University Of California, San Diego

NIH Research Projects · FY 2020 · 2020-09

Project Summary/Abstract Plant natural products (NPs) are important sources for the discovery and development of small molecule medicines. Analysis of the genome data implies that nature's synthetic potential has been largely underestimated, and the majority of NPs have been unexplored. Over the past twenty years, many approaches have been developed to more efficiently discover novel NPs from microbial organisms. However, none of these strategies are applicable to predicting or activating biosynthetic pathways that are cryptic or of very low efficiency under normal conditions in plants. Plant NPs are believed to play an indispensable role in plants' innate immunity and defense framework. In response to the recognition of pathogens or damage by the pattern recognition receptors (PRRs), the plant activates the biosynthesis of NPs that function as defensive molecules such as antimicrobials. PRRs are surface-localized, ligand-binding, receptor-like kinases or proteins that recognize and respond to molecular signals in the environment. Genome analysis indicates that plants encode a huge number of PRRs, with the function of more than 95% being unknown even in the model plant Arabidopsis thaliana. If we can activate the downstream pathways of the unknown PRRs, plant NPs that are produced as defense or signaling molecules under various situations will be activated and discovered. Therefore, we propose to develop a strategy to engineer and redirect plant immune signaling to discover novel plant NPs. The central hypotheses are 1) plant perception complex/immune signaling pathway can be functionally reconstituted in the baker's yeast Saccharomyces cerevisiae; 2) plant PRRs can be engineered to recognize altered stimulus; and 3) the signaling and metabolic pathways downstream of target plant PRRs can be activated through introducing the engineered PRR and the corresponding stimulus. With expertise in synthetic biology and NP biosynthesis, we will verify the hypotheses and demonstrate this strategy through executing the following three specific aims, using Arabidopsis thaliana as the testbed: Aim 1, establish a yeast platform that enables functional reconstitution of plant immune complex and high throughput phenotyping; Aim 2, engineer plant immune receptors so they can be activated by known stimulus; Aim 3, implement the chimeric immune receptors into the model plant for plant NP and biosynthesis discovery. The project will generate 1) discovery of novel plant NPs that may not be synthesized under normal conditions, and their native functions; 2) strategies for engineering plant pattern recognition receptors that can activate various plant immune and metabolic responses; 3) insights into how the highly complex plant signaling pathways (immune, perception, growth factor, plant hormone, etc.) are correlated and regulated. The development of this methodology is a significant step towards my long-term goals: (1) to advance the foundational understanding of phytochemical synthesis, (2) to promote the discovery of novel phytochemicals for pharmaceutical applications, and (3) to develop microbial bio-production of phytochemicals of high value as an economic approach.

NIH Research Projects · FY 2024 · 2020-09

Low back pain (LBP) is a complex condition that affects 65-85% of the population, and is the leading musculoskeletal condition contributing to disability in the United States. Seventy-five percent of individuals undergoing treatment for this condition experience suboptimal or poor outcomes in the form of disability and deficits in functional capacity, including strength and endurance of the lumbar musculature. The most common initial treatments for individuals with chronic LBP are exercise-based rehabilitation, and pharmacological management in the form of analgesic medications. Although these two conservative treatment modalities are often concurrently prescribed, the influence of analgesic medications on the capacity of muscle to adapt in response to exercise is unknown. Importantly, in healthy individuals, some of these medications have been shown to inhibit muscle protein synthesis, metabolism, and stem cell function. The influence of medications may explain the variability in muscle- specific and clinical outcomes associated with exercise-based rehabilitation in this population. To address these current gaps in the literature, we propose to define medication usage patterns and clinical outcomes across individuals with chronic low back pain who are participating an exercise-based rehabilitation program. Specific Aim 1 will investigate the influence of symptom interference, psychosocial factors, and diagnosis on analgesic medication use relative to exercise in individuals with LBP. Specific Aim 2 will evaluate the influence of medication type, dose, and timing on exercise performance. Finally, Specific Aim 3 will determine if medication type, dose, and timing influences the magnitude of muscle hypertrophy and clinical outcomes after completion of a 12-week resistance exercise program. Determining the impact of common analgesic medications on muscle hypertrophy, exercise performance, and clinical outcomes is an important step in optimizing conservative management in individuals with low back pain. This information will also be applicable to a variety of musculoskeletal conditions for which similar treatment strategies are employed. This contribution is significant because it is the first step in a precision medicine approach aimed at establishing appropriate and targeted exercise and analgesic medication prescriptions for reversing muscle impairments that obstruct patient recovery. This proposal is innovative because it aims to fill a large gap in knowledge regarding the influence of analgesic medication on muscle adaptation in individuals with pain and pathological muscle.

NIH Research Projects · FY 2025 · 2020-09

PROJECT SUMMARY/ABSTRACT Metalloproteins carry out many cellular functions that are central to biology and human health, While our knowledge of how metalloproteins function has grown immensely thanks to technological advances, we still possess only a superficial understanding of the interplay between protein structure/dynamics and metal coordination/reactivity, As a result, it has been challenging or even impossible (a) to predict the functional mechanism of metalloproteins simply by looking at their structures, (b) to emulate or improve upon the structures and functions of metalloproteins by de nova design, and (c) to understand how complex bioinorganic functions may have emerged on simple peptide/protein scaffolds during natural evolution, The overarching goal of the proposed research program is to address these three challenges by designing and constructing protein scaffolds with complex metal-based functions from scratch, Toward this end, we have recently developed/adapted two powerful approaches to metalloprotein design, Metal-Centered Protein Assembly (MCPA) and MachineLearning- guided Design of Metalloproteins (MLDM), which allow novel protein structures to be built around metal active sites rapidly and with atomic accuracy, In the proposed research, we will further develop these "metalcentered" protein design strategies (and establish their generalizability) by constructing de nova protein scaffolds that will provide access to diverse metal active sites with tunable primary coordination spheres, secondarysphere environments and global structures/properties that are difficult to attain with other protein design strategies, We will use these protein scaffolds to build new metalloenzymes for challenging ester, amide and phospho-ester bond hydrolysis reactions (Specific Aim 1 ), for redox reactions involving dioxygen binding and activation (Specific Aim 2), and for abiological catalytic transformations (e,g,, hydride and carbene transfer) (Specific Aim 3), These efforts will uncover fundamental structure-function relationships that govern diverse metalloprotein activities, lead to better understanding of how bioinorganic complexity arises in simple protein scaffolds, and furnish new-to-nature reactivities.

