University Of California Los Angeles

NIH Research Projects · FY 2025 · 2021-09

PROJECT SUMMARY/ ABSTRACT Trauma is a leading cause of death and disability in Sub-Saharan Africa (SSA), particularly in Cameroon, where a higher burden of injury is reported compared to similar settings in the region. Injury research focused on prevention and improvements in trauma care, such as trauma Quality improvement (QI), have led to significant reductions in the burden of injury in high-income countries. Yet, there remain critical gaps in the current trauma research infrastructure in SSA due to limited training opportunities. The Sustainable Trauma Research, Education, and Mentorship Program (STREaM) will seek to fill this gap, building on an existing long-term partnership between the University of California and the University of Buea (Buea) to provide innovative training to Cameroonian post-graduate candidates with a focus on novel, cutting edge quantitative tools. STREaM Cameroon program will aspire to establish a cadre of graduate trainees with multidisciplinary expertise in Injury prevention and control, quality improvement, and quantitative methods that can address limitations posed by the time-dependent, dynamic, and incomplete nature of trauma-related data. The program will leverage recent advances in research methodologies, such as machine learning and implementation science, that are particularly suited to trauma research. STREaM Cameroon aims to accomplish the following objectives:1) Train a critical mass of multidisciplinary scientists in trauma research through MPH, PhD, and post-doctoral pathways who will form the foundation for an Injury Center at the Buea; 2) Develop and implement a combination of short, medium, and long-term quantitative and trauma research curricula co-taught by U.S. and Cameroonian faculty to sustainably strengthen existing offerings at the Buea; 3) Provide mentored research opportunities for trainees to apply quantitative skills to trauma QI projects utilizing the partnership’s existing research and data collection infrastructure in Cameroon; and 4) Integrate trainee scholars into a robust scientific network through existing international organizations and the creation of a Cameroonian Trauma Network to serve as an ongoing community of practice. During the five-year program, a total of 2 post docs, and eight PhD and Master’s level students per year will be trained using a team mentoring approach. Master’s and PhD students will take part in online courses throughout their training, administered through the University of California Berkeley and University of California San Francisco’s Clinical and Translational Science Institute. All students will participate in mentored research. Additionally, post-docs will spend one semester at Berkeley receiving in-person training to prepare them for faculty positions at Buea. Upon completion of the STReaM program, graduates will successfully engage in innovative, evidence-based research to improve the quality of trauma care and reduce the burden of injury among vulnerable populations in SSA. STReaM Cameroon graduates will thus be trained and equipped to mentor the next generation of scientists in trauma research, playing a critical role in influencing healthcare practices and policy locally and internationally.

NIH Research Projects · FY 2025 · 2021-09

NETWORKING CORE: PROJECT SUMMARY/ABSTRACT The overarching objective of the KUH-ART Networking Core is to bring together all NIH-funded trainees (Kidney/Urology/Hematology) for formal and informal opportunities to learn, communicate, interact, and collaborate in a vibrant scientific community. This Core’s responsibilities are twofold, to: 1) ensure the development of key infrastructure and operations that will provide peer networking and outreach; and 2) support ongoing communication and events across the range of NIH trainees and activities of KUH-ART TL1 and facilitate access to all Professional Development and Training Core programs. The Specific Aims are: Specific Aim 1. To establish a digital platform to facilitate learning and social networking across all trainee levels. After a review of available components for a learning platform, we propose to develop our system around two robust software packages: Canvas (for repository building), and Slack (an integrated messaging tool). This foundation will create a virtual community for KUH-ART trainees, fostering communication that is driven by the trainees themselves. We will plan to work with other funded U2C sites to reach consensus towards a shared digital platform architecture to link trainees across our sites. Specific Aim 2. To facilitate communication between KUH-ART trainees and their mentors to promote long-term trainee engagement, commitment and professional accomplishment. Aligned closely with Professional Development Core efforts, we will use networking opportunities to facilitate career development, including alumni and other key individuals that will foster trainees’ biomedical research insights and trajectories in different ways (e.g., academic; industry; government; non-governmental organizations). Specific Aim 3. To create a seamless path for communications across KUH-ART partner institutions and networking across external programs. Across existing programs at UCLA, Cedars-Sinai Medical Center, Charles Drew University, and the UCLA-Harbor Medical Center/Lundquist Institute, we will operationalize methods to streamline communications, activities, content curation and delivery for sharing within our KUH-ART network. Trainees will be able to interact, both online and in-person, with individuals within the UC2, as well as across other training programs. The successful implementation of this Networking Core will ensure that NIH-funded trainees in biomedical sciences will be connected, digitally and otherwise, in a community that fosters their learning, communication, mutual support, scientific growth, and career development.

NIH Research Projects · FY 2024 · 2021-09

PROJECT SUMMARY/ABSTRACT Myocardial infarction (MI) predisposes patients to ventricular tachycardia/fibrillation (VT/VF) and sudden cardiac death. After MI, alterations within the cardiac sympathetic nervous system (SNS) have been tightly linked to VT/VF. These alterations include inflammation, structural and functional remodeling within the stellate ganglion, and heterogeneous remodeling of intramyocardial sympathetic nerves in the scar-border zone. These result in enhanced and dysfunctional cardiac sympathetic neurotransmission that lead to VT/VF. Although spinal afferent signaling is enhanced after MI, the arrhythmogenic potential of spinal afferents (via maladaptive interactions with cardiac sympathetic nerves) has not been explored. Based on novel data from our group, the goal of this proposal is to test the hypothesis that chronic enhanced cardiac afferent signaling is the primary driver of sympathetic neural remodeling and dysfunction that causes VT/VF. Pilot studies from our group using epicardial resiniferatoxin (RTX) to deplete cardiac TRPV1 afferents in porcine support the rationale that persistent afferent signaling (beyond the acute ischemic phase) plays a central role in shaping the neural and cardiac substrates that lead to VAs. We will test our hypotheses using novel tools from a multidisciplinary team of investigators in 3 aims, in porcine with MI. In aim 1, we will determine whether post-MI structural, neuroinflammatory, and functional neuronal remodeling within stellate ganglia are caused by persistent TRPV1 afferent signaling. In aim 2, we will determine whether persistent cardiac TRPV1 activation amplifies intramyocardial neurotransmitter release to increase VT/VF risk. This will be accomplished using simultaneous cardiac electrophysiologic mapping and real time in vivo detection of intramyocardial Norepinephrine and neuropeptide Y levels. We will determine whether TRPV1 afferent depletion attenuates arrhythmogenicity by normalizing neurotransmitter release patterns. In aim 3, we will define the optimal site of RTX delivery for clinical management of VT/VF [Epicardial vs. Stellate Ganglion vs. Epidural application]. This will guide clinical translation of afferent neuromodulation. The results of this proposal may shift how arrhythmogenesis is approached after MI, and guide the development of new therapies that prevent altered afferent signaling after MI to fill a major clinical gap.

