Ut Southwestern Medical Center

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY Acute coronary syndrome (ACS) is common and a cause of significant morbidity and mortality worldwide. ACS is treated routinely with percutaneous intervention followed by dual antiplatelet therapy and high-intensity lipid- lowering statin therapy for 12 months. The post-ACS period is highly vulnerable, and rates of morbidity and mortality remain high despite the availability of effective treatments. Non-adherence to post-discharge medications is a major preventable cause of morbidity and mortality in the post-ACS period. Moreover, adverse outcomes and non-adherence rates are higher among individuals from low-income groups and among racial/ethnic minorities. The polypill strategy has shown promise in improving adherence to medications and reducing cardiovascular risk in primary and secondary prevention settings. Nonetheless, polypill-based strategies have not been evaluated for individuals in the vulnerable post-ACS period, when adherence to dual antiplatelet therapy and high-intensity statins is particularly critical. Furthermore, optimal strategies for the implementation of a polypill approach and its acceptance in the clinical community by different stakeholders are not known. To address this knowledge gap, we propose a type 1 hybrid effectiveness-implementation, multi-center, randomized trial to test the feasibility and effectiveness of a polypill-based strategy for post-ACS management. We will utilize a flexible polypill containing a high-intensity statin, aspirin, and P2Y12 inhibitor. The once-daily polypill will be added to baseline medical therapy. The primary endpoint will be composite clinical outcomes, including all-cause mortality, ischemic events, and bleeding events over 12 months. Additionally, we will evaluate the polypill acceptability, preferences, cost, and lessons among providers and patients.

NIH Research Projects · FY 2025 · 2025-08

Hepatocellular carcinoma (HCC) is the major histological type of liver cancer, caused by viral (HBV, HCV) and metabolic (alcohol, metabolic dysfunction-associated steatotic liver disease [MASLD]) etiologies. The high mortality rate is attributable to failed early cancer detection, which is increasingly challenging for the current “one-size-fits-all” HCC screening owing to the rapidly changing etiological landscape and growing etiologically heterogeneous at-risk patient populations. Our prior simulation study showed that individual risk-based HCC screening is cost-effective. However, new tools to precisely evaluate the risk according to confounding factors, particularly etiology, are urgently needed. We previously developed etiology-agnostic HCC risk biomarkers, hepatic transcriptome-based Prognostic Liver Signature (PLS) and serum proteome-based Prognostic Liver Secretome signature (PLSec), which were successfully validated in phase 3 biomarker studies. Subsequently, we developed etiology-specific “plug-in” biomarkers for patients with cured HCV and MASLD, which substantially improve the etiology-agnostic HCC risk prediction. PLS/PLSec family biomarkers are therapeutically modifiable, and used as endpoints in clinical trials and studies of HCC chemopreventive agents. These results warrant further expansion of this approach to other major etiologies, HBV and ALD, and non- cirrhotic MASLD for comprehensive etiology-adjusted HCC risk prediction. Cholangiocarcinoma (CCA) risk factors remain largely unknown, as evidenced by the absence of clinically recognizable risk conditions in approximately half of the CCA patients, highlighting an urgent unmet need for CCA risk biomarkers. To address these unmet needs, our objectives are to develop a strategy for HCC risk assessment in cirrhosis and non- cirrhosis patients with the major viral and metabolic etiologies, and develop resources for CCA risk biomarker discovery. Aim 1. Develop and validate etiology-specific HCC risk biomarkers in cirrhotic and non-cirrhotic chronic liver disease patients: we will develop and validate tissue/serum-based “plug-in” HCC risk biomarkers and their integration with the etiology-agnostic PLSec as etiology-adjusted HCC risk assessment tools in cirrhosis and non-cirrhosis patients with HBV, ALD, and MASLD. Tissue/serum samples for CCA risk biomarker development will also be collected. Aim 2. Determine cost-effectiveness of etiology-adjusted HCC screening: by utilizing our established Markov models, we will determine the clinical utility of etiology-adjusted risk- stratified HCC screening, and identify optimal individualized screening strategies. We expect to establish a new strategy of comprehensive etiology-adjusted HCC risk prediction and resources for CCA risk biomarker discovery, which will collectively lead to a transformative improvement in the prognosis of this deadly cancer type.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY Millions of pregnant women worldwide harbor at least one type of parasite infection. In countries where helminth infections are prevalent in pregnant women, infants have reduced response to immunizations against multiple diseases. Helminth infections in pregnant mothers are implicated in this reduced vaccine efficacy in infants and children. However, very little is known about the factors that drive alterations in fetal immune programing and infant immune responses. The goal of this proposal is to fill this knowledge gap using a tractable experimental system in mice that we have developed. We leveraged our expertise in parasite-virus co-infection to establish a model of maternal helminth infection and our goal is to discover mechanisms that underly difference in fetal immune programming that occur with prenatal exposure to infections. We found that offspring exposed prenatally to maternal helminth infection have reduced susceptibility to influenza virus infection. We hypothesize that maternal helminth infection independent of in utero transmission alters immune programming in offspring through alterations to maternal and fetal microbiota. We will test this hypothesis with two aims. The first aim is to determine replication and inflammatory response to influenza virus in the lungs of offspring with and without prenatal helminth exposure. Because intestinal helminth infections change the microbiome of infected mice and the fetal microbiome is acquired from the nursing mother, the second aim is to determine the contribution of the helminth-altered microbiota to changes in offspring antiviral responses. At the completion of this study, we anticipate identifying immunological mechanisms underlying transgenerational imprinting of offspring immunity. Furthermore, this work will inform efforts to improve immune responses in children in helminth endemic areas to infection and vaccination.