NIH Research Projects · FY 2024 · 2020-09

Project Summary of the Parent Award Most cellular behaviors and functions rely on cell signaling. A direct approach to detect this event is to record cellular electrical potentials that are associated with various ionic kinetics during signal processing. It has been shown that a wide range of high profile diseases, such as epilepsy, episodic ataxia, Alzheimer's, and Parkinson's, may result from dysfunction of voltage-gated sodium, potassium, and calcium channels. Although qualitative knowledge of the motions of these ions has been well studied, a quantitative understanding is still missing because of the lack of tools that would allow high-spatiotemporal-resolution sampling of ion motions inside cells. My group is dedicated to developing a soft electronic interface for cells and tissues. This synthetic electronic interface will have similar mechanical properties to the biology, and can organically fuse with the target cells and tissues, which will not only result in higher signal to noise ratio but also longer recording time than conventional rigid and bulky recording systems. This five-year project aims to develop an innovative cellular interface that is composed of an array of highly sensitive three- dimensional field effect transistor (FET)-based sensors on a stretchable substrate. We use this innovative cellular interface to test the hypothesis that ionic kinetics, including the speeds of ionic diffusion through ion channels in the cell membrane, ion drift driven by ion pumps, and inter-cellular signal propagation, entail crucial quantitative information associated with disorders of electrogenic cells, such as neurons, cardiomyocytes, and electrically excitable endocrine cells. The sensors can simultaneously record different positions of a single cell or among different cells in a cellular network, thus enabling us to measure and calculate the time- or speed-related kinetic factors of the ions (i.e., the time at which the ions move in or out of the cell membrane and the speed at which they do, respectively). Also, using an FET design, we can amplify the recorded signal directly at the targeting location, realizing as much as ten-fold signal amplification. Furthermore, we can differentiate the specific ionic species that are actively functioning inside and outside of the cells by coating the surfaces of the FET sensors with phospholipid bilayers that have the corresponding ion channels, allowing the specific ions to permeate the cell membrane, which would result in a change in electrical potential that could be recorded by the FET sensors. The information acquired will help gain new insights in cellular communications, with profound implications for brain sciences, cardiac physiology, and clinical practices.

NIH Research Projects · FY 2024 · 2020-08

Modified Project Summary/Abstract Section HIV cure efforts will likely continue to be futile if we ignore the inflammatory mechanisms sustaining the persistence of HIV. Scientific Premise: A common driver of inflammation for persons with HIV (PWH) is Cytomegalovirus (CMV), which almost universally co-infects PWH. During this coinfection, subclinical CMV replication is frequent and profoundly impacts the immune system, including several CMV-driven mechanisms that promote HIV persistence, even during antiretroviral therapy (ART). Some of these mechanisms could skew the HIV provirus towards preferentially integrating into CMV specific CD4+ T cells. Also, as CMV specific CD4+ T cells comprise a large proportion of all CD4+ T cells, so understanding how they contribute to HIV persistence would be essential for HIV cure efforts. Strengths of the proposed research are that it will use state-of-the-art methods and will leverage prior NIH-investments to collect appropriate biospecimens and data as part of an ACTG-funded, randomized trial of the anti-CMV drug letermovir (A5383, Co-chairs: Gianella, Hunt) as well as anti-CMV vaccine Triplex (A5355, Chair: Sara Gianella). Study Design: Our project is designed to carefully and rigorously elucidate the CMV-driven mechanisms that impact HIV persistence. Aim 1 will determine how various viral antigens (CMV, Influenza, EBV and HIV) directly induce clonal expansion of HIV-infected CD4+ T cells ex vivo. Aim 2 will assess the indirect effect of suppressing CMV with letermovir or vaccine on HIV reservoirs and T cell repertoire in vivo. To clarify mechanistic pathways of ex vivo and in vivo observations in Aims 1 and 2, we will characterize specific immunologic mechanisms associated with clonal expansion and inflammation in association with CMV and HIV persistence. Overall Objective: HIV cure efforts will likely be futile if we ignore the inflammatory mechanisms that sustain the HIV reservoir. This project is in line with NIH OAR priorities because it will assess the mechanisms by which viral antigens (CMV, EBV, Influenza and HIV) influence HIV persistence through expansion of CD4+ T cells that carry HIV DNA (Aim 1). Further, we will determine the benefits of suppressing CMV to decrease immune dysfunction and HIV cell reservoirs (Aims 2 and 3). Impact: The proposed project will have meaningful impact by determining how suppressing CMV with letermovir may influence inflammation, immune dysfunction, and HIV reservoirs. Generated results will advance both the HIV cure and PWH health agendas.

NIH Research Projects · FY 2025 · 2020-08

Abstract Improving the demographics of the biomedical workforce is critical for enhancing educational experiences, fostering scientific discovery and innovation, increasing the benefit of research on health disparity populations and public trust. While academic institutions have an important role in this mission, the representation of faculty from underrepresented backgrounds is low and has remained stagnant. The overall goal of the UC San Diego (UCSD) Raising Advancement and Parity for Infectious Disease Researchers (RAPID) Faculty Development Program is to improve the demographics of the biomedical research workforce in infectious diseases. The UCSD RAPID Program will provide effective mentorship, activities to develop critical academic skills and research training experiences to participants to enhance their development of successful research programs focused on infectious diseases and success in obtaining independent extramural funding. RAPID will recruit underrepresented early career faculty and transitioning postdoctoral scholars from a national pool to participate in professional skill and research development activities in a summer institute program. The RAPID program is directed by two principal investigators (PIs) and four co-investigators (co-Is) with extensive experience in mentoring and training postdoctoral scholar, residents and junior faculty and success in creating and implementing faculty development and mentoring programs specifically for underrepresented trainees. The PIs / co-Is have successfully led extramurally funded training programs; and are actively engaged in NIH-sponsored infectious diseases research; five of the PIs are from backgrounds underrepresented in the biomedical research workforce. The specific objectives of the UCSD RAPID Program are to enhance the demographics of the biomedical workforce by providing participants with critical academic skills to enhance their success in developing multidisciplinary research programs focused on infectious diseases. We propose three specific aims. Aim 1. To improve the demographics of the biomedical workforce by continuing to recruit underrepresented early career faculty and transitioning postdoctoral fellows from local and national pools who have infectious diseases scientific expertise aligned with those of our research mentors. Aim 2. To continue to enhance professional skill development and effective mentorship of early career infectious disease researchers by utilizing evidence-based strategies including a faculty research and career advancement plan, effective mentorship and by improving knowledge and skills in various professional development areas important for academic and research success. Aim 3. To continue to improve research training and research self-efficacy of mentees through immersion in effective strategies to enhance the development of robust research programs, acquire sustainable grant writing skills and success in obtaining extramural funding. The aims proposed in the UCSD RAPID Program renewal will continue to enhance participants academic and research success, and in obtaining independent NIH or equivalent funding to support multidisciplinary infectious disease research.

