University Of Southern California

NIH Research Projects · FY 2025 · 2016-09

RNA silencing is a gene regulatory mechanism by which small RNAs (18-30 nucleotides) and their Argonaute protein co-factors modulate the expression of both foreign and endogenous mRNAs. Small RNAs play a critical role in maintaining proper gene expression by identifying fully or partially complementary mRNAs and targeting them for either transcriptional or post-transcriptional regulation. The role of RNA silencing in gene regulatory pathways is conserved across most eukaryotes and is thus of fundamental importance to the developmental and cellular biology of humans. C. elegans is an excellent system to study RNA silencing because of its short generation time, its transparency which is ideal for microscopy, and the powerful genetic tools available for genome manipulation. In C. elegans germ cells, proteins involved in RNA silencing are organized into sub- compartments of perinuclear condensates, with each sub-compartment playing a unique and critical role. Many protein factors have been identified that localize to these structures, yet we know little about how they are organized and assembled. In the first part of this proposal, we will identify factors and conditions that promote assembly of RNA silencing components into perinuclear condensates. We will further identify the RNAs in each sub-compartment, with the ultimate goal of dissecting the trajectory of a targeted mRNA through each of its phases: beginning with transcription, continuing through this assemblage of perinuclear condensates, and ultimately with translational repression or degradation by the RNA silencing pathway. Because there are ~27 C. elegans Argonaute proteins, many of which colocalize at P granules, we will next identify the factors contributing to sorting of small RNA into the appropriate Argonaute proteins. This sorting is critical because many Argonaute proteins bind different small RNAs from one another, target distinct groups of mRNAs, and can have very different regulatory effects on these target mRNAs. Finally, we will focus on how protein modifications such as phosphorylation and methylation can regulate RNA silencing pathways, including affecting localization, interacting partners, and dynamics of Argonaute proteins and other key factors. Together, the proposed experiments will uncover the key details of how RNA silencing pathways are organized, how the specificity of the pathways is defined, and what mechanisms regulate these pathways. This work will lead to a better understanding of how small RNAs modulate gene expression in healthy cells, which can ultimately be applied to discerning how changes in these pathways cause misregulation of genes in humans and transition to a disease state.

NIH Research Projects · FY 2026 · 2016-07

The Southern California Clinical and Translational Science Institute (SC CTSI) is submitting this revision for a third cycle of Clinical and Translational Science Award (CTSA) funding at a time of dramatic growth and opportunity at our hub. The SC CTSI encompasses the University of Southern California (USC) and Children’s Hospital of Los Angeles (CHLA), in close partnership with the Los Angeles County Department of Health Services. Our vision is to be a leader in clinical and translational research to benefit all populations within our local communities. Our approach builds on past success, acknowledging the changing landscape of clinical and translational research (CTR), the priorities of the CTSA program, and the evolving needs of our researchers, trainees, patients and communities. Our scope leverages strengths in clinical, health system, and community research, education and training, within the overarching theme of mitigation of disease burden. We approach this theme working with our local communities, different health systems, and multiple scientific disciplines to improve health care and outcomes. Our impact encompasses academic productivity as well as benefit to our workforce, health systems, patients, and communities. To pursue our vision in the context of our scope and themes, we propose six specific aims: (1) Workforce Development: Train a highly skilled workforce with the knowledge, skills, and attitudes to conduct rigorous and reproducible research focused on the evolving health needs of local communities. (2) Collaboration and Engagement: Create a culture in which team-based research, engaging all stakeholders and following sound principles of team science, is the standard approach to addressing complex challenges in health and research. (3) Integration: Engage our local communities to establish clinical research priorities; identify barriers to research; and develop, demonstrate and disseminate innovative approaches to assure fully partnered clinical research across communities and the lifespan. (4) Methods and Process: Apply principles of quality and process improvement to clinical and translational research to develop and share novel approaches to enhance efficiency, quality and impact. (5) Informatics: Provide an agile information ecosystem that encompasses research, clinical care, communities and their environment, providing a holistic view of health and disease and serving as the engine for discovery, innovation and insight. (6) CTSA Hub: Participate in CTSA network activities, conduct multi-site studies, adopt successful models from peers, and develop, demonstrate and disseminate innovative approaches. Achieving these aims will advance the discipline of CTR directed at improving health in all populations within our local communities.

NIH Research Projects · FY 2026 · 2016-07

The Southern California Clinical and Translational Science Institute’s Institutional Career Development (ICD) Program operates within the University of Southern California and Children's Hospital Los Angeles. We operate in the heart of Los Angeles, where the population faces serious challenges: 20% live below the federal poverty level, 30% are under 18 years old, and 57% of adults do not complete high school. The disease burden is high and amplified by local conditions linked to poor disease outcomes: neighborhood poverty levels, crime rates, low access to and engagement in healthcare. Thus, we aim to: 1) develop leaders who conduct rigorous and reproducible clinical translational research (CTR) that identifies and overcomes translational barriers to improve the health of all populations within our local communities, 2) empower Scholars to sustain CTR careers, and 3) increase Scholar ability to work effectively with the population surrounding our institutions. Based on these aims, we expand the ICD Institutional Ecosystem with state-of-the-art Education and Mentor Resource Centers and Advisory and Faculty Boards with strong educational CTR expertise and broader representation of educational backgrounds and scientific expertise. We propose to train 4 new Scholars per year for three years each through NIH, institutional, and departmental funds. The ICD Program builds on a successful three-course series emphasizing CTR research methodology, rigor and reproducibility, team science, communication skills, and research in the local populations surrounding our institutions, combined with a comprehensive career development program. Scholars enroll in a Master’s or Certificate program in Clinical, Biomedical, and Translational Investigations. New ICD training opportunities include healthcare delivery science, health data science, precision medicine, and Quality by Design. A robust distance education platform is in place for recording, archiving, and disseminating educational materials; it also supports Scholars in developing oral communication skills and disseminating their research. Experiential opportunities include interactions with SC CTSI core experts in, e.g., digital recruitment, community engagement, regulatory knowledge, community mentors, and visiting scholar research presentations at other CTSA institutions. Scholars-Mentor teams use Individual Development Plans to guide career progression throughout the program. Barriers to career progression are identified and addressed through a novel Barriers Mitigation Board which informs scholars' resilience for long-term career success. We have created robust tracking and evaluation processes that inform and advance the program. Data show transformative and widespread institutional change due to ICD Scholars and alumni transitioning to independent research careers with robust research funding, academic productivity, and advancement. More broadly, we have contributed regionally and nationally to training and career development in CTR by sharing tools and best practices and leadership in CTSA committees and working groups. We look forward to expanding this success in the next funding cycle.