NIH Research Projects · FY 2025 · 2025-08

Project Summary Protein-protein interactions (PPIs) are fundamental to nearly all cellular functions, and disruptions caused by mutations often lead to disease. Despite decades of research, a significant portion of the human PPI network remains unknown. The challenges in elucidating the human interactome stem from the vast number of potential interactions, high false-positive rates in high-throughput experiments, and the presence of weak, transient interactions that evade experimental detection. Leveraging breakthroughs in protein structure prediction using Deep Learning (DL) and extensive genomic data for coevolutionary analysis, we have developed pipelines for de novo PPI screening. Our method has shown superior performance compared to large-scale experimental screens and has provided valuable insights into yeast and bacterial pathogen proteomes. This proposal aims to enhance our pipeline and extend its application to resolve the human interactome. First, we will leverage the unprecedented volume of sequence and structural data to transform our methods for proteome-wide PPI screening in humans. We will utilize petabytes of untapped genomic sequence data from draft eukaryotic genomes and genomic reads to enhance the statistical power of coevolutionary analysis. To efficiently perform proteome-wide predictions, we will develop fast and accurate DL networks for PPI prediction by adapting RoseTTAFold and AlphaFold networks and augmenting the PPI training datasets with domain- domain interactions from over 200 million AlphaFold models. Preliminary results indicate that these strategies can drastically boost our pipeline's performance, positioning us to uncover novel interactions in humans. Second, we will address the challenge of weak and transient interactions, particularly those mediated by short linear motifs (SLiMs). We will compile training datasets for biologically significant but weak interactions, detect interaction-mediating phosphorylation sites, and develop specialized DL networks to recognize these sites and weak interactions. We will integrate predicted interactions with experimental data and other bioinformatic analyses to catalog SLiMs in human proteomes and explore their functional roles. Third, we will leverage the predicted human interactome to identify genetic variants that disrupt PPIs and cause disease. We will adopt and develop tools to predict PPI-disrupting mutations based on evolutionary data and physicochemical properties of the interface. These predictions will be integrated with the vast amount of human and mouse genotype-phenotype data, particularly data from the Sequencing Populations to Accelerate Research and Care (SPARC) program led by our McDermott Center at UT Southwestern. This approach will provide mechanistic insights into poorly understood diseases, aiding patient diagnosis. In summary, we will develop and release a suite of computational tools to overcome current challenges in predicting human PPIs, use these tools to resolve the human interactome and catalog SLiM functions, and integrate our findings with patient sequencing data to uncover novel disease mechanisms.