NIH Research Projects · FY 2024 · 2020-08

The ability to store and retrieve sequentially related information is arguably the foundation of intelligent behavior. It allows us to predict the outcomes of sensory situations, to achieve goals by generating sequences of motor actions, to 'mentally' explore the possible outcomes of different navigational or motor choices, and ultimately to communicate through complex verbal sequences generated by flexibly chaining simpler elemental sequences learned in childhood. Sleep extracts invariant features from the learned information, leading to the generation of explicit knowledge and insight. Despite remarkable progress, including work by PI and co-PI of this project, many critical questions remain about role of sleep in memory and learning. Here we propose to address these questions through the development of computational models that are probed and validated through in vivo experiments in mice. We will explore the hippocampal (HC) and neocortical (NC) mechanisms underlying how sequences are acquired and subsequently consolidated through off-line replay during Slow Wave Sleep (SWS) in a manner that minimizes interference between overlapping and/or reversed sequences and how NC may chain sequence fragments together. We combine computer modelling (Bazhenov) of spiking neural networks that mimic awake and SWS brain dynamics, including NC slow oscillations and HC Sharp Wave Ripples (SWR), with high density neural ensemble recordings (McNaughton) in mice, in a controlled behavioral setting including sequence learning and subsequent, chemogenetically induced SWS, which makes it possible to observe how learned sequence representations in NC evolve spontaneously over prolonged periods of SWS. The PIs have been collaborating on and discussing this topic for the past several years, resulting in specific hypotheses that can be explored in real brains. The project outcome will provide a better understanding of how knowledge is extracted from experience, what brain circuits are involved and how brain dynamics are shaped by the development of a rich internal model of the world, including the ability to predict the outcomes of current situations and one's own actions in that context. RELEVANCE (See instructions): The ability to store and retrieve sequentially related information is the foundation of intelligent behavior and brain executive function. Deficits in this ability, resulting from disruption of brain circuits, are seen in depression, schizophrenia and PTSD. Better understanding of the mechanisms and brain dynamics underlying the acquisition, consolidation and retrieval of sequential information will lead to interventions to improve cognitive performance, memory and learning in healthy subjects and patients with mental illness.

NIH Research Projects · FY 2024 · 2020-08

ABSTRACT Support is requested for an interdisciplinary effort to understand the key molecular and developmental events that regulate blood and vascular cells in inflammation, hemostasis and thrombosis with a focus on adhesive signaling. The four Projects will: 1) Test the hypothesis that direct interactions between Rap1 and talin1 plays an important role in platelet, leukocyte, and endothelial cell functions in inflammation, hemostasis and thrombosis. 2) Use newly developed imaging modalities to enable quantitative dynamic footprinting of the surface of neutrophils in contact with substrate to assess adhesion receptor clustering and conformation in response to specific molecular adaptor-adhesion receptor interactions. A particular focus is the structure-function of kindlin-3, the gene mutated in human leukocyte adhesion deficiency Type 3, and its relationship to talin. 3) An Early Stage Investigator will test the hypothesis that genetic inactivation of Krit1 or Heg1 in adult mice will protect against experimental inflammation or thrombosis. In collaboration with a structural biologist, he will extend studies to test the feasibility of pharmacologically disrupting the HEG1-KRIT1 complex to mimic the effects of genetic inactivation of these genes. 4) To assess the role of SHARPIN and associated components of the LUBAC linear ubiquitination complex in the functions of platelets and endothelial cells in inflammation, hemostasis, and thrombosis. This project will test the hypothesis that this newly-identified regulator of platelet and endothelial cell functions contributes to inflammation, hemostasis, and thrombosis. A scientific core unit, led by a world leader in murine models of inflammation, hemostasis, and thrombosis, will provide the individual projects with in vivo models and expertise required to establish the patho- physiological relevance of these novel molecular mechanisms.

NIH Research Projects · FY 2025 · 2020-08

Schmidt – Project Summary Radical species play important roles in biological systems linked not only to dysfunctional cell proliferation and other disease pathways, but also in essential healthy processes necessary for life. Understanding the reactivity profiles of open-shell carbon, oxygen, sulfur, and other heteroatomic-centered radical intermediates is crucial to understanding how these processes occur and to propose reasonable mechanisms for currently ill-defined pathways. Studying and understanding reactivity profiles of radical intermediates can also result in the development of new synthetic methodologies with the potential to streamline and make the synthesis of existing pharmaceuticals more efficient and provide access to the next generation of therapeutics and tools for imaging, diagnosis, treatment, and prevention. This proposal is built on the prior and concurrent efforts of the PI’s research group using phosphorous-based reagents to unmask carbon and heteroatom-centered radicals from untraditional precursors. This general platform has achieved the regioselective construction of C-N bonds which are present in a substantial portion of FDA approve pharmaceuticals and are often involved in the mode of biological activity. These radical-mediated approaches leverage the favorable thermodynamics of atom-transfer processes to achieve new bond formations from common chemical functionalities. Future studies will continue to explore the potential of this general platform by investigating the ability of other common functional groups to be analogously unmasked to achieve new bond formations. We anticipate that this work may lead to new strategies in complex molecule construction for use in the preparation of new molecular therapeutics and tools in chemical biology.

NIH Research Projects · FY 2026 · 2020-08

Glaucoma is a leading cause of blindness, worldwide. The only proven glaucoma treatment is intraocular pressure (IOP) reduction. Elevated IOP is caused by increased aqueous humor outflow (AHO) resistance at the trabecular meshwork (TM) of the trabecular AHO pathways. Medications can be used to lower AHO resistance through these pathways, but patients can be medically non-responsive for unclear reasons. Trabecular ablation was developed as a safe and logical treatment, but IOP-lowering efficacy is limited in large, well-controlled clinical trials. Thus, current glaucoma therapies are not effective enough, and there are insufficient tools to fully assess AHO anatomy and physiology across the entire eye to understand why. Aqueous angiography (AA) is an AHO visualization method that has shown segmental AHO over the entire eye with high-flow (HF) and low-flow (LF) regions. LF regions have been linked to glaucoma treatment success. However, while AA provides gold-standard AHO information, it is an invasive method with risks. Thus, we must derive a biologically-focused anterior segment AHO structure/function relationship and re-frame segmental AHO assessment as a non-invasive structural test to fill this gap. To do this, specialized optical coherence tomography (OCT) approaches must be taken to overcome the complex, large, and three-dimensional AHO pathway anatomy. Thus, our central hypothesis is that improved understanding of the ocular structures that determine segmental AHO (particularly LF regions) in normal and diseased eyes can improve current and lead to new glaucoma therapies. The objectives are to understand the structural determinants and identify biomarkers of segmental AHO, use this knowledge to test glaucoma treatments, and create new tools to better evaluate AHO pathways in humans. In Aim 1, we will use AA, OCT, and lipid emulsion (LE) OCT-angiography (OCTA) in ex-vivo human eyes to define the AHO pathway structures that define segmental AHO LF and HF subtypes. These areas will then be tested using trabecular ablation to identify the best locations for improving outflow facility and reducing IOP. In Aim 2, we will use OCT and OCTA in wild-type and glaucoma mice with high IOP to define AHO pathway structures that define segmental AHO in a pathophysiological state. These areas will then be studied using glaucoma IOP- lowering drugs. In Aim 3, we will develop a new robotic anterior segment OCT (AS-OCT) tailored to human AHO anatomy with high spatial resolution, optimal spectral range to reach the desired depth, and robust safety features. Robotic control improves speed, feasibility, and reliability. Early-stage clinical performance and repeatability testing will be performed in healthy volunteers and glaucoma patients using body-position-induced IOP alteration to iteratively optimize the operation protocol. This proposal brings together the optimal team. Dr. Zhang is a bioengineer who has successfully designed many custom OCT systems, including for the anterior segment, to improve ocular anatomical and physiological assessment. Dr. Huang is a clinician-scientist who developed AA, has published on clinical AS-OCT, and cares for glaucoma patients.

