University Of California, San Diego

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY Pneumonia is the most common cause of hospitalization due to infection in the US and the most common cause of infection-related death. Mortality in healthcare-associated pneumonia (HAP) is 13% overall and 36% in patients admitted to the ICU. Bacterial lung infections are also a frequent complication of prolonged mechanical ventilation required in patients after major surgery, traume, and severe lung injury due to viral pneumonias (e.g. SARS-Cov2); mortality in such ventilator-associated pneumonias (VAP) is even more grave. Two leading bacterial causes of HAP/VAP are the Gram-negative nosocomial pathogens Pseudomonas aeruginosa (PA) and Acinetobacter baumannii (AB), both frequently highly multidrug-resistant and can develop resistance to last line carbapenems. Gram-negative bacterial HAP/VAP is frequently complicated by neutrophil- and cytokine driven hyperinflammation and associated lung damage—which when severe is designated “acute respiratory distress syndrome” (ARDS). There are no standard clinically proven therapies to support the host immune system in clearing severe bacterial pneumonia while simultaneously suppressing the hyperinflammation that leads to lung tissue destruction. Here we describe a highly innovative drug concept for critically ill patients with severe PA and AB pneumonia with a unique multifold mechanism of action: biomimetic human macrophage membrane-coated nanoparticles (MΦ-NP). MΦ-NP are made by wrapping cell membranes derived from human macrophages around biodegradable polymeric cores, retaining their membrane lipid bilayer and full repertoire of surface structures and receptors, just on a nano (~1/50,000th) scale. The natural biomimicry imparts to the MΦ-NP the ability to bind, sequester and neutralize bacterial toxins, lipopolysaccharide (LPS), and host-derived proinflammatory cytokines, a tripartite mechanism of action to curb harmful inflammation, preserved tissue integrity, and facilitate bacterial clearance. Here we describe our extensive prior published and preliminary results that strongly support the novel therapeutic concept of MΦ-NP for the treatment of severe Gram- bacterial pneumonia in ICU patients, and how the proven team at San Diego-based Cellics Therapeutics will support our Clinical Development Plan at every step of the pathway toward an investigational new drug (IND) application and entry into Phase 1 clinical trials to meet this critical unmet medical need. In Aim 1 we will study the capacity of MΦ-NP to preserve lung epithelial and endothelial barrier integrity and function upon pneumonia challenge, including work in novel 3D human iPSC derived organoids. In Aim 2, we will examine the ability of MΦ-NP to block excessive alveolar macrophage and neutrophil-driven inflammation but preserve their antibacterial function against MDR Gram- pathogens. Finally in Aim 3, we will conduct in vivo analysis of the benefits of intratracheal (IT) and/or intravenous (IV) MΦ-NP therapy on mortality, bacterial clearance, and lung inflammation/damage in murine models of MDR Gram- pneumonia and perform key studies to assess PK/PD and toxicity profile of MΦ-NP administration.

NIH Research Projects · FY 2024 · 2023-07

Project Summary The inflammasomes are cytoplasmic multi-protein complexes that can sense and be activated by microbes or tissue damage, which then leads to the activation of caspase-mediated inflammatory pathways involving the release of cytokines IL-1β and IL-18. Although the pro-inflammatory role of inflammasomes have been well established in innate immune cells, recently, several studies have uncovered a role for different inflammasome components in regulating many different T cell responses, a key part of adaptive immunity. Specifically, a subset of T cells called regulatory T cells (Tregs), which are known for their ability to suppress immune responses and inflammation, were shown to be affected by their cell intrinsic inflammasome components. Even though the critical role of Tregs in establishing tolerance to a wide range of innocuous foreign antigens from commensal microbes and food in the gut has long been well-recognized, the function of the NLRP3 inflammasome in Treg-mediated control of intestinal homeostasis remains an open question. Based on preliminary data, it was hypothesized that NLRP3/inflammasome could serve as an integral determinant in controlling Treg biology and that induction of NLRP3 in intestinal Tregs would be specifically required for their control of Th17 responses in the intestine. To test this hypothesis, the first aim will elucidate the function of NLRP3 in controlling Treg biology in the gut in heath and disease using both loss-of-function and gain-of- function approaches through employing two novel mouse models that have been recently generated in the lab: mice with Treg-specific deletion of NLPR3 and mice with Treg-specific expression of constitutively active NLRP3. Two different Th17-dependent disease models: anti-CD3 induced intestinal inflammation and Citrobacter rodentium infection model will be employed. As such, the biological impact of NLRP3 depletion or constitutive activation in Tregs on the other immune cells in the intestinal system under both physiological and pathological conditions will be elucidated. In the second aim, the molecular mechanisms underlying NLRP3- mediated control of Treg biology will be investigated. First, as IL-1b, a component of the NLRP3/inflammasome pathway was also found to be selectively induced in intestinal Tregs under inflammation, I will determine the potential role of Treg-derived IL-1b in controlling intestinal homeostasis. Next, the potential involvement of inflammasome-independent vs. –dependent mechanism underlying NLRP3-mediated Treg biology will also be examined. Finally, as the heterogeneous nature of Tregs is now well appreciated, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) studies will be conducted to determine if there is a specific subset of Tregs that expresses NLRP3 or whether NLRP3 induction is a common feature for all intestinal Tregs under inflammation. Collectively, this study will provide mechanistic insights into the underappreciated anti-inflammatory role of NLRP3 in intestinal Tregs and will undoubtedly facilitate the development of future therapeutics for inflammatory bowel disease and other human intestinal disorders.