NIH Research Projects · FY 2025 · 2025-08

Molecular Mechanisms of Wntless in Zaki Syndrome and Wnt secretion Approximately 3% of live births are affected by structural birth defects. The underlying pathological mechanisms and effective pharmacologic prevention, however, remain largely elusive. Zaki Syndrome is an inborn error marked by severe developmental abnormalities, including brain malformations, facial dysmorphisms, limb deformities, and growth retardation, posing a significant threat to children's health. This syndrome was identified in 2021 and is caused by homozygous mutations in the WLS (Wntless) gene, leading to disturbances in the Wnt signaling pathway, which is critical for embryonic and fetal development. WLS is a transmembrane protein essential for the maturation and secretion of Wnt proteins, which play a crucial role in cell differentiation during developmental process. WLS binds tightly to the modified Wnt proteins, facilitating their intracellular trafficking and extracellular secretion. Moreover, a Glycogen Synthase Kinase 3 inhibitor named CHIR99021 has been shown to restore development in the Zaki disease models. Interestingly, missing body parts in mouse embryos were regenerated, and the growth of organs resumed normally. Since it was identified not long ago, how Zaki syndrome mutations affect WLS for reduced Wnt production remain unclear, moreover, the exact mechanisms of Wnt release from WLS, an indispensable step in the human development, is not yet understood. In this project, we will use multi-faceted approaches to elucidate how Zaki syndrome-causing mutations affect the activity of WLS and whether these mutations specifically alter the secretion of certain Wnt proteins more than others. We will study all six mutations and assess how they influence WLS. Additionally, we will test our hypothesis that phospholipids mediate Wnt release from WL using synthetic probes and artificial lipid environments. Furthermore, three Zaki syndrome-causing mutations are in the C-terminus of WLS. We hypothesize that these mutations disrupt the interaction between WLS and its intracellular binding partners, interfering with WLS trafficking. To investigate this, we will delineate the trafficking step each mutation disrupts and identify novel WLS binding partners and post- translational modifications involved in its trafficking. Overall, our results will provide significant insights into the mechanisms underlying Wnt secretion and Zaki syndrome in the embryonic development. Our findings may also contribute to the design of therapeutic strategies to target WLS for the treatment of Zaki syndrome and thus improve children’s health.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY This project will investigate the impact of dihydrouridine (D) modifications in tRNA on a newly discovered post- transcriptional regulatory mechanism called P-site tRNA-mediated decay (PTMD), and the resulting effects on mitochondrial metabolism and cancer metastasis. PTMD is a pathway wherein specific arginyl-tRNAs recruit the CCR4-NOT complex to ribosomes translating mRNAs rich in CGG, CGA, and AGG arginine codons, resulting in reduced translation and accelerated turnover of these transcripts. Since mRNAs that encode components of mitochondrial ribosomes and the respiratory chain are rich in these codons, reduced efficiency of PTMD results in an increase in mitochondrial activity. Recently, activation of mitochondrial respiration was shown to drive metastasis in clear cell renal cell carcinoma (ccRCC), but how metastatic ccRCC cells upregulate mitochondrial activity remains unclear. Overexpression of multiple dihydrouridine synthase (DUS) enzymes that introduce D modifications at specific positions in tRNAs is also strongly associated with poor patient survival in ccRCC. Moreover, DUS overexpression is associated with upregulation of transcripts rich in CGG/CGA/AGG arginine codons, including those encoding mitochondrial proteins, indicative of PTMD impairment. Based on these findings, we hypothesize that DUS overexpression results in D hypermodification of tRNAs, reducing their ability to recruit the CCR4-NOT complex, and thereby increasing the translation and stability of CGG/CGA/AGG-rich mRNAs encoding components of mitochondrial ribosomes and the respiratory chain. In ccRCC, the increase in mitochondrial metabolism and respiration that results from this translational reprogramming is predicted to promote metastasis, resulting in poor patient outcomes. To investigate this hypothesis, our research program will examine how altering DUS enzyme activity affects tRNA D modifications, overall tRNA metabolism, and the PTMD pathway in human and mouse ccRCC cells, documenting the effects of both individual and combinatorial D modifications at multiple tRNA positions. Using ccRCC models, we will evaluate the impact of gain and loss of DUS enzyme activity, as well as mutations in the CCR4-NOT subunit CNOT3 that impair PTMD, on mitochondrial activity and metastasis in this malignancy. Cryo-electron microscopy (cryo-EM) will be used to investigate the molecular mechanisms whereby D hypermodification of tRNAs influences tRNA structure and CCR4-NOT recruitment. Altogether, these experiments will provide a mechanistic understanding of the impact of dihydrouridine modifications on PTMD and ccRCC pathogenesis, potentially revealing new therapeutic vulnerabilities in this malignancy. We have assembled a complementary team of experts in RNA biology, post- transcriptional regulation, metabolism, cancer biology, and structural biology to accomplish these aims, and we are eager to collaborate with other groups in the RNAMoDO program to investigate how additional RNA modifications impact normal physiology and cancer.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY/ABSTRACT Dyspnea on exertion (DOE) and exercise intolerance are hallmark symptoms of heart failure with preserved ejection fraction (HFpEF). The mechanisms of these symptoms are unknown, and no therapeutic strategy exists for these debilitating symptoms. As such, NHLBI working groups recommend prioritizing studies that advance understanding of HFpEF-related (patho)physiology and the primary causes of symptoms in these patients so that novel therapeutics can be developed. DOE and exercise intolerance are also very common symptoms of obesity. Obesity has reached epidemic levels and affects four-in-ten American adults. The prevalence of obesity rises to eight-in-ten adults in the HFpEF population yet, the role of obesity in provoking symptoms of DOE and exercise intolerance in HFpEF patients has, thus far, been neglected. Human studies demonstrate that obesity affects breathing mechanics, whereby lung volume subdivisions and maximal expiratory flow are decreased, which increases the risk of expiratory flow limitation, dynamic hyperinflation, and an altered breathing pattern during exercise. All these obesity-related mechanical ventilatory constraints ultimately 1) increase the oxygen (O2) cost of breathing and 2) impose a mechanical ceiling on ventilation (V̇E) during exercise, which could provoke DOE and reduce exercise capacity. Thus, we hypothesize that obesity is likely a significant contributor to DOE and exercise intolerance in patients with HFpEF. To date, the O2 cost of breathing and the effect of obesity-related mechanical ventilatory constraints on DOE and exercise intolerance remains untested in patients with HFpEF. Therefore, the overall aim of this K99/R00 proposal is to 1) investigate the O2 cost of breathing and examine how this impacts DOE and peak exercise capacity in patients with HFpEF, and 2) reduce obesity-related mechanical ventilatory constraints to potentially reduce DOE and increase exercise capacity in patients with HFpEF. To accomplish these goals, we will 1) investigate the interaction of HFpEF (underlying changes in pulmonary function) and obesity (obesity-related changes in pulmonary function) on the O2 cost of breathing during eucapnic voluntary hyperpnea, and its association with DOE during constant load exercise and peak exercise capacity, and 2) investigate the effects of breathing a low density helium-oxygen gas mixture (HeO2: 21% O2 and 79% He), which reduces obesity-related mechanical ventilatory constraints (HeO2 increases maximal expiratory flow, reduces the work of breathing, decreases expiratory flow limitation & dynamic hyperinflation, and increases VT expansion), on DOE during constant load exercise and peak exercise capacity. We anticipate these investigations will 1) further understanding of the role of obesity in provoking symptoms of DOE and exercise intolerance in HFpEF patients, 2) identify new mechanisms underlying symptoms of DOE and exercise intolerance, which could dramatically alter conventional thinking about the primary causes of these symptoms in patients with HFpEF, and 3) provide new targets for independent investigation so that novel therapeutic strategies can be developed and enable new paradigms for personalized therapy in HFpEF.