NIH Research Projects · FY 2024 · 2020-08

The overall goal of the NINDS-proposed UC San Diego Leading the Advancement of Underrepresented Neuroscientists for Change (LAUNCH) program is to effectively mentor and train individuals underrepresented in neurosciences in critical career development skills and research to enhance the development of competitive neuroscience research programs and success in obtaining independent extramural research funding in a visiting scholars program. LAUNCH will utilize asset models and evidence-based strategies to enhance effective mentoring, career skill development, and research training. LAUNCH is directed by five PIs with a history of mentoring and training junior faculty and postdoctoral fellows and success in creating and implementing career development and mentoring programs specifically for underrepresented minority (URM) trainees and women. All PIs have successfully led extramurally funded training programs; four of the five PIs are actively engaged in NIH-sponsored biomedical research, 3 PIs are women, and two PIs are from URM backgrounds. The overall goal of the NINDS-proposed UC San Diego Leading the Advancement of Underrepresented Neuroscientists for Change (LAUNCH) program is to effectively mentor and train underrepresented early career neuroscientists in critical career development and research skills to enhance the development of research programs and success and in obtaining independent extramural research funding. The specific objectives of the UCSD LAUNCH program are to increase the representation of scientists from backgrounds underrepresented in neurosciences in obtaining effective mentorship, critical career development skills, research training and grant funding. Three specific aims are proposed. Aim 1 is to recruit underrepresented junior faculty and transitioning postdoctoral fellows who have neuroscience scientific expertise aligned with those of our research mentors in the areas of Alzheimer's disease and related dementias, cellular, developmental and molecular neurosciences and computational and systems neurosciences, particular strengths of UC San Diego. Aim 2 is to use asset models and evidence-based strategies to enhance career skill development and effective mentorship of participants using a Faculty Research and Career Advancement Plan to identify short- and long-term career and research goals, engage in effective mentorship with a 3-membered mentoring team, and extend knowledge and skills in specific career development areas. Aim 3 is to promote research training and research self-efficacy of participants by extending research knowledge, skills and strategies through direct training with a UCSD faculty research mentor and immersion in activities that will enhance research progress, collaborations and networking, grant writing skills, and as well as publication strategies that will accelerate successful research program development and submission of an NIH or equivalent grant. LAUNCH includes PIs with extensive experience in program and career development and neuroscience research, a strong cohort of UC San Diego faculty neuroscience researchers and career mentors from underrepresented backgrounds.

NIH Research Projects · FY 2024 · 2020-08

In recent years there has been increased awareness and concern about the “epidemic of loneliness” among older adults and other general population, but the prevalence is even higher among people with schizophrenia. Loneliness is a significant risk factor for medical comorbidity, cognitive dysfunction, reduced functional capacity, lower well-being, and earlier mortality. The mortality risk associated with loneliness is double that for obesity, and equivalent to smoking 15 cigarettes per day. Notably, many of the deleterious effects associated with loneliness parallel those associated with schizophrenia and aging. This convergence raises a question of whether loneliness significantly contributes to the deficits in health, cognition and functional capacity, physiologic function, and well-being among middle-aged and older adults with schizophrenia. The proposed project is the first comprehensive study of the nature, longitudinal stability, and deleterious impact of loneliness in schizophrenia. Given recent conceptualizations of schizophrenia as a systemic disorder resulting in accelerated aging, and the manner in which loneliness may evolve over the life-course, the focus for this study will be on the effects of loneliness with age among middle-aged and older adults with schizophrenia (n=120) as well as age-comparable non-psychiatric comparison (NC) subjects (n=90). The study employs a longitudinal burst design, with in-person visits and assessments of key variables at baseline, 6-, and 12-months. For seven days following each of the three primary study visits, smartphone-based Ecological Momentary Assessment (EMA) will be used to measure loneliness, social activity, and mood in real-time. Our primary aims include determining the associations of schizophrenia and aging with persistent loneliness, and the degree to which the associations are independent of social isolation and depressive symptoms. The other primary aim is to determine the association of persistent loneliness over 6- and 12-months with levels and patterns of biological markers of health, medical comorbidity, cognitive dysfunction, functional capacity, and health-related quality of life. Hypotheses predict schizophrenia being associated with worse and more persistent loneliness, and that persistent loneliness will be associated with worse biological markers of health and other outcomes. We also expect these associations to increase with advancing age. Stability and temporal relationships between acute loneliness, social activity, and mood measured in real-time using EMA, and associations of these patterns with those from the standard in-person measures will also be assessed. The data from this project will fill a critical unmet need for empirical data to guide the content and focus of efforts to prevent and reduce deleterious biological and longer-term health outcomes and diminished well-being in older adults with schizophrenia. Together, this study represents a significant and innovative step in furthering efforts toward more effective, comprehensive, individualized prevention and treatment of loneliness and its adverse effects in middle-aged and older adults with schizophrenia.

NIH Research Projects · FY 2024 · 2020-08

Project Summary Congenital Heart Disease is the most common congenital anomaly in newborn babies, accounting for one third of all major congenital anomalies. Despite recent congenital heart disease genetic studies highlighting the critical role of cardiac transcriptional and chromatin regulators during heart development, our understanding of how these developmental regulators interact to create the dynamic gene regulatory networks that mediate heart development remains to be fully elucidated. Thus, we propose to define and assay the cardiovascular developmental regulators and their gene regulatory networks that direct the development of the vast array of cardiovascular cell types creating the mammalian heart. To achieve this goal, a multi-disciplinary experimental and computational systems biology approach will be implemented to: (1) elucidate gene regulatory networks that establish the cardiogenic cellular hierarchy of the developing mammalian heart, (2) investigate the spatiotemporal organization of the cardiogenic cellular hierarchy during mouse embryogenesis and heart morphogenesis and (3) functionally examine how distinct cardiovascular developmental sources create specific cardiovascular lineages contributing to the developing heart.

