University Of Texas Hlth Ctr At Tyler

NIH Research Projects · FY 2026 · 2026-06

Tissue factor (TF), the primary initiator of the blood coagulation cascade, is carefully regulated to prevent aberrant coagulation activation. However, pathological conditions including bacterial and viral infection induce intravascular TF expression and lead to thrombosis. As TF-induced thrombosis is a major cause of acute myocardial infarction, ischemic stroke, and pulmonary embolism, improved understanding of the mechanisms of pathological TF activation may lead to new therapeutic targets. Pyroptosis, a form of inflammatory cell death, drives TF-mediated intravascular coagulation activation in bacterial sepsis. Emerging studies also implicate inflammasome activation in viral infections, but its role in TF activation is unknown. Our preliminary studies demonstrate that ORF3A, an accessory viral protein induce TF activation in a phosphatidylserine (PS)-dependent mechanism that requires TMEM16F, similar to PS-dependent TF activation in pyroptosis. In Aim 1, my lab will investigate the underlying mechanisms that govern ORF3a-induced TF activation emphasizing the key roles of programmed-cell death. Lipid peroxidation and its highly reactive end products such as 4-hydroxy-2-nonenal (HNE) are involved in various forms of programmed cell death including pyroptosis. However, the role of HNE, the most stable and toxic reactive aldehyde produced during lipid peroxidation, in pyroptosis-associated TF and coagulation activation is not known. Our preliminary data showed that HNE induces PS-dependent TF activation in LPS-primed macrophages and causes intravascular coagulation activation in mice. However, the complete mechanism by which HNE induces PS externalization and TF activation is not known. In Aim 2, my lab will use chemical and genetic approaches to investigate whether HNE-induced TF activation and intravascular coagulation activation is mediated through programmed cell death. Although lipid peroxidation plays a central role in cell death and coagulation activation in bacterial sepsis, a therapeutically targetable enzyme responsible for the unbridled lipid peroxidation and generation of pathological levels of reactive radicals such as HNE is not known. In Aim 3, my lab will use genetically modified mice deficient in lipid peroxidation and HNE formation to investigate TF-dependent pathologic coagulation activation and thrombosis during sepsis. A successful completion of these studies will help delineate a common pathway involved in pathologic TF activation across varied pathogenic infections and will also help identify a specific therapeutically targetable enzyme to attenuate TF activation in disease.

NIH Research Projects · FY 2025 · 2025-07

Abstract: The incidence and mortality of empyema or pleural sepsis has steadily risen over the past several decades. While, after antibiotics, surgery is widely accepted as the first choice to treat empyema in adults, up to 30% of patients are poor candidates for both surgery and conventional high dose intrapleural fibrinolytic therapy (IPFT). Substituting non-surgical drainage of pleural fluid with a low-dose Alteplase (ALT)-based intervention could positively affect the survival of patients with advanced-stage empyema. Our preclinical studies in three rabbit models of pleural injury have demonstrated that Docking Site Peptide (DSP) increases the efficacy of Alteplase (ALT) up to 8-fold by affecting Plasminogen Activator Inhibitor 1 (PAI-1). Next, we determined that a decrease in intrapleural inflammation coincides with successful treatment with ALT/DSP in a model of advanced- stage empyema (effective bolus dose of ALT is unknown; >13.5 mg). Thus, targeting both pleural fibrosis and inflammation may result in a further increase in the efficacy of ALT in our preclinical model, which closely recapitulates empyema in humans. Increased levels of the Triggering Receptor Expressed on Myeloid Cells 1 (TREM-1) and proinflammatory biomarkers in pleural fluids of patients with empyema and rabbit models of empyema indicate TREM-1-mediated activation of inflammation. A TREM-1 peptide inhibitor, GF9, will be tested with ALT/DSP (ALT/DSP/GF9) in rabbit models of acute and advanced-stage empyema in order to further increase the efficacy of ALT. This milestone driven MPI proposal is focused on preclinical testing and optimization of a novel therapeutic strategy (Two-Target Fibrinolytic Therapy; T2FT), concurrently targeting two distinct mechanisms that contribute to disease severity and therapeutic outcomes of several thrombotic and fibrotic pathologies (R61), followed by the development, formulation and testing of a novel T2FT Product (DSP/GF9) suitable for rapid translation to clinical trials (R33). Our hypothesis is that simultaneous targeting of TREM-1 and PAI-1 mechanisms with short peptides GF9 and DSP is a clinically tractable strategy to increase the efficacy of ALT in the treatment of empyema. Our objective is to develop a T2FT Product (DSP/GF9) that, in combination with low dose of ALT, is suitable for treatment of high-risk patients with advanced-stage empyema. T2FT offers a novel pharmacological option for patients who are recommended for surgery but either decline or are at too high a risk for surgery or high ALT dose IPFT. Our hypothesis will be tested and objective achieved in three specific Aims: (i) Development and preclinical validation of a low dose T2FT in a rabbit model of acute, early- stage empyema (R61); (ii) Optimization and preclinical validation of low dose T2FT for advanced-stage empyema in a rabbit model (R61); (iii) GMP-friendly pilot production, stability, formulation, toxicity, and efficacy studies of low dose ALT single injection T2FT treatment for translation to clinical application (R33). This is a genuine University/Industry collaboration that focuses on the development and commercialization of a novel treatment. UTHSCT (Contact PI: Dr. Komissarov) contributes a validated rabbit model of empyema, ALT/DSP methodology, and matching funds. SignaBlok (PI: Dr. Sigalov) contributes well-tolerable formulations of GF9, a novel mechanism-based TREM-1 inhibitory peptide that has been validated preclinically in multiple inflammation- associated pathologies, and over 13 years of industrial experience to serve as a business accelerator and steer the project towards the market. The anticipated product, a GMP-friendly low-dose T2FT for empyema will be manufactured in a pilot. If successful, this project could elucidate a Catalyze-guided bench-to-bedside pathway towards industry.