NIH Research Projects · FY 2025 · 2025-08

SUMMARY Neuron loss is a frequent result of spinal cord injury (SCI). A fundamental but unresolved challenge is how to restore the lost neurons and repair the neural circuits after SCI. Stem cell-based transplantation has limitations on immune compatibility, neuronal survival, and functional integration. The long-term goal of this proposal is to define a regenerative strategy by using a patient's own scar-forming cells without cell transplantation. In response to SCI, perivascular cells proliferate and migrate into the lesion core to form the fibrotic scar. Scar formation is initially beneficial by restricting damage but ultimately detrimental to neural regeneration through acting as a physical and chemical barrier to axonal regeneration and growth. The goal of this high risk but high reward project is to define methods to convert these fibroblasts into neurons. Aim 1 will focus on reprogramming of fibroblasts into progenitors in vivo. Stem cell factors will be examined. Aim 2 will focus on direct neuronal conversion of fibroblasts in vivo. Several key neurogenic factors will be examined for induction of neurons. Results of this work may reveal a regeneration-based therapeutic strategy by targeting the fibrotic scar after SCI.

NIH Research Projects · FY 2026 · 2025-08

PROJECT SUMMARY This proposal focuses on actions of the sympathetic nervous system (SNS) to control ghrelin secretion. Ghrelin is a hormone produced primarily by enteroendocrine “ghrelin cells” in the lining of the stomach. Understanding the mechanisms that control ghrelin secretion is highly significant given ghrelin’s key roles in regulating metabolic processes, including eating, physical activity, and blood glucose. Ghrelin engages hedonic eating behaviors, ghrelin action is required for the usual rebound food intake following a fast, and ghrelin increases exercise endurance and regulates food intake after exercise. Also, ghrelin prevents life- threatening hypoglycemia in mice subjected to chronic caloric restriction. Previous work has identified the SNS as a primary driver of increased ghrelin secretion in response to fasting. We showed that norepinephrine (NE), which is released from SNS nerve terminals originating in the celiac ganglion, activates β1-ARs (adrenergic receptors) on ghrelin cells to stimulate ghrelin secretion during a 24h fast and a chronic caloric restriction protocol. Despite this, specific aspects of how the SNS regulates ghrelin secretion remain unknown. The overall goal of this proposal is to close these gaps in knowledge and provide a comprehensive understanding of SNS-driven ghrelin secretion. In Aim 1, we will determine how fasting and exercise change SNS innervation of ghrelin cells, using a combination of histochemistry, neuroanatomical tract tracing, and transcriptomics. In Aim 2, we will identify the specific SNS neuronal populations responsible for ghrelin secretion during fasting and exercise. This will be achieved by determining the requirement of ghrelin cell β1-AR and NPY Receptor subtype 5 (NPY5R) for fasting-induced and exercise-induced stimulation of ghrelin secretion and for the ensuing effects of this secreted ghrelin on rebound food intake after fasting, food intake after exercise, and exercise endurance. Also, we will use chemogenetics to manipulate (inhibit and separately, stimulate) activity of the different celiac ganglion neuronal populations that innervate ghrelin cells. In Aim 3, we will determine if the SNS works coordinately with insulin to regulate ghrelin secretion. This will be achieved by disrupting the presumed usual balance between SNS and insulin required for appropriate ghrelin secretion. To do this, we will generate mice with ghrelin cell-specific deletion of either insulin receptors, β1-ARs, or both. Using both in vivo models and primary gastric mucosal cell cultures from those mice, we will evaluate ghrelin secretion in response to NE and insulin and under conditions that include a fast-refeed model and diet-induced obesity. Overall, our studies will identify the SNS subtypes that innervate ghrelin cells, those synaptic and transcriptional changes within ghrelin cell-innervating SNS neurons and ghrelin cells occurring as a result of caloric restriction and exercise, the requirement of ghrelin cell β1-ARs and NPY5Rs for fasting-induced and exercise-induced ghrelin secretion, food intake, and exercise endurance, and how the SNS and insulin coordinately regulate ghrelin secretion during fasting, postprandially, and in diet-induced obesity.