NIH Research Projects · FY 2025 · 2021-09

PROJECT SUMMARY Proposed is a five-year research career development plan focused on evaluating the mechanisms of thyroid autoimmunity during cancer immunotherapy. The candidate, Dr. Melissa G. Lechner, M.D., Ph.D., is an Assistant Professor of Medicine in Endocrinology at the University of California, Los Angeles (UCLA). This proposal builds upon her strong background and provides new training in mouse models of autoimmunity, advanced transcriptomic and proteomic techniques, and bioinformatics. During the award term, Dr. Lechner will be mentored by Dr. Maureen Su, M.D., a leader in the field of autoimmune disease and experienced physician scientist with a track record of mentoring more than 30 students, post-doctoral fellows, and junior faculty. She will have additional support from co-mentor Dr. Greg Brent, M.D., a renowned thyroid researcher, and a strong team of advisors with technical and content expertise. Immune checkpoint inhibitor (ICI) therapies have revolutionized cancer treatment, but their use is limited by the development of unwanted autoimmune side effects seen in up to 60% of patients. These immune-related adverse events (IrAE) interrupt cancer treatment and lead to organ dysfunction, hospitalization, and even death. The cause of IrAEs remains unknown, however, recent data suggest that toxicity can be uncoupled from anti- tumor effects. Thyroiditis, a common IrAE, is ideal for studying mechanisms of IrAE development because of the ability to directly sample immune infiltrates in the thyroid by fine needle biopsy and to compare with Hashimoto’s thyroiditis (HT), a well-described spontaneous thyroid autoimmune disease. Interestingly, ICI-thyroiditis has both similar and distinct features from HT. Dr. Lechner developed a mouse model that recapitulates human IrAEs from checkpoint immunotherapy, including multi-organ immune infiltrates and autoantibodies. Using this model, she has identified a role for RORg+ Th17 and Tc17 cells and T peripheral helper (TPH, CXCR5-ICOS+PD1+) cells in IrAEs. These cell populations have previously been associated with spontaneous autoimmune diseases, including HT, but not yet IrAE. Additionally, studies in patients with checkpoint-inhibitor thyroiditis showed intrathyroidal T cell accumulation and increased RORg+ T cells. Therefore, in Specific Aim 1, Dr. Lechner will determine the role of RORg+ Th17 and Tc17 and TPH cells in IrAE development using a mouse model and analysis of thyroid-infiltrating cells patients with ICI-thyroiditis vs. HT. The absence of autoantibodies to known thyroid antigens (e.g. thyroid peroxidase thyroglobulin) in many ICI-thyroiditis patients also suggests immune attack against yet unidentified targets. Thus, in Specific Aim 2, Dr. Lechner will identify the antigen targets in ICI thyroiditis, evaluate immune responses to these antigens, and compare them known antigens in HT. With this work, Dr. Lechner aims to advance our understanding of mechanisms underlying thyroid autoimmune disease and checkpoint immunotherapy toxicities, and obtain the skills needed to become an independent investigator.

NIH Research Projects · FY 2025 · 2021-09

Project Summary/Abstract Dr. Tikvah Hayes is a postdoctoral research fellow in the laboratory of Dr. Matthew Meyerson at the Dana-Farber Cancer Institute and the Broad Institute. Her long-term career goal is to reduce cancer-associated mortality and suffering by determining the mechanisms of cancer development and identifying attractive therapeutic strategies for better patient care. To accomplish this goal, Dr. Hayes uniquely leverages both functional genomics and molecular biology methods to answer fundamental questions related to cancer biology. The human epidermal growth factor receptor (HER) family of receptor tyrosine kinases (RTK) is frequently altered in cancer. Targeted panel sequencing of patient tumors has revealed a number of activating alterations in both EGFR and HER2. As a consequence, several generations of molecularly targeted EGFR and HER2 therapies have been designed and have proved efficacious for some patients with either EGFR- or HER2-mutant cancers. However, a subset of patient-observed HER family variants lacking a reported function persist and in the absence of functional data are classified as variants of unknown significance. It remains unknown whether all EGFR and HER2 missense mutations are oncogenic drivers and are sensitive to clinical EGFR or HER2-targeted therapies. This proposal aims to functionally and mechanistically characterize the role of EGFR and HER2 missense variants in promoting oncogenesis and resistance to tyrosine kinase inhibitor (TKI) therapies. Aim 1 will seek to nominate alternative strategies for patients harboring rare EGFR mutations where no clinically approved EGFR- targeted therapy exists. Aim 2 will evaluate the oncogenic capacity of rare EGFR variants. Finally, in Aim 3, HER2 variant oncogenic capacity and TKI sensitivity will be interrogated. The proposed research will greatly improve our understanding of how RTK missense variants promote cancer development and resistance to targeted therapies. Dr. Hayes will learn new techniques which will include organoid culturing, in vivo cell line xenografts, intrathoracic lung injections, tumor imaging and tissue processing/staining, while simultaneously enhancing her career development through training in grant-writing, science communication, and leadership. During the K99 phase, Dr. Hayes’ research and training will be carried out under the primary mentorship of Dr. Matthew Meyerson, a leader in cancer genomics, and will be additionally complemented by collaborations with experts in high- throughput genetic screening, clinical genomics, structural biology, and in vivo mouse modeling, as well as mentoring from an advisory committee consisting of Drs. Michael Eck, William Hahn, Pasi Janne, and Carla Kim.

NIH Research Projects · FY 2025 · 2021-09

Training Core Abstract The broad goal of KUH-ART is to prepare our trainees to become leaders in cutting edge research in the nephrology, urology and hematology areas. Our trainees will have either a clinical background or basic science background combined with an interest in solving medically relevant questions in the KUH area. UCLA KUH-ART will consolidate existing fragmented research training programs under one umbrella and create a larger regional entity where trainees are part of an interactive cohort. The Specific Aims of the KUH-ART are: 1. Guide trainees in developing a strong foundation of knowledge in biological and health sciences relating to different aspects of kidney, benign urologic and benign hematologic diseases. 2. Provide individualized hands-on mentored research training in each trainee’s focus area of basic, translational, clinical or computational research. 3. Develop trainees’ scientific writing and communication skills for presentations, publications, and grants (see Professional Development Core). 4. Maintain an interactive and supportive academic environment that promotes the development of team research skills and collaborative experience needed for successful, independent scientific careers as members and leaders of interdisciplinary teams. 5. Develop a KUH community through a versatile instructional and mentoring platform geared to the trainees, mentors, the KUH scientific community and other research stakeholders at UCLA and nation-wide (see Networking Core). 6. Devise and implement comprehensive tracking and ongoing evaluation in multiple areas of the program by structured feedback from trainees, mentors, Internal and External Advisory Boards and NIDDK to identify weaknesses and institute continuous quality improvement. We aim to prepare outstanding pre- and postdoctoral scholars for research careers in benign KUH and allied disciplines, promote multidisciplinary team research, and expand research workforce with both physicians and non-clinician investigators pursuing or newly attracted to KUH research. Our goal is to attract an outstanding group of pre- and postdoctoral applicants who seek a cross-training experience across the research spectrum from basic sciences and translational medicine to health services and informatics. We have carefully selected 56 outstanding mentors who have a record of commitment to biomedical research training in the KUH and related areas. The proposed new UCLA KUH-ART integrates and mutually potentiates the previously fragmented research training and career development enterprise at UCLA and affiliated institutions. Ultimately, our graduates will accelerate the volume, pace, and translation into practice of scientific discoveries and innovations that improve the care and outcomes of patients across the lifespan, from children to the elderly.