NIH Research Projects · FY 2025 · 2016-07

OVERALL ABSTRACT The overall goal of this Program Project is to develop novel statistical methods for integrating multi-omic data to address etiology, prognosis, and treatment of cancer through a collaboration of four closely related projects and four shared cores (see inset). The four projects can be broadly described as spanning the spectrum of analysis challenges including feature selection, mediation, interaction, and characterization. The first of these, “High-Dimensional Regression for Data Integration,” develops new strategies for the analysis of longitudinal -omic data incorporating external functional information, maintaining a rigorous inferential foundation. The second project, “Integration of Omic Data to Estimate Mediation or Latent Structures,” develops novel latent factor and mediation models using high-dimensional omic data or GWAS summary statistics to identify and distinguish genotype, exposure and omic effects. The third project, “Integration of Omic Data in the Analysis of Gene x Environment Interaction,” incorporates gene expression and other -omics data into powerful multi-step approaches to scan for interactions leveraging exposure or disease marginal associations. Project 3 will also add novel approaches to identify transcriptional interactions, hierarchical GxE models with heredity constraints (i.e., requiring interactions to include the corresponding main effects), and extensions to longitudinal, survival, and quantitative traits. The fourth project, “Statistical Methods for Genome Characterization,” automates annotation of gene function using phylogenetic inference to identify new cancer- specific regions of conserved DNA methylation. Project 4 also proposes a novel approach for agnostic pathway gene set enrichment analysis. These projects will be supported by four cores: Administrative Core (A), Functional Annotation Core (B), Computation and Software Development Core (C), and Data Analysis and Research Translation Core (D). Core B will maintain up-to-date copies of key bioinformatics resources and will develop a software application that will provide a single unified portal for creating annotation files that integrates data from multiple resources. Core C will assist with high-volume computing needs and will develop user-friendly software packages that implement novel methods. Core D will focus on translation of new methods, both by supporting applications to real cancer datasets and by developing materials for training outside investigators in the use of our methods and software. Our proposed work will have both methodological and substantive importance. On the one hand, we will develop novel statistical methods that will be applicable to a wide range of cancer epidemiology studies and clinical trials. These methods will, for example, allow more powerful discovery of genetic associations and interactions through leveraging biological information from other sources. They will have translational significance in the areas of risk prediction and targeted interventions. Our program is designed to be highly integrative, with the various projects and cores being inter-related, so that together they will be more informative than any of them could be on their own. Program members have access to extraordinary data resources at USC and elsewhere, assuring that the methods we develop will be motivated by, and applicable to, important questions arising in current cancer research.

NIH Research Projects · FY 2025 · 2016-07

During fetal development and early childhood, growth of the bony skull accommodates a rapid expansion of the underlying brain. This is accomplished first by progenitors that grow the individual skull bones, and then by stem cells residing in the flexible bony joints called sutures. In a common birth defect called craniosynostosis (1 in 2000 live births), loss of the cranial sutures results in bony fusions that impede brain growth, thus leading to cognitive impairment if left untreated. Surgical correction involves invasive and risky surgeries on infants to break apart the fused bones. Unfortunately, the skull bones often re-fuse, necessitating repeated surgeries. There is thus a critical need to better understand the causes of craniosynostosis, such that we can develop therapies that minimize repeated surgical interventions. In the previous funding cycle, we generated and characterized the first zebrafish model of Saethre-Chotzen Syndrome, which preferentially affects the coronal suture. In so doing, we pinpointed early changes in the growth rates of the embryonic skull bones as a major cause of suture fusions. In this renewal we address three outstanding questions in the field of craniosynostosis. In Aim 1, we investigate the embryonic origins of the suture stem cells that grow and maintain the skull. While suture stem cells have been studied at postnatal stages, whether they arise from progenitors at the tips of growing bones, or alternatively from migrating cells, remains debated. By generating the first single-cell transcriptomes of the developing mouse and zebrafish coronal sutures, we have uncovered conserved embryonic cell types and molecular markers for suture progenitors. Using new lineage tracing tools in mouse and fish, we will test that bone front progenitors expressing ETS-family transcription factors are the origin of suture-resident stem cells. In Aim 2, we investigate how the Saethre-Chotzen genes Twist1 and Tcf12 regulate the transition from bone front progenitors to suture stem cells. Preliminary data reveal that Twist1 and Tcf12 upregulate the Bmp antagonists Grem1 and Noggin during suture formation, suggesting that tighter regulation of Bmp signaling is essential to slow bone growth and prevent fusions. Using mouse conditional genetics and new zebrafish mutants, we will test that direct regulation of Grem1 and Noggin expression by Twist1 and Tcf12 is necessary and sufficient for regulated bone growth and normal suture formation. In Aim 3, we address a central mystery of the craniosynostosis field – why do particular mutations tend to affect only particular sutures? By generating and contrasting new zebrafish models for 11 coronal and 7 midline craniosynostosis genes, we will test whether coronal suture formation is particularly sensitive to mutations that perturb the rate of bone growth. To do so, we will make use of new zebrafish transgenic reporters that allow quantitative in vivo measurements of osteoblast addition and suture formation. A strength of the proposal is the unique team of experts in zebrafish, mouse, and human craniofacial genetics. By using model organisms to understand the developmental bases for diverse types of craniosynostosis, we strive toward developing more targeted treatments for craniosynostosis patients with particular genetic mutations.

NIH Research Projects · FY 2025 · 2016-06

ABSTRACT Diversification of our immune system requires two primary DNA recombination pathways: V(D)J and class switch recombination (CSR). Both V(D)J and CSR have several poorly understood intermediate steps. These intermediate steps are the basis for the most disease-relevant aspects of these pathways because they are inherently unstable. Static structural biology approaches alone are not sufficient to understand the instability of these intermediates. The dynamic approaches described here permit us to understand these unstable intermediates that are key to both inherited and acquired (neoplastic) diseases of the V(D)J and CSR pathways. From an applied standpoint, the understanding gained in this proposal positions us to eventually use biochemical systems to generate improved antibodies against pathogenic viruses and bacteria. Important for the current proposal, over 85% of human lymphoid malignancies are B cell in nature, and we have shown that the breakage phase at the two chromosomes arises by a confluence of failures in the V(D)J and Ig CSR mechanisms. The chromosome break at the immunoglobulin locus is typically due to failures during the synapsis steps as the RAG complex prematurely releases the ends. Failures can also occur in the RAG hand- off to the NHEJ pathway (for joining the ends). We study all of these aspects of RAG function in this proposal. The other chromosome break arises due to the off-target behavior of the CSR enzyme called activation-induced deaminase (AID), which we study in the second Project of this proposal. The Lieber lab has done key biochemistry on all of the enzymes mentioned above. We are the first and only lab to reconstitute the entire V(D)J pathway using fully purified enzymes. Despite beautiful recent atomic structures of RAG and AID proteins, the dynamic action of these enzymes and how they fail is the gap that remains. In addition to neoplasms, diseases caused by RAG and AID enzymes are responsible for over one-third of inherited human immune deficiencies called SCID. My lab has used the current funding period to develop in-lab capability to use our unique purified proteins for V(D)J and CSR in high resolution single molecule assays, specifically cryo-EM and sm-FRET. In 2019 and 2020, we published the first sm-FRET in which not only the proteins but also the dynamic sm-FRET were done in my lab. My lab also now has full cryo-EM abilities, which would be relevant at the later stages of the current proposal. We also can carry out the relevant biochemical steps in this proposal on mono- and polynucleosomal substrates in addition to naked DNA. In Project 1, we dissect the key vulnerable points in the RAG synapsis steps and their hand-off to the NHEJ pathway. In Project 2, we study the independent process of Ig class switch recombination (CSR). The Lieber lab was the first to discover kilobase length chromosomal R-loops at switch sequences. We are the only lab able to reconstitute the entire CSR pathway using purified substrates and proteins. We apply our cumulative technologies to ask key questions about how CSR occurs and how it fails in disease states.