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY Combined PET/MR, enabling simultaneous PET and MRI, has the potential to at least match the diagnostic performance of reviewing separate PET/CT and MRI scans, in a single integrated exam of the heart. This will substantially reduce the patient burden, exam costs, and radiation compared to serial imaging on PET/CT and MRI, and benefit the workup of multiple heart diseases. Further, by enabling accurate spatial overlap of PET and MR images, and the ability to generate gold standard metabolic measures from extended dynamic PET scans, PET/MR could outperform interpretation of serial scans. However, quantitative accuracy of tracer uptake on PET images from PET/MR studies frequently is lower than that from reference standard PET/CT. The primary cause of this discrepancy are errors in MR-based corrections for PET signal attenuation. MR- based attenuation corrections suffer from artifacts due to metallic cardiac implants, breathing motion, and limited lung signal, which can all propagate into the reconstructed PET image. This is an important problem, since PET/MR may have limited efficacy in the workup of patients with heart diseases if PET image quality and quantification does not match PET/CT systems. The overall objective of this proposal is to develop a comprehensive PET attenuation correction scheme, using the signal from an external PET source and the patient, to enable precision PET imaging during cardiac PET/MR exams. The method utilizes hardware, image reconstruction, and deep learning algorithms to directly measure and correct for PET attenuation based on physics principles alone, without using prior data or assumptions. The specific aims include: 1) fabricating a device that can rapidly position and remove an external PET source in a PET/MR that is practical and safe for patient imaging, 2) developing algorithms for real-time hardware optimization and deep learning enhancement that ensure robust PET quantification for all exams, and 3) evaluating the proposed attenuation correction scheme on the workup of patients with the infiltrating disease, cardiac sarcoidosis. We focus on cardiac sarcoidosis, as these patients often have a cardiac defibrillator implanted before imaging, particularly challenging attenuation correction methods, and PET and MRI are the standard of care for workup. We will assess our algorithms with phantoms, simulations, and prospective FDG-PET/MR and PET/CT studies of sarcoidosis patients. Successful completion of these aims will enable realization of PET/MR as a comprehensive integrated workup of cardiac sarcoidosis and heart diseases overall.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY Lower grade gliomas, as well as the high grade gliomas that arise from them, are now diagnostically defined by the presence of mutations in genes encoding isocitrate dehydrogenase (IDH) enzymes. Mutant IDH enzymes synthesize the oncometabolite (R)-2HG. (R)-2HG accumulates to millimolar levels in IDH-mutant glioma cells and inhibits 2-oxoglutarate-dependent enzymes, including the TET and KDM dioxygenases that catalyze DNA and histone demethylation, respectively. Thus, (R)-2HG cells causes chromatin hypermethylation and epigenetic reprogramming. IDH mutations occur first in the series of genetic alterations that cause lower grade gliomas, suggesting that they play an important role in tumor initiation. However, our understanding of the precise targets of (R)-2HG-induced epigenetic reprogramming that drive neural cell transformation is limited. This limitation is tied to the difficulty in using primary samples from established tumors to retrospectively study tumor initiation. To address this issue, we created a genetic mouse model of astrocytoma and performed time- resolved single-cell multi-omics analyses of the alterations caused by mutant IDH during premalignancy and tumor initiation. We found that mutant IDH repressed neuroblast and interneuron cell lineages and expanded oligodendrocyte precursor cells prior to tumor formation. Moreover, we found that oligodendrocyte precursor cells, but not neuroblasts and interneurons, were permissive to transformation. These data suggest that altered lineage specification of neural progenitor cells may be a key mechanism of glioma promotion by IDH oncogenes. To identify molecular changes that cause this effect, we performed a cross-species transcriptomic analysis of IDH-mutant and IDH-wildtype tissues. We identified mutant IDH-induced silencing of a lineage- specific transcription factor that is required for interneuron differentiation. This silencing event was associated with DNA hypermethylation of an associated CpG island. Based on these findings, we hypothesize that epigenetic reprogramming by (R)-2HG drives glioma initiation by inhibiting neuronal specification of neural progenitor cells, thereby expanding the pool of oligodendrocyte precursor cells that are susceptible to transformation by glioma-associated mutations. We will test this hypothesis through three specific aims. In Specific Aim #1, we will examine the relationship between DNA hypermethylation and silencing of the identified interneuron-specifying transcription factor in human and mouse samples. In Specific Aim #2, we will test whether ectopic expression of this transcription factor reverses mutant IDH-induced lineage reprogramming of neural progenitor cells in vivo. In Specific Aim #3, we will ask if altered neural progenitor cell lineage priming drives gliomagenesis downstream of IDH mutations and whether a gene involved in this process may serve as a biomarker of response to mutant IDH inhibitors, which have shown anti-glioma activity in the clinic. If successful, our work may reveal the molecular and cellular dynamics that drive IDH-mutant glioma initiation and nominate new approaches to monitor and predict response to IDH inhibitor therapies.