NIH Research Projects · FY 2025 · 2021-09

PROJECT ABSTRACT The proposed training program aims to provide professional training through academic curricula, research experiences, and continuing education courses in industrial hygiene and environmental health sciences to graduate students and industrial hygienists in the Southern California region, and to recruit diverse undergraduate and graduate students to join the graduate school pursuing master and doctoral studies in occupational and environmental health sciences related fields. The Southern California Superfund Research Program (SCSRP) will build on the strong educational and research environments at the University of California Los Angeles (UCLA) and the well-established UCLA Industrial Hygiene and Environmental Health and Sciences (EHS) programs to develop a modern and multidisciplinary training program for students and the community of industrial hygienists. Our mission is to prepare next-generation professionals for effective management of stressors caused by emerging technologies such as nanotechnology. Our multidisciplinary team includes the highly diverse faculty members and student population at UCLA, UC Irvine (UCI) and California State University Fullerton (CSUF) and Long Beach (CSULB). Our faculty team has a proven track record in mentoring students with a combined total of more than 350 trained graduate and undergraduate students and postdoctoral fellows. Our team consists of industrial hygienists, environmental scientists, population health experts and community partners. Our training will focus on occupational exposures and effects, digital learning techniques, practices and protection guidance regarding engineered nanomaterials, emerging infectious agents, and nanotechnology- enabled products including consumer electronic products and their related waste to be managed at the generation and disposal stages. It is essential to provide proper training on the hazards of exposure to new materials used in emerging and rapidly changing technologies and their effective control strategies for workers, industrial hygienists, and the students, who will make up the future workforce. Our program broadens the scope of current educational approaches with new and unique training regarding emerging technologies which are unavailable in our other existing training programs. We anticipate training 6, 7 and 8 graduate students in years 1, 2, and 3-5 respectively. This includes 2-3 nine-month trainees and 4-5 summer trainees per year. We also will recruit a diverse population of undergraduate students, with openings to 4-5 students per year with the 5-day training workshop. During the five-year program period, we anticipate providing 37 training positions for master and doctoral students; and for undergraduate students, providing them with 24 training opportunities in the 5- day workshop in the hopes of future recruitment into graduate school. We will also train more than 100 industrial hygiene professionals through the continuing education courses. Upon completion of our program, participants will be well-trained industrial hygienists influential in the next generation workforce. These outcomes will aid the expansion of the existing educational programs in industrial hygiene and environmental health sciences.

NIH Research Projects · FY 2024 · 2021-09

A major challenge in neuroscience is to uncover how defined neural circuits in the brain encode, store, modify, and retrieve information. Adding to this challenge is the fact that neural function does not operate in isolation from but rather within living, behaving animals. To tackle this challenge, significant advancement of neural, behavioral, and computational tools is needed along with new experimental approaches to enable the detailed study of neural circuits within the context of complex behavior and naturalistic, ethologically relevant environments. This proposal aims to do exactly this by designing, implementing, and sharing a highly innovative, community driven, neuro-behavioral recording and real- time processing platform capable of uninterrupted, months-long wireless recording of neural and behavioral activity across a colony of animals in large, naturalistic environments. We will develop a new generation of ultra-light weight, fully wireless miniature microscopes (Miniscopes) for neural imaging in truly naturally behaving animals. These wireless Minsicopes will be powered remotely through power-over-distance technology and capable of imaging neural activity with single cell resolution across thousands of neurons. In combination with transgenic mouse lines, these wireless Miniscopes will continuously record neural activity across months as animals live, uninterrupted, in large, enriched environments. An extensive array of behavioral devices will be developed and natively integrated into the platform for animal tracking, parsing complex behaviors, and detecting animal-environment interactions. All tools and techniques built for this project will be actively shared through our open-source website and workshops. Neural and behavioral data will be processed, in real-time, through a novel computational framework (hardware and software) and shared openly through an online database accessible to the neuroscience community. Pilot experiments using this platform will investigate the long-term formation, stability, and generalization of hippocampal cognitive maps within ethologically relevant environments. Once validated, subsequent experiments will incorporate tasks proposed by the neuroscience community encompassing both basic science and investigation of neurological disorders. A single dataset generated with this platform will track a colony of animals’ complex behavior and neural activity through learning, recall, sleep, social behavior, and aging. This novel approach has the potential to fundamentally transform the way neuroscience research is thought about, implemented, and shared and will undoubtedly provide new insight into neural function and disorder.

NIH Research Projects · FY 2025 · 2021-09

PROJECT SUMMARY/ABSTRACT Social dysfunction is a core feature of schizophrenia. Many individuals with schizophrenia experience social disconnection, a lack of social contact with friends and family. Social disconnection is associated with reduced quality of life and many negative health effects, but most current treatments do little to address it. The development of new interventions is currently hindered by a lack of scientific understanding about how differences in the way individuals’ brains process information contribute to social disconnection, and a lack of biomarkers associated with social functioning. Recent research in non-clinical social neuroscience points to a compelling model that may help to explain social disconnection in schizophrenia and would provide the basis for a new biomarker of social dysfunction. Specifically, research using functional magnetic resonance imaging (fMRI) and inter-subject correlation (ISC) analysis methods shows that people whose brains tend to respond more normatively to dynamic, naturalistic stimuli (e.g., video clips) tend to have more social connections, perhaps because more other people experience the world in a similar way, whereas people with less normative responses tend to have fewer social connections. Converging evidence suggests that many individuals with schizophrenia are likely to have less normative responses to such naturalistic stimuli, which could help to explain why social disconnection is common in the disorder. However, the ISC method has not yet been used to study social dysfunction in schizophrenia. This project will fill this research gap by translating ISC research methods from non-clinical research in order to investigate how ISCs relate to social disconnection in schizophrenia. Individuals with schizophrenia (N=200) and matched healthy controls (N=100) will each complete one fMRI scan during which they will view naturalistic video stimuli and complete two established paradigms that assess important domains of social processing: social cue perception and mentalizing. We will characterize ISCs based on responses to the naturalistic video stimuli and characterize brain activity related to social cue perception and mentalizing using standard analyses. The study will test whether ISCs differ between the two participant groups and evaluate to what extent group ISC differences relate to individual differences in social connection. We will also characterize ISC normativity for each member of the schizophrenia group, using the control group as a reference, to assess whether brain response normativity is associated with social disconnection, and whether individuals’ degree of social disconnection can be predicted from it. The project will also test whether an ISC-based measure is more sensitive to individual differences in social disconnection than established fMRI measures. Results from this project will improve understanding of how brain activity relates to social dysfunction in schizophrenia. ISC measures are also expected to constitute a biomarker of social dysfunction that may be useful for identifying individuals at high risk of social disconnection, targeting treatments toward individuals most likely to benefit from them, or assessing outcomes in future clinical trials.

NIH Research Projects · FY 2026 · 2021-09

PROJECT SUMMARY/ABSTRACT – Overall The prediction, detection, management and prevention of persistent post-concussive symptoms (PPCS) represent some of the most important neurological challenges in the science of traumatic brain injury (TBI) today. For the purposes of this application, PPCS will refer to post-concussive symptoms lasting ≥3 months, consistent with the National Institute of Neurological Disorders and Stroke Common Data Elements for concussion. We approach this using the concept of endophenotypes, quantitative behavioral traits characterized by objective measures using blood-based, imaging or autonomic measures or other techniques. Understanding the endophenotypes of PPCS will provide opportunities for early identification and potentially for intervention, treatment and prevention. The overarching goal of this application is to develop a predictive algorithm for PPCS endophenotypes in early and middle adolescents (EMA) to inform clinical screening, management and future research. Our specific aims are: Specific Aim 1. In a Development Cohort, develop and characterize individual objective biomarkers predictive of PPCS by combining biomarkers with symptom clusters and neuropsychological function. Biomarkers will be examined in 3 Research Cores: Autonomic, Imaging and Blood- based. Specific Aim 2. To develop and characterize endophenotypes of PPCS in EMA by combining two or more objective biomarkers with symptom clusters and neuropsychological measures. Specific Aim 3. To prospectively validate endophenotype biomarkers from Aims 1 and 2 in a broad group of EMA with concussion (Validation Cohort). Specific Aim 4. To create a clinically useful risk stratification algorithm using validated biomarkers, in conjunction with symptoms and neurobehavioral function, which will predict the development of PPCS. The Development Cohort will be recruited from existing concussion and sports medicine clinics at 6 sites within the Four Corners Youth Consortium (4CYC). This cohort will include subjects presenting from 0-12 months after concussion, will likely be enriched in those with PPCS, and has proven feasible for recruitment into an observational prospective registry. The Validation Cohort will be recruited from the same clinics but also expanded to primary care clinics/networks and emergency departments (acutely/subacutely) and followed to a chronic time point. With this broader and more generalizable cohort, the candidate blood-based, imaging and autonomic biomarkers from the Development Cohort will be tested and validated. It is from these 2nd cohort data that a predictive algorithm (likely combining clinical and biomarker measures) will be developed.