NIH Research Projects · FY 2026 · 2016-05

PROJECT SUMMARY/ABSTRACT Regulation of stem cell functions is crucial for tissue formation, growth, and homeostasis. In many tissues and organs, stem cells give rise to transit amplifying cells (TACs), an undifferentiated progenitor population. TACs function as transient but indispensable integrators of stem cell niche components. However, we have limited understanding of how mesenchymal stem cells (MSCs) interact with TACs and provide feedback to MSCs in regulating tissue homeostasis. The adult mouse incisor provides an excellent model for stem cell study because it grows continuously. MSCs are a Gli1+ cell population surrounding the neurovascular bundle (NVB) near the proximal region in the adult mouse incisor, making it an ideal model in which to investigate the regulatory mechanisms of MSCs. The NVB may secrete signaling molecules, providing a niche for MSCs in the adult incisor. However, the functional significance of signaling molecules from the nerve within the NVB and the molecular mechanism by which they regulate MSCs are largely unknown. Significantly, our preliminary data shows that the trigeminal nerve secretes Fgf1, which acts directly on MSCs via FGFR1 to regulate tissue homeostasis, as loss of Fgfr1 in Gli1+ MSCs leads to retarded incisor growth, similar to the phenotype seen with compromised innervation. Fgf signaling regulates important downstream epigenetic regulators such as Arid1a and Arid1b to control the fate of TACs. Furthermore, loss of Arid1a specifically inhibits Wnt5a signaling, which may provide feedback to MSCs. Importantly, we have recently discovered that Runx2+/Gli1+ cells in the adult incisor are MSC niche cells, strategically positioned to coordinate MSC-to-TAC transition. Our study suggests that Runx2 is regulated by the epigenetic regulator Arid1b and controls p53 activity to mediate MSC-to-TAC transition and feedback to MSCs. Collectively, based on our preliminary data and taking advantage of well-established animal models, we propose to test the hypotheses that Fgf signaling from the trigeminal nerve regulates MSCs in the adult mouse incisor, Arid1a and Arid1b act downstream of Fgf signaling to control MSC-to-TAC transition, and Arid1b-Runx2 interaction regulates p53 activity to control TAC differentiation and feedback to MSCs to maintain tissue homeostasis. We propose the following specific aims to test our hypotheses. Specific Aim 1: To investigate whether Fgf signaling from the trigeminal nerve plays a crucial role in regulating MSCs in the adult mouse incisor. We will explore the molecular mechanism of Fgf signaling and its downstream targets in regulating the fate of MSCs to maintain mesenchymal tissue homeostasis. Specific Aim 2: To determine the role of Fgf- regulated Arid1a and Arid1b activity in controlling the MSC-to-TAC transition and maintenance of incisor tissue homeostasis. We will explore the mechanisms by which TAC fate is altered and their impact on MSCs in Arid1a and Arid1b mutant mice. Specific Aim 3: To investigate the molecular mechanism by which Arid1b regulates Runx2 expression and Runx2-regulated p53 signaling to control TAC differentiation. We will also investigate the functional significance of p53 in regulating TACs and the fate of MSCs in adult mouse incisors.

NIH Research Projects · FY 2025 · 2016-05

Enhancing regenerative capacities is a fundamental goal in medicine. As yet, the principles of salamander regeneration to augment mammalian healing are not directly applicable. Here we propose using lizards, more closely related to mammals yet exhibiting remarkable regenerative capabilities, as model organisms in a set of studies aimed at manipulating skeletal regeneration capacities. While both salamanders and lizards regenerate their tails, salamanders regenerate near-perfect copies of original tails, while regenerated lizard tails are known as an “imperfect replicates” with several key anatomical differences compared to originals. The most striking of these “imperfections” concerns the lack of dorsoventral patterning and segmentation in regenerated lizard tail skeletons. Progress made under our original proposal identified the signals regulating regenerated skeletal tissue induction and patterning, creating the first dorsoventrally-patterned regenerated lizard tails. This renewal proposal focuses on later stages of skeletal maturation that, given the proper signals, culminate in segmentation. Our recent comparative analyses indicate that regenerated skeleton segmentation is dependent upon three distinct milestones: (1) perichondrium patterning, (2) cartilage hypertrophy, and (3) periosteum formation. Both salamander and lizard regenerated tail skeletons begin as unsegmented cartilage elements. Our preliminary findings suggest a novel role for spinal cord meningeal tissues in regulating skeleton segmentation. Regenerated salamander, but not lizard, meninges contain specialized cell populations capable of recreating embryonic segmentation signals in adjacent perichondrium and initiating a signaling cascade that transforms the entire regenerated skeleton. Some of these signals induce cartilage hypertrophy in salamander cartilage before anti- ossification processes that dominate lizard skeletons have the chance to stagnate cartilage maturation. Other signals missing in lizard tails allow salamander bone cells to survive and promote periosteum development. Based on this comparative analysis, we hypothesize the feasibility of mechanistically based interventions to shift the “imperfectly” regenerating lizard tail to phenocopy the “perfectly” regenerating salamander tail. The Aims are: (1) Introduce patterning to regenerated lizard tail perichondrium by supplementing adult spinal cord meninges with embryonic segmenting cells; (2) Induce regenerated lizard cartilage hypertrophy by interrupting anti- maturation signals that result in dysregulated cartilage development; and (3) Promote periosteum formation within regenerated lizard tails by inducing bone cell survival and recruitment. An integrated approach is proposed, incorporating a unique, asexually reproducing lizard species with in vivo surgical manipulations to deliver cells and bioactive agents toward manipulating skeletal development. We believe that this approach will produce the first regenerated lizard tails with skeletons exhibiting cartilage maturation and segmentation. These studies will contribute towards mechanistic understanding of a vertebrate regenerative process, and may lead to improving skeletal healing in non-regenerative organisms, including humans.

NIH Research Projects · FY 2025 · 2016-05

Abstract This is a renewal application for the USC-Buck Geroscience Training Program in the Biology of Aging T32 Training Grant which was first funded as of May 1st, 2016. The training program is an unique cooperative venture of the University of Southern California's Leonard Davis School of Gerontology (USC) and the Buck Institute for Research on Aging (Buck). In 2014, in a truly joint venture, we created the very first dedicated Biology of Aging Ph.D. program in the USA. Students take courses at both institutions, many in person but also in a fully interactive on-line format and undertake first-year lab. rotations at both campuses before selecting a mentor and lab. at USC or the Buck. As we come to the end of the fourth year of our T32 grant we are pleased to report that our young PhD program is comprised of a current PhD student body of 41 PhD candidates. Although our inaugural admission to the program was in 2014, we have already graduated 7 PhD students and expect another 6-7 to graduate with their doctoral degrees by the end of the current grant period – average time to degree completion is 5 years. Thirteen predoctoral trainees and six postdoctoral trainees have been supported by our T32 grant. The goals of our Biology of Aging program are as follows: 1) To train pre-doctoral and post-doctoral researchers who will become leaders in the biology of aging field. Our training encompasses biochemistry, molecular biology, molecular genetics, physiology, neurobiology, computational biology, immunology, and pathology; 2) To enable students and post-doctoral fellows to become experts in the theory and methods of one specific area of biological research, but also enable them to incorporate methods and approaches from other disciplines of cutting-edge areas of aging research; 3) To provide our students and post- doctoral fellows with training which incorporates familiarity with the theory, methods, and data of the multiple aging disciplines that are essential to dealing with national issues arising from the aging of the population (e.g. susceptibility to, or poor outcomes from, viral diseases such as COVID-19) as well as insuring individuals a long, healthy life: 4) To provide predoctoral and postdoctoral trainees with structured curriculum and research experiences that lead to mastery of the knowledge, methods, analytic approaches, and theory of the gerosciences; 5) To provide both predoctoral and postdoctoral trainees structured exposures that allow them to gain understanding of the knowledge, methods, and theory of other relevant gerontological disciplines (sociology, psychology, public policy, elder-law, elder-economics, etc.) through scheduled activities such as the weekly Multidisciplinary Research Colloquium in Aging, and courses, such as GERO 592 – “Multidisciplinary Perspectives on Current Research in Gerontology.”; 6) To develop demonstrable research competence, emphasizing ethics, the responsible conduct of research, and methods for enhancing reproducibility through participation in research projects with mentors and development of independent research projects. Through these training goals, we expect our trainees to become leaders in the next generation of aging researchers.