NIH Research Projects · FY 2025 · 2025-07

Radiation therapy is the mainstay in the treatment of lung, breast and esophageal cancers, types of lymphoma and tumors that metastasize to the lungs. Each year in the US, there are an estimated 252,950 new cases of lung cancer and 313,510 cases of breast cancer. Acute and chronic lung injury, due to radiation of normal lung tissue, occurs during cancer treatment. The resulting tissue damage is a major cause of morbidity and occasional mortality. Lung injury and consequent pulmonary fibrosis (PF), resulting from lung irradiation is one of the major causes of impaired quality of life after cancer treatment. While every effort is made to minimize the radiation dose to areas of the lung which do not contain cancer, some normal lung damage ultimately occurs. Although a variety of medications have been evaluated in animal models to mitigate radiation-induced lung toxicity, none have been sufficiently compelling to gain FDA approval. Ionizing radiation induces alveolar epithelial cell (AEC) damage leading to radiation-induced lung injury (RILI). This results in lung tissue barrier dysfunction, secretion of various pro-inflammatory and pro-fibrotic cytokines. This in turn leads to activation and differentiation of lung fibroblasts to activated myofibroblasts or fibrotic lung fibroblasts (fLfs), resulting in excessive extracellular matrix (ECM) deposition. These changes promote radiation-induced PF (RIPF). Increased p53 levels occur in damaged AECs and induce senescence and apoptosis. p53 is reciprocally suppressed with increasing proliferation and resistance to apoptosis of fLfs. A Cav1 scaffolding domain 7-mer peptide (CSP7) suppresses p53 in injured AECs, preventing senescence and apoptosis, and restores baseline p53 expression in fLfs from IPF lungs, reversing established PF. CSP7 is well-tolerated in mice, rats, and dogs, and completed phase 1a human safety, tolerability, and PK testing without adverse effects (NCT04233814) and currently going through safety and limited efficacy (phase 1b) testing in patients with IPF (NCT05954988) in U.S. and Europe. Thus, our work provides robust proof of rigor and reproducibility and validates development of targeted intervention. Our objective is to test the beneficial effects of CSP7 that confer protection against RILI and RIPF and develop a novel peptide intervention for cancer patients undergoing thoracic radiation. We hypothesize that CSP7 will inhibit lung injury and resolve PF caused by ionizing radiation. We will test our hypothesis in two Specific Aims: 1) determine the ability of CSP7 to inhibit radiation-induced lung injury (RILI) and prevent development of PF in mice and 2) assess if CSP7 resolves radiation-induced established pulmonary fibrosis (RIPF) in mice. The RILI destroys functional units of lung and worsens function, which is already marginal in many lung cancer patients, leading to less physical activity, increased breathing medications, supplemental oxygen, and/or mechanical ventilation. The preventive effect of CSP7, if proven by the proposed project, provides a novel p53-targeted therapy for RILI and RIPF. The findings from this project are essential to determine whether CSP7 can provide a more reliable and effective intervention that can be further developed for cancer patients with RILI and/or RIPF.

NIH Research Projects · FY 2025 · 2024-07

Venous thromboembolism (VTE), which comprises deep vein thrombosis (DVT) and pulmonary embolism (PE), is the third most common cause of vascular death after a heart attack and stroke. VTE is responsible for 300 000 deaths annually in the USA alone. Although the development of direct oral anticoagulants has improved the treatment of VTE, there are still significant bleeding risks associated with anticoagulant therapy. A better understanding of the pathogenesis of VTE would aid in developing novel, effective and safer drugs. Although the etiologic factors of DVT codified by Virchow’s triad, i.e., hypercoagulability, blood stasis, and endothelial cell dysfunction, are still relevant, recent studies suggest that DVT is primarily a thromboinflammatory-mediated event. This opens a new possibility that suppression of thromboinflammation may be an ideal approach to prevent and treat VTE. The endothelium is an important contributor to thromboinflammation in DVT. Our recent studies show that Gab2 (Grb2-associated binder2), a signaling adapter protein, plays a central and key role in integrating inflammatory signaling initiated by diverse inflammatory stimuli in endothelial cells. Our studies identify for the first time that Gab2 mediates the assembly of the CBM (CARMA3-BCL10-MALT1) signalosome in endothelial cells in response to inflammatory stimuli. Gab2-mediated CBM signalosome not only leads to the activation of NF-kB and prothrombotic gene expression but also exocytosis of P-selectin and VWF via activation of the Rho signaling pathway. In vivo studies show that global deficiency of Gab2 or inhibition of MALT1 in the CBM signalosome by specific pharmacological inhibitors protects against LPS- and S. pneumoniae infection- induced inflammation and inferior vena cava (IVC) ligation-induced venous thrombosis. These studies identify novel inflammatory signaling mechanisms and suggest they could play a crucial role in venous thrombosis. However, many knowledge gaps exist still in our understanding of these mechanisms and their contribution to VTE. We hypothesize that endothelial Gab2-MALT1-mediated signaling plays a crucial role in thromboinflammation and contributes to the pathogenesis of VTE and targeting Gab2-MALT1 signaling by pharmacological inhibition of MALT1 will have therapeutic potential in preventing and treating VTE. The specific aims are to (1) elucidate molecular mechanisms by which Gab2 mediates thromboinflammatory signaling in endothelial cells, (2) determine the role of endothelial Gab2-MALT1 signaling in venous thrombosis using cell-specific Gab2 and MALT1 knockout mice, (3) assess the influence of the Gab2-MALT1 signaling on venous thrombus resolution and vein wall injury. The proposed studies will employ innovative experimental approaches and unique transgenic mice Impact: Our proposed studies will provide novel insights into thromboinflammatory signaling in endothelial cells and other relevant cell types. Elucidating the role of Gab2- MALT1-mediated signaling in thromboinflammation and venous thrombosis would aid in developing novel and ideal therapeutic drugs to prevent and treat VTE without increasing bleeding risk.