NIH Research Projects · FY 2025 · 2021-09

The Sustainable Academic Capacity Building for Excellence through Research and Training (SACERT) Program will be under the leadership of two US based highly experienced Principal Investigators. SACERT goals are to increase timely progression to completion of doctoral degree among pre-doctoral students, and to improve the educational and mentoring experiences of 12 participating institutions in South Africa. The focus of SACERT is chronic stress and non-communicable chronic mental disorders including substance abuse, depression, and posttraumatic stress disorder across the life course. SACERT responds directly to current national governmental initiatives to train pre-doctoral students who are at the dissertation stage in the mental health field. We focus particularly on building capacity of scholars in the nursing, social work, occupational therapy, psychology, psychiatry, and public health fields to conduct translational mental health-related research via two pathways, Tracks A and B. We will provide short-, medium-, and long-term research training which includes coursework and research training in an intensive 3-month in-residence training at UCLA and a long-term mentorship (Track A), as well as annual workshops in South Africa (Track B). The Specific Aims are to: 1) Implement a two-year multidisciplinary training program at UCLA and in South Africa for four pre-doctoral Scholars (“Track A,” who will be post- master’s degree, with approved dissertation proposals) per year (cumulative n=16) to: a) enhance their research skills in the areas of chronic stress and non-communicable chronic mental health disorders, b) support their research productivity during the two-year tenure, and c) strengthen their relationships with mentors; 2) Implement a training model involving annual virtual and/or in-person modular workshops for the Aim 1 Scholars (n=4/year) and mentors (n=4/year) and additional Scholars who will be master’s and predoctoral students (“Track B”; n=36/year for four years; cumulative n=144) and faculty (n=36/year), to: a) strengthen research and mentoring skills related to chronic stress and non-communicable chronic mental health disorders, b) build and sustain a supportive network of Scholars and mentors across universities, and c) disseminate the results of Scholars’ and mentors’ research related to chronic stress and non-communicable chronic mental health disorders; 3) Provide mentorship training to Scholars’ mentors (n~16/year) to: a) enrich the mentor-scholar dyad, b) increase capacity in South African university environments, and c) promote sustainability of our research mentorship model; and 4) Evaluate these training and mentorship efforts with regard to: a) time to degree, productivity related to publications and grant proposals; sustainability of training and mentoring (Track A) and b) knowledge and skills gained (short- and long-term), and satisfaction with educational and mentoring experiences (Tracks A & B).

NIH Research Projects · FY 2025 · 2021-09

PROJECT SUMMARY A promising strategy to improve neuromodulation therapies (e.g. deep brain stimulation) in Parkinson’s Disease (PD) is to develop stimulation paradigms that target specific neural signals. Most previous work has aimed to identify and reduce pathologic signals. An unexplored alternative approach is to identify and enhance neural signals that promote movement. Several scenarios known to improve movement in PD patients are the presence of visual movement targets, rhythmic auditory stimuli, and motivational incentives. The goal of this proposal is to capitalize on these scenarios to identify biomarkers of movement facilitation that may serve as targets for future neuromodulation therapies. This approach has potential to provide novel therapies for symptoms refractory to current treatments, such as freezing of gait. Previous work examining neural mechanisms of movement facilitation in PD have yielded inconsistent results. This may be due to a failure to account for well-known heterogeneity in behavioral benefits across PD patients and the assumption that different cueing phenomena exert motor benefits through a single neural mechanism. The studies proposed here test the overarching hypothesis that 3 different types of cues (visual targets, rhythmic auditory stimuli and reward incentives) facilitate movement through distinct neuroanatomic circuits and electrophysiological mechanisms, by leveraging known variability in behavioral cueing benefits across patients. Aim 1 is to demonstrate behavioral dissociations between the 3 forms of movement facilitation within patients and relate variability in cueing benefits to integrity of dissociable neuroanatomic circuits as measured by resting state and diffusion tensor magnetic resonance imaging (MRI). Aim 2 is to characterize the electrophysiological correlates of behavioral benefits for the different cue types using electroencephalography (EEG) and intraoperative electrophysiological recordings obtained during implantation of deep brain stimulator in the globus pallidus internus. This work will augment my prior skills in task fMRI, transcranial magnetic stimulation (TMS) and electrophysiology by extending training in multiple modalities (high density EEG, resting state fMRI, DTI); build my analytic skills in advanced multivariate statistics; and advance my expertise in PD motor physiology. My mentorship team comprises experts in PD neurophysiology and neuromodulation therapies, and non-invasive studies of inter-individual differences in motor neurophysiology. Coursework in multivariate statistics and seminars in advanced EEG and neuroimaging applications will further my development. The environment at UCLA has a rich interdisciplinary neuroimaging community, state-of-the-art image acquisition facilities including Ahmanson-Lovelace Brian Mapping Center and Staglin Center for Cognitive Neuroscience and a renowned clinical Movement Disorders Division. The career development plan forges a path to become an independent physician-scientist, using multiple modalities to characterize neurophysiologic biomarkers of heterogeneous disease features in Parkinson’s disease to improve therapy development and delivery.

NIH Research Projects · FY 2024 · 2021-09

ABSTRACT Single-cell RNA sequencing (scRNA-seq) provides genome-wide information about gene expression at the resolution of individual cells. The unprecedented scope of these data is revolutionizing our understanding of development and tissue homeostasis as well as diseases like cancer. A major issue with scRNA-seq, however, is the shear scale of the data, consisting of ~20,000 gene expression measurements in thousands to millions of cells. Effective computational approaches are clearly required to translate data of this size and complexity into actionable biological insights. For instance, scRNA-seq data are approximately 20,000-dimensional, and as a result all available analysis pipelines rely on multiple dimensionality reduction steps. This usually entails a combination of linear tools like PCA and non-linear techniques like t-SNE and UMAP. The data is generally reduced to between 10- and 100-D for data analysis (e.g. clustering into distinct cell types) and 2-D for visualization. The problem, however, is that dimensionality reduction can lead to loss of information. We recently showed that this loss of information is dramatic: for any given cell, over 95% of its neighbors are changed in the process of dimensionality reduction. This complete change in the structure of the data can introduce significant noise and bias into the analysis, and suggests the critical need for alternative approaches. The premise of this application is that reducing bias in scRNA-seq data analysis will maximize our ability to extract meaningful information from the data. In this proposal, we focus on developing new algorithms to address three specific steps in the typical analysis pipeline: (1) Dimensionality Reduction: Our hypothesis is that deep neural networks can be explicitly trained to maximize the amount of information that can be retained for both data analysis and visualization. (2) Feature Selection: Not all genes are equally informative for downstream analyses, so researchers generally choose a subset of genes based on variation in the population. We have shown that standard approaches to selecting genes convolve true biological variation with technical noise from the experiment. We hypothesize that statistical models based on our understanding of sources of technical noise can be used to select more informative genes. (3) Cell clustering: Clustering the data to determine cell types is critical, but cells with different identities often form complex, overlapping geometries in gene expression space that are difficult for existing algorithms to resolve. Our hypothesis is that new clustering tools, guided by prior knowledge and leveraging innovations in clustering from image segmentation, can overcome this problem. We will build these new tools and test them against existing benchmark datasets and novel data generated by our experimental collaborators. We will also integrate these tools into popular scRNA-seq analysis packages. Successful completion of the proposed work will allow the field to extract more biologically relevant information from the burgeoning set of scRNA-seq datasets.