NIH Research Projects · FY 2025 · 2016-04

Genome instability refers to changes in chromosome sequence, structure, or number that affect normal cell function. Such instability is characteristic of cancer, as well as certain developmental and neurological defects, and aging. Data from multiple organisms suggests that DNA replication stress is a key contributor to genome instability. Mechanisms that stabilize replication forks, prevent abnormal divisions, and promote DNA repair are a primary barrier to disease; therefore, understanding their function and the consequences of their disruption has direct relevance to human health. This proposal employs an established model cell biology system, the fission yeast S. pombe, to characterize how living cells respond to replication stress. S. pombe is a well-established genetic model for chromosome biology that shares many features with human cells. Significantly, nearly all the genes under study have orthologues in humans that have been associated with disease.. A key aspect of the approach is to use live cell imaging to characterize the response to replication stress and characterize its long term consequences. The overarching goal is to understand the dynamics of replication stress and its resolution in normal and mutant cells. This includes determining how the cell deploys molecular mechanisms to allow damage resolution and ensure chromosome segregations. We address the cellular and genetic consequences of division under stress; investigate how replication occurs late in G2 or mitosis to facilitate resolution; and examine the three-dimensional organization of repair structures. We have previously shown that the pericentromere is a fragile site, and we have expanded that to examine the ribosomal DNA and the role of phase separation in contributing to gene integrity, as well as identification of other fragile regions. A novel component is the analysis of replication stress during meiosis as a contributor to chromosome rearrangements associated with birth defects and infertility. By combining this cell biological approach with superb yeast gene-discovery tools, and identifying the molecular events that lead to abnormal divisions and further stress, this project tackles a critical gap in current understanding. What are the pathways that contribute to different responses to stress and their associated pathologies and how do they affect the biology of living cells? Together, these studies provide a holistic picture of how conserved proteins interact to maintain genome stability in a eukaryotic cell, identifying markers and risk factors for human disease.

NIH Research Projects · FY 2026 · 2015-09

Summary The Harmonized Diagnostic Assessment of Dementia for the Longitudinal Aging Study in India (LASI-DAD) is the first and only nationally representative and publicly available panel dataset on late-life cognition and dementia in India, purposefully designed for comparative analysis. We have drawn a sample of community- residing older adults 60+ years of age from 22 states in India and administered the Harmonized Cognitive Assessment Protocol (HCAP) originally developed by the Health and Retirement Study, a common cognitive test battery used by an international network of researchers, enabling new and innovative comparative studies. We have successfully completed two waves of data collection and released the data to the larger research community through the Gateway to Global Aging Data website. In this application, we aim to prepare for and collect Wave 3 of LASI-DAD. We will conduct follow-up interviews with all participants and recruit newly age-eligible and refresher samples, as done in Wave 2. Our overarching goals are to develop a first rate, longitudinal study of late-life cognition and dementia in India and to provide rich, high-quality data to the larger research community to advance our understanding of risk factors of late-life cognitive decline and AD/ADRD. Considering a relatively high mortality rate, our goal of studying cognitive aging over time, and need to capture interactions between dementia risk factors and social and physical contexts, we propose to lower the age threshold, recruit older adults at ages 55 and older, and expand the sample to achieve the necessary power. Altogether, we propose to recruit N=7,000 older adults at ages 55 and older, representative of the country. For Wave 3, we propose to bring further innovations in expanding an already comprehensive set of risk factors and improving measurements. Specifically, taking advantage of technological innovations in mobile sensing, we will collect novel data on (1) indoor environment (i.e., air pollution, temperature, humidity); (2) daily active and sedentary behaviors and digital biosignals (i.e., rest-activity rhythms, heart rate variability, oxygen saturation); and (3) egocentric audio recordings (centered around a certain person) from which we will capture social interactions, affect states, and background sounds. As with Waves 1 and 2 data, all generated data from Wave 3 will be released to the wider research community. We plan to host a series of webinars and capacity- building workshops, to train next-generation scientists. Altogether, LASI-DAD will provide an unprecedented opportunity to study risk factors for AD/ADRD and cognitive decline, especially in understudied groups with low literacy and education, enabling all interested researchers to investigate the relative contributions of key risk and resilience factors for AD/ADRD, generating new insights into the deterioration of cognitive abilities and dementia onset.

NIH Research Projects · FY 2024 · 2015-08

Modified Project Summary/Abstract (The abstract contained no specific references to the in vivo mouse experiments and therefore is unchanged): O-GlcNAc modification is a dynamic protein-modification that is absolutely required for embryonic development in mammals, and is misregulated in diseases, including diabetes, neurodegeneration and cancer. Although approximately 1,000 proteins are modified by O-GlcNAc, the effects of the vast majority of these modifications on protein function are completely unknown. The long-term goal of our research program is to fill in these missing gaps by determining the biochemical consequences of O-GlcNAc on proteins that are key to human disease. To accomplish this goal, we use a combination of carbohydrate and synthetic protein chemistries to build O-GlcNAc modified proteins for subsequent biological experiments. This chemical approach is uniquely enabling, as it is currently the only way to generate homogeneous and site-specifically O-GlcNAc modified proteins. We have been very successful and have used synthetic proteins to determine that O-GlcNAc has a multifaceted role in preventing the amyloid aggregation of proteins in neurodegenerative diseases. Specifically, we have found that O-GlcNAc both directly inhibits the aggregation of amyloid forming proteins and activates the activity of certain small chaperones. In this proposal we will continue to build on these discoveries. In Aim 1, we will determine how O-GlcNAc inhibits the early stages of α-synuclein amyloid formation. In Aim 2, we will test whether O-GlcNAc alters the structure/toxicity relationships of α-synuclein amyloids. In Aim 3, we examine how O-GlcNAc alters the small heat shock protein interactome. Finally, in Aim 4, we will determine if O-GlcNAc can rescue the activity of mutant chaperones that cause Charcot-Marie-Tooth disease. At the conclusion of these independent aims, we will have further unravelled the mechanisms by which O-GlcNAc inhibits protein aggregation and provided critical data to support the ongoing efforts to target O-GlcNAc therapeutically.

NIH Research Projects · FY 2024 · 2015-07

PROJECT SUMMARY The calvarial bones of the infant skull are separated by fibrous connective tissue joints called sutures and fontanelles. These joints are critical for early reshaping of the skull during birth and brain growth. Improper fusion of these joints, both premature and delayed, results in craniofacial deformities seen in numerous genetic disorders. In this proposal, we aim to study the relatively uncharacterized role of calvarial connective tissue (CT) to better understand its role in calvarial joint development and pathology. We hypothesize that lineage-dependent, regional signaling from CT orchestrates distinct differences in morphology, mechanism of fusion, and susceptibility to abnormal closure among calvarial joints. Using both cutting-edge multiomics technology and mouse genetics, we will resolve differences across calvarial joint CTs in both normal and disease contexts. Syndromes featuring premature suture fusion (craniosynostosis) and delayed fontanelle closure are commonly associated with variants in Fibroblast growth factor receptor 2 (FGFR2). Although most research thus far has focused exclusively on the role of Fgfr2 in the bone, our lab has revealed its importance in developing joint CT, including tendon and ligament. We will, therefore, apply these findings to study the role of Fgfr2 in calvarial CT using both loss- and gain-of-function alleles in mice. Our preliminary data shows that Fgfr2 loss-of-function in the neural crest cells (NCC) blocks normal contribution of CT fibroblasts to the advancing bone fronts in the anterior fontanelle (AF) resulting in its patency. Conversely, our gain-of-function model featuring the Fgfr2M391R variant in Bent bone dysplasia syndrome (BBDS) shows that activation in the NCC leads to multi-suture synostosis, most interestingly in sutures where only CT (and not bone) is NCC- derived. Conversely, Fgfr2M391R activation in mesoderm does not affect suture patency. The NCC-specific nature of these phenotypes suggests regional, lineage-dependent regulation of CT. In this proposal, we aim to identify and characterize gene expression and regulatory networks within CT fibroblast subtypes, as well as their spatial arrangements and fate trajectories, in different sutures and fontanelles. We predict that regional regulation of Wnt, Fgf, and retinoic acid signaling pathways play a key role in the organization and fusion of normal sutures by affecting cell fate potential. Additionally, we will explore the novel concept that non- canonical, nuclear signaling of Fgfr2 orchestrates these processes via differential gene regulation in calvarial CT fibroblasts. This study is expected to show that CT fibroblasts are signaling centers that direct calvarial joint development and underlie region-specific fusion patterns in congenital skull deformities.