NIH Research Projects · FY 2025 · 2024-06

Project Summary: Respiratory viruses such as influenza and SARS-Cov-2 pose a continuing and substantive threat to human health in the US and globally. Respiratory viral infection triggers host innate and adaptive immune responses, which are the critical antiviral defense mechanisms to control virus replication and spread. This R21 proposal seeks to identify the critical host immune modulators following influenza A virus (IAV) infection. In this project, we will investigate transcription factor Runx3 regulation of lung conventional dendritic cell (DC) subset-2 (cDC2) in priming non-Th1 CD4+ T cell subsets during IAV infection. We recently generated an inducible Runx3 global knockout (KO) mouse model and reported that Runx3 KO resulted in a huge reduction (>85%) in numbers of lung CD8+ cytotoxic T cells during IAV infection but increased the numbers of lung CD4+ T and innate immune cells as well as the levels of pro-inflammatory cytokines. As a result, the general Runx3 KO mice tended to have a better survival outcome following IAV infection, although not statistically significant. Since lung CD8+ cytotoxic T cells play a central role in the clearance of IAV, our findings suggest that Runx3 KO may augment type-1 immunity to compensate for the loss of lung CD8+ cytotoxic T cells. We further found that Runx3 was strongly expressed in CD11c+ immune cells from IAV-infected mouse lungs. Lung CD11c-expressing cells include DCs and tissue resident alveolar macrophages (TR-AMs). Our new preliminary data indicate that Runx3 is not expressed and could not be induced by Th1 and Th2 cytokines in isolated TR-AMs but is expressed and readily inducible in activated DCs. Furthermore, CD11c-specific Runx3 KO mice were largely (62.5%) resistant to a lethal IAV infection, while all the littermate control mice succumbed to the lethal IAV infection. Our findings suggest that Runx3 deficiency in CD11c+ lung DCs may augment host immunity for a better clearance of IAV. As Runx3 expression is mainly restricted to cDC2, we hypothesize that Runx3 plays an important role in lung cDC2 development, maturation and priming of non-Th1 CD4+ T cell subsets, through which impacts host immune responses and the outcomes of IAV infection. We expect that cDC2-specific deficiency of Runx3 would suppress Th2 and Treg responses and result in a host immune balance skewing to Th1 immunity, which would favor for an effective IAV clearance and be beneficial to the outcomes of lethal IAV infection. We will test the novel hypothesis by using the CD11c- and cDC2- specific Runx3 KO mouse models. The proposed studies have not been explored previously and will enable us to identify novel factors and pathways that prevent optimal immunity against IAV infection. The proposal will also lead to a comprehensive understanding of Runx3 regulation of T cell immunity during respiratory viral infection and thereby will advance the field.

NIH Research Projects · FY 2026 · 2024-03

Clotting factor VIIa (FVIIa) initiates the activation of the coagulation cascade by binding to the procoagulant cofactor tissue factor. Recombinant FVIIa is a clinically approved drug for treating bleeding in hemophilia patients with inhibitors and other bleeding disorders. It is also used off-label to treat severe bleeding associated with surgery, liver disease, and intracerebral hemorrhage. We have discovered that FVIIa also binds to the anticoagulant cofactor, endothelial cell protein C receptor (EPCR). FVIIa binding to EPCR modulates protein C/activated protein C-mediated anticoagulant pathway. Our studies also established that FVIIa-EPCR activates protease-activated receptor 1 (PAR1)-induced biased cell signaling, resulting in anti-inflammatory and vascular barrier protective effects. Interestingly, our recent studies revealed that FVIIa-EPCR-PAR1-mediated biased signaling induces the release of extracellular vesicles (EVs) from endothelial cells (EEVs). These vesicles are found to exhibit hemostatic and anti-inflammatory properties. EVs are increasingly recognized as important mediators of intercellular communication, play an important role in various pathophysiological processes, and likely have immense therapeutic potential. Understanding the biogenesis and release of FVIIa-generated EVs, characterizing their cargo, interactions with recipient cells, and their behavior in vivo is crucial for assessing their role in pathophysiology and fully capitalizing on their therapeutic and drug delivery potential. The proposed aims are designed to address these important knowledge gaps. Our overall hypothesis is that FVIIa-released EVs contribute to hemostatic, anti-inflammatory, and vascular barrier protective effects by communicating with other cell types by transferring their unique cargo. These EVs hold therapeutic potential in treating bleeding disorders, inflammation, and hemophilic arthropathy. The specific aims are, Aim 1: Investigate the hypothesis that FVIIa- released EEVs are unique and distinct from EEVs released by other coagulation proteases. Aim 2: Elucidate the mechanism of FVIIa-released EV biogenesis, phosphatidylserine (PS) enrichment of FVIIa-released EEVs, and their distribution and fate in vivo. Aim 3: Determine the role of FVIIa-released EEVs in hemostasis and inflammation and elucidate potential mechanisms. Aim 4: Determine the effect of FVIIa-released EEVs in the treatment of hemophilic arthropathy (HA) and explore the potential contribution of miR10a, found in the cargo of FVIIa-released EEVs, to this process. In these proposed studies, we will employ an unbiased omics approach to characterize FVIIa-released EEVs. We will also use loss- and gain-of-functional studies, unique transgenic mice, and murine model systems of bleeding, hemophilic arthropathy, and inflammation. The knowledge gained from our studies will not only lead to more efficient and cost-effective clinical treatments for hemophilia patients but also lead to novel therapeutic strategies for bleeding and inflammatory disorders. Our studies will contribute to a paradigm shift in our current understanding of proteases-induced cell signaling and their potential to affect cellular processes in distant cells through communication via EVs.