NIH Research Projects · FY 2024 · 2020-07

Extremely high-throughput mapping of protein, RNA, and chromatin interactions in health and disease Abstract This Catalyst project aims to removing a major bottleneck in understanding diabetes and its complications, by developing the technologies to map diverse molecular interactions in the disease-relevant cells at the genomic scale. These proposed technologies, collectively called PRACI (Protein, RNA, and chromatin interactions), will enable a typical research lab to map genome-wide protein-protein, RNA-protein, RNA-RNA, and RNA- DNA/chromatin interaction networks from a given cell type within 1 months’ time. PRACI enables typical labs to compare molecular interaction networks between health and disease states. Without PRACI, genome-wide mapping of even a single type of interactions from a disease-relevant cell type remains a formidable task. I will systematically map molecular interactome changes related to diabetes related vascular complications, using hyperglycemia and chronic inflammation-induced irreversible alterations vascular endothelial cells as a testbed system. I anticipate to reveal which components of the multiscale molecular networks are responsible for the sustained dysregulation of gene expression in dysfunctional endothelial cells. Such information will lead to new perspectives to diabetic wound healing, given the established roles of endothelial dysfunction to diabetic wounds and the relative accessibility of vasculature. I anticipate that these technologies and their enabled discoveries will contribute to and inspire transformative changes in the study of Diabetes, Endocrinology, and Metabolic Diseases.

NIH Research Projects · FY 2024 · 2020-07

Pancreatic ductal adenocarcinoma (PDA) is a highly lethal human malignancy, typically diagnosed at an advanced stage and known to be largely unresponsive to chemotherapy and ionizing radiation. Recent genomic characterization of PDA reveals that between 20-25 % of PDA harbor recurrent mutations in genes, including BRCA1/2, PALB2, and ATM, which are critical for homologous recombination (HR), an important form of DNA repair. In many patients, these may be germline mutations. This subgroup of PDAs, termed HR-deficient PDA, has emerged as a defined biological entity associated with increased chemoresistance and a more aggressive disease course. The defects in HR observed in these tumors impart cells with a specific vulnerability to PARP inhibitors and platinum-containing therapy. Still, as observed in the case of many other targeted therapies, only a fraction of HR-defective patient tumors respond to PARP inhibition. More so, many patients that initially respond eventually often develop resistance and progress. Therefore, novel therapies which can be effective against HR- defective PDA, alone or in combination with PARP inhibitors or other combinatorial regimens, are urgently needed. We have recently determined that inactivation of the HR pathway is associated with overexpression of polymerase theta (PolƟ, also known as POLQ) in PDA. POLQ is a key enzyme that regulates an alternative pathway of DNA repair, known as the alternative non-homologous end-joining (Alt-NHEJ) pathway. Data from our group indicates that in the setting of defective HR, Alt-NHEJ becomes a critical pathway responsible for the repair of DNA breaks. Furthermore, we show that POLQ inhibition in HR-defective tumor cells demonstrates a synthetic lethality phenotype, not observed in cells with intact HR. In this proposal, we present exciting new data that knockdown of POLQ is synthetically lethal in PDA cells deficient for Brca1, Brca2, Atm, and Palb2 genes. POLQ knockdown significantly inhibited growth of both Brca2- and Atm-deficient tumors cells in vivo. Further, POLQ knockdown significantly upregulated the cGAS-STING pathway in HR-deficient PDA and promoted T cell infiltration. Here, we plan to examine the unique role of POLQ in pancreatic cancer biology and its role as a novel therapeutic target in HR-defective pancreatic cancers. We will also evaluate the antitumor effect of combining POLQ inhibition with: i) current standard cytotoxic chemotherapies, ii) PARP inhibition, and iii) immunotherapy. An important goal of this proposal is to generate a set of data for proof-of-concept that targeting POLQ in a valuable therapeutic strategy in HR-defective pancreatic cancer, as POLQ inhibitors are currently in development for clinical use.

NIH Research Projects · FY 2024 · 2020-07

Project Summary and Relevance Project Summary: The broad, long-term objective of this collaborative project is the discovery of small molecule therapeutics that can replace antibodies as inhibitors of the PD-1 checkpoint. To date, no small molecules have been approved for this application, although the benefits of small molecules over biologicals in drug therapy is clear. This project capitalizes on the existence of a large collection (up to 30,000 samples) of structurally unique marine microbial metabolites that have shown to be a solid source for the development of anticancer agents. This collection, available at the Scripps Institution of Oceanography, UCSD, from Dr. William Fenical will be interfaced with the cancer biology lab of Dr. Yin Lu at the Nanjing University of Chinese Medicine, to screen for selective inhibitors using a commercially-available cell-based bioassay for PD-1 binding. When active metabolites are discovered, they will be screened in a variety of secondary assays to show selective binding. Finally, verified PD-1binding inhibitors will be produced in multi-milligram amounts by large-scale cultivation and provided to Dr. Lu for evaluation in mouse and rat xenograph models of select cancers. Relevance: This project aims to improve on the immunotherapy of cancer by discovering small molecules that selectively bind to the protein PD-1, which when bound to PDL-1 is responsible for the deactivation of the immune system. Replacing the current antibody (protein) therapy with a small molecule drug is likely to improve treatment efficacy and will clearly reduce drug cost.

NIH Research Projects · FY 2024 · 2020-07

Background: Strong evidence indicates physical activity (PA) reduces risk of bladder, breast, colon, endometrium, esophagus, gastric, and renal cancer, and there is moderate evidence for lung cancer. Individuals aged 40+ who are inactive are at high risk of developing cancers 58,65 but only 1/3 meet guidelines for PA;5-15 thus, they are an important group to target. While effective PA interventions exist, interventions often work only for some individuals or only for a limited time,16-18 thus establishing the need for interventions that can account for dynamic, idiosyncratic PA determinants in order to support each person’s PA. In response, we developed JustWalk, a modular adaptive mobile health (mHealth) intervention that makes daily N-of-1 adjustments to support PA for each person. JustWalk is based on Social Cognitive Theory (SCT) with N-of-1 adaptation driven by a mathematical dynamical model of SCT, which we have developed and validated. JustWalk can perform N-of-1 adaptation based on our innovative use of control engineering methods, which we call a control optimization trial (COT). We have a digital platform and empirical justification for our next step: to evaluate, in a randomized controlled trial (RCT), whether using a COT approach to continuously optimize a PA intervention to each individual is superior to an intervention that is identical but lacks the COT methods. Primary purpose: Evaluate differences in minutes/week of moderate-to-vigorous intensity PA (MVPA) among the COT- optimized vs. non-COT groups at 12 months. Hypotheses: We hypothesize significantly higher minutes/week of MVPA in the intervention arm (COT) relative to control (non-COT) as measured via ActiGraph (powered for effect size of ≥0.32). Methods: We will conduct this RCT with 386 adults aged 40+ who are inactive and overweight/obesity. This is a high-risk group who would benefit from a PA intervention for cancer prevention and who would benefit from an adaptive intervention because of the idiosyncratic and dynamic nature of PA that is pronounced within this group. Assessments will be conducted at baseline, 6, and 12-months using a hip-worn ActiGraph for assessing minutes/week of MVPA, as justified by guidelines. Implications: This research is highly significant because our intervention would be the first scalable PA intervention squarely grounded in SCT with N-of-1 adaptation driven by a mathematical dynamical model version of SCT. Further, favorable results would justify use of our COT methods for other complex and highly idiosyncratic and dynamic behaviors such as weight management, smoking, or substance abuse. Finally, our work should improve understanding of engagement with digital health tools. This research is highly innovative as we would be the first to conduct a COT and to empirically evaluate its utility in an RCT.