NIH Research Projects · FY 2024 · 2021-09

1 ABSTRACT 2 3 There is growing incidence of neurodevelopmental disorders (NDD). Causes for NDDs include ischemic 4 placental disorders (IPD) with fetal/intra-uterine growth restriction (FGR/IUGR), perinatal asphyxia, and 5 hypoglycemia. Exploration of connections between aberrant placental health and NDDs has occurred. Besides 6 the intra-uterine environment (IUE), genetic mutations also contribute to a subset of NDDs, forming an IUE-gene 7 paradigm. We have focused on the neuronal glucose transporter isoform 3 (GLUT3; gene: glut3). Glut3 gene 8 mutations are reported with NDDs/cognitive disabilities. Glut3 mutations with exposure to an adverse IUE may 9 portray expansive effects upon NDD endophenotypes. Development of diagnostics and early dietary 10 interventions is much needed. We have shown that IUGR and hypoxia-ischemia perturb developing brain glut3 11 expression perturbing neurobehavior. We also created murine glut3 deletions, that reduced trans-placental 12 glucose transport leading to postnatal NDD (excitatory autism spectrum disorders), where small extracellular 13 vesicles (sEVs) fueling diagnostics, and ketogenic dietary intervention are being explored. We next disengaged 14 placental glut3 gene from neural-specific glut3 mutations towards deciphering independent neural mechanisms 15 behind NDDs. We also created glut3 expressing human brain organoids from induced pluripotent stem cells 16 (iPSCs). Assessing pre-clinical ketogenic dietary effects targeting NDDs, will yield novel results. To achieve this 17 goal, we will test the hypothesis, that IUE and neural glut3 mutations/dependency cause NDDs by 18 perturbing neurodevelopment with a potential for amelioration. The aims are: 1) a. To investigate changes 19 in cell numbers per cell type and cell-specific transcriptomics in cerebral cortices (CC) with neural progenitor 20 cellular (NPC) absence of glut3 by using nestin-driven conditional null postnatal mice. This will be accomplished 21 by 10X genomics single cell (sc) RNA-sequencing and bioinformatic analyses, followed by in-situ hybridization 22 (ISH)/immunohistochemical (IHC) detection of major changes in key transcribed/translated products in specific 23 cell types. b. To assess administration of prenatal versus postnatal ketogenic diet as an early intervention in 24 ameliorating NDD. 2) a. To explore neural processes and cellular profile in CC with or without MoMCR/IUGR in 25 targeted absence or overexpression (OE) of glut3 in excitatory neurons/NPCs using Emx1-driven conditional 26 null and OE mice during the life course from embryonic and postnatal to the adult. This will entail deconvoluting 27 bulk CC RNA-seq with ISH/IHC, with non-invasive detection of perturbed transcriptome/proteins in circulating 28 sEVs. b. To examine the impact on CSF/plasma metabolomics, neuronal function and neurobehavior in the adult 29 offspring. 3) a. To develop cortical organoids from control iPSCs with glut3 OE and/or glut3 deletions, and 30 examine cellular profiles by deconvoluting organoid RNA-seq with scRNA-seq and ISH/IHC. b. To interrogate 31 the effect of hypoxia and hypoglycemia with/without ketones/lactate on iPSCs, NPCs and cortical organoids.

NIH Research Projects · FY 2025 · 2021-09

PROJECT SUMMARY Anterior uveitis is the most common form of intraocular inflammation in children. Children tend to have more chronic courses than adults and thus require more frequent examinations for screening and monitoring of inflammation. Clinical grading of anterior chamber (AC) inflammation, both cell and flare, is currently performed at the slit lamp utilizing the widely accepted Standardization of Uveitis Nomenclature (SUN) Working Group criteria. However, this system has limitations since it is non-continuous and semi-quantitative. A rapid, reproducible, and quantitative technique to evaluate inflammation is of paramount importance in children as they are often unable to cooperate with prolonged examination at the slit lamp. This K23 Mentored Patient-Oriented Career Development Award proposal seeks to evaluate objective measures of intraocular inflammation to improve the diagnosis and monitoring of anterior uveitis in children. This award will provide Dr. Edmund Tsui, a uveitis specialist and Assistant Professor at the Stein Eye Institute at the University of California, Los Angeles, with the protected research time and formal coursework towards a Master’s of Science in Clinical Research to establish himself as an investigator in patient-oriented research in uveitis. This award will provide Dr. Tsui with the support to achieve the following goals: 1) to learn biostatistics and epidemiology, 2) to become skilled at image acquisition, processing and analysis, 3) to learn about the design and implementation of clinical trials. Dr. Tsui has assembled an outstanding multi-disciplinary team of mentors to ensure that he will achieve these goals. His mentorship team consists of Dr. Gary N. Holland (Professor of Ophthalmology and an expert in pediatric uveitis), Dr. Srinivas R. Sadda (Professor of Ophthalmology and a world-leader in ophthalmic image processing and analysis), and Dr. Deborah K. McCurdy (Professor of Pediatrics, Division of Pediatric Rheumatology and an expert in pediatric arthritis). We will pursue the following specific aims: 1) develop a standardized, reproducible technique using anterior- segment optical coherence tomography to quantify AC cells, 2) longitudinally evaluate AC flare using laser flare photometry, and 3) create a predictive risk stratification model based on objective measures of intraocular inflammation. The long-term goal is that these results would support the use of objective measures in routine clinical practice and as endpoints in clinical trials. Ultimately, earlier detection and improved monitoring of uveitis in children can prevent permanent vision loss and disability. This research will lead to the submission of an R01 grant prior to the end of the K23 award to enable Dr. Tsui to become an independent clinician-scientist.

NIH Research Projects · FY 2025 · 2021-09

ZIP8 is a transmembrane importer of divalent metals into the cytosolic space through the cell membrane and from subcellular compartments. Although GWAS data implicate hypofunctional ZIP8 mutations in a myriad of serious pathologies, there is a paucity of mechanistic studies investigating its functions during homeostasis or pathologic conditions. We have created two novel ZIP8 knockout (KO) mouse models in order to study this transporter, an inducible whole-body KO and a lung epithelium-specific KO, and our preliminary data indicate significant roles of ZIP8 in lung host immunity, splenic iron recycling, and placental nutrient transport. Specific Aim 1. Define the functions of ZIP8 as a metal transporter in the immune response to lung infections. ZIP8 expression is higher in the lung than in any other organ system, but its biological function is unknown. Our preliminary data show that lung ZIP8 is located primarily in the alveolar epithelium, where it imports iron from the alveolar space, is upregulated with both inflammatory stimuli and gram-negative bacterial infection, and is important for induction of the antioxidant enzyme manganese superoxide dismutase by lipopolysaccharide (LPS). We will characterize ZIP8-mediated transport of Fe, Zn, and Mn during both homeostasis and LPS lung injury using radioactive metal tracers, and study the effects of ZIP8 on the outcomes of gram-negative bacterial and fungal lung infections. Specific Aim 2. Define the role of ZIP8 in splenic macrophage erythrophagocytosis and iron recycling. Our preliminary data show that spleen ZIP8 is primarily expressed in macrophages, ZIP8 deletion induces splenic iron sequestration within red pulp macrophages and serum iron restriction, and spleen ZIP8 expression is regulated by splenic iron levels. We will identify the location, activity, and regulation of ZIP8 within splenic macrophages. Using mouse models of altered iron handling with iron overload, iron deficiency, and hemolysis, we will also characterize the function of ZIP8 in iron recycling during both baseline homeostasis and stress. Specific Aim 3. Define the contribution of ZIP8 to maternal-fetal nutrient transport in the placenta. The placenta is the second highest ZIP8-expressing tissue type in humans, and global ZIP8 ablation in mice is embryonic lethal. Our preliminary data show that placental ZIP8 is expressed in syncytiotrophoblasts, indicating a key role of ZIP8 in the transport of nutrient metals from maternal circulation to the embryo. We will use a novel trophoblast specific ZIP8 KO mouse to define the role of ZIP8 in placental transport of Fe, Zn, and Mn, perform confirmatory studies using primary human trophoblasts, and investigate ZIP8 regulation by maternal iron status. Our proposal will answer fundamental questions about the pathophysiologic functions of this critical metal transporter in metal-mediated lung host immunity, splenic iron recycling, and placental transport of nutrient metals. The findings will inform our clinical approaches in diagnosing and managing the many pathologies associated with disrupted metal homeostasis.