NIH Research Projects · FY 2026 · 2015-05

Project Summary/Abstract Sound pressure produces force across the mammalian cochlear partition, creating a vibratory traveling wave that propagates longitudinally up the cochlear duct. The key feature distinguishing this process from the non- mammalian cochlea is amplification, whereby forces produced by thousands of outer hair cells (OHCs) sharpen and amplify the traveling wave. Our overarching objective is to understand how and why the complex biomechanics of the 3D multi-cellular and acellular arrangement that form the organ of Corti work together to create cochlear amplification, ultimately shaping the signals within the inner hair cells (IHCs) and auditory nerve. Specifically, we will determine how this process, which stems from the broadly-tuned basilar membrane, creates sharper frequency tuning. This question is significant on a basic science level because these biophysical processes underlie the ability to hear sounds just above the Brownian motion of molecules in air with an exquisite frequency resolution. This question remains unsolved and is clinically important because hearing loss, typically due to loss of cochlear amplification, reduces the understanding of speech in noisy environments. Our central hypothesis is that the afferent auditory nerve signal is not fully described by basilar membrane vibration. In aim 1, We will measure the vibration from 15-20 sequential IHC stereociliary bundles and from the center of the basilar membrane at the same longitudinal locations using OCM in vivo. We will assess whether IHC bundle vibration matches basilar membrane vibration. In aim 2, We will measure calcium levels in type I afferent auditory nerves under the IHCs in vivo during the presentation of sound stimuli using two-photon fluorescence imaging. We will correlate the spatial distribution of changes in calcium with the vibratory responses of IHC bundles collected within the same mouse. Together, these data will be interpreted to test our hypothesis. If our hypothesis is true, IHC bundles will vibrate differently than the basilar membrane and this difference will vary with the relative proportion of cochlear amplification. Furthermore, we expect auditory nerve activity to correlate with IHC stereociliary bundle stimulation and not necessarily basilar membrane vibration.

NIH Research Projects · FY 2024 · 2015-04

Project Summary Improved understanding of the neurobiological systems involved in excessive caloric consumption is critical for developing novel prevention and treatment strategies for obesity. Traditionally the field has focused on hypothalamic and brainstem substrates that control `homeostatic' food intake that occurs in response to energy deficits. In addition to studying these classic feeding centers, it is critical to also identify the systems through which higher-order brain regions regulate reward-driven food seeking and consumption based on learned, incentive, and hedonic cognitive factors. This project investigates the hippocampus (HPC) as a critical brain substrate integrating memory processes and feeding-related signals to regulate conditioned food- motivated behavior, including appetitive responses linked with excessive caloric intake and obesity. Our focus is on two HPC subregions that intersect feeding behavior and memory: the ventral HPC CA1 (CA1v) and the dorsal CA3 (CA3d). Our findings from the previous funding cycle identify a role for CA1v projections targeting the medial prefrontal cortex (mPFC), lateral hypothalamic area (LHA), and lateral septum (LS) as pathways functionally relevant to feeding behavior 1-3. Aim 1 experiments will advance these findings to identify the role of three HPC projection pathways (CA1v -> mPFC, LHA, LS) in HPC-dependent associative learning tasks that are relevant to excessive caloric intake and are based on categorically separate food-associated stimuli, including [1] interoceptive energy status cues, [2] external contextual cues, and [3] social-based olfactory cues. In addition to the appetitive associative memory processes described above, HPC-dependent meal- related episodic memory (recalling who, what, when, and where surrounding a meal) powerfully influences feeding behavior 4-8. Results from the previous funding cycle identified a neural pathway through which gastrointestinal (GI) vagus afferent nerve (VAN) signaling, traditionally studied in the context of meal size control, promotes HPC-dependent memory 9. Our preliminary results support the hypotheses that [1] the stomach-derived hormone ghrelin acts via GI VAN signaling to promote meal-related episodic memory, and [2] medial septum (MS) cholinergic signaling is a relay connecting GI VAN signaling and HPC function. These hypotheses are investigated in Aim 2 experiments using an innovative combination of state-of-the-art methodologies, including in vivo fiber photometry-based imaging of novel fluorescent genetically-encoded sensors for acetylcholine (ACh) 10,11 and stomach distention-dependent electrical VAN stimulation. The extent to which these ventral and dorsal HPC pathways converge through shared collateral projections, and/or common downstream targets is examined in Aim 3 experiments that utilize neural pathway tracing approaches to [1] map the collateral and 2nd-order projections of CA1v projections to mPFC, LHA, and LS, and [2] identify downstream projections of CA3d neurons that encode GI VAN signaling. Overall results from these three interconnected aims will identify novel neural systems that intersect memory and feeding behavior.

NIH Research Projects · FY 2025 · 2014-09

Most measures of adult health and longevity in the United States lag well behind those of other wealthy countries. Despite widening recognition of this crisis, we have only a limited understanding of its causes and few strategies to reverse them. This proposal, a renewal of the highly successful Network on Life Course Health Dynamics and Disparities in 21st Century America (NLCHDD) funded for the past ten years by the National Institute on Aging, lays out a plan to further develop the scientific groundwork, human capital, and data and analytic infrastructure to answer critical questions about the U.S. health and longevity crisis. Our overarching objective over the next five years is to strengthen and focus the NLCHDD to generate new evidence and disseminate data and analytic resources to better understand the trends and disparities in U.S. adult health and longevity across the life course and social and geographic contexts. We will do so through four specific aims. First, we will direct attention and resources toward five targeted scientific questions that will shed light on the multi-layered determinants of the troubling trends and growing disparities in U.S. adult health and longevity. These questions (described in detail in the proposal) focus on how social and geographic contexts—separately and collectively—shape trends and disparities in adult health and longevity across the life course. Second, we will strategically expand the interdisciplinary Network of emerging established scientists who will collaborate to investigate the key scientific questions. Third, we will provide development and training opportunities for Network scientists via pilot grants, grant proposal mentoring, working groups, and annual meetings. Fourth, we will develop and disseminate data and analytic resources to foster innovative research on the key scientific questions and advance science in this critical area. Our Network is innovative in its focus on the multi-layered contextual determinants of trends and disparities in adult health and longevity across the life course; in its openness and evolving nature; in its efforts to incorporate emerging investigators with more established ones; and in its central concern for support, mentoring, and development of emerging scholars. This emphasis on human capital development is reflected in all aspects of the Network's organization and operation. Our Network is also unique in its attention to focusing on research that can inform policies and interventions and provide the foundation for future research advances. Finally, our Network is unique in that it will facilitate the expansion, integration, and public dissemination of new and existing data resources for population health determinants across social and geographic contexts. The renewal Network brings together a PI team and four sites that span the U.S. with substantial experience in developing large-scale population health research and complementary scientific strengths connected to the Network’s aims. Using its complementary strengths, developmental maturity, and geographic representation, the NLCHDD leadership and overall Network is poised to make important scientific inroads over the next five years on the U.S. population health and longevity crisis.