NIH Research Projects · FY 2024 · 2020-07

PROJECT SUMMARY High-grade serous ovarian cancer (HGSOC) is the leading cause of death from gynecologic malignancies. Most patients initially respond to chemotherapy after surgery, yet ~80% will recur with disease that becomes resistant to treatment. Immune therapies have shown great promise, but with limited efficacy in HGSOC. The HGSOC tumor microenvironment (TME) is highly immuno-suppressive and this is hypothesized to promote tumor immune evasion. We have developed two new implantable syngeneic mouse ovarian tumor models that will allow for the molecular analysis of tumor- and host-specific signals driving immune evasion. By selecting for aggressive growth in mice, we have extensively characterized KMF cells (gains in genes for KRas, Myc, and FAK) that exhibit many phenotypic similarities to HGSOC; intrinsic chemo-resistance and potent immune suppression. We will focus on FAK (focal adhesion kinase), a tyrosine kinase canonically supporting cell motility signaling. FAK is the fifth highest amplified gene in HGSOC and greater than 65% of patients exhibit elevated FAK mRNA with poor prognostic significance. Using pharmacological FAK inhibitors, FAK knockout, FAK re-expression, complementation, and bioinformatic analyses of KMF cells in tumor-bearing mice, we find that FAK drives the expression of a select group of cytokines and tumor-associated surface proteins involved in regulating tumor growth and immune evasion. Inhibiting FAK results in decreased myeloid-derived suppressor cell (MDSC) recruitment, increased CD4 and CD8 T cell tumor infiltration, and decreased expression of PD-L1, CD112, and CD155 checkpoint regulatory proteins on KMF cells in vivo. These changes are consistent with a normalization or reprogramming of the ovarian TME by FAK inhibition in a tumor-intrinsic manner. FAK inhibition also prevents bloody ascites formation in the KMF model. A second newly-developed T antigen-driven FAK floxed mouse ovarian carcinoma model (MOVCAR) revealed that FAK loss prevents tumor growth in syngeneic low-T mice. FAK-null MOVCAR tumors were infiltrated by CD45+ leukocytes, and when evaluated in immune-deficient mice, orthotopic FAK-null MOVCAR tumor growth was enhanced. This proposal will test the hypothesis that tumor-intrinsic FAK activation facilitates immune-suppressive related changes to the TME. Aim-1 will use a new inducible FAK expression system to evaluate FAK nuclear localization- and kinase-dependent signals driving malignancy, chemokine expression, and MDSC recruitment. Aim-2 will test the role CD112/CD155 immune checkpoint protein expression and whether FAK inhibition may combine with antibodies to TIGIT (T cell immunoreceptor with Ig and ITIM domains) to limit tumor growth via effects on T cells. Aim-3 will use an inducible knockout of FAK, of the related Pyk2 kinase (new model), or inducible expression of kinase-inactive FAK in mouse endothelial cells, with the KMF implantable tumor model, to test stromal FAK and Pyk2 signaling on the TME. These mouse studies, with analyses of patient tumors, will provide important insights on the role of FAK inhibition to enhance immunotherapy efficacy for HGSOC.

NIH Research Projects · FY 2025 · 2020-07

Enter the text here that is the new abstract information for your application. This section must be no longer than 30 lines of text. The Pathways in Biological Sciences (PiBS) Training Program at UCSD is a T32 Training Program funded since 2020 that evolved from the successful 40+ year Cell and Molecular Genetics (CMG) Training Program. PiBS provides an enhanced practices pathway to produce leaders in biology careers, including: academic and industrial research, education, writing, consulting, and policy. Trainees comprise a select subset of 30 UCSD Biological Sciences PhD students, conducting research in a variety of pressing problems in foundational and translational biology by the use of mechanistic molecular approaches. Students are invited to become PiBS Trainees at the end of their first year, soon after choosing a thesis advisor, for a two-year PiBS-supported period, followed by maintained Trainee status for the remainder of their PhD. PiBS aims to instill and amplify six core competencies, including critical thinking, knowledge acquisition, experimental ability with emphasis on rigor, reproducibility and quantitation, effective communication, leadership through team building and collaboration, and career development. To this end, the PiBS program will conduct a variety of Trainee-specific activities: yearly one-on-one meetings with the PiBS Director, BGGN290 - a class for in-depth analysis and critique of invited seminar speakers, a twice-yearly public colloquium of Trainee research presentations, a yearly Trainee-organized Symposium of invited leaders from a chosen field, scientific writing workshops, a path-to-career workshop, career information and networking guidance, a white-board “jam” to enhance clear exposition of science, and a yearly “One Book-One Program” group discussion of a mutually chosen book. The PiBS mission includes oversight mechanisms to evaluate the success and effectiveness of the PiBS program to measure effective impartation of the core competencies required for Trainee success, and to select and evaluate our PiBS Training faculty to ensure their involvement, rigorous scientific approaches, and competency to serve as PhD mentors. PiBS Trainee outcomes will be clearly documented, continuously curated, securely stored, and available through web-based resources to best self-assess our progress, facilitate dissemination, and inform future Trainees about the most impactful choices for their individual career goals. The PiBS mission is deeply dedicated to maximizing the impact of our Trainees both immediately and as the future leaders of biological science and biology-oriented careers.