NIH Research Projects · FY 2024 · 2023-07

The dystonias overall are a rare neurologic disorder. Cervical dystonia (CD), sometimes called “spasmodic torticollis”, is one of the most common forms of dystonia. CD is characterized by the partial loss of voluntary control of the neck musculature producing abnormal postures and/or movements of the head in the form of head tremor. In addition to these overt motor abnormalities, the disorder is also associated with non-motor symptoms including pain, fatigue, anxiety, and depression. Treatment options for CD are suboptimal. Many oral medications have been tried but their efficacy is minimal and limited by dose-dependent adverse side effects. Botulinum neurotoxin (BoNT) injections repeated every 3-4 months are the primary treatment of choice. Although BoNT is highly efficacious for many patients, for a variety of reasons about 1/3 of patients discontinue BoNT treatment, and of those who continue treatment about 1/3 are unsatisfied with the response. Because treatment options are suboptimal, there is an active effort to find better strategies for treating CD, as evidenced by dozens of active trials listed on ClinicalTrials.gov. However, the most common clinical outcome assessment used to measure motor abnormalities – the Toronto Western Spasmodic Torticollis Rating Scale (TWSTRS) – does not capture head tremor. Also, as with most clinical rating scales, the TWSTRS is an intrinsically subjective assessment and therefore suffers from inter-rater variability. This reduces our power to detect treatment effects in clinical trials. Technology-based objective measures have the potential to circumvent this variability. Advances in computer vision technology have enabled the measurement of head orientation/rotation from 2-D images of the face in conventional video recordings. One of the long-term objectives of our group is to leverage these advances to develop software that can capture and quantify motor abnormalities across multiple types of focal dystonia. We are calling this system the Computational Motor Objective Rater (CMOR). In this project specifically targeting CD, our aims are 1) to evaluate CMOR’s convergent validity with patient reports of severity of abnormal head posture and head tremor and 2) to determine CMOR’s sensitivity to changes in severity associated with interventions. To accomplish these aims, we will conduct CMOR analyses of motor symptoms from video recordings of 100 CD patients enrolled in a separate Dystonia Coalition project to evaluate the variability of efficacy of BoNT. That project will also acquire patient reports in the form of a patient centered outcome with specific questions about the two motor features of CD and the patient’s global impression of change (PGIC) in response to each BoNT treatment. Collectively the results will provide important information about CMOR’s validity and a quantitative basis for sample size estimates for future clinical trials in CD.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY / ABSTRACT Translational cancer research that improves patient health requires a multi-disciplinary approach that advances innovative discoveries from (A) basic research to (B) preclinical validation (often utilizing biobanked tissue) to (C) clinical implementation via entrepreneurship and commercialization. But surgeons rarely receive formal training in biobanking and entrepreneurship, and few programs are designed to formally train surgeons in the cancer biology and the tumor microenvironment (TME). Recognizing these critical gaps in training surgeon- scientists, the Department of Surgery and the Moores Cancer Center (NCI-Designated Comprehensive Cancer Center) and the Department of Surgery at the University of California San Diego (UC San Diego) propose a new program to support training for MD/DO surgeon-scientists who show objective evidence of a commitment to a career in academic surgical oncology for a two-year training program. We will create the Surgical Oncologists as Scientists (SOAS) Training Program centered on formal training in three topics: 1) the TME; 2) biobanking; and 3) innovation/entrepreneurship. The rationale for TME training is that increasingly, the oncologic surgeon- scientist needs to thoroughly understand details of how the TME plays significant roles in cancer initiation, progression, metastasis, response to therapies, and serves as novel targets for anti-cancer drugs. The rationale for training in biobanking is that academic surgeons are frequently asked to collaborate in research because their unparalleled access to human specimens, which must be properly banked in a dedicated biorepository. Finally, the rationale for innovation/entrepreneurship training involves the critical need to ensure that research training of surgeon-scientists has real-world translational relevance—that is, we need to demonstrably improve cancer care, not merely improve understanding. This rationale leverages the metropolitan San Diego area as the third largest assembly of components necessary to successfully translate (i.e., commercialize) innovations into Food and Drug Administration (FDA)-approved clinical realities. San Diego includes a plethora of biotech startups (hundreds spun out of UC San Diego), Angel investors, private equity and venture capital firms, contract research organizations, and local networking activities. The SOAS program will be co-led by a surgical oncologist/translational scientist and a PhD scientist that bring complementary, but unique skills in science and experience in innovation. Research training will occur within one of 14 Faculty Mentor’s laboratories, each of which has solid, continuous R01 NIH funding, and each has a strong record of successful mentorship. Also, Trainees will develop co-mentoring relationships with at least one of our 9 Entrepreneurial Liaison Advisors, each of whom has practical experience with translation (e.g., patents, start-ups). The SOAS Training Program will train collaborative surgeon-scientists to become future leaders in academic surgery and oncology to actively participate in translating innovative new discoveries into clinical cancer care.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY Acute myeloid leukemia (AML), diagnosed in over 20,000 US citizens each year, has a 5-year survival of only 20-30%. Despite decades of research, the effective treatment of AML remains a significant unmet clinical need, with standard of care underscored by high relapse and mortality rates due to the persistence of treatment- resistant leukemic stem cells (LSC) that drive the disease. Work by us and others, and the existence of a large genomic subgroup represented by mutations in RNA splicing genes, in combination present compelling evidence to suggest that deregulated control at the level of RNA metabolism is a feature that defines and mediates aspects of disease pathology. RNA binding proteins (RBPs) are core effectors of post-transcriptional regulation that execute precise control of gene expression by modulating RNA properties that include splicing, polyadenylation, localization, degradation and translation, and as a class can enforce an extremely diverse network of regulatory pathways. One specific class of RBPs functions within stress granules, membraneless cytoplasmic structures that are composed of RBPs and mRNAs to orchestrate post-transcriptional programs mediating adaptive cellular responses. Through a combination of genetic screens and in vivo studies, we recently discovered that LSCs selectively depend on the ability to form stress granules for their survival and proliferation. We therefore hypothesize that stress granules play a critical role in AML pathogenesis and that stress granule proteins represent a vulnerability that can be exploited in novel targeted therapeutic strategies. In this project, we aim to define the dynamics and functional requirements for stress granules in the leukemic stem cells of highly treatment refractory MLL-rearranged (MLL-r) AML. We will first perform a series of in vitro stress granule formation and in vivo cell engraftment studies assays using acutely isolated MLL-r AML and normal HSCs to identify stress granule dynamics and characteristics across primitive to more committed AML and normal hematopoietic cells. We will uncover mRNAs bound selectively in stress granules, define and functionally validate putatively key LSC- specific stress granule-interacting proteins, including one candidate we have already identified, and map the role of novel LSC-specific stress granule proteins and RNAs sequestered in them, in LSC function. Lastly, we will systematically screen for novel stress granule-relevant RBPs that underlie the function of relapsed LSCs. Our study will thus define the role of stress granule RNA and protein components and the gene expression networks they control to promote leukemia pathogenesis, thereby identifying novel potential therapeutic targets in AML.

NIH Research Projects · FY 2026 · 2023-07

ABSTRACT Severe neonatal hyperbilirubinemia (SNH) and necrotizing enterocolitis (NEC) are the most common causes of morbidity in newborns worldwide, with both symptoms being linked to human breast milk (HBM). Enteral formula feeding is a direct biomarker for the induction of NEC in preterm newborns, while HBM protects against NEC. In newborns, HBM suppresses UDP-glucuronosyltransferase (UGT) 1A1 expression, the only transferase capable of conjugating bilirubin, thus contributing to the development of hyperbilirubinemia. Humanized UGT1 (hUGT1) mice that express the human UGT1A1 gene mimic what is observed in humans with neonatal hUGT1 mice developing SNH. As an animal model to examine the mechanisms that lead to regulation of the UGT1A1 gene, we have documented that the UGT1A1 gene is repressed in liver tissue, which plays a key role in total serum bilirubin (TSB) accumulation. While approximately 10% of the neonatal hUGT1 mice develop Kernicterus Spectrum Disorder (KSD), which is lethal, most of the newborns are healthy, have normal reproductive cycles, and represent an excellent model to study the underlying mechanisms linking UGT1A1 expression to SNH. New findings from our laboratory have demonstrated that the delay in intestinal UGT1A1 expression is controlled specifically by the nuclear receptor transcriptional corepressor protein, NCoR1. When NCoR1 is rendered non-functional through genetic knockout experiments in the intestines, neonatal TSB levels are normal and intestinal UGT1A1 is dramatically induced, resulting from intestinal epithelial cell (IEC) maturation. The delay in intestinal UGT1A1 in neonatal hUGT1 mice is a direct result of breast milk, since formula feeding leads to significant induction of UGT1A1. HBM plays a key role in the development of SNH by blocking bilirubin metabolism while simultaneously protecting newborns against NEC. Thus, we hypothesize that the underlying mechanisms leading to SNH are also linked to the underlying mechanisms that regulate NEC. This may not be a coincidence but crucially important to understand, since bilirubin is a potent antioxidant that could combat oxidative stress induced intestinal inflammation, which leads to NEC. Thus, the focus of our efforts will determine if complimentary cellular mechanisms are tied to the development of both SNH and NEC. The major focus areas, based upon current publications and preliminary findings, will be to tie the role of microflora, TRL4 signaling, HBM oligosaccharides, and neonatal IEC maturation, with the control and regulation of SNH and NEC. The experiments outlined are anticipated to lead to a greater understanding of these syndromes, made available using novel mouse models and advanced technology that will allow us to connect the early biological events after birth leading to the developmental control of SNH with those same processes that will be tied to the onset of NEC. Because there does not exist effective therapeutic interventions for the treatment of either SNH or NEC, the long-term goal of this work and the unraveling of the mechanisms leading to these syndromes will be to use this information to improve the development of effective therapy.