NIH Research Projects · FY 2026 · 2024-03

Pleural fibrosis is the scarring of the pleura resulting in restrictive lung disease and impaired lung function. The pathophysiological mechanism of pleural fibrosis is unclear. The interactions between resident and inflammatory cells, profibrotic mediators and coagulation factors, and fibrinolytic pathways are integral to pleural remodeling and fibrosis. Increasing evidence affirm the critical role of pleural mesothelial cells (PMCs) in pleural fibrosis development, mainly through a process termed mesothelial to mesenchymal transition (MesoMT). MesoMT is characterized by increased expression of α-smooth muscle actin (α-SMA)/collagen 1 (Col-1)/fibronectin (FN), and enhanced cell migration/invasion. Currently, there are no pharmacologic treatments for this disease. Therefore, identification of novel targets and therapeutic strategies is an important goal for the public health. However, there is a fundamental knowledge gap in mechanisms controlling MesoMT during pleural fibrosis. Our preliminary data strongly support that dedicator of cytokinesis 2 (DOCK2) is a crucial regulator of MesoMT to promote pleural fibrosis. In primary human PMCs (HPMCs), DOCK2 was induced by the potent MesoMT inducer TGF-β. DOCK2 knockdown blocked TGFβ-induced MesoMT maker expression and cell migration. Snail as a transcriptional factor controlling epithelial to mesenchymal transition was found critical in TGF-β-induced MesoMT. DOCK2 knockdown inhibited TGF-β-induced Snail expression and activation of Smad2/3 and NF-κB signaling, which have been shown to upregulate Snail expression in various cell types. DOCK2 knockdown also suppressed TGF-β-induced Rac1 activation in HPMCs. In addition, we found that DOCK2 was dramatically induced in the fibrotic pleura of human pleuritis patients and in pleural fibrosis models induced by Streptococcus pneumoniae (Strep), carbon black/bleomycin (CBB), and TGF-β. DOCK2 knockout mice were significantly protected from Strep-induced pleural fibrosis. Based on these findings, our overall hypothesis is that DOCK2 mediates MesoMT and increases PMC migration/invasion to promote pleural fibrosis, which will be tested in three specific aims. In Aim 1, we will determine if DOCK2 promotes pleural MesoMT via upregulation of Snail. Further, we will test whether DOCK2 increases Snail through activating Smad2/3 and NF-κB signaling. In Aim 2, we will test if DOCK2 promotes pleural MesoMT with increased cell migration/invasion. Specifically, we will determine if DOCK2 mediates TGF-β-induced cytoskeletal reorganization, migration, and invasion via activating Rac1. In Aim 3, we will test the hypothesis that DOCK2 knockout blocks pleural fibrosis via inhibiting MesoMT in vivo. We will determine if general and mesothelial cell-specific DOCK2 knockout mice are protected from Strep, CBB, and TGF-β induced pleural fibrosis through suppressing MesoMT in vivo. Completion of the proposed studies will establish the pivotal role and mechanisms of DOCK2 in promoting pleural fibrosis by regulating MesoMT, which may ultimately contribute to the identification of novel targeted therapies for this important but refractory clinical problem.