NIH Research Projects · FY 2026 · 2014-04

ABSTRACT The USC Norris Comprehensive Cancer Center has a long history of commitment to and support for National Clinical Trials Network (NCTN) trials that extends beyond 20 years. It has served as the home of the USC UG1 Lead Academic Participating Site (LAPS) grant during the last reporting period and of the U10 NCTN support grant prior to that. The three areas of emphasis for the USC UG1 LAPS are (a) to provide scientific leadership across the NTCN through innovative and impactful clinical trials and though service on NCTN related committees; (b) to provide leadership in biomarker development and in integration of new technologies in NCTN trials; (c) to ensure robust accrual to NCTN trials with particular emphasis on expanding patient enrollment, while optimizing data quality and timeliness. The USC UG1 LAPS has demonstrated robust accrual to NCTN trials with over 500 patients recruited during the previous reporting period. Multiple accrual enhancement strategies have been implemented, and additional ones are planned. USC UG1 investigators have led or been part of the leadership of high impact trials such as SWOG/CALGB 80405 for colorectal cancer, SWOG 1815 for biliary tract cancer, and SWOG 1937 for urothelial cancer. They have also demonstrated exceptional leadership in leveraging NCTN trials clinical and specimen databases to generate biomarker results that have the potential to further advance the respective fields of investigation. For example, biomarker results from SWOG/ALLIANCE 80405 have identified prognostic and predictive markers on tissue and in blood which can further guide future drug development and therapeutic planning for colorectal cancer. In the genitourinary cancers space, innovative biomarkers developed by USC investigators while leveraging our unique liquid biopsy shared resource represent important scientific advances to enrich the patient populations for future trials. Our mentorship of early career investigators, along with our active involvement in the Experimental Therapeutics Clinical Trials Network (ETCTN), ensure that we continue to bring and lead innovative trials within the NCTN. Lastly, we continue to build on our long-standing tradition of excellence in community outreach and engagement and innovative approaches to enhance enrollment into clinical trials. The USC NCCC growing satellite network along with the facilitated referral model that we have created will position us well to continue to expand our clinical trial accrual. Furthermore, we will continue our contribution to clinical trials for rare tumors such as liver cancers, urothelial, penile, testicular, and sarcomas thanks to the expertise of our investigators and our large patient population.

NIH Research Projects · FY 2025 · 2014-04

PROJECT SUMMARY The broad goal of the proposed experiments is to identify key molecules that allow mammals to detect basic taste stimuli and generate electrical responses. Taste stimuli are detected by taste buds located on the tongue and oral cavity that contain distinct cell types, including the Type III taste receptor cells (TRCs) generally believed to mediate sour taste. Molecular mechanisms of taste reception have been a subject of intense investigation over the last 30 years, with great strides made in identifying receptors for bitter, sweet, umami and sodium taste. The receptor for sour taste was more elusive. In the last two grant periods, we identified Otop1 as a candidate sour receptor, and showed that it encoded a novel proton-selective ion channel (OTOP1), expressed in Type III TRCs. Our results from the last grant period showed that in Otop1 knockout mice (Otop1-/-) responses of isolated taste receptor cells and of the gustatory nerve to acids were strongly attenuated, confirming a key role of OTOP1 in sour sensing. However, we found no change in taste behavior to acid stimuli in Otop1-/- mice. In addition to acid stimuli, Type III TRCs also respond to high concentrations of salts. Of these, ammonium chloride, a breakdown product of amino acids that is a strong taste stimulus, is known to change the pH of the cell cytosol. In the last grant period we showed, quite unexpectedly, that OTOP1 is strongly activated by ammonium chloride, through a mechanism distinct from the pH-gating observed in response to acid stimuli. We also showed that gustatory nerve responses and behavioral aversion to ammonium chloride are attenuated in Otop1-/- mice. These results lead us to hypothesize that OTOP1 functions as a general pH sensor in the gustatory system, where it mediates response to taste stimuli that change extracellular or intracellular pH. We test this hypothesis through three aims. The first aim is focused on identifying pharmacological tools that can be used to activate or inhibit OTOP1 channels using a structured-guided virtual screen and patch clamp recording of heterologously expressed OTOP1 channels. Successful completion of this aim will provide new tools to assess the contribution of OTOP1 to the detection of other taste stimuli under Aims 2 and 3, complementing experiments with Otop1-/- mice. Aims 2 and 3 examine the contribution of OTOP1 to the detection of two stimuli previously shown to be mediated by Type III TRCs, water, and carbonation, using patch clamp recording of HEK-293 cells expressing OTOP1 channels and isolated taste receptor cells (Aim 2) and gustatory nerve recording, swallowing and taste behavior (Aim 3). The successful completion of these aims will lead to a comprehensive understanding of the mechanisms by which Type III taste receptor cells detect a wide range of non-canonical taste stimuli. The identification of taste modifiers may be used to enhance palatability of food, reducing the need to add sweeteners that contribute to the development of diabetes or salts that contribute to hypertension.

NIH Research Projects · FY 2025 · 2013-12

Endothelial cells (ECs) play a critical role in regulating vascular functions. We and others have demonstrated that, through epigenetic and transcriptional regulations, laminar pulsatile shear stress (PS) induces athero- protective genes to maintain EC homeostasis, whereas disturbed flow with oscillatory shear (OS) elevates athero-prone genes to cause EC dysfunctions. We have performed single-cell RNA sequencing (scRNA-seq) analyses to demonstrate that the transcriptomic effects of PS are distinct from those of OS. In addition, we have shown that PS caused enrichments of histone active mark (H3K27ac) at genes related to EC homeostasis and histone repressing mark (H3K9me3) at genes related to inflammation. We also demonstrated that the PS- induced H3K9me3 is dependent on the nuclear envelop proteins lamin/emerin. These findings have led to our hypothesis that PS and OS modulate EC functions through the coupling of lamin/emerin and chromatin to recruit histone modifiers, thus leading to differential changes in histone epigenetics and the associated genomic and transcriptomic regulations, and hence the opposite functional outcomes. The couplings between lamin/emerin and chromatin/genome can transduce the mechanical signals from physical space into genome space for gene and cell fate regulations. In order to test our hypothesis, we will conduct ChIP-seq to identify the lamin/emerin associated genome regions (LEAGRs) under PS and OS, and determine the LEAGR-associated histone modifications (i.e., epigenome). To visualize the differential flow-modulations of the dynamic interaction between LEAGRs and lamin/emerin in single live cells, we will employ endonuclease-deficient Cas9 (dCas9) together with small guide RNAs (sgRNAs) and engineered biosensors to track the dynamics of the histone profiles of these genomic loci, particularly those related to EC homeostasis or inflammation. We will then determine the roles of the locus-specific epigenetic profiles in regulating the transcriptome and cellular functions under different flows. We will conduct studies in vivo on aorta arch (OS) and thoracic aorta (PS) in mice to validate our in vitro results, and assess their impacts on atherogenesis by using atherosclerotic mouse models. Specifically, the MR (magnetic resonance)-guided FUS (focused ultrasound) (MRg-FUS) system will be used to remotely and noninvasively activate the inducible shRNA and CRISPRa/i (CRISPR activation or interference) systems to manipulate lamin/emerin and locus-specific histone epigenetics at local tissue areas of mouse with partially ligated carotid arteries to examine their functional roles in vivo. Accordingly, three specific aims are proposed: 1) In vitro investigation of lamin/emerin and EC epigenome/transcriptome under different flows, 2) Imaging of locus- specific epigenetic and chromatin remodeling in single live ECs, 3) In vivo examination and validation of the epigenome/transcriptome regulation in mouse atherosclerosis models. With the integrated multi-omics, single- cell imaging, and noninvasive locus-specific modulation, we will be able to identify and mitigate the key molecules to develop mechanomedicine for vascular diseases.