NIH Research Projects · FY 2025 · 2023-07

Delineating a parietal-anterior cingulate-claustrum circuit underlying cognitive control and attention Treatments are urgently needed for cognitive dysfunction in psychiatric patients. Given the link between such dysfunction and outcome in patients, large numbers of clinical trials were conducted with companies attempting to be ‘first-to-market’. In the rush however, preclinical studies used had limited validity to the cognitive domains reportedly targeted. Thus, circuit-engagement of the cognitive domain tested was rarely if-at-all verified and all clinical trials to-date have failed. New paradigms have emerged with reported relevance to domains affected in psychiatry, but little opportunity to validate circuits underlying these behaviors, let-alone drugs that modulate such circuits and behavior, have arisen. This application will utilize a circuit-targeted approach to confirm the utility of the 5-choice continuous performance test (5C-CPT) to measure cognitive control and attention across multiple psychiatric disorders. Specific Aim 1 will optimize the touchscreen 5C-CPT for parametric manipulation. The 5C-CPT exists for mice, rats, and humans, with EEG & fMRI versions. The task has always been standard however, primarily in 5-hole operant chambers, but a touchscreen version with parametric manipulations within the task would improve translatability to human testing and enable task performance-based consistency. Backward masking of stimuli have been used in cognitive control tasks previously, but only recently used in human 5C-CPT studies. Here, we will demonstrate that such masked trials enable parametric assessment of 5C-CPT performance in mice. Specific Aim 2 will determine the pharmacological sensitivity of the touchscreen 5C-CPT. After developing the task, it is important to confirm that it is sensitive to manipulations, including those available for use in humans for pharmacological predictive validation. We demonstrated that modafinil improves healthy human participant performance of the standard 5C-CPT, while scopolamine impairs mouse performance. Here, we will confirm that modafinil and scopolamine similarly affect this masked touchscreen 5C-CPT, while predicting that a dopamine D4 receptor agonist would improve cognitive control. We will confirm that modafinil rescues scopolamine-induced deficits, avoiding receptor tautological complications. Specific Aim 3 will confirm the role of the anterior cingulate cortex (ACC)claustrum and claustrumparietal cortex (PC) circuit underlying this masked touchscreen 5C-CPT performance. Consistent with human CPTs, we confirmed the necessity of the PC for mouse 5-choice (5C-)CPT performance. We hypothesize that a ACC to claustrum projection is important during more cognitively demanding trials (from parametric manipulations), while a claustrum to PC projection occurs is important for selecting whether to respond or not during trials. Using fiber photometry and optogenetic techniques, we will confirm both the activation and necessity of this circuit respectively, including changes in activity as a direct result of pharmacological manipulation. Thus, circuitry underlying cognitive control will be identified, as will pharmacological treatments affecting this circuit that are readily testable in healthy human participants.

NIH Research Projects · FY 2026 · 2023-06

Project Summary Peripheral nerve injuries, as a result of trauma, tumors, or other medical conditions, require 50,000-200,000 surgeries annually, and may cause complete or partial paralysis. The autograft is the current "gold standard" but requires additional procedures to harvest the graft, can be challenging to perform in a pediatric population, and often leads to neuroma formation and loss of function at the donor site. The goal of this project is to validate the materials and methods to fabricate pre-clinical polymeric three-dimensional (3D) nerve conduits with an embedded wireless sensor for continuous monitoring of functional recovery to be used in infants/children. The 3D printed vascularizable nerve conduits mimic the micro-architecture of nerve tissues, are embedded with wireless sensors for in situ monitoring, and can perform biomimetic functions to augment nerve regeneration therapies. Currently, there is no clinical solution for monitoring the success of a neural graft therapy after surgery. Specific Aim 1 will focus on optimizing 3D-bioprinted nerve conduit fabrication and performance using commercial-grade biomaterials for clinical translation. To fabricate such a conduit in this aim, we will use a Rapid Projection, Image-guided, Direct-printing (RaPID) platform that can 3D-print the entire nerve conduit in mere seconds and will match the patient’s specific size and shape. The conduit will have linear micro-channels along the length for axon growth and side micro-holes for vascularization. Specific Aim 2 will validate generation of pediatric patient-specific conduits based on volumetric defect. In this aim, we will coordinate the collection of MRI data among pediatric patients from birth to 18 years of age, both sexes, and with peripheral nerve injuries involving the head and neck, upper limbs, and lower limbs. Based upon the MRI data collected, personalized pediatric nerve conduits will be 3D bioprinted to validate the RaPID system and provide evidence for planned FDA regulatory review. Specific Aim 3 will develop a wirelessly powered and controlled sensor to detect electrical impulses across a nerve defect. In this aim, we will attach wireless sensors via a polymeric cuff design to the distal end of an injured mouse sciatic nerve to assess the rate and robustness of nerve fiber growth across the therapeutic repair site. Developing this implantable sensor will pave the way for integrating diagnostics with therapeutics for surgical interventions. The final deliverable at the completion of this proposal will be to have the manufacturing specifications, source material specifications, sizing limits, testing and release specifications for 3D bioprinted nerve conduits with wireless sensing to support a pre-submission meeting with FDA followed by a 510(k) filing.

NIH Research Projects · FY 2025 · 2023-06

PROJECT SUMMARY/ABSTRACT Most therapies that target microbiome composition do not have a detectable impact on the gut microbiome and are not robust to the interpersonal diversity and plasticity of the community in human hosts. To develop a better mechanistic understanding of the microbe-host relationship and more effective microbiome-mediated therapies, approaches based on functional modulation of the gut microbiome are necessary. However, these approaches have been difficult to develop. Attaining long-term engraftment in the luminal environment has proven to be quite difficult, and even once engraftment has been achieved, a change in physiology or improvement of pathologic phenotype has not yet been demonstrated. There is a critical need for a tool that will allow investigators to “knock-in” functions into the gut microbiome and investigate their effects on the luminal milieu and, ultimately, physiology in conventionally-raised hosts in non-sterile conditions. The investigators propose a novel approach to address this need by using native bacteria as chassis for the introduction of specific functions into the luminal environment. The proposal's innovation is a new strategy that allows the quick and effective “knock-in” of a beneficial function in a sustained manner into conventional hosts. To date they have demonstrated that tractable native bacteria can be engineered to express a beneficial function ex vivo, reintroduced to the host, engraft the entire gut of the host, and deliver an intended beneficial function. These functions can affect host physiology, help determine the effect of specific bacterial functions and potentially alleviate disease. The central hypothesis of this proposal is that long-term colonization and functional change in the gut microbiome of a conventional host can be performed effectively with engineered native bacteria. In the next five years, the investigators will continue the development of this technology and better understand the chassis-host interactions that will aid in the development of live bacterial therapeutics for clinical use. First, the investigators will engineer regulatory systems for the transgene of interest, including a sense and control, protein secretion, and biocontainment circuit. They will test whether these systems function in vivo in hosts that are in a non-sterile environment. In addition, they will assess the natural biocontainment of engineered native bacteria among co-housed hosts. Second, they will determine how the niche for a bacterial chassis affects function delivery and whether multiple functions can be delivered by the same chassis or whether different chassis are necessary for the delivery of multiple functions. Finally, the investigators will determine the role of microbial community in amplifying the effects of a transgene of interest in gnotobiotic mice. The expected outcome of the proposed studies is attainment of fundamental biological knowledge of how the gut microbiome can be functionally manipulated. These studies will have a positive translational impact because they will demonstrate that synthetic biology approaches can lead to the development of curative interventions to some of the most debilitating and costly chronic diseases.