NIH Research Projects · FY 2025 · 2021-09

PROJECT SUMMARY The reprogramming of somatic human cells to induced pluripotent stem cells (iPSCs) by only four transcription factors (TFs) Oct4, Sox2, Klf4, and cMyc (OSKM) is one of the most striking remodelings of gene regulatory networks. The remarkable ability of OSKM to reprogram diverse somatic cell types into iPSCs that are functionally indistinguishable from embryonic stem cells indicates that OSKM leverages a fundamental mechanism for network remodeling that may be generally applicable to all cell fate transitions. Previous studies of reprogramming have identified the crucial role of cooperative TF binding in repressing somatic programs and activating pluripotent ones. However, associating TF binding dynamics and epigenomic remodeling with key bifurcation events during reprogramming is confounded by the highly heterogeneous nature of the reprogramming process and the lack of knowledge regarding how the transition from somatic to pluripotent regulatory programs occurs in individual cells. In this project, we aim to model the regulatory network underlying the cell fate change of reprogramming using three types of single-cell multi-omic profiles generated from critical time points during reprogramming. We will interrogate the network leveraging natural perturbation of reprogramming and pluripotency by genetic variants. Genetic variation is well known to modulate the regulatory network of pluripotency and contributes to the variability of cellular phenotypes and differentiation capacity of iPSC lines. We will generate population-scale single-cell joint profiling of RNA and DNA methylation (snmCT- seq), joint profiling of RNA and chromatin accessibility (scRNA + ATAC-seq) and single-nucleus joint profiling of chromatin conformation and DNA methylation (sn-m3C-seq), allowing the cell-type-specific determination of transcriptome, chromatin accessibility and methylation states at regulatory elements, as well as enhancer-gene looping to connect non-coding variants to their regulatory target. To integrate OSKM binding with the single-cell transcriptomic and epigenomic dynamics, we will determine the allele-specific binding of TFs and histone modifications using a pooled-alleles ChIP-seq strategy. We will use Dynamic Regulatory Events Miner (DREM) to construct predictive models by integrating transcription factor-gene interaction information with time- and pseudotime-series genomics data. To determine the genetic regulation of the reprogramming network, we will apply the novel statistical method FastGxE to distinguish cell-type-specific from the shared genetic component of gene expression regulation, to enhance the sensitivity for identifying cell-type-specific quantitative trait loci (QTLs). To test the regulatory network, we will experimentally determine the function of network hub genes and non-coding variants using high-throughput CRISPR interference and precise variant replacement experiments. Our proposed project integrates diverse approaches including single-cell multi-omics, computational modeling, and genetic engineering, and will likely provide new insights into the mechanism by which TFs remodel regulatory networks of cell type identity and serve as a model for similar analyses in other systems.

NIH Research Projects · FY 2025 · 2021-09

PROJECT SUMMARY/ABSTRACT Episodic memories integrate the content of human experience in space and time and constitute the core of one's identity. Memory formation involves processing, and constructing interpretations of the incoming information in our daily lives and is one of the first functions compromised in neurodegenerative diseases such as Alzheimer's Disease. With population aging, we face a “Cognitive Tsunami” of millions of people with memory disorders. Thus, understanding neural mechanisms of memory, and finding interventions that enhance these processes is a critical endeavor with the potential to improve the lives of countless people world-wide. Although it is established that memory is critical for cognitive well-being, and sleep is critical for memory consolidation, the underlying mechanisms in the human brain are poorly understood. Research on memory and sleep so far has suffered from a gap between non-invasive cognitive research in humans and detailed electrophysiological research in animals. Moreover, most human studies are dominated by stimulus response methodologies where the presented stimuli constitute limited, discretized, aspects of memory. This approach, albeit well-controlled, is far from the rich narrative of episodes we experience. Thus, to mechanistically probe human memory consolidation, it is imperative to (a) employ methodologies that incorporate the continuous and multimodal nature of experience; (b) identify relevant neural activation patterns and how they are transformed and reactivated during sleep; (c) establish means to causally modulate memory processes during sleep. Building upon our exploratory U01 project, this proposal seeks a breakthrough in our understanding by going beyond the state-of-the-art, and via the application of integrative and multidisciplinary approaches. It capitalizes on a highly unique opportunity to record and modulate neuronal activity of a large number of single neurons and neuronal assemblies in the human brain. In parallel, it exploits the high dimensionality of the data as an asset through the use of cutting-edge Deep Learning (DL) algorithms, which have emerged as promising analysis tools. Specifically, the project will investigate the presence, and decoding, of distributed neural patterns associated with memory for different aspects of experience during wakefulness and identify their reactivation during sleep. The proposal aims to selectively modulate memory via application of novel closed-loop stimulation in sleep in concert with the DL model predictions. We anticipate that this project is poised to shed light on the relationship between sleep and memory, and its modulation from a novel perspective. Such an ambitious goal can only be achieved with unrivaled combination of experience, access to a clinical setting, and interdisciplinary collaborations such as those proposed in this project. By combining the opportunity to stimulate and record neural activity with the computational power of artificial intelligence, this project aims to offer findings with far reaching implications for basic neuroscience and contribute to the development of novel therapies for human memory disorders.