NIH Research Projects · FY 2026 · 2024-01

Project Summary Vascular smooth muscle cell (VSMC) phenotypic modulation, a phenotypic switch from a differentiated contractile phenotype to a proliferative phenotype, contributes to vascular remodeling and the development of diverse vascular diseases such as atherosclerosis, hypertension, and restenosis following angioplasty. However, the molecular mechanisms that control VSMC phenotypic modulation are poorly understood. Our exciting preliminary data strongly support a novel role of Runt-related transcription factor 3 (RUNX3) in VSMC phenotypic modulation. RUNX3 belongs to the ‘Runt domain’ family of transcription factors that act as regulators of gene expression in several important developmental pathways. We found that RUNX3 expression is significantly increased by platelet-derived growth factor-BB (PDGF-BB), a potent stimulator of VSMC phenotypic modulation. Knockdown of RUNX3 reversed PDGF-BB-inhibited expression of SMC contractile markers. In addition, RUNX3 knockdown blocked PDGF-BB-induced VSMC proliferation. These data demonstrate that RUNX3 is essential for PDGF-BB-induced VSMC phenotypic modulation and cell proliferation in vitro. In addition, RUNX3 overexpression blocked myocardin-induced α-SMA expression and promoter activity, suggesting that RUNX3 regulates VSMC contractile marker expression through myocardin/SRF signaling. RUNX3 knockdown also inhibited PDGF-BB induced expression of c-Myc, a crucial driver of VSMC proliferation. The PDGF-BB-induced activation of NF-κB and phosphorylation of GSK3β, important pathways in regulating c-Myc levels, were adversely affected by RUNX3 knockdown. RUNX3 expression was activated in the media and neointima VSMCs following the left common carotid artery injury in C57BL/6 mice. RUNX3 deficiency (RUNX3-/-) dramatically inhibited injury-induced neointima formation, suggesting that RUNX3 plays a critical role in injury-induced neointima formation and vascular remodeling in vivo. These data together strongly support a novel hypothesis that RUNX3 induces VSMC phenotypic modulation by suppressing VSMC contractile marker expression and promotes VSMC proliferation via c-Myc, leading to neointima formation/vascular remodeling, which will be tested by three Specific Aims. Aim 1: Determine the molecular mechanisms underlying RUNX3 function in modulating VSMC phenotype by testing the hypothesis that RUNX3 regulates VSMC phenotypic modulation via suppressing myocardin/SRF-mediated transcriptional activation of VSMC marker genes. Aim 2: Test the hypothesis that RUNX3 upregulates c-Myc expression through NF-κB and GSK3β/β-catenin signaling to promote VSMC proliferation. Aim 3: Test whether RUNX3 is essential for carotid artery ligation/wire injury-induced vascular remodeling using global, VSMC-specific, and endothelial cell-specific RUNX3 knockout mice. Taken together, this project will shed new lights on the pathogenesis of vascular remodeling after vessel injury, which may ultimately lead to the identification of novel targets for therapeutic treatment of various cardiovascular diseases related to vascular remodeling.

NIH Research Projects · FY 2026 · 2023-12

Project Summary Nontuberculous mycobacteria (NTM) including Mycobacterium avium complex (MAC) are among the most difficult to treat etiological agents associated with pulmonary disease. Just between 2008-2015, the annual NTM lung disease incidence increased from 3.13% to 4.73% per 100,000 persons, and the annual prevalence changed from 6.78% to 11.7%. The current American Thoracic Society guidelines recommend a macrolide- ethambutol-rifamycin combination therapy for treatment of pulmonary MAC, where therapy continues for 12- months after converting one’s sputum culture to negative (no growth or microbiological clearance). We performed a meta-analysis and found that despite an average 18–23-month long therapy duration, the sustained sputum culture conversion rates at the end of therapy were only 54% with the macrolide containing regimen and 32% with macrolide-free regimens. Thus, there is need for safe, more effective, and shorter-course regimens for treatment of MAC pulmonary disease. However, there is a knowledge gap in the pharmacokinetics/pharmacodynamics-based guidelines on dose and combination regimen composition as well as information on the synergy/antagonism between the drugs, at the given dose, in the combination. As a result, the treatment regimen for MAC infections is largely empirical and driven by clinical experience. To fill in the knowledge gap, we devised a programmatic approach for unbiased screening of the drugs (old, new, and/or repurposed) for efficacy against MAC to perform dose selection using the principle of pharmacokinetics/pharmacodynamics. We use a pre-clinical hollow fiber system model of MAC (HFS-MAC) in tandem with a mouse model of MAC, clinical trial simulations, and time-to-extinction modeling using pre-clinical and clinical data to design and rank efficacious combinations of drugs for MAC killing and accurate estimates of therapeutic duration. The safety and toxicity profile of the drugs we propose to advance, in this grant proposal, for treatment of MAC pulmonary disease is well documented, data on human population pharmacokinetics are available, and the mechanism of action and the effective tissue penetration are also available for most of the proposed drugs. Thus, exposure targets for maximal kill, identified in the pre-clinical models can be translated to a clinical dose to treat patients with MAC pulmonary disease in a relatively shorter timeframe. We aim to shorten the therapy duration for pulmonary MAC from the current >18 months to <6 months.

NIH Research Projects · FY 2026 · 2023-12

Project Summary: The envelope (Env) glycoprotein exposed on the surface of HIV-1 virions is essential for virus entry into susceptible cells and is the primary target of neutralizing antibodies, small molecules, and fusion inhibitors. The structural dynamics of Env promote HIV-1 entering susceptible cells via membrane fusion and facilitate antibody evasion. However, a lack of knowledge about the time-resolved structural dynamics and allostery of Env impedes the attempts to comprehend the mechanisms by which Env enables virus entry and facilitates immune evasion. Env is trimeric, in which each protomer is composed of two subunits: exterior gp120 for binding to cellular receptors/coreceptors and membrane-anchored gp41 for driving fusion. Upon interacting with cellular receptors/coreceptors, gp120 undergoes large-scale conformational changes, further activating a series of fusion-promoting structural refolding in gp41. Refolding in gp41 progresses from a prefusion state through intermediates to the post-fusion that is generally believed to drive membrane fusion. Structures of Env have provided atomic details of Env conformations at fusion endpoints. However, substantial knowledge gaps in the Env-mediated fusion mechanism cannot be bridged by conventional structural tools. These gaps include time, sequence, reversibility, transitional paths, and transient intermediate steps of structural changes of Env. The proposed research is based on the hypothesis that Env is a highly cooperative dynamic machine in which conformational changes reflected in gp120 and gp41 during fusion occur in well-ordered spatial and temporal equilibrium. Single-Molecule Fluorescence Resonance Energy Transfer (smFRET) studies with fluorescent labels placed on gp120 demonstrated that native Env intrinsically interchanges between multiple conformations and has responsive conformational sampling to CD4 activation, neutralizing antibodies, and inhibitors. This project will elucidate spatiotemporal information of Env in its native state, with focused investigations on the less- studied gp41 and its association with gp120, and ultimately provide a time-resolved stepwise spatial framework of the fusion process. Multiple synergic methods, including smFRET in the context of intact virions, an integrated enhanced sampling molecular dynamics (MD)-smFRET, AI-guided multiscale simulations/modeling for mapping Env allostery, cell-based virological assays, and photophysical analysis will be used. The research is built upon recently established minimally invasive smFRET imaging of Env using genetic code expansion combined with click chemistry. It will be further extended to multi-perspective for monitoring gp120-gp41 associated cooperativity and capturing structural changes of gp41. The conformational dynamics of Env will be monitored from three different structural perspectives. Neutralizing antibodies and fusion inhibitors will be used to facilitate revealing conformational cooperativities of Env and spatiotemporally resolving individual fusion intermediates. The expected results will provide new insights about the time-resolved structural dynamics and allostery of Env that can inform the design of Env-centric interventions such as vaccines, antibody therapy, and anti-viral drugs.