NIH Research Projects · FY 2026 · 2023-06

PROJECT SUMMARY/ABSTRACT This resubmission responds to PAR-MH-21-135 (Development of Psychosocial Therapeutic and Preventive Interventions for Mental Disorders, R61/R33), addressing the PAR by sequentially testing a new intervention that is translated from basic science and that uses a multi-modal approach to assessing and modifying an objectively measured target. The overarching goal is to evaluate a new blended mobile intervention that is aimed at improving introspective accuracy (IA) in people with psychotic disorders, with the ultimate goal of improving functional outcome. Introspective accuracy is the degree to which one’s self-assessment of task performance or abilities corresponds with objective data. Our group and others have demonstrated that poor IA is a strong and independent predictor of functional disability. Yet, there are currently no treatments that directly target IA. Basic experimental research and other lines of evidence suggest IA is malleable, and that improvement in task-based IA transfers to untrained tasks. This project’s premise is that task-based IA training could be delivered in a remote mobile health format and coupled with coaching in applying improved IA to real- world functional behaviors, creating a novel avenue for functional rehabilitation in psychotic disorders. We have developed and completed usability testing of iTEST, a novel blended mobile intervention. iTEST integrates graduated drill-and-practice training delivered on a mobile device that targets IA with personalized coaching in applying IA to everyday compensatory behaviors. In the R61 phase, we will recruit people with psychotic disorders with at least minimal functional impairment. We will first conduct a pilot study to finalize a fully ready-for-deployment version of iTEST. Next, we propose an open trial of iTEST, evaluating whether the intervention leads to clinically significant changes in task-based IA along with transfer to an untrained task (target mechanisms). We will also determine the dose of intervention needed to achieve clinically significant improvement in IA targets, by evaluating change at 8, 12, or 16 weeks. If go/no go criteria (clinically significant increases in trained and untreated introspective accuracy) are met in the R61 phase, the R33 phase includes a randomized controlled trial contrasting iTEST with a control condition that provides training in goal setting and cognitive compensation but does not include task-based IA training. We will evaluate whether iTEST leads to greater improvement in IA and functional outcome, whether these improvements are sustained at follow up, and whether increases in IA mediate improvements in functional outcome. This project responds directly to NIMH Strategic Aim 3.1, by evaluating a new intervention that targets functioning by modifying an objectively measured target. Our project also responds to the NIMH Digital Health Priority Area by advancing mobile interventions for cognitive rehabilitation. If effective, iTEST could be integrated with many cognitive training and other rehabilitative interventions to boost impact on functional outcomes.

NIH Research Projects · FY 2026 · 2023-06

PROJECT SUMMARY / ABSTRACT Primary lung cancer is by far the leading cause of cancer death worldwide, with approximately 150,000 deaths yearly in the United States. When symptoms arise, the lung cancer survival rate at five years is a dismal 17%. Lung cancer screening with low-dose CT has been shown to reduce mortality from lung cancer among high- risk patients as the cancer is typically caught early, in stage IA. Definitive diagnosis requires tissue sampling, and despite risks of pneumothorax, sampling is often performed by percutaneous transthoracic lung biopsies under CT guidance. Since sampling can cause immediate perilesional hemorrhage and obscure views of the lesion, there is little room for error. However, current procedural challenges, involving translating the patient in- and-out of the bore repetitively for frequent freehand needle adjustments and advancements, introduce errors, take significant time, cost, and confers ionizing radiation and risk of complications to the patient. The purpose of this project is to develop an autonomous needle biopsy procedure performed under artificially intelligent robot guidance, optimizing for patient safety and targeting accuracy. The approach involves (i) a highly dexterous, force-sensitive redundant robot design with an active needle placer that operates inside the CT scanner, and can articulate and steer needles for any thoracic approach or patient position; (ii) an artificially intelligent planner that finds new, less traumatic, and safer approaches to biopsy lesions in a patient-specific manner, and (iii) closed-loop CT-image feedback control to precisely steer needles to suspect lesions. The work of this project is to be carried out via the following Specific Aims: (1) develop the force sensitive robot based on our previous robotic designs and validate on real human cases for reachability and safety analysis, (2) develop metrics and algorithms for planning needle biopsy approaches in a patient- specific way, and (3) develop high-fidelity breathing phantoms across biologically relevant variables and compare the automated robotic approach to freehanded needle placement a user study. The proposed approach offers a solution that could significantly broaden the approach direction and positioning of needles for biopsies. The semi-autonomy provides significant value by computing a variety of factors in planning the approach that optimizes accuracy and safety, including patient anatomy, safety from sensitive structures, and depth of insertions --- all of which can also have a significant effect on patient health during screening, who are already have compromised pulmonary status or have elevated risk of acute pneumothorax. Finally, the integration of machine learning, automation, and robotics reduces the variation between clinicians, leverages population data to make data-backed informed plans, and can reach super- human precision while reducing procedure time and ionizing imaging. Our long-term goal is to evaluate how the semi-autonomous approach can be advantageous to, more effective than, and/or affordable to traditional manual biopsy approaches. The outcome of this project will be a validated system ready for a clinical study.

NIH Research Projects · FY 2025 · 2023-06

Neural circuits are formed by directed growth of axons and dendrites and subsequent assembly of synapses between selected pre- and postsynaptic neurons at precise anatomical and subcellular locations. Although tremendous progress has been made in identifying the key axon guidance cues for nervous system development in the past two decades, the signaling and cell biological mechanisms of axon guidance still remain partially understood. The incomplete knowledge of how growth cones signal to respond to specific cues hinders our ability to apply the knowledge from axon guidance studies to repair circuits and restore function after traumatic injury and in neurodegenerative disorders. We found that Wnt family morphogens are axon guidance cues and the planar cell polarity pathway mediates Wnt function in axon guidance. We also found that Wnt signaling regulate axon regrow after spinal cord injury in adulthood and planar cell polarity signaling regulates the assembly of glutamatergic synapse formation. We plan to use Wnt/PCP signaling as a tool to address unsolved fundamental questions in growth cone guidance and understand its expanded role in adult axon regeneration. Aim 1: How PCP components create asymmetric signaling to mediate growth cone turning in development. Aim 2: Interactions between Wnt/PCP pathway and canonical Wnt pathway and the Shh pathway in A-P guidance. Aim 3: Role of Wnt/PCP signaling in functional recovery after spinal cord injury.