NIH Research Projects · FY 2025 · 2013-09

SUMMARY/ABSTRACT: USC TCORS OVERALL In response to new FDA landmark policies targeting tobacco products with flavors and other youth-attracting features, the non-combustible market is evolving in ways that could perpetuate adolescent and young adult (AYA) use. Shifts to the non-combustible tobacco market include the emergence of modern oral nicotine products (ONPs; flavored nicotine pouches, non-therapeutic gums, lozenges, gummies) with rapidly increasing sales, e-cigarettes and ONPs with novel flavors and higher nicotine concentrations (e.g., concept flavors with ambiguous flavor names that are difficult for the FDA to classify but offer fruity sensations and e-cigarettes with >6% nicotine), and novel marketing platforms (TikTok and other social media that highly engage AYAs). USC TCORS responds to these challenges with a theme of “Informing regulation of the evolving market of non-combustible products to protect young people.” The overall Center specific aims are: Aim 1) Conduct four interrelated projects that will: (a) determine how modern ONPs and e-cigarettes impact AYA tobacco product use uptake, escalation, abuse liability, and poly-use patterns across populations; (b) identify product characteristics and marketing approaches that amplify these impacts; Aim 2) Augment our Center’s infrastructure with three cores that will optimize the productivity and impact of our regulatory science (Administrative Core, Measures and Materials Core, Data Processing and Analysis Core); and Aim 3) Develop the next generation of tobacco regulatory scientists via developing the careers of doctoral and post-doctoral trainees, and investigators transitioning to tobacco regulatory science (TRS). Collectively, USC TCORS will provide key evidence determining whether availability of certain non-combustible product classes (e.g., new ONPs), types (e.g., products that can be used discreetly), characteristics (e.g., e-cigarettes and ONPs in concept flavors), and marketing strategies (e.g., social media influencers) increase AYA’s risk of initiating and progressing along the tobacco use trajectory. This research will directly inform FDA’s responses to numerous e-cigarette, ONP, and other illegally marketed non-combustible products. It will provide rigorous actionable evidence to guide FDA decisions on pending marketing applications from tobacco product companies. The data will also inform FDA policies regarding which illegally marketed products should be targeted as enforcement priorities. These achievements will build upon our successful USC TCORS Centers that, since 2013, has published 237 peer reviewed articles (166 of these published since 2018). Further, we have a substantial track record of: (a) providing foundational evidence informing FDA’s development of new policies; and (b) rapidly adapting our research to inform FDA revision of previous policies to keep pace with the evolving market; this is evidenced by 31 citations of TCORS research in FDA policy documents. FDA Scientific Areas: Behavior, Addiction and Marketing

NIH Research Projects · FY 2025 · 2013-08

ABSTRACT: Idiopathic pulmonary fibrosis (IPF) is an age-associated disease characterized by progressive accumulation of scar tissue in the lungs. High morbidity rates in patients with IPF mandate more effective treatments. A new paradigm implicates accumulation of alveolar epithelial cells (AECs) that are compromised by loss of endoplasmic reticulum (ER) chaperone glucose-regulated protein 78 (GRP78), a master regulator of proteostasis, in the pathogenesis of lung fibrosis. However, the molecular mechanisms and metabolic landscapes characteristic of age-related PF have not been identified. Our goal in this project is to use alveolar epithelial type II (AT2) cell-specific Grp78-KO mice, modeling the age-specific GRP78 reductions seen in AECs, to establish how GRP78-loss impairs mitochondrial bioenergetics and biosynthesis, leading to development of an aging phenotype in AT2 cells and subsequent lung fibrosis. Perturbed proteostasis and activation of ER stress response signaling known as the unfolded protein response (UPRER) have been suggested as one possible mechanism underlying observed AEC abnormalities. We found that GRP78 is downregulated accompanied by activation of ER stress/UPRER in AT2 cells from IPF patients and aged mice/human individuals. We further show that GRP78 undergoes reactive oxygen species (ROS)-induced carbonylation (the most common form of oxidative stress-induced damage to proteins) in AT2 cells from IPF patients and aged mice. In our model, AT2 cell-specific Grp78-KO mice develop aging-associated phenotypes including disrupted proteostasis, mitochondrial dysfunction, abnormal mTOR signaling and metabolism, apoptosis and senescence in AT2 cells with subsequent lung fibrosis. In this study, we highlight an emerging theme that GRP78 loss-disrupted proteostasis leads to gradual decline of mitochondrial function and metabolic fitness, which in turn is tightly linked with phenotypic changes of AECs (apoptosis and senescence) with the endpoint of lung fibrosis. The use of Grp78-KO mice to model GRP78 loss in AECs allows us to rigorously examine how impaired proteostasis promotes development of an aging phenotype in AT2 cells. Guided by our published and unpublished results, we hypothesize that age-related AEC-specific downregulation of GRP78 induces unresolved ER stress/UPRER, which in turn dysregulates metabolism and overactivates mTOR leading to AEC dysfunction and subsequent lung fibrosis in IPF. We propose the following specific aims to address this hypothesis: AIM 1: To identify mechanisms whereby disturbed GRP78-dependent mitochondrial function and metabolism in AEC promote the development of PF. Aim 2: To characterize the role and mechanisms of GRP78 reduction in mediating AEC aging phenotype and PF. Aim 3: To determine the therapeutic potential of targeting GRP78 loss-mediated pathways in age-associated PF in vivo and in vitro. The proposed studies will provide rationale for how therapeutics that target metabolism might achieve specificity for pro-fibrotic cells as anti-IPF agents.

NIH Research Projects · FY 2025 · 2013-07

PROJECT SUMMARY The nervous system fine-tunes synaptic output to ensure reliable communication, partly through kinase-drive protein phosphorylation. Alterations in phosphorylation dynamics profoundly affect neurotransmitter release, synaptic vesicle recycling, synaptic growth and plasticity, and are closely associated with neurodevelopmental and neurodegenerative disorders. The evolutionarily conserved DYRK1A kinase plays a critical role in neurodevelopment and is implicated in several neurological conditions, including autism, Down syndrome, intellectual disabilities, and Alzheimer’s disease. Despite its importance, the precise mechanisms by which DYRK1A regulates synaptic function remain unclear, and its physiological substrates are largely unidentified. Using Drosophila as a model, our previous work demonstrated that the DYRK1A homolog, minibrain kinase (MNB), is essential for synaptic transmission, modulating clathrin-mediated and bulk vesicle endocytosis through the phosphorylation of synaptojanin. To advance our understanding of MNB functions in vivo, we developed an innovative approach that integrates proximity labeling with phosphoprofiling to identify novel physiological substrates and pathways regulated by MNB in neurons. Building on these preliminary findings, this proposal aims to investigate two novel MNB-regulated pathways at the synapse: selective autophagy and neuropeptide release. Aim 1 will examine the role of MNB/DYRK1A in regulating autophagy at the synapse. We hypothesize that MNB phosphorylation of a protein required for selective autophagy facilitates the removal of damaged synaptic components and toxic aggregates. Additionally, we will investigate the role of MNB-dependent phosphorylation in modulating TDP-43 aggregation in a fly model of frontotemporal dementia and amyotrophic lateral sclerosis. Aim 2 will determine and validate MNB/DYRK1A's role in regulating neuropeptide release. The proposed research will provide critical insights into MNB's regulatory roles at the synapse, offering new perspectives on the molecular mechanisms of synaptic activity and potential therapeutic avenues for neurodegenerative diseases. Additionally, our innovative kinase substrate identification method can be broadly applied to other kinases, offering a powerful tool for future studies.