NIH Research Projects · FY 2025 · 2023-09

Research Abstract: The spike/fusion glycoproteins residing on the surface of human enveloped viruses are targets of immune response and are the focus of researchers developing vaccines and antiviral treatments. The conformational dynamics of spike proteins drive the entry of enveloped viruses into cells via viral membrane fusion and facilitate antibody recognition. However, the lack of deep insights into dynamics has prevented a complete elucidation of the molecular mechanism by which spike proteins promote virus entry. Many viruses, such as coronavirus SARS-CoV-2, respiratory syncytial virus (RSV), and HIV-1, share a similar viral fusion mechanism (type-I) mediated by their respective spike proteins. These spikes undergo dramatic structural changes, and the energy released from conformational transitions overcomes the fusion kinetic barriers. However, our understanding of the multi-step fusion process mainly relies on individual structural snapshots of spike proteins at fusion endpoints. How these endpoints are correlated in a time-resolved manner and the order and frequency of conformational events underlying virus entry remain largely elusive. The proposed research extends our efforts to explore viral membrane fusion and is supported by our experience probing the conformational dynamics of the SARS-CoV-2 spike (S) and HIV-1 envelope (Env) glycoproteins. The overarching goal of this project is to integrate our knowledge into a generic working model that will describe a time-resolved stepwise framework of the type-I fusion mechanism, in which the conformational trajectories of fusion proteins are explicitly defined in space and time. We pioneered the use of the single-molecule Förster resonance energy transfer (smFRET) to study S and revealed multiple S conformations on the virus. We delineated sequential transitions of S from closed to open conformations upon activation by cellular receptors. We provided the first experimental evidence of decelerated transition dynamics from open states, suggesting increased stability of the fusion-reactive open state to be part of the SARS-CoV-2 adaption strategies. Here, we will use an integrated platform of smFRET and virus-to-cell fusion in combination with computational and structural tools to reveal the conformational plasticity S adapts during virus evolution and to visualize the conformational trajectory S undergoes during fusion. We will perform comparative studies on another respiratory virus - RSV fusion (F) protein, with interest in other type-I spike proteins of newly emerging viruses. We will elucidate conformational events and transition dynamics of F-mediated viral membrane fusion and evaluate whether conformation- presentation of F-based vaccine candidates represents the predominant state exposed to the host. The studies are expected to allow us to identify the common and divergent traits of the S- and F-mediated fusion processes that will advance our knowledge and help us define the common theme of the type-I fusion mechanism. We envision that this program of research using different advanced technologies will reveal unrecognized insights into virus entry that lay the foundation for advances in anti-viral interventions, in line with the mission of NIGMS.

NIH Research Projects · FY 2026 · 2023-03

PROJECT SUMMARY (30 lines) Dr. Jarett Berry is a Professor of Medicine in the Division of Cardiology at UT Southwestern Medical Center. Over the last 13+ years, he has led a successful program of research that has been supported through sustained funding from the NIH and/or the American Heart Assocation. He has established a successful research program characterizing the impact of exercise on the risk for heart failure with preserved ejection fraction. He has held leadership roles at UT Southwestern and nationally. Furthermore, he has mentored numerous trainees at all levels, facilitating their transition to indepdnence as evidenced by their own independent research careers. Beginning in 2019, he was named the new PI of the Dallas Heart Study, where he is leading a multidisciplinary effort to characterize the biology of healthy aging in a large, multiethnic cohort. He also developed and serves as the director of the DHS Exercise Testing Laboratory where his lab performs comprehensive exercise testing on DHS participants. His current research is funded by a large institional commitment that supports the 3rd examination of the DHS. His research is also supported by additional funding from the NIH. Therefore he is well positioned to lead an expansion of his mentoring program that will be supported by this K24 mechanism and support his long-term career goals: (1) Lead a major research program focused on the prevention of heart failure with preserved ejection fraction (HFpEF); (2) Improve the understanding of the mechanisms contributing to low exercise capacity in middle age and identify targeted strategies for treatment; and (3) Develop a new generation of clinical investigators equipped with knowledge and skill set to conduct high-quality, patient oriented cardiovascular research. During this award period, the PI will acquire additional leadership training and gain exposure to advanced imaging techniques using high-field, 7T MRI through attending focused training experiences and hands-on work with his advanced imaging colleagues. Based on prior research established by the PI, the central hypothesis of this application is that exercise intolerance in older HFpEF patients reflects the natural history of low exercise capacity in midlife. The Specific Aims of the proposal are the following: Specific Aim #1: Characterize peripheral mechanisms of reduced exercise capacity in otherwise healthy middle-aged and older adults at increased risk for HFpEF. DHS participants will complete (1) functional measurements [VO2 kinetics and oxygen extraction (AVO2 difference) at submax exercise]; and (2) structural measurements (skeletal muscle volume, muscle fat infiltration). A subset DHS participants will also undergo additional functional in vivo measurements of mitochondrial function using our established 7T MRI/MRS platform. Specific Aim #2: Compare the peripheral mechanisms of EI in patients with established HFpEF with otherwise healthy adults with similar/matched peak V02 using the same measurements as in Aim 1. Trainees will gain experience in patient- oriented research and participate in informal and formal research training experiences led by the PI as part of his institutional role in mentoring trainees in the CTSA.