NIH Research Projects · FY 2026 · 2023-06

7. PROJECT SUMMARY The long-term goal of the proposed career development award is to provide the training necessary to develop an independent research program investigating how chronic pain is related to dementia risk. Such research is timely given recent links between chronic pain and a doubled risk of dementia due to Alzheimer's disease (AD). Chronic pain may lead to general, AD-unspecific, neurodegeneration that increases susceptibility to AD dementia, supported by studies linking chronic pain to smaller brain volumes in adults. Alternatively, recent animal studies suggest that the biological processes underneath chronic pain may promote amyloidosis and tau seeding, but there is less focus on the relationship of chronic pain and AD-related neurodegeneration in humans. A training emphasis focused on incorporating biological measures will complement my existing expertise in chronic pain, cognitive aging, and advanced statistical analysis to conduct this research program. The proposed training goals are to: 1) attain proficiency in neuroanatomy and neuroimaging relevant to aging and AD; 2) obtain competence in assessment and biology of pain; and 3) establish a multidisciplinary program studying brain changes and AD risk. Training will involve a combination of formal coursework, and hands-on activities, and discussion with mentors and other field experts. The Department of Psychiatry at the University of California San Diego is an ideal environment for the proposed training activities with access to world-renown researchers and research centers focused on chronic pain, neuroimaging, and Alzheimer's disease as well as an excellent departmental record of career development for junior researchers. The proposed project will examine how chronic pain relates to indicators of general neurodegeneration and AD-related neurodegeneration across independent samples of older adults including the Framingham Heart Study, the Religious Orders Study/Memory Aging Project, and the Vietnam Era Twin Study of Aging. Aim 1 will examine how chronic pain relates to indicators of general neurodegeneration, including brain age, an estimation of age based on thickness/volume across a wide arrange of AD-unspecific brain regions, as well as neurofilament light, a protein released during neurodegeneration. Aim 2 will examine how chronic is associated with indicators of AD-related neurodegeneration. Indicators include AD brain signatures capturing thickness/volume and mean diffusivity in AD-vulnerable brain regions, biomarkers of amyloid and tau, and diagnosis of mild cognitive impairment and AD dementia. Analyses will help clarify how chronic pain contributes to dementia risk, either through general neurodegeneration or AD-related neurodegeneration. Multiple datasets will improve the rigor of analyses by allowing for replication.

NIH Research Projects · FY 2025 · 2023-06

ABSTRACT The incidence of LC in never-smokers (LCINS) has been increasing but the etiology of this cancer type is largely unknown. We have generated exciting preliminary data showing that exposure to house dust mites (HDM), the most common indoor aeroallergen worldwide, not only provokes allergic reactions and inflammation in the lungs, but also induces pro-tumor inflammation and DNA damage, and accelerates lung cancer (LC) development in three preclinical mouse models of LC at a dose within the range of the annual human HDM exposure. We identified that HDM genomic DNA is present in the tumors of a high percentage of LCINS patients and that it is a strong activator of the AIM2 inflammasome and inducer of IL-1β secretion. Based on these new findings, we hypothesize that long-term exposure to HDM increases the risk of LC development in susceptible hosts (i.e., mice and humans genetically predisposed to LC or co-exposed to other lung carcinogens). Our objectives in this proposal are: 1) to investigate the cellular mechanisms by which chronic HDM exposure changes the lung microenvironment and makes it conducive to LC development, 2) to determine whether HDM has mutagenic effects by studying the mutational signatures potentially linked to HDM exposure in mice in vivo and in human lung organoids in vitro, and 3) to translate these findings to LCINS patients by identifying the composition of the lung tumor microenvironment (TME) and the mutational signature profiles in a subgroup of patients with signs of prior exposure to HDM. Our long-term goal is to increase public awareness of the risk that chronic exposure to HDM may pose for the development of LCINS. Thus, we propose the following three specific aims (SA): in SA- 1, we will test whether HDM exposure changes the cellular composition of the lung TME, in SA-2, we will determine whether HDM exposure induces somatic mutations in lung epithelial cells, and in SA-3, we will evaluate whether HDM exposure can be used as a biomarker for diagnosis, prognosis, and targeted therapy in LCINS patients. The expected outcomes of this work are 1) to identify the cellular mechanisms by which HDM exposure promotes LC development in susceptible hosts, 2) to demonstrate that chronic exposure to HDM is a new environmental risk factor for LCINS, 3) to provide strong scientific support for the development of novel preventive (e.g., HDM avoidance) and therapeutic (e.g., anti-HDM vaccine, anti-IL-1β antibodies, and NLRP3/AIM2 inhibitors) interventions in LCINS patients chronically exposed to HDM, and 4) to expand the investigations of exposure to other aeroallergens as potential risk factors in LC.

NIH Research Projects · FY 2026 · 2023-06

ABSTRACT/PROJECT SUMMARY Bronchopulmonary dysplasia (BPD), a chronic lung disease, is the most common major complication of preterm birth affecting at least one fourth of infants born with a birth weight less than 1500g. Many premature infants with BPD will continue to have persistent respiratory symptoms and decreased lung function into adulthood. These life-long complications of BPD create significant health burden and necessitate extensive health care utilization. Currently, there is no effective prevention or personalized treatment for BPD. Not every premature infant develops BPD, and this individual variability in BPD susceptibility is likely explained by complex interactions between environmental, cellular, genetic, and epigenetic factors. Supplemental oxygen administration, while lifesaving in the neonatal period, remains a key determinant of BPD pathophysiology. Exposure of the immature lung to increased levels of oxygen elicits an inflammatory response resulting in abnormal lung development. However, the lung immune cells, specifically those involved in the innate immune response, and their accompanying gene expression programs that provide protection against BPD are not completely known. The overall objective of this proposal is to identify and characterize specific lung myeloid cells and their gene programs that provide protection to oxygen-induced lung injury. Our hypothesis is that the innate immune response activated in the lung differs between premature infants who develop BPD and those that are resilient to disease. Based on our novel finding that genetic loss of function of Triggering Receptor Expressed on Myeloid cells 2 (TREM2) is protective in hyperoxia-induced lung injury, we propose that inhibition of TREM2 signaling may be exploited to modulate the innate immune response to prevent abnormal lung development. In Aim 1 we will employ single cell RNAseq and TREM2-deficient mice to define how TREM2 regulates gene expression and severity of lung injury after neonatal hyperoxia exposure. In Aim 2 we will apply novel approaches using myeloid p53-deficient mice exposed to neonatal hyperoxia and interrogate epigenomic modifications using ATACseq and ChIPseq to identify the regulatory mechanisms by which TREM2 directs a pathogenic immune response on a transcriptional level. Lastly, to establish proof-of-principle for the translational potential of therapeutic targeting of TREM2 we will test a TREM2 blocking antibody in vivo and assess recovery from hyperoxia in room air (Aim 3). Further investigations of the conservation of gene regulatory pathways between mice and humans will provide a sound rationale to use these gene pathways to develop targeted therapies. This project will identify unique gene regulatory networks of lung myeloid cells that support a regenerative immune response in the developing lung. These findings will elucidate novel pathways of neonatal lung resilience after hyperoxia, which will inform the development of more targeted management of multifactorial BPD.