NIH Research Projects · FY 2025 · 2025-07

PROJECT SUMMARY Liver cancer incidence is rising globally, with an overall survival rate of about 20%. Developing new therapeutic strategies is therefore critical to improve treatment response and increase survival. Our lab has identified a novel metabolic vulnerability in liver cancer which could pave the way for new mechanisms of therapy. Starving tumors of the essential amino acid tryptophan (Trp) completely abrogates liver cancer growth in genetically engineered mouse models as well as syngeneic xenografts. Importantly, the vast majority of bodily Trp is metabolized and not used for protein synthesis. Therefore, we broadly tested adding back various Trp metabolites to identify those that were critical for tumor growth. We discovered that the novel oncometabolite indole-3-pyruvate (I3P) is the only downstream product of Trp capable of rescuing liver cancer growth. However, the growth-promoting effects of I3P are significantly stronger in vivo than in vitro, suggesting that it has a non cell-autonomous mechanism of action. I surveyed multiple different immune cell types relevant to the liver cancer microenvironment and found that I3P may play a critical role in modulating macrophage polarization. My studies will therefore focus on defining the role of I3P-mediated macrophage phenotypes in the immune response to liver cancer.

NIH Research Projects · FY 2025 · 2025-07

PROJECT SUMMARY/ABSTRACT Although IgE-mediated HSRs are the most feared, most drug HSRs are non-IgE-mediated and often require only dosage and administration adjustments rather than complete drug avoidance. Clinical similarities between IgE- and non-IgE-mediated immediate HSRs lead to misclassification, unnecessary drug avoidance, less effective treatments, and increased costs. Recent research has emphasized the role of non-IgE receptors, such as MRGPRX2, in mast cell (MC) activation. MRGPRX2, expressed primarily on skin MCs, is a ligand for positively charged drugs like vancomycin, fluoroquinolones, and some neuromuscular blocking agents. MRGPRX2 activation requires sustained and high tissue drug concentrations, often surpassing therapeutic levels. This discrepancy may stem from differences in MRGPRX2 expression or functionality. It is unknown if individuals with an MRGPRX2 ligand-mediated HSR exhibit elevated MRGPRX2 expression levels in sera and skin MCs or heightened sensitivity to other MRGPRX2 ligands, suggesting a definable hyperreactive phenotype. Using vancomycin infusion reactions (VIR) as a prototypical MRGPRX2 ligand-induced HSR, this proposal aims to compare MRGPRX2 expression levels in sera and skin MCs and skin test dose responses to other MRGPRX2 ligands in subjects with VIR compared to vancomycin-tolerant controls. The research rationale is based on preliminary data suggesting that VIR subjects have a significantly lower vancomycin skin test dose threshold for a positive response than vancomycin-tolerant subjects, raising the possibility that these individuals may also exhibit lower thresholds and increased sensitivity to other MRGPRX2 ligands. A multiphase study will be conducted by three U.S. Allergy Centers. In the UG3 Phase, Aim 1 will validate a vancomycin skin test with an optimal vancomycin concentration to discriminate VIR subjects with an ROC ≥0.8. Aim 2 will optimize and validate an immunofluorescence (IF)-based assay for quantifying MRGPRX2 in skin MCs with a reproducibility coefficient of variation of <10% for MRGPRX2 staining intensity. Once the UG3 Milestones are accomplished, the project will move into the UH3 Phase. Aim 3 will compare MRGPRX2 expression levels in sera and skin MCs using the validated IF assay from Aim 2 and determine their correlation with vancomycin skin test dose responses in VIR and vancomycin-tolerant subjects using the validated skin test from Aim 1. Lastly, Aim 4 will determine if VIR subjects exhibit skin hyperreactivity to other MRGPRX2 ligands apart from vancomycin. The expected outcomes will significantly advance the understanding of the MRGPRX2-mediated drug HSR mechanism and provide a comprehensive methodology for studying other non-IgE-mediated HSRs. Ultimately, the long-term goal is to advance knowledge of immediate drug HSR mechanisms and develop diagnostic tools that can identify non-IgE-mediated HSRs, thus preventing misclassification and unnecessary drug avoidance.