NIH Research Projects · FY 2025 · 2022-09

OVERALL Project Summary The Southwest Center for Agricultural Health, Injury Prevention, and Education (SW Ag Center) is a well- established organization based at the University of Texas Health Science Center at Tyler. The SW Ag Center will build on over 25 years of service in Public Health Region 6 (Arkansas, Louisiana, New Mexico, Oklahoma, and Texas) through the proposed work. The mission of the SW Ag Center is to improve the safety and health of agricultural, forestry and fishing (AgFF) workers. This is accomplished through an integrated program of research, intervention, translation, surveillance, and outreach activities that engage and leverage a network of strategic partners who represent the interests of a diverse worker population and a wide range of AgFF production. The Center is positioned to expand its connections with industry segments, state departments of agriculture, cooperative extension, trade associations, and service providers. The proposed scope of work is responsive to the current funding announcement and is organized around the theme “Leveraging strategic partnerships to advance best practices that promote and protect the health and safety of diverse AgFF populations.” The SW Ag Center team consists of multidisciplinary faculty, staff, investigators, regional advisors, and extension partners who are organized to foster cohesive, coordinated, and synergistic operations. Proposed research includes two basic science projects led by experienced PIs. They will (1) investigate the role of bacterial extracellular vesicles from organic dust in lung inflammation and (2) characterize and compare worker health status on western US dairy farms. The SW Ag Center portfolio includes three intervention projects aimed at different regional audiences: These projects address (1) health disparities among commercial fishermen, (2) safety climate in grain handling facilities, and (3) safety considerations for agricultural pilots and operators. The Center's translation project focuses on hearing conservation for independent contract loggers and surveillance research will integrate motor vehicle crash and injury data in AgFF sectors. The regional capacity for AgFF research will be strengthened through the Center's pilot feasibility program. Outreach activities will develop pragmatic approaches to move research findings and best practices into the workplace. Early-stage professionals will also be supported through outreach mini grants, internships, practicum experiences and capstone projects. Research and outreach will be guided and continuously improved by a cohesive and coordinated evaluation plan. The SW Ag Center is equipped with the necessary experience and resources to identify practical solutions to persistent and emerging issues while cultivating effective partnerships with diverse AgFF groups.

NIH Research Projects · FY 2024 · 2021-07

PROJECT SUMMARY Empyema (EMP) is increasing in frequency worldwide and is associated with a mortality rate of up to 20% in patients older than 65 years. Thoracic surgery for treating EMP is invasive and many patients have co-morbidities that preclude its use. Bleeding remains a major concern and occurs in up to about 5-15% of EMP patients treated with intrapleural fibrinolytic therapy (IPFT). These factors offer a premise for the identification of more effective, well-tolerated forms of IPFT that better address the molecular mechanisms governing intrapleural fibrinolysis, particularly in advanced-stage EMP. The need for more efficacious, innovative forms of IPFT represents a gap in the field that is of high priority and addressed in this project. The objective of our study is to identify novel interventions that improve therapeutic outcomes in subjects with EMP using a fibrin-targeted delivery of encapsulated plasminogen activators (PAs) combined with ultrasound sonofibrinolysis (US) in a validated model of Streptococcus pneumoniae induced EMP in rabbits. Liposomal carriers with single chain (sc) tissue (sctPA) and urokinase (scuPA), and resistant to plasminogen activator inhibitor 1 “molecular cage” type complexes with α-macroglobulin (αM/uPA) will be tested. Our preliminary data demonstrate that (i) transthoracic US or sctPA- based liposomes (TELIP) with nanomolar affinity to fibrin improve therapeutic outcomes of an otherwise ineffective dose of fibrinolysin; (ii) US promotes intrapleural formation of αM/uPA, which correlates with success of IPFT in pleural injury. Our hypothesis is that combining intrapleural delivery of low doses of a fibrinolysin encapsulated within fibrin targeted carriers with ultrasound sonofibrinolysis will additively increase the intrapleural half-life of plasminogen activators and rate of fibrinolysis, enhancing the efficacy of IPFT in acute and chronic S. pneumoniae induced EMP. The hypothesis will be tested in three Specific Aims: 1. Determine the minimal effective doses (MEDs) of echogenic liposomal carriers for treatment of S. pneumoniae induced EMP in rabbits. 2. Identify the ultrasound mechanical index and treatment schedule that optimizes outcomes of IPFT in rabbits with S. pneumoniae induced EMP. 3. Use the additivity of transthoracic ultrasound and fibrin- targeted carrier delivery to increase the efficacy of IPFT in S. pneumoniae induced EMP. Our project team consists of two groups with expertise in translational research, IPFT, management of EMP, therapeutic commercialization, and liposomal carrier formulation and delivery. By applying state-of-the-art biochemical, biophysical, physiologic, tissue analysis and imaging techniques, we will accomplish the Research Plan to address the current gaps in empyema treatment and expand our understanding of sonochemical mechanisms. If, as expected, this project succeeds, a new, well-tolerated, more effective and clinically tractable paradigm for IPFT will emerge that may ultimately improve outcomes in patients with empyema.