NIH Research Projects · FY 2025 · 2021-09

Although enrollment in private Medicare plans has risen from 12.8% in 2004 to 37.5% in 2019, the health consequences of large numbers of older Americans enrolling in these plans are not clear. This is of particular concern for high-risk patients, people with selected chronic conditions that place them at higher risk of adverse outcomes. Private Medicare plans are typically managed care plans that receive a capitated payment for each plan enrollee and therefore face financial incentives to control costs. Although high-risk patients could potentially benefit if some private Medicare plans are able to improve health outcomes through care coordination or by steering patients to high-quality health care providers, they could also be adversely impacted if some private Medicare plans achieve cost savings by reducing provision of necessary or preventive care. This Career Development Award proposal, “Private Medicare Plans and Health Outcomes for Older Adults,” focuses on leveraging new data—from private Medicare encounter claims, a state all-payer claims database, and the private Medicare risk adjustment system—in order to better understand how private Medicare plans impact health outcomes for older adults, particularly among high-risk patients. This work will focus on evaluating the performance of specific private Medicare plans—as opposed to evaluating private Medicare plans as a whole—something made possible by the recent availability of comprehensive health care claims data from private Medicare plans. Examining plan-specific effects will allow for a more complete understanding of whether there are specialized private Medicare plans that can improve health outcomes for high-risk patients. The research aims encompass three areas: 1) estimating plan-specific effects of private Medicare plans on quality of care and patient outcomes, 2) evaluating the performance of private Medicare plans that specialize in improving health outcomes for high-risk patients, and 3) using prediction methods to quantify the potential for favorable selection by private Medicare plans. This work will make use of quasi- experimental methods to estimate whether enrollment in specific private Medicare plans is associated with better health outcomes; for example, by studying patients who transition from an employer- sponsored plan to a private Medicare plan, or patients who switch from traditional Medicare to a private Medicare plan. This award will also support additional training toward three career goals that support the research aims: 1) developing expertise in measurement of health care quality and improvement of patient outcomes, 2) acquiring knowledge of clinical management of high-risk patients, and 3) building skills in statistical methods used for prediction and modeling health outcomes. These goals will be achieved through coursework, mentorship, seminars, and research, among a highly productive group of health economics and health policy scholars at a leading institution.

NIH Research Projects · FY 2025 · 2021-09

PROJECT SUMMARY Regeneration of native skin elements – hair follicles, sweat glands and adipose tissue, is a highly thought after outcome of wound healing. While, in principle, very large skin wounds in adult mice can spontaneously regenerate new hair follicles and new adipocytes, commonly studied small wounds in mice and clinical wounds in humans heal with a far less desirable fibrotic scarring. If and how adult skin wounds can be directed to replace the natural tendency for healing with a scar with regeneration of native skin elements remains unknown. This application is inspired by a serendipitous discovery that adding an antigen to our novel biomaterial, the Microporous Annealed Particle (MAP) hydrogel, can induce regeneration of new hair follicles when added into normally fibrotic small mouse skin wounds. This immunomodulatory MAP gel provides wound-resident immune cells with the molecular triggers that elicit an adaptive immune response to enhance macrophage responses. Further, our studies on naturally regenerating very large skin wound model show that macrophage-fibroblast interactions are essential for stimulating new hair follicle regeneration. Through an integrated bioengineering, bioinformatic and experimental approach, this application will focus on testing our new hypothesis that by engineering MAP gels to have specific immune triggers, interactions between T-cells, macrophages, and fibroblasts in the wound can transform normally profibrotic healing response into highly desirable regenerative response. The first aim of the proposed research is to mechanistically establish the lymphocyte and macrophage subsets and the molecular signaling pathways required for MAP formulations we have created to elicit hair follicle regeneration. This will be achieved using bioinformatic analyses of transcriptomics, proteomic, and functional profiling at single-cell resolution. confirmed with in vivo loss of function/ transgenic mouse studies lacking key immune pathways or cells MAP gels. The second aim is to engineer new types of immunomodulatory MAP gels designed to maximally induce T-cells and macrophage pro-regenerative signals while minimizing pro-fibrotic signals using a high-throughput in vitro assay. The third aim is to determine how MAP gel-induced immune signals enhance lineage plasticity of wound fibroblasts that is prerequisite for new hair regeneration. This will be achieved via an advanced bioinformatic analysis on single-cell transcriptomic data and functional gain- and loss-of-function studies on wound immune cells and fibroblasts. The study premise is based on newly accepted-for-publication and extensive preliminary data. The proposed studies are significant because they will establish new immune cell-driven mechanism for enhancing fibroblast plasticity and activating embryonic-like regeneration of native skin elements in adult wounds. The proposed studies are innovative because they will establish new types of immune-modulating biomaterials, and new paradigm of biomaterial-triggered regenerative response in adult tissues. In the future, the results of this study will drive the development of next-generation immune-modulating wound biomaterials for potential clinical use.

NIH Research Projects · FY 2024 · 2021-09

Project Summary/Abstract Genome instability increases the rates of mutations, chromosomal rearrangements, and aneuploidy and drives many age-related human diseases, including cancer. The challenges of replicating our genome and epigenome with each cell division requires molecular pathways that ensure the propagation of stable genomes to daughter cells. To date, the roles of mammalian noncoding RNAs (ncRNAs) in the maintenance of genome stability is incompletely understood. We propose that filling this gap is essential to expand our knowledge of human development and homeostasis and to identify novel risk factors that contribute to human disease. In fission yeast, the RNA interference (RNAi) pathway acts during DNA synthesis at the repeats of pericentromeres via locally produced ncRNAs to establish the heterochromatin needed for genome stability. It is unclear if similar cell cycle-specific RNAi mechanisms of genome stability are present in mammals. In preliminary studies, we used mouse stem cell systems to map high-confidence interactions of the RNAi effector Argonaute (Ago) proteins with ncRNAs. We determined that Ago binds directly to pericentromeric ncRNAs. Furthermore, we found that pericentromeric ncRNAs are overexpressed during DNA synthesis in Ago-deficient cells and observed multiple signatures of genomic instability caused by full Ago depletion. In parallel, previous studies in mouse models have established that overexpression of pericentromeric ncRNA suffices to cause genomic instability and tumorigenesis. Based on these intriguing findings, we hypothesize that pericentromeric ncRNA expression, established via cell cycle-specific Ago regulation, is critical for the maintenance of genomic stability in mammalian cells, analogous to fission yeast. In this RO1 research project, we examine the potential roles of RNAi in preventing genomic instability caused by accumulating pericentromeric ncRNA and/or disruption of local heterochromatin structure. We propose to define cell cycle- specific Ago activities to elucidate the molecular triggers for pericentromere regulation and to determine how pericentromeric ncRNAs contribute to genome stability. In Aim 1, we will determine how and when Ago functions at pericentromeres for the establishment of heterochromatin. In Aim 2, we determine the direct molecular consequence of Ago recruitment to chromatin. Finally, in Aim 3, we will elucidate how ncRNAs control Ago activity at pericentromeres during cell cycle progression. These innovative studies will answer the long-standing question of whether the mammalian RNAi pathway contributes to the maintenance of pericentromere heterochromatin and genome stability and will break new ground in our understanding of RNA- mediated gene regulation. We predict these studies will drive and yield a framework for future strategies to modulate pericentromeric ncRNA in disease settings.

NIH Research Projects · FY 2025 · 2021-09

ABSTRACT. The broad, long-term objectives of this K01 project are to improve the health of Apache American Indians through a study that examines the association between cancer (CA) outcomes and Arsenic (As), co- metals, and nitrate on the San Carlos Apache (SCA) reservation in Arizona. The study setting has an extensive history of hard rock mining since the early 1900s when uranium (U), copper, silver, and asbestos were extracted. Anthropogenic causes and naturally occurring elements can cause movement of As and co-metals into the environment and may result in adverse health effects. Arsenic is a known carcinogen and is associated with diabetes, adverse reproductive outcomes, and cardiovascular disease. A main goal of this pilot study is to develop and implement an exposure assessment tool (EAT) to study cancers and to use in the future to examine the association between exposures and multiple adverse health outcomes. The specific aims are to: 1) characterize historical water data by time and recorded As, Cd, Pb, U, and nitrate concentration levels from 1981-2021, 2) examine the association between chronically elevated As, Cd, Pb, U, and nitrate in water and CA outcomes (bladder, kidney, prostate, lung, breast, and skin), 3) analyze and apply a Geographic Information System (GIS) model to map high-risk (As, Cd, Pb, U, nitrate) areas based on this EAT, and 4) provide study findings to tribal members and leaders. A retrospective pair matched case-control (N = 160) design will be employed. Decades of As, Cd, Pb, U, and nitrates concentration levels recorded by the US Environmental Protection Agency (EPA), tribal EPA, and US Geological Survey from areas known to have elevated As, co-metal and nitrate concentration levels will be collected. Local tribal health/Indian Health Service (IHS) records will be examined for CA diagnoses and mortality (using ICD codes) reported by the IHS, tribal health, private health records, state CA registries, and mortality records of the past 10 years. Study controls will be selected from SCA enrollment data and matched to cases by sex and age. Odds Ratios will be reported using logistic regression to determine associations between exposure risk and outcomes. A dose response between chronic As, Cd, Pb, U, and nitrate water ingestion and reported cancers are anticipated. This is the first local study to retrospectively examine water contaminant levels in relation to multiple CA outcomes. The data will form the foundation for an R01 intervention study to educate, screen, and identify risks for adverse health outcomes among residents. Findings will be disseminated to tribal members and leaders, healthcare facilities, and the general population. This study has the potential to augment prevention efforts, intervention, education, monitoring/surveillance, and can support policy development and legislation. The project will reach a nationally underserved population in the biomedical, social, behavioral, and clinical sciences and is in alignment with training diverse scientists in fields per the NCI grant purpose and mission. The study addresses CA disparities in an underserved community while advancing scientific knowledge.