NIH Research Projects · FY 2024 · 2020-07

PROJECT SUMMARY/ABSTRACT: This K08 application is designed to provide Dr. Robert Dorschner, MD, the scientific training and professional development required to become an independent investigator in the field of cutaneous host defense. The advent of methicillin resistant staphylococcus aureus (MRSA) has significantly increased the morbidity of skin and soft tissue infections (SSTIs). There is a great need for innovation to better understand host defense of the skin and to develop alternative therapies. Neutrophils are a key component of cutaneous host-defense, yet neutrophil-targeted therapies are lacking. The long-term goal of this proposal is to train the PI through a project that will advance an understanding of innate mechanisms that regulate neutrophil recruitment and activation in cutaneous inflammation and infection. His preliminary data demonstrate that the leukocyte surface protein ECRG4 promotes early neutrophil recruitment to cutaneous injury and regulates CD44 expression. The central hypothesis is that ECRG4 enhances the inflammatory response to contain and eliminate cutaneous infection through its ability to amplify neutrophil recruitment and regulate CD44 signaling. The rationale for this project is that a determination of novel neutrophil recruitment mechanisms will enable therapeutic targeting of molecules like ECRG4 for neutrophil-directed therapies to enhance host defense against antibiotic resistant microbes. Dr. Dorschner will apply molecular and cell biology techniques to ECRG4 KO mice and human leukocytes to: 1) Determine the role of ECRG4 in host defense against cutaneous staph aureus infection, 2) Assess its regulation of neutrophils with in vivo and ex vivo models, and 3) Define the effect of ECRG4 regulated CD44 expression on neutrophil recruitment and function. These findings will demonstrate a novel mechanism controlling early inflammatory responses to infection that can be translated to the development of anti-infective therapies. To achieve this, Dr. Dorschner has assembled an interdepartmental mentoring team with experience launching junior investigators into independent research careers. His primary mentors from the Department of Surgery are Dr. Brian Eliceiri, PhD, an expert in immune cell trafficking and inflammation, and Dr. Andrew Baird, PhD, an expert in wound healing. Additional clinician-scientist mentors from the Department of Dermatology provide further expertise in cutaneous immunity and inflammation research and clinician-scientist career development. This training plan implements 1) acquisition of scientific and technical expertise in neutrophil biology and signaling using mouse and human models 2) training in grant writing, clinical research and biostatistics 3) generation of data for a successful R01 submission, and a 4) planned transition to independence through ongoing professional development. This work takes place within the outstanding scientific environment at UCSD in the Departments of Surgery and Dermatology. This training plan builds on Dr. Dorschner's previous research and clinical training to position him as a leading clinician-scientist with an independent R01-funded research program focused on neutrophil driven cutaneous inflammatory responses.

NIH Research Projects · FY 2025 · 2020-07

Project Summary The laboratory led by PI Galia Debelouchina has the following long-term objectives: 1) The development of structural biology methodology to study complex and dynamic biological assemblies in vitro, and 2) The extension of these methodologies for structural biology investigations in the cellular environment. Our methodology development combines solid-state nuclear magnetic resonance (NMR) spectroscopy with state- of-the-art chemical biology tools for the comprehensive description of biological systems both in vitro and in cells. Over the next five years, we plan to accomplish the following goals: 1) Elucidate the molecular basis of heterochromatin formation and regulation. Heterochromatin compartments are associated with gene silencing and repetitive DNA sequences, and their formation is a vital step in cell differentiation and development. Recent hypotheses suggest that they are formed through a process called liquid-liquid phase separation and that a central player in this process is the heterochromatin protein 1 (HP1) family. Our goal is to understand how HP1 proteins orchestrate a complex network of interactions with each other, with chromatin, and with other protein binding partners to regulate the material properties of heterochromatin environments and their implications for gene silencing. We will tackle this goal using NMR spectroscopy, chemical biology, cell biology and computational tools to obtain a comprehensive molecular view of heterochromatin interactions. In the process, we also hope to develop new NMR-based tools to characterize dynamic and heterogenous biological systems such as those formed by HP1 proteins. 2) Development of NMR-based tools for structural biology in cells. Here, we plan to focus on the development and implementation of a technique called targeted dynamic nuclear polarization (DNP), which allows us to zoom in on a specific protein in the cellular environment and to increase its NMR signals selectively over the cellular background. We plan to apply this technique to study protein-membrane interactions in whole bacterial and mammalian cells. Ultimately, we aim to develop targeted DNP as a tool to build an atomic resolution picture of the cellular milieu and to investigate changes in protein structure and dynamics in health and disease.

NIH Research Projects · FY 2024 · 2020-07

Summary Bioprinting plant virus nanoparticles for immunotherapy and relapse prevention of ovarian cancer High grade serous ovarian cancer (HGSOC) is the most common and severe form of ovarian cancer and women with HGSOC have a poor prognosis. Immunotherapy approaches that induce systemic antitumor immunity, in particular those that prevent relapse, are urgently needed for HGSOC. We propose to employ plant virus-like nanoparticles (VLPs) combined with slow release antigen depots as a cancer vaccine approach to launch sys- temic antitumor immunity during remission to block relapse. Our data indicate that intraperitoneal (IP) admin- istration of plant VLPs in a mouse model of ovarian cancer modulates the tumor microenvironment to relieve immunosuppression and generate adaptive anti-tumor immunity and memory against tumor antigens. The VLPs are non-infectious, non-cytotoxic, and non-cytolytic, but the highly repetitive nature of the proteinaceous VLPs triggers innate immune activation and associated adaptive immune response. Building on this, we will develop a VLP biopolymer formulation to enable effective immunotherapy following surgical debulking in HGSOC. We will incorporate irradiated tumor cells as source for patient specific tumor antigens; the cells will be delivered together with the VLPs which act as adjuvant to launch long-lasting anti-tumor immunity. The proposed immu- notherapy implant will be produced through an innovative 3D bioprinting technique; specifically, rapid, microscale continuous optical bioprinting (µCOB). This platform offers control over both the topographical complexity and the cellular and material composition of the scaffold at micron-level resolution. Our rapid 3D bioprinting process allows for photopolymerization of multiple biocompatible materials, and facilitates incorporation of VLPs and/or cells. The engineering design space and tunability of this approach is impeccable; in particular the implant will be designed so that therapeutic doses are released in programmed intervals (prime/boost) vs. continuous slow release. We will fulfill three specific aims: 1) Bioprint VLP biopolymer implants and test various configurations to optimize slow, continuous release vs. staged, e.g. weekly release of the therapeutic VLPs. The implants will undergo rigorous quality control and reproducibility testing and released VLPs will undergo structural analysis and biological testing. 2) Evaluate efficacy of the immunotherapy implants vs. soluble VLPs will be evaluated using mouse model of ovarian cancer (ID8vegf/defb29). Immunological investigation will provide insights into the mechanism of the immunotherapy. 3) To further explore vaccine parameters and model very low endogenous patient antigen loads during remission, we will bioprint biopolymer implants to deliver VLPs and antigen (from irradiated cells) prior to challenge with ID8vegf/defb29 cells. For future translational approaches, patient tumor from surgical debulking and/or patient neoantigen peptides would be used. The clinical significance is high: we envision a simple modification to the current treatment work-flow, where small degradable vaccine implants are left in the intraperitoneal (IP) cavity during surgery or administered subcutaneously (SC) post-surgery, or both.