NIH Research Projects · FY 2024 · 2020-07

Project Summary/Abstract Non-urban populations are given little attention in many aspects of medical practice. Rural communities often lack the infrastructure for developing and sustaining a preventive approach to occupational disease and injury, particularly for specific work sectors such as agriculture, where the hired and/or migrant workforce may constitute the majority. Northeast Texas, home to about 1.5 million people spanning 35 counties, is considered the largest rurally distributed population in the state, and is also one of the unhealthiest. There is a considerable need to train medical students and graduates in general, and occupational medicine residents in particular, to be competent in knowledge and skills pertaining to rural and migrant populations, who have special cultural needs and considerations. As the region’s only university medical center, the University of Texas Health Science Center at Tyler (UTHSCT) is home to some of the latest developments in patient care and community health, medical and health education, and biomedical and clinical research. There is a physician shortage in rural counties throughout Northeast Texas, and UTHSCT has the responsibility of training the future generation of physicians. The occupational medicine residency program at Tyler (OMR) is one of seven ACGME-accredited graduate medical education (GME) programs sponsored by the institution. The overall objective and mission of the program is; ‘to increase the number of occupational medicine physicians who have adequate experience and sufficient competence to enter the practice without direct supervision, while adding a special focus on training in the occupational health needs of the rural workforce, to help serve the population of Northeast Texas and beyond’. This is in alignment with the overall mission of the institution. Specific aims of the program are to: 1. Increase the number of board certified occupational medicine graduates able to engage in evidence based and independent practice in various settings including the proportion remaining in Texas and rural areas, 2. Enhance a robust residency experience in rural / agricultural occupational health, safety, protection and promotion. There remains a recognized burden of occupational injury and illness in general and in agriculture specifically. This proposal is considered responsive to the Funding Opportunity Announcement PAR-15-352 by addressing a critical gap in Occupational Medicine Residency (OMR) trained physician workforce needs (core discipline). The proposed program will integrate agricultural safety and health by implementing a multi-faceted training approach that relies upon an inter-professional educational team effort, while also leveraging the strengths of the NIOSH-supported Southwest Center for Agricultural Health, Injury Prevention and Education to achieve a significant impact on continued workforce expansion.

NIH Research Projects · FY 2024 · 2017-09

Empyema is a bacterial infection of the pleural space, a serious complication of pneumonia that carries a mortality rate of up to 20%, the incidence of which continues to increase worldwide. Intrapleural fibrinolytic therapy (IPFT) involving the delivery of plasminogen activators has been used to expedite drainage of loculated pleural effusions, including empyema. Using a new model of Streptococcus pneumoniae-induced empyema in rabbits we developed a single-dose IPFT with a plasminogen activator inhibitor 1 (PAI-1)-targeted adjunct, which is 8-fold more effective than PA alone for treatment acute empyema. We also validated the ability of our Fibrinolytic Potential Assay (FPA) to predict the success of IPFT in patients with empyema. Interestingly, the efficacy of IPFT in our model of advanced-stage empyema is decreased by 40-50%, similar to what has been observed in patients. This is, in part, due to a significant decrease in the rate of intrapleural fibrinolysis. To mitigate the risk of bleeding complications associated with an increase in the dose of PA, we propose multiple injections of low-dose PAI-1-targeted IPFT to treat advanced-stage empyema. Our objective is to identify effective PAI-1-targeted IPFT for advanced-stage empyema. Our hypothesis is that successful IPFT in advanced-stage empyema requires fibrinolytic activity sustained over a longer period of time and neutralization of PAI-1. The hypothesis will be tested in four Specific Aims: 1. Maximize the efficacy of IPFT in advanced- stage empyema in rabbits by targeting both the slow rate of fibrinolysis and PAI-1, 2. Develop novel PAI-1 targeting peptides to optimize IPFT in advanced-stage empyema, 3. Determine the mechanisms that result in increased resistance to IPFT in advanced-stage empyema, and 4. Using the Fibrinolytic Potential Assay to identify candidates for IPFT prior to treatment. We will select a dosing schedule and use two validated PAI-1 targeting adjuncts (monoclonal antibodies (mAbs), and a docking site peptide) to decrease the dose of PA, test these mechanisms for additivity in PAI-1 targeting to maximize efficacy, and test the efficacy of PAI-1 targeting peptides selected using phage display technology. We will use the FPA to analyze samples from Phase 2 Clinical Trial “A Study to Evaluate LTI-01 in Patients with Infected, Non-draining Pleural Effusions” (ClinicalTrials.gov; NCT04159831). We will use state of the art biochemical techniques to analyze pleural fluid and plasma from human patients and our unique model of empyema to investigate the molecular interactions of fibrinolysis of advanced-stage empyema. Our team has the biochemical, pulmonary and technical expertise to successfully accomplish the proposed work. The project addresses key gaps in our current understanding of the pathogenesis of pleural organization, optimization of IPFT and development of a new diagnostic approach to predict outcomes of IPFT. This project is positioned to shift the paradigm of treatments available for patients with extensive pleural loculation, failed drainage, and advanced-stage empyema.