NIH Research Projects · FY 2025 · 2023-06

Glaucoma is one of the leading causes of irreversible blindness for which the lowering of intraocular pressure (IOP) is the only proven treatment. Since elevated IOP is a critical risk factor for glaucoma, several animal models have been developed to study the cellular, vascular, and electrophysiologic responses of the retina to acute IOP elevation. While these models have elucidated the relationship between ocular perfusion and retinal function as well as many of the cellular pathways activated in response to acute IOP related exposure, there are significant differences in optic nerve structure and composition across species, limiting the translation of these findings to the human disease. This project will study the impact of IOP elevation in the living human eye for the first time by utilizing the unique resources developed by the Living Eye Project. This project provides experimental access to the human eye in vivo in research-consented brain-dead organ donors prior to organ procurement. Following enucleation, the Living Eye Project provides access to the same eyes for ex vivo analysis of cellular and tissue responses. Our principal hypothesis is that acute IOP elevation results in deformation of the optic nerve head (ONH), and this deformation drives mechanosensitive mechanisms within the lamina cribrosa (LC) and peripapillary sclera that initiate pathologic remodeling of the LC, which injures the axons of retinal ganglion cells traversing this mechanically dynamic region. These mechanosensitive pathways will be characterized using spatial transcriptomics for the first time in the human eye alongside immunohistochemistry and protein analysis. We predict that increased IOP initiates a profibrotic, inflammatory phenotype and transcriptomic alterations that regionally colocalize with the connective tissue density within the LC and are associated with the magnitude of IOP-induced deformation of the ONH measured in vivo. Our unprecedented opportunity to measure structural and biomechanical parameters of the human ONH in vivo and perform ex vivo evaluation of the cellular mechanobiology of the same tissues will provide the first direct experimental link between ONH mechanical strain and the molecular and cellular responses of ONH tissues that drive remodeling, which is critical to the development and progression of glaucomatous optic neuropathy. Defining this “mechanotranscriptome” in the human ONH will critically assess the translational value of animal models for studying mechanotransduction as well as define the human cellular and molecular mechanisms of ONH remodeling needed to guide the development of novel therapeutics designed to enhance the resilience of the ONH to pressure-related stress.

NIH Research Projects · FY 2026 · 2023-06

Alzheimer's Disease (AD) and related dementias (ADRD) are characterized by progressive structural changes of brain tissue that results in a debilitating loss of cognitive and functional abilities and has profound social and economic implications. While hallmark AD pathology (e.g. beta amyloid depositions and neurofibrillary tangles) are remarkably pronounced at the cellular level, there are currently no successful non- invasive brain imaging techniques to report these microstructural changes. Diffusion magnetic resonance imaging (dMRI) is a widely available non-invasive clinical imaging method with this potential, as it is sensitive to the subtle motion of water within the complex brain gray matter (GM) and white matter (WM) tissue architecture. In principle, dMRI can report both the local tissue structure and the long range connectivity of neural tracts in order to identify pathology and determine the effects of AD on functional brain networks. Unfortunately, the clinical utility of the standard dMRI methodology is severely compromised by its lack of specificity to microstructural tissue changes below the image resolution. Recently, however, we have developed a novel acquisition and analysis method called Joint Estimation Diffusion Imaging (JEDI) that is highly sensitive to microstructural features of GM and GM/WM border regions, and also provides improved connectivity maps from WM. JEDI is easily implemented on a clinical scanner and we have recently incorporated it into a first study on subjects ranging from cognitively normal (CN) to Mild Cognitive Impairment (MCI) to early AD in order to assess its ability to detect changes in these groups. Two critical steps in extending the clinical utility of JEDI in AD are: 1) To characterize the relationship between the JEDI data and specific tissue microstructural features in order to develop quantitative clinical metrics and 2) To develop efficient acquisition protocols for both microstructural sensitivity and limited patient scan time. That is the focus of this proposal, which will involve three lines of work: 1) Numerical computer simulations of the JEDI experiment in realistic tissue models that will allow us to efficiently optimize the acquisition protocol for maximum specificity and minimal time; 2) Validate these optimizations through in-vivo evaluation of normal aging processes in the ferret and in ex-vivo radiologic-pathologic analysis in post-mortem human tissue from patients with different stages of AD; 3) Incorporate these optimizations into the JEDI acquisition and analysis of human protocols on our clinical scanners with specific application to examining the prodromal microstructure tissue changes across the aging-MCI-AD continuum. By enabling a reliable, validated and clinically viable method for the quantitative characterization of subtle brain tissue changes across the aging-MCI-AD continuum, JEDI will significantly enhance our ability to understand the earliest neurodegenerative features of AD and provide new insights into its causes, consequences, and possible treatment targets.

NIH Research Projects · FY 2026 · 2023-06

PROJECT SUMMARY Craniosynostosis syndromes are a group of devastating developmental disorders characterized by craniofacial abnormalities and strabismus, or eye misalignment. The most common craniosynostosis syndromes, including Apert Syndrome, are associated with genetic mutations in fibroblast growth factor receptor 2 (Fgfr2). Strabismus in Apert syndrome patients is difficult to treat due to high surgical failure rates. Sadly, untreated strabismus is closely correlated with amblyopia, vision loss, and significant functional and psychosocial difficulties that negatively impact quality of life for patients. It is unclear how abnormal FGFR2 signaling is associated with strabismus in patients with Apert syndrome. These patients have abnormal bony orbits and abnormal extraocular muscles (EOM) because of a known Fgfr2 mutation; however, it is not well understood how abnormal FGFR2 signaling, abnormal bony orbits, and abnormal EOM clinically manifest as strabismus. Previous research shows atypical EOM, specifically smaller EOM and myofiber disorganization, in both human Apert patients and in the Apert mouse model. Scientific investigations will focus on identifying the contributing determinants that govern abnormal EOM structure and function in Apert syndrome and the key factors that cause EOM disease using a mouse model for Apert syndrome. EOM anatomy and function will be analyzed using MRI, histology, and muscle functional studies. Mutant mice that only express the Fgfr2 mutation in muscle, muscle stem cells, bone, or innervating neurons will be used to characterize the contributions of abnormal FGFR2 signaling in different tissues to altered EOM structure and function in Apert syndrome. A novel gene therapy that specifically targets the abnormal Fgfr2 mutation in Apert syndrome will also be tested in our Apert mouse model using similar techniques. Dr. Rudell has proposed a career development plan to reach her goal of becoming an independent clinician scientist with an expertise in EOM physiology. Her research background in synaptic development in skeletal muscle intersects perfectly with her clinical interests in pediatric ophthalmology and EOM disease. Her department is extremely supportive of her career goals at the University of California San Diego, with access to outstanding mentors and research facilities. Her career development plan includes coursework and hands-on research projects in genetics and muscle biomechanics. Her mentors are leading scientists and clinicians in muscle physiology, craniofacial genetics, and pediatric ophthalmology, with excellent training records. They are unequivocally committed to Dr. Rudell’s success as an independent clinician scientist.