NIH Research Projects · FY 2025 · 2021-08

PROJECT SUMMARY This project addresses the need for a better understanding of the causes of major depressive disorder (MDD) as a way to improve diagnosis and treatment for the world's leading cause of disability. Genetic approaches, a path to identifying causal factors and hence finding novel treatments, are proving successful in some psychiatric disorders, but their application in MDD poses challenges, due to the condition's heterogeneity and the importance of environmental factors. Success requires studies that take into account heterogeneity by assessing multiple clinical features, and include measures of environmental risk factors. Furthermore, genetic studies need to expand their reach to include multiple, ethnically diverse populations, so as to identify additional risk loci, enable fine-mapping and the identification of likely causal variants, and expand the use of polygenic predictors of disease to more populations. NIMH, in issuing PAR-20-026, “Genetic Architecture of Mental Disorders in Ancestrally Diverse Populations”, recognizes this need and in response to this call, we have established an international collaboration of investigators from South Korea and the United States, with a strong track record of large-scale psychiatric genetic research in East Asia. We will create the largest East Asian cohort available for the discovery of new MDD genes, increase the diversity of genetic discovery efforts (a step towards reducing health disparities), and perform exhaustive analyses to identify likely causal variants and genes involved in MDD. The aims of the consortium are as follows: Aim 1: To collect from South Korea DNA samples and phenotypes from 10,000 women with severe recurrent MDD and from 10,000 matched, screened, controls. We will obtain a comprehensive set of clinical features and risk factors, a deep set of phenotypes that provide a powerful resource for gene identification. Aim 2: We will genotype samples, map risk loci for MDD in the Korean sample, identify sources of heterogeneity and examine how genes and environment interact to cause MDD. Aim 3: Identify genetic loci specific for MDD in a meta-analysis of East Asian cohorts, and refine likely sets of causal variants by using trans-ancestry fine-mapping in cohorts of different ethnicities.

NIH Research Projects · FY 2025 · 2021-08

ABSTRACT The future challenges of genomic science are enormous. Data sets continue to grow; with high-throughput technologies, and Biobank datasets, studies with105 cases and107 markers will soon be commonplace. Electronic health record (EHR) datasets are also rapidly expanding. Health data will soon be routinely collected from mobile and wearable devices, dramatically increasing their volume and utility. This data is critically important for advancing the understanding of human diversity and disease. Precision health and predictive medicine raise the stakes even further. It is imperative that all genomic researchers in the 21st century have a command of the quantitative and computational Big Data tools necessary for genomic research at this scale. The goal of this program is to provide training in next generation mathematical and statistical theory and computational methods for genomics and Big Data analysis. The program is designed for (1) researchers at the postdoctoral and early career level; (2) more senior biomedical researchers transitioning to more quantitative genomic research, with the goal of acquiring new research skills or updating existing knowledge; and (3) more senior computational scientists who wish to apply their methods in a new domain, and gain contacts among researchers active in those fields. Our program is useful for those trainee researchers whose career focus is computational methods development, but will also be useful for those researchers who want to add a genomics methods development component to their research program. We propose to create a one-week workshop on genomics and next generation computational statistics for Big Data to be held on the campus of the University of California, Los Angeles. The week will include a program of lectures, tutorials, hands-on teaching labs and exercises, and project-based one-on-one sessions with Program Faculty genomic scientists. The participants will be provided with 1) training in statistical and mathematical genomics theory; 2) training in the use of statistical and computational methods and tools to analyze genomic data; 3) training in computational methods development; 4) exposure to cutting edge research; 5) opportunities to consult, collaborate, and build mentoring relationships with Program Faculty genomic experts from multiple institutions and specialties. All materials from the one-week course will be recorded and made freely available online for access to any interested researcher. A central goal of the program is to help increase diversity in the biomedical workforce. We will plan a vigorous outreach effort with our well-established network of outreach partners to attract diverse participants. Our very diverse Program Faculty will aid in our diversity outreach and effective mentoring efforts. In addition, we plan to offer a series of Diversity Scholarships to attract participants from groups under-represented in the sciences. We will also offer diversity scholarships to host faculty from minority-serving institutions, to form partnerships and to assist them in putting our tutorials and educational tools to use in their home institutions.

NIH Research Projects · FY 2025 · 2021-08

ABSTRACT For patients with mild cognitive impairment (MCI) and Alzheimer’s Disease (AD) there are few effective treatments for memory enhancement. Strategies that directly manipulate neural activity are promising but currently have serious limitations. Deep brain stimulation (DBS) of the entorhinal cortex (ERc), a part of the brain important for memory, in a small sample of patients has been shown to improve memory, but DBS is highly invasive and requires neurosurgery. Other neuromodulation techniques that do not require surgery are limited in that they target only surface brain structures. In MCI and AD, it is the deep brain structures, including the ERc and the hippocampus (HC) that are most affected. Low intensity focused ultrasound pulsation (LIFUP) uses acoustic energy waves with frequencies higher than humans can hear to penetrate the skull to effect specifically targeted deep brain regions. Therefore, LIFUP could be targeted at the deep brain structures critical for episodic memory formation, the same regions that are affected in MCI and AD. We are the first to do just this and our preliminary data shows that LIFUP: increases perfusion of the ERc; increased functional connectivity of the ERc/HC memory network and may improve behavioral memory performance. Our LIFUP set-up is safe to use inside a magnetic resonance imaging (MRI) machine which allows for simultaneous brain modulation and real- time measurement of the modulation using MRI. We will use each participant’s structural brain MRI to aim LIFUP at the ERc. This will allow us to directly test the effects of LIFUP on activity in the ERc, in other brain regions connected to the ERc (e.g. HC), as well as on blood flow in the HC and other brain areas important for memory. Applying this to patients with MCI, we will try to determine the dose, booster effect and duration of LIFUP effects on brain and blood flow, structure and function, determine whether these LIFUP-related changes improve memory in this population and evaluate the effect of LIFUP on blood-based biomarkers of AD-related neurodegeneration. Understanding how the parameters of LIFUP dose and booster session effect the impact and duration of LIFUP on brain, biomarker and memory performance will be a significant step towards constructing a comprehensive clinical trial. The ability to change the activity and blood flow of brain regions by targeting them with LIFUP would be an important step towards developing a non-invasive memory prosthetic that would make a very significant contribution to AD treatment.