target. Lastly, in Aim 3 we will develop the first NatB pharmacological inhibitors for evaluation in vitro, and in iPSC derived neurons. We use state-of-the-art computational approaches in combination with experimental high-throughput screening to identify molecules that can inhibit NatB acetylation of αS with minimal effects on AcN of other proteins. These molecules will serve as essential research tools and as lead therapeutic candidates for PD and ADRDs.

NIH Research Projects · FY 2025 · 2024-09

Precision medicine initiatives are growing exponentially in medical care systems. Genetic testing for both somatic and germline testing have allowed providers to provide both tailored preventative and treatment plans for patients related to various disease conditions. Medically underserved populations (those experiencing health disparities) are largely interested in testing even with having limited knowledge of testing. Still, many of the interventions and research efforts to improve these disparities have solely focused on individuals’ attitudes and knowledge of testing. Based upon findings in my predoctoral research (F99 phase), intervention efforts may be more successful at addressing testing disparities at the interpersonal and system levels via agency and normative influence. Thus, the goal of the K00 proposal is to better characterize environmental, interpersonal, and institutional facilitators and barriers that impact genetic testing utilization especially at the clinical level within the implementation of novel service delivery approaches, while also developing strategic partnerships with local genetic providers and community partners their current communication strategies and work to develop materials and communication campaigns to promote genomic engagement with medically underserved populations and testing their efficacy with panel data. Aim 1 seeks to characterize clinical facilitators and barriers for novel innovative genetic testing service delivery approaches among a) providers and b) all eligible patients to develop impactful interventions to improve perceived agency for genetic testing uptake. Using a sequential qualitative and quantitative approach, I will interview both community practice providers (n=15, Aim 1a) and patients (n=20, Aim 1b) engaged with the Telegenetics program to better understand rationale of ordering testing, experiences, and affective responses, and then develop and distribute a survey for both providers (n=100) and patients (n=200) to test associations between uptake and facilitators and barriers. Aim 2 will build strategic local partnerships with genetic testing service providers as to a) assess current engagement strategies and developed engagement strategies for medically underserved populations and b) test messages that emphasize normative influence and agency on testing intention. The first phase of Aim 2 will assess Penn’s Telegenetics program, the Basser Center BRCA program, and Abramson Cancer Center Community Outreach and Engagement arm communication and engagement strategies around cancer genetic testing service delivery, using a formative, process, and outcome communication evaluation (Aim 2a). Next, building upon connections made in Aim 2a, I plan to work with community leaders through a community participatory research model and asset mapping approach to co-create materials and test their effects with a Qualtrics panel (n=500 participants, Aim 2b). Subsequently with lessons learned, I argue some of these strategies could be scaled to national partners and other healthcare systems to promote genetic testing service delivery with a variety of other medically underserved communities.

NIH Research Projects · FY 2025 · 2024-09

Project Summary About 50% of high grade serous ovarian cancers (HGSOC) exhibit defects in homologous recombination (HR; e.g. BRCA1/2 mutations). Approximately 20% HGSOC and 50% of serous endometrial cancer (EMCA) exhibit CCNE1 amplification. About 50% clear cell ovarian cancer (CCOC) have ARID1A loss. My research goal is to exploit genetic vulnerabilities in gynecological cancers with scientifically rational drug combinations. First, CCNE1 amplification promotes loss of G1-S checkpoint and increased reliance on the G2-M checkpoint for survival. Ovarian and endometrial cancers with CCNE1 amplification are platinum resistant with poor outcomes. I will test new therapies that exploit survival pathways critical for survival in CCNE1 oncogene addicted cells. I will also determine if other biomarkers in addition to CCNE1 correlate with response to effective targeted therapies. Second, rare gynecological cancers lack preclinical models for drug discovery. We will expand our existing PDX and organoid platform to include rare tumor types. We will also test new strategies that exploit the genetics of these rate tumor types such as low-grade serous ovarian cancer. In addition, I will perform deep genomic and transcriptomic studies to identify biomarker signatures that predict response to DNA Damage Response (DDR) inhibitor combinations using PDXs and patient samples from an ongoing phase IB clinical trial. I will also identify new targets for ARID1Amut clear cell ovarian cancer using a CRISPR screen targeting functional protein domains. Lastly, PARP inhibitors (PARPi) represent a significant advance in ovarian cancer treatment with HR deficiency; however, tumors ultimately acquire resistance. I showed that combination PARPi-ATRi overcomes PARPi resistance in cell lines and PDX models (Nature Commun, 2020) which led to Phase II clinical trial. We will now determine if combination therapy can be augmented by activating the immune system. We will test new strategies such as radionucleotides to overcoming PARPi resistance. Lastly, we will further evaluate a non-invasive molecular imaging tool to predict response to PARPi therapies. In summary, these studies have a significant impact to advance cancer therapies for women with gynecological malignancies into the clinic.

NIH Research Projects · FY 2025 · 2024-09

Project Summary/Abstract Injuries to soft tissues represent 45% of all musculoskeletal injuries per year. Fatigue loading causes damage at the microscale to collagen fibrils, which makes the tendon more susceptible to rupture. Changes to the native tendon composition are often associated with injury risk. In the aging tendon, interfibrillar structures between fibrils (e.g., glycosaminoglycans (GAGs)) have been shown to decrease, in association with alterations to interfibrillar mechanics and rupture rates. While GAGs may not play a direct role in elastic mechanics, they have been postulated to promote fibril sliding by retaining water and increasing fibril spacing and lubrication, meaning that they provide an important load-bearing mechanism in tissues with aligned fibrils. This sliding mechanism may protect against repetitive, viscoelastic processes that cause tendon damage, namely fatigue, by reducing overall load to individual collagen fibrils. Yet, the connection between GAGs and fatigue-induced rupture remains unelucidated. The goal of this proposal is to define the multiscale interplay between GAGs, interfibrillar load transmission, and fatigue rupture in intact and healing mature and aged tendons. Our overall hypothesis is that GAGs modulate fibril spacing which enables sliding between aligned fibrils and protects against fatigue-induced microdamage and eventual rupture in intact and late-stage healing tendons. The proposed aims would innovate preclinical evaluations of multiscale tendon mechanics and augment the scientific understanding of micromechanical changes that precede injury in aging and healing tendons. The Aims are: Specific Aim 1: In mature and aged Achilles tendons, define the role of GAGs in preventing damage accumulation and eventual rupture during fatigue loading. Specific Aim 2: In the healing Achilles tendon, define the role of GAGs in preventing damage accumulation and eventual rupture during fatigue loading. In both aims, we will couple state-of-the-art biomechanical testing of a high-throughput rodent model with rigorous micromechanical and histological measures of interfibrillar sliding and structures. We will use findings from these techniques to inform and refine computational shear-lag models of tendons to further explore the role of GAGs in fatigue loading. These exciting and innovative studies will elucidate the role of GAGs in interfibrillar sliding, microdamage, and eventual rupture in Achilles tendons undergoing fatigue loading. Further, these studies will increase our understanding of mechanisms that lead to injury in aging and healing tendons, which is essential to our understanding of how tendon injuries occur, to improve interventions preceding injury, and enhance future therapeutic strategies following tendon injury.