NIH Research Projects · FY 2026 · 2023-06

PROJECT SUMMARY A diverse educational and scientific community including people with different life experiences, cultural backgrounds, and ethnicities is vital for developing a robust workforce that can address the technological and social challenges of the U.S. in a new global and interconnected economy. Unfortunately, there is tremendous disparity in the U.S. scientific community in which individuals from disadvantaged economic and social backgrounds, with disabilities, and from some ethnic groups (i.e., African, Native, and Latino Americans) are underrepresented and therefore unable to contribute their talents. Therefore, a forceful approach should be developed to correct the lack of diversity within the scientific community. A starting point for this approach is at colleges and universities where students from underserved communities that do not have the same resources to support higher education begin their education. Indeed, the socio-economic reality of underprivileged students is likely to negatively impact their interest in research. To overcome the obstacles of preventing the pursuit of scientific careers, we are proposing the establishment of a “Maximizing Access to Research Careers” (MARC) program at UC San Diego with the mission is to unlock the potential of students from underrepresented ethnic groups in science, from disadvantaged socio-economic backgrounds and students with disabilities. The proposed MARC program is directed at motivating, training, mentoring, and facilitating the transition of undergraduate students from college to a Ph.D. program. This new MARC program at UC San Diego will be built on the success of 14 years of experience obtained from an undergraduate “Initiative for Maximizing Student Development” (IMSD) program. The proposed MARC program is composed of two consecutive phases to accomplish our goals. An initial Pre-MARC “Boot Camp” training where students acquire the fundamental scientific skills to be successful in research activities (Phase 1), which is followed by immersing scholars into a rich scientific environment by participating in a research project under the supervision and mentorship of internationally recognized, productive, and well-funded investigators with outstanding training records (Phase 2). In this setting, trainees enhance their initial scientific training by gaining expertise in experimental planning, time management, data collection, interpretation, reproducibility, presentations, and ethics, with the final goal of enrolling in a Ph.D. program. These phases will be accompanied by leadership and career development training to increase students’ self-identity and self-efficacy as scientists, thus supporting their pursuit of a research career.

NIH Research Projects · FY 2026 · 2023-06

PROJECT SUMMARY Drug abuse and HIV infection co-exist and are difficult to study due to challenges in people living with HIV (PLWH) who abuse drugs. One of the prime areas of pathogenic interactions of HIV and drugs of abuse is the brain, which carries additional study limitations. To obtain rigorous data on the effects of HIV and cocaine on the brain, we will utilize well-studied nonhuman primate animal model, Simian immunodeficiency virus (SIV)- infected and uninfected control rhesus monkeys, in the presence or absence of cocaine. Single cell sequencing assays enable cell type-specific analysis of the role of specific cell types in both healthy brain function and disease. The overall objective of this proposal by multidisciplinary team of investigators is to reveal the single cell determinants of brain in the context of viral persistence in SIV/cART/cocaine non-human primates. Simultaneous single-cell RNA sequencing and single-cell Assay for Transposase- Accessible Chromatin sequencing (scMultiome-seq) will be carried out on cells isolated from the prefrontal cortex (PFC), striatum, and hippocampus from each animal. Data will be processed and analyzed to derive cell type-specific regulatory programs and changes in these programs that regulate neuropathogenesis in the primate brains. These studies will provide unique and valuable insights into SIV/cocaine/cART interactions in the brain while also providing crucial experimental validation of the findings in humans. Successful completion of these innovative single-cell studies and data analyses methods will generate a single cell transcriptome and epigenome atlas of cellular part list for three NIDA-relevant brain regions, PFC, striatum, and hippocampus. These results will illuminate novel insights into transcriptomic and epigenetic landscapes of CNS and how they are altered by HIV and cocaine use.

NIH Research Projects · FY 2026 · 2023-06

PROJECT SUMMARY Autism spectrum disorder (ASD) is one of the most common neurodevelopmental disorders, diagnosed in one in 44 children in the United States. Sex is among the most significant risk factors for ASD, with males being three to five times more likely than females to manifest the disorder. While epidemiological data documenting these sex differences in autism are abundant, there is currently little understanding of the fundamental differences between male and female biology that contribute to the sex biases in autism prevalence, severity, and clinical presentation. Based on mounting evidence implicating i) important microglial contributions to neurodevelopment, ii) sex-biased microglial activation in individuals with ASD, and iii) our preliminary findings regarding microglia- specific sex-linked gene expression, this proposal is built around the central hypothesis that genetic sex differences in microglia contribute the male bias in ASD. Sex chromosomes may be especially important drivers of sexual dimorphism in human brain development. For one, ASD manifests at an early age, before the puberty-associated increase in sex hormone production. Further, progressive chromosome Y aneuploidy (e.g. XY, XYY, XYYY, XYYY) leads to incrementally increased incidence of ASD. These observations suggest a significant role for chromosome Y for presenting ASD-related behaviors. Yet, there is a gap in knowledge about Y-linked genes and their contribution to sex dimorphism outside the reproductive tract and to ASD pathophysiology. Therefore, the project goal is to test the hypothesis that increasing chromosome Y dose in human microglia in vitro (Aim 1) and in a xenotransplantation model (Aim 3) results in microglial pathology, neuropathological defects, and ASD-associated behavioral deficits. Delineating genome wide transcriptional disruption and genome wide reorganization (Aim 2) will further uncover how chromosome Y-linked genes contribute to microglia-specific gene networks and expand our knowledge on Y- linked genes associated with ASD. The long-term goal is to generate a framework for studying genetic sex differences in microglia and their contributions to sex-biased brain development. A deeper understanding of the contribution and molecular regulation of microglia in ASD will lay the groundwork to ultimately identify novel potential sex-specific interventions to improve the outcomes for individuals with ASD. The proposed research will take place in the Coufal and Glass laboratories at UC San Diego. The Coufal lab expertise is in human induced pluripotent stem cell models of neuroimmunology, and the Glass lab has expertise in tissue-resident macrophage gene regulation and epigenetics. Through graduate coursework, mentorship, and hands-on learning, Celina will gain experience in stem cell modeling systems for human brain cell types and for approaching large datasets from a quantitative perspective. These skills will be valuable for the completion of the proposed research and for Celina’s future career as a physician-scientist.