NIH Research Projects · FY 2025 · 2025-07

PROJECT SUMMARY Syphilis, caused by the spirochete Treponema pallidum subsp. pallidum (T. pallidum), is an important cause of stillbirth, preterm delivery, and neonatal death. In untreated syphilis in pregnancy, histopathologic findings of necrotizing funisitis, proliferative vascular changes in the villi, acute or chronic villitis with a predominance of CD8 T cells, and increased villous macrophages of fetal origin (Hofbauer cells) are described. Little is known about transcriptional dysregulation of immune cells in the dynamic immune microenvironment of the placental interface along a spectrum of clinical syphilis disease and treatment. The objective of this proposal is to address knowledge gaps by elucidating T pallidum-driven changes in the maternal-placental-fetal immune transcriptome, linking maternal syphilis stage, treatment timing, treponemal burden, placental histopathology, and neonatal outcomes. The central hypothesis is that adverse neonatal outcomes from syphilis, such as preterm birth, correlate with placental pathology, high treponemal burden, and transcriptional dysregulation of CD8+ T cell and Hofbauer cell populations in the placenta. In Aim 1, placental histopathologic phenotypes will be defined and correlated with treponemal burden and neonatal outcomes along a spectrum of clinical disease and compared to healthy controls. In Aim 2, differential placental gene transcriptional profiles will be linked to histopathologic placental abnormalities, preterm delivery, and congenital syphilis. As Medical Director of Perinatal Infectious Diseases at a maternity center with an annual delivery volume of over 12,000, Dr. Adhikari oversees the clinical evaluation and management of approximately 150 patients with syphilis in pregnancy every year and has collected robust preliminary clinical data. With the full support of UT Southwestern Medical Center, the Clinical and Translational Science Award Program, the Department of Obstetrics and Gynecology, and the Green Center for Reproductive Biology Sciences, as well as local and national mentors and expert advisors, Dr. Adhikari has a rich environment in which to engage in individualized mentorship and career development, formal coursework and hands-on learning to succeed. Research and training will be completed under the guidance of a robust mentorship team, including experts in placental biology, infectious diseases in pregnancy, and genomics. This K23 award will provide the training and resources needed for Dr. Adhikari to launch a successful career as an independent investigator to better define the maternal-placental-fetal immune response to infection at the cellular and molecular level and link these findings to adverse pregnancy outcomes such as preterm birth and congenital infection.

NIH Research Projects · FY 2026 · 2025-07

PROJECT SUMMARY / ABSTRACT TITLE: Exploring Pathophysiology and Treatment Approaches in Mild Autonomous Cortisol Secretion Adrenal tumors are found in ~5% of the adult population and up to 20% of patients with obesity, diabetes, and hypertension. Most of these comprise adrenal cortical adenoma. Mild Autonomous Cortisol Secretion (MACS) is a prevalent condition, defined as failure to suppress cortisol ≤1.8 mcg/dL after a 1-mg dexamethasone suppression test. MACS is usually discovered during biochemical workup of incidental adrenal tumor. MACS is linked with weight gain, hypertension, impaired glucose metabolism, insulin resistance (IR), nearly 3-fold increase in cardiovascular events, and more than 10-fold increase in mortality. MACS has a well-established association with IR. However, the pathophysiologic link between MACS and IR remains incompletely characterized. Some studies show that IR, hyperinsulinemia, and the anabolic effects on adrenal tissue, which has insulin-like growth factor (IGF)-1, IGF-2, and insulin receptors, offer possible pathophysiological links. Other studies conclude the inverse pathway – that dysregulated cortisol secretion in MACS elicits excess adiposity and IR. Adrenalectomy is the only available treatment option for MACS, but it leads to inconsistent outcomes. To date, there is no prospective data comparing adrenalectomy to pharmacological weight loss and its effects on IR and dysregulated cortisol secretion in MACS. Further investigation into the relationship of the “adrenal-insulin axis”, and how cortisol and IR relate to one another, is urgently needed. Tirzepatide, a novel dual glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide-1 (GLP-1) receptor agonist, is the most effective FDA-approved agent for treatment of obesity (with or without diabetes). We hypothesize that weight loss with tirzepatide will improve IR, but weight loss will not normalize dysregulated cortisol secretion. To directly test this, we will conduct a pilot randomized trial to compare the effect of adrenalectomy vs weight loss with tirzepatide on IR, steroid profile, body composition, muscle strength, and cardiometabolic profile in patients with MACS. We will also perform a prospective interventional case-control study to compare the effect of tirzepatide on weight loss, body composition, and cardiometabolic changes in patients with MACS vs matched controls following 6-month treatment. The studies proposed in this K23 proposal will provide valuable insights into the pathophysiology of MACS, and in turn identify better treatment strategies. In parallel, the proposal will allow me to get in-depth training in assessing cardiometabolic and adrenal metabolome outcomes in patients with MACS, skills necessary to achieve my long-term career goal of becoming an independent clinical investigator and leader in adrenal disorders. This proposal builds on my prior clinical and research experience and leverages a strong mentorship team that is invested in my professional development. My 5-year training and mentoring plan includes formal coursework, professional development, and mentored research, with defined milestones to ensure productivity, progress, and successful transition to investigational independence.