NIH Research Projects · FY 2025 · 2013-07

PROJECT SUMMARY/ABSTRACT We propose to assemble a multi-PI/PD Linked Clinical Research Center (LCRC) at the University of Southern California (USC) and Saint Luke’s Mid America Heart Institute (MAHI) in Kansas City – high volume centers committed to enrolling patients in clinical trials. The USC-MAHI LCRC will leverage CTSI programs at both USC and MAHI, while also bringing in implementation science experts from Washington University in St. Louis, and the University of California San Francisco (UCSF) to build an educational platform that spans our centers and trains the next generation of clinical researchers in cardiothoracic surgery. This unique LCRC will increase the capacity of the CTSN to successfully conduct trials in regions with high disease burden, low socioeconomic status, ethnic and racial diversity. The specific aims of the USC-MAHI LCRC are to (1) leverage USC’s experience within the CTSN and its synergistic relationship with MAHI to increase the CTSN’s capacity to successfully conduct clinical trials in areas of high disease burden, low socioeconomic status, and ethnic and racial diversity, (2) foster the development of the affiliate site in the performance of randomized control trials, trial mechanics, and increase the affiliate’s ability to independently participate in federally sponsored trials in areas of need and high disease burden, (3) assemble a collaborative team of expert researchers at USC, MAHI, and the NHLBI K-12 T4 Implementation Science research programs that will apply innovative implementation science research methodology designed for sustainably improving the population-level translation of future CTSN studies, and (4) establish a development platform that is inclusive with respect to gender and race for the next generation of independent cardiothoracic implementation science researchers at both the primary and affiliate sites. These specific aims will require building a large multidisciplinary team spanning multiple institutions. Aim 1 will be conducted through the robust multidisciplinary clinical networks at both the primary and affiliate site, while Aim 2 will involve an innovative and novel mentoring plan between the primary and affiliate site, which leverages multiple entities, including the Clinical and Translational Science Institutes at both sites. Aim 3 will be accomplished by bringing experts in implementation science at USC, MAHI, Washington University in St. Louis, and the University of California San Francisco into the CTSN infrastructure to assist with trial design and execution. Healthcare policy and economic experts at MAHI and the Schaeffer Center for Health Policy & Economics at USC will also engage the CTSN. Aim 4 will be addressed through the formation of a Clinical and Implementation Research Skills Program Plan which, while based at USC, will leverage resources across multiple institutions including the clinical trial, community engagement, and KL2 programs at the Southern California and Frontiers Clinical and Translational Science Institutes, the Mid America Heart Institute Cardiovascular Outcomes Research Fellowship (T32 program), and our experts in implementation science.

NIH Research Projects · FY 2025 · 2012-09

The health, social and economic issues associated with dementia, and the disparate burden of dementia across different racial/ethnic populations, are of such magnitude and complexity that they require a vantage point from multiple disciplines. Generating scientific evidence to advance dementia research requires rigorous methods applied to the best available data. The University of Southern California’s Alzheimer’s disease and Alzheimer’s disease Related Dementias Resource Center for Minority Aging Research (USC AD/ADRD RCMAR) brings a distinct capacity for integrating theories and tools from myriad disciplines including but not limited to economics, sociology, and gerontology, using large, complex data sets, and applying rigorous panel data and quasi-experimental methods to generate innovative AD/ADRD research. Our interdisciplinary faculty have the support and expertise to advance research in our focus area: pathways by which social, behavioral and economic factors, and policies and health systems affect disparities in risk of AD/ADRD, and affect disparities in the health, health care and economic outcomes of persons living with dementia. We build upon our successful 10-year history of advancing the research and careers of early stage investigators. We bring together the infrastructure, leadership, interdisciplinary expertise and resources to: (1) increase the number and scholarly achievements of early stage investigators and; (2) develop new, innovative lines of dementia research. The USC AD/ADRD RCMAR is housed in the Schaeffer Center for Health Policy and Economics, which brings together expertise in AD/ADRD from across USC’s schools, and maintains a large data core, analytical programming team, and external affairs team to support AD/ADRD research and disseminate findings for impact. To this we add resources and leaders from our partner NIA funded centers: USC’s Roybal Center for Behavioral Interventions of Aging, Alzheimer Disease Research Center, Center for Economic and Sociodemographic Study of AD/ADRD, and USC/UCLA Center on Biodemography and Population Health. Importantly we have partnered with Spelman College, Howard University, and California State University Fullerton. Their junior researchers and senior scholars and leaders are uniquely positioned to bring different perspectives and broaden the field of AD/ADRD research. We propose a set of interrelated activities across three cores: (1) a Leadership and Administration Core to provide leadership, management, communication, and evaluation systems for achieving our goals; (2) a Research Education Core to selectively provided pilot research awards to junior scientists and team-based mentorship and professional development to support rigorous research; (3) an Analytical Core to develop new data and analytical resources to support innovative dementia research.

NIH Research Projects · FY 2025 · 2012-07

PROJECT SUMMARY/ABSTRACT Our dentition plays important daily roles in speech, mastication, and determination of facial shape and expression. The tooth root is essential for the proper function of the dentition because it anchors the tooth within the maxilla or mandible. In addition, the root helps transmit and balance occlusal forces through periodontal ligaments and serves as a passageway for the neurovascular bundle that supplies blood and innervation to our teeth. To date, we have limited understanding of the regulatory mechanisms of root development and patterning. Understanding the signaling mechanism that regulates the fate of progenitors during tooth root development and patterning, and how signaling pathway disruption can lead to craniofacial malformations, will advance stem cell-mediated tooth root regeneration. Importantly, we have identified Gli1+ progenitors that are crucial for the development and patterning of roots. These progenitors are heterogenous and may have different functions. To gain a comprehensive understanding of all progenitor cells and their roles in tooth root development, we developed a spatiotemporal single-cell atlas of neural crest lineage diversification and cellular function during this process. Building on this work and preliminary data, we have designed studies to test the hypotheses that (i) FGF signaling from the trigeminal nerve directly controls progenitors during root development; (ii) Piezo1 and Piezo2 function downstream of FGF signaling to control the fate of progenitors; and (iii) Kdm6b and Ezh2 antagonistically regulate Trp53 expression downstream of FGF signaling to regulate root elongation and patterning. We propose the following three specific aims to test our hypotheses. Specific Aim 1: To investigate how FGF signaling from the trigeminal nerve controls the fate of progenitors during root development. We will also investigate how FGF- regulated downstream target genes exert their functional specificity in regulating root development. Specific Aim 2: To investigate the functional significance of Piezo1 and Piezo2 as FGF signaling mediators in regulating the fate of progenitors during root development. We will elucidate the molecular mechanism(s) by which signals from the dental mesenchyme control root development. Specific Aim 3: To investigate how Kdm6b controls the fate of progenitors during root development. We will also investigate the antagonistic interaction between Kdm6b and Ezh2 in regulating Trp53 to control root patterning and uncover the regulatory mechanism by which Trp53 controls progenitors in root development.