NIH Research Projects · FY 2026 · 2023-06

In cancer, macrophages play a multifaceted role in disease progression and response to therapies. Tumor- associated macrophages (TAMs) serve several pro-tumoral functions including the expression of factors promoting growth, immune suppression and angiogenesis. A high TAM burden in the tumor microenvironment is often associated with poor prognosis and therapeutic resistance to certain immunotherapies. Moreover, TAMs are emerging as a target for anti-cancer therapeutics. Overall, an imaging probe that can non-invasively detect TAM burden could help stratify patients and personalize treatments to improve response rates. Recently, our laboratory has developed novel molecular probes enabling sensitive and precise imaging of inflammatory foci in vivo. We synthesized functionalized fluorocarbon nanoemulsions incorporating a fluorous-encapsulated radiometal chelate (FERM). Pre-formed FERM nanoemulsion rapidly captures zirconium-89 into the fluorous phase. The highly hydrophobic nature of fluorocarbons helps exclude competition from water, cations, lipids and proteins that contribute to the dissociation of 89Zr from the carrier. By encapsulating the radiometal inside the volume of nanoemulsion droplet one can achieve a high payload and cell detection sensitivity, with low background. Following an intravenous injection of FERM, nanoemulsion droplets are scavenged by phagocytic macrophages. The labeled cells accumulate at inflammatory sites resulting in sensitive and quantifiable positron emission tomography (PET) signals reflecting predominantly macrophage burden. Preliminary PET results from our lab demonstrate excellent sensitivity and versatility of the FERM probe in a diversity of inflammation rodent models, including solid tumor, acute infection and autoimmune disease. Building on these results, our project has three Aims: Aim 1. 89Zr FERM formulation. We will perform FERM nanoemulsion formulation optimization and scale-up. We will also develop optimal radiopharmacy methods to maximize labeling efficiency of FERM and product yield. Aim 2. Biological characterizations. Cell-based assays will be performed to evaluate potential toxicity of 89Zr FERM. Moreover, we will characterize the in vivo blood half-life, probe stability, and preliminary dosimetry. Aim 3. In vivo immuno-oncology studies. We will characterize the effectiveness of FERM for TAM detection and quantification, responsiveness to treatments that deplete TAM burden, and the probe’s potential for predicting response to immunotherapeutic interventions in multiple murine solid tumor models. Parallel phenotypic profiling of FERM-labeled cells in the tumor will be performed. The proposed studies will generate essential data needed to drive potential clinical translation of the FERM imaging biomarker for use in future immuno-oncology clinical trials.

NIH Research Projects · FY 2025 · 2023-06

PROJECT SUMMARY/ABSTRACT This proposal is for a new training program that capitalizes on our major local strengths in respiratory physiology and pulmonary disease. Over time, the field of physiology and pathophysiology has evolved to solve new problems identified from clinical management of lung airway, interstitial and vascular diseases and to extend the new discoveries from genetic, genomic, cell and molecular studies to define pathogenic mechanisms and develop novel therapeutic interventions for lung diseases. We remain focused on the importance of integrated function and systems biology and thus we use the concepts of physiology as an integrator across respiratory science studied at multiple levels. With the success of our recent T32 and recruitment efforts, our respiratory science has broadened to include strength in genetics, (epi)genomics, molecular and cellular biology. While we view our science as cutting edge, we pride ourselves on the fact that our trainees do not just focus on a single molecule or gene but rather keep in mind the importance of integrated function and translational research. Our MPIs include diverse strengths in Pulmonary, Sleep, Genomics, Critical Care, Physiology and Respiratory Science. The MPIs have mutual respect, complementary expertise, shared vision for scientific progress and a strong commitment to developing a superb next generation of leaders with rich diversity. To improve the quality of mentoring, we also removed less effective mentors while adding more R01-funded preceptors and formalizing the levels of faculty participation based on success in research training, research productivity and current research funding. We have made both Sleep and Pediatrics as major scientific foci, addressing major national shortages in these areas. We utilize individual development plans, overseen by the MPIs, Preceptors and senior advisors, for all of our trainees to empower people with diverse backgrounds. We promote collaboration between MDs and PhDs, ensure that everyone has experience and competency in inter-, trans- and multi-disciplinary research, and ensure all of our trainees have a strong foundation in physiological approaches that provides a clinical context for research problems studied at any level. We promote cohesiveness, team spirit and a unique identity for our trainees via common activities involving all of our trainees and mentors/preceptors such as frequent scholarly meetings, career development sessions and quarterly retreats. We are committed to a training program that includes every phase of academic career development, from ‘cradle to grave’ including developing junior faculty into independent investigators, and even improving the mentoring skills in our senior faculty. We also remain committed to diversifying the next generation of respiratory scientists as demonstrated by our long- term track record and recent recruitments. The lack of a robust pipeline for multidisciplinary researchers who can apply modern integrative approaches to problems in respiratory science is a crisis which has been further amplified by the COVID pandemic, but it is a challenge that we are well-qualified and eager to address.

NIH Research Projects · FY 2026 · 2023-06

Project Summary Growth factor (GF)-based therapies hold great promise for tissue engineering, cancer treatment, and regenera- tive medicine but controlling their activity and selectivity can be challenging. GFs act as ligands for membrane- receptors controlling signaling cascades that drive gene expression and cellular functions, such as proliferation and differentiation. Tools that can selectively activate or suppress GF-mediated signaling activity in cells are needed to achieve control over the activity of these molecules and improve their therapeutic properties. Heparan sulfate (HS) proteoglycans (PGs), while often overlooked, are uniquely suited for this purpose, as they often serve as coreceptors for GFs at the cell surface. By promoting the formation of complexes between GFs and their receptors, they balance competing signaling pathways and regulate cellular responses. While the structure and activity of HS on cells can be controlled, to some extent, through genetic engineering of their biosynthesis, chemical tools for remodeling cell-sulfate HS to attain GF-binding specificity would be much mor general and better suited for therapeutic applications. This project establishes such tools, termed neoPG chimeras, that will be able to selectively activate or inhibit GF signaling activity in cells. This will be achieved by taking advantage of the GF-binding selectivities of recombinant HS polysaccharides produced through systematic mutation of HS biosynthetic enzymes in laboratory cell lines. The recombinant HS polysaccharides will be harvested, character- ized for GF binding specificity and merged with functional elements for targeting to the cells. Membrane targeting neoPG chimeras will be developed to promote GF association with receptors at the cell surface and promote GF signaling activity (Aim 1). Lysosome-targeting neoPG chimeras will be used to drive extracellular GFs into the cells for degradation, thus inhibiting signaling activity (Aim 2). The focus of this study will be on establishing and validating neoPG chimeras as actuators of signaling by members of the Fibroblast Growth Factor family of pro- teins in the context of cellular proliferation and differentiation. However, many other classes of GFs require cell surface HS for function and the new tools are expected to find broad application in many different aspects of biomedical research and GF-based therapies.

NIH Research Projects · FY 2026 · 2023-05

Global proteomics mass spectrometry data sharing infrastructure - Project Summary Technological developments and the increased pace of data generation in mass spectrometry (MS) now enable systematic probing of the human proteome, thus contributing to the characterization of biomolecular mechanisms required for the development of therapeutic responses to disease. Recognizing the scientific necessity of open data to enable new discoveries and to establish the reliability of published results, the proteomics community embraced data sharing as a common practice. The authors of thousands of papers have already publicly re- leased the underlying MS data using the resources that we propose to support and extend: the MassIVE repos- itory of mass spectrometry data and the ProteomeCentral data portal for the global ProteomeXchange consor- tium of MS data repositories. In this project, we propose to develop new proteomics MS data infrastructure, standards, workflows and data indexes to substantially advance FAIR (Findable, Accessible, Interoperable and Reusable) access to proteomics MS datasets. First, we will develop new community standards for representation of dataset metadata and for the detailed description of proteomics identifications and abundances detected in available datasets, including peptides, proteins, isoforms and post-translational modifications. We will also ex- tend workflows for dataset submission, processing and indexing to enable advanced queries by each dataset’s detected proteomics identifications. Second, we will create new infrastructure for researchers to share controlled access proteomics datasets from studies of human subjects where there may exist a significant risk of the data being identifiable. Third, we will extend the ProteomeCentral data portal to support the new dataset structures, metadata and indexes allowing for the global integration of the new levels of information across all Proteo- meXchange repositories.