NIH Research Projects · FY 2024 · 2020-07

PROJECT SUMMARY / ABSTRACT Diamond-Blackfan anemia (DBA) is a unique example of a bone marrow failure disorder that improves with drug treatment. Glucocorticoids increase red blood cell production in most DBA patients, but the underlying mechanism of clinical efficacy was unclear until recently. I identified a phenomenon where mouse burst forming unit-erythroid (BFU-E) cells progress through a continuum of developmental states during transit-amplification; glucocorticoid treatment decreases the degree of developmental progression per cell cycle, resulting in a greater number of transit-amplifying cell divisions before the onset of erythroid terminal differentiation (Developmental Cell, 2019). Conversely, TGFβ treatment of BFU-Es increases rate of developmental progression and decreases overall BFU-E proliferative capacity. My findings defined a novel developmental biology paradigm where rate of progenitor cell developmental progression regulates balance of proliferation and differentiation, and total cellular output. Insights into the mechanisms by which glucocorticoids and TGFβ regulate proliferative capacity remain elusive, and the conclusions from my mouse erythropoiesis studies must be directly tested in human erythropoiesis. I will identify the target genes of glucocorticoid and TGFβ signaling in BFU-Es using nascent transcriptome profiling and chromatin occupancy and architecture profiling. Furthermore, I will use single cell RNA sequencing of normal and DBA patient bone marrow hematopoietic progenitor cells to compare glucocorticoid and TGFβ effects on mouse erythropoiesis and human erythropoiesis. My proposed studies will: (i) contribute broadly to our understanding of pathophysiology and treatment principles in bone marrow failure, (ii) further develop a novel field within developmental biology that arose from my earlier postdoctoral work, and (iii) provide ample opportunities for mechanistic and translational follow-up for my transition to independence. I am a physician-scientist seeking K08 support for mentored research under the guidance of Dr. Harvey Lodish and Dr. Stuart Orkin. This mentored period of 80% research and career development, and 20% clinical time, will ensure I acquire the skills required to become a successful independent principal investigator. Drs. Lodish and Orkin are internationally recognized mentors, together training >200 successful independent investigators; both received the American Society of Hematology Basic Science Mentor Award. My training will occur at two world- class institutions, the Whitehead Institute for Biomedical Research, and the Dana-Farber/Boston Children's Cancer and Blood Disorders Center. Both are rich with opportunities for young scientists to train, pursue highly impactful science, and foster long-lasting collaborations. I will also be guided by a committee of researchers that are all leaders in their fields: Drs. David Bartel (RNA biology), Peter Reddien (developmental biology), and Akiko Shimamura (bone marrow failure). The support of this K08 award will allow me to focus on maturing my research and strengthening my career development during this critical last stage of mentored training. At the conclusion of my award period, I will be optimally positioned for achieving success as an independent physician-scientist.

NIH Research Projects · FY 2024 · 2020-07

Project Summary The degradation of misfolded proteins in the endoplasmic reticulum (ER) by the ER-associated degradation (ERAD) pathway prevents potentially toxic proteins from entering the secretory pathway. ERAD, however, cannot clear all proteins from the ER. For example, some proteins, such as aggregation-prone proteins, large polymers and fibrillar proteins, are resistant to degradation by ERAD and must be disposed of by alternate disposal pathways. As aggregation prone proteins have been to linked to neurodegenerative diseases, understanding how these alternate disposal pathways function is of medical importance. ER autophagy (ER-phagy) is a disposal pathway that degrades ER domains and aggregation-prone proteins. How specific domains, on the continuous network of the ER, are targeted for degradation is unknown. We have found that a non-canonical form of the COPII coat, that contains SEC24C-SEC23, works with receptors on the ER to target domains for autophagy. ER-phagy sites (ERPHS) on the ER are distinct from the ER exit sites where secretory cargo is loaded into canonical COPII coated vesicles that traffic to the Golgi. Our findings suggest that ER structure may be important for the formation of ERPHS. Additionally, mutations in several ER shaping proteins, associated with hereditary spastic paraplegias (HSP), lead to defects in ER-phagy. These findings suggest a link between ER-phagy, the formation of the ERPHS and HSP. In this proposal I describe several aims that are designed to address the role that ER structure plays in the formation of ERPHS and the link between ERPHS formation and HSP. Specifically, we will perform live cell imaging and mass spectroscopy experiments to characterize the ERPHS and their cargo. Misfolded proteins, known to be degraded by ER-phagy, will be analyzed. To date six ER autophagy receptors have been identified. Our studies will address when SEC24C interacts with the autophagy machinery and which of the six known receptors interact with SEC24C. Our biochemical studies may lead to the identification of new proteins that interact with SEC24C during ER autophagy. Autophagy reporters, imaging analysis and biochemical studies will be used to address the role that ER organization and ER shaping proteins play in ER-phagy and ERPHS formation. The proteins we will analyze in Aim 2 and Aim 3 are associated with HSP and HSP-like neuropathies. In total, these studies will shed light on the link between ER structure, ERPHS formation and HSP.

NIH Research Projects · FY 2024 · 2020-07

Abstract Objectives: The Advanced Data Analytics Program To (ADAPT) will enhance behavioral and social sciences research, by training a diverse next generation of data scientists who will learn interdisciplinary skills needed for successful careers in behavioral and social sciences health-related data science. Rationale: San Diego is a hub for genomics, mobile technology, behavioral health research and data science in Southern California, yet no data science curriculum for behavioral scientists currently exists. The ADAPT program will fill this gap and intersect the areas of health sciences, informatics, computer science, and statistics in Southern California. Design: ADAPT will educate doctoral students in the behavioral and social sciences to build and further expand an ecosystem for big data analytics that promotes finding, accessing, interoperating, and reusing digital objects and responsibly computing with human subjects’ data in cloud environments. The ADAPT program will be based at the University of California, San Diego (UCSD), with faculty collaborators from San Diego State University. It will be based on two joint doctoral programs (JDPs) at these universities (Clinical Psychology and Public Health/Behavioral Health). Dual mentoring by faculty with expertise in behavioral and social sciences and computer science, biomedical informatics, or statistics will ensure a truly interdisciplinary focus that will cover team science and responsible conduct of research. Key Activities: Trainees will gain expertise through coursework, research experience during rotations and external internships, mentoring and other activities. Existing data science courses were selected for the curriculum, which will also include a new course in cloud-based human subjects’ data computing. Through individualized development plans, ADAPT trainees will work with their faculty mentors to tailor the curriculum and career paths according to students’ interests and skills. Data science coursework will utilize elective course slots in the JDP curricula, will typically be completed in years 1 and 2 of the JDPs. They will provide the foundational knowledge needed for academic and industry rotations and for the start of the trainees’ research phase. Projected Number of Trainees: 6 first or second year JDP students Planned Duration of Appointments: 3 years, renewed annually based on good academic standing Intended Trainee Outcomes: Metrics for success will include number and quality of publications, and rate of academic milestone completion. Trainees who complete the ADAPT program will possess the scientific knowledge needed to be a behavioral health data scientist, understand ethical and regulatory aspects of computing with protected health information, and will become critical members of scientific teams working in academia, government, for-profit and non-profit research institutions.