NIH Research Projects · FY 2025 · 2025-07

Cardiac ATTR amyloidosis (ATTR-CA) is caused by the aggregation and deposition of the protein transthyretin in the heart, which leads to arrhythmias, congestive heart failure, and death. Although there are an estimated 25% of individuals over 80 years old that have these cardiac deposits, and there are 1.5 million at-risk Black individuals in the US who harbor a hereditary pathological transthyretin variant, ATTR-CA is often misdiagnosed, diagnosed too late, or never at all. This diagnostic problem is likely due to the variable ATTR-CA clinical presentation and the lack of simple, specific, and inexpensive diagnostic tests. This issue is exacerbated in Black and Hispanic communities, which are more likely to harbor a pathological gene variant but have been historically overlooked. The laboratory of PI Dr. Lorena Saelices Gomez has used the structures of cardiac fibrils extracted from ATTR-CA patients to design a peptide probe (Transthyretin Amyloid Detection 1, or TAD1) that robustly detects transthyretin aggregates in plasma of ATTR-CA patients. Our aim now is to validate TAD1 as a biomarker for ATTR-CA, bringing our technology a step closer to clinical application. In Aim 1, we will determine the ability of TAD1 to identify ATTR-CA in a cohort of Black and Hispanic individuals with heart failure. This cohort (n>600) has been extensively evaluated in the Screening for Cardiac Amyloidosis with Nuclear Imaging in Minority Populations (SCAN-MP) study (R01HL139671, NCT03812172), the largest NIH funded ATTR-CA screening study for underrepresented minorities with heart failure, directed by co-PIs Drs. Mathew Maurer and Frederick Ruberg. We will capitalize on the biobanked samples and the comprehensive phenotypic and genotypic evaluation of this cohort to determine the diagnostic value of TAD1. We will assay plasma samples using our TAD1 assay and compare it to the current reference diagnostic test, PYP scintigraphy. In a subset of patients with elevated TAD1 signal, we will leverage a novel, highly-specialized imaging test for ATTR-CA using positron emission tomography (PET) imaging, to detect early ATTR-CA and investigate the interaction of ttr genotype with TAD1 levels. For Aim 2, our objective is to translate our TAD1 assay into a high throughput diagnostic ELISA tool, scalable for clinic use. We will first screen a polyclonal antibody panel generated in our laboratory and generate a fibril-specific monoclonal antibody from the best candidate. We will then optimize our peptide probes by yeast surface display. Finally, we will select the best probe and combine it to the monoclonal antibody to setup an ELISA assembly. We will validate this assembly with the samples used to develop the original TAD1 assay and the SCAN-MP cohort’s samples. The identification of ATTR-CA through a secure, affordable, and highly responsive test like this will facilitate early diagnosis. This, in turn, allows for the timely initiation of effective treatments during the initial stages of the disease when they are most beneficial.

NIH Research Projects · FY 2026 · 2025-07

PROJECT SUMMARY/ABSTRACT This proposal details a career training plan for Dr. Walter Chen, a neonatologist at UT Southwestern, to become an independent physician-scientist studying metabolic organelles and how they contribute to liver homeostasis and disease (e.g., inborn errors of metabolism [IEMs]). Dr. Chen received his M.D. and Ph.D. degrees from Harvard and MIT, respectively, and completed Pediatrics residency at Boston Children’s Hospital. He then completed his Neonatal-Perinatal Medicine fellowship at UT Southwestern. During his fellowship, Dr. Chen initiated his postdoctoral research under the mentorship of Dr. Ralph DeBerardinis at UT Southwestern. Dr. DeBerardinis is an internationally recognized expert in the study of human metabolism and IEMs using advanced metabolic techniques, such as stable isotope tracing. Dr. DeBerardinis has mentored numerous trainees, many of whom have become successful academic investigators. Under this award, Dr. Chen will be supported by Dr. DeBerardinis and a co-mentor Dr. Hao Zhu, who is an expert in liver biology. These mentors, as well a multidisciplinary advisory team, will provide scientific expertise and guidance that will facilitate Dr. Chen’s career development. In this proposal, Dr. Chen will learn stable isotope tracing techniques and how to use mouse models to study liver biology, which will be critical for his transition to independence. At UT Southwestern, Dr. Chen will have access to all the resources and expertise needed to conduct his research and develop as an independent investigator. This research proposal will investigate an uncharacterized mitochondrial protein in cellular and hepatic physiology that has connections to an IEM and is implicated in type 2 diabetes. Preliminary studies indicate that this protein regulates valine and isoleucine catabolism, an important metabolic pathway in the liver. Aim 1 will define the function and mechanism of action of this protein using cultured cells. Aim 2 will investigate the effects of losing this protein on core metabolic processes, such as mitochondrial respiration. Aim 3 will determine the role of this protein in hepatic physiology by studying liver-specific knockout mice. This work will elucidate the mechanism, function, and role of this uncharacterized mitochondrial protein in cellular and hepatic physiology, thus providing insights that will advance our understanding of how dysfunction of this protein can contribute to human disease. Through this award, Dr. Chen will develop the skills necessary to become an NIH-funded independent investigator.

NIH Research Projects · FY 2025 · 2025-07

Project Summary Bats serve as reservoirs for numerous viruses that spill over to humans and cause disease. The immune adaptations that allow bats to control viral infections without developing disease are not clearly defined. This project aims to investigate cell-intrinsic antiviral mechanisms in bats, focusing on interferon-stimulated genes (ISGs) and their evolutionary adaptations. We will examine the antiviral properties of RTP4, a rapidly evolving RNA-binding protein that inhibits flaviviruses, which have been associated with bats for decades but are relatively understudied compared to other viral zoonoses. Through biochemical, genetic, virological, and cell biological approaches, we will determine the antiviral molecular mechanism of RTP4 and assess the functional diversity of ISGs across multiple bat species. Successful completion of this project will significantly advance our understanding of bat immunity by defining the molecular mechanisms underlying a bat-flavivirus arms race, and by expanding the known repertoire of antiviral bat ISGs. These outcomes will set the stage for future mechanistic studies and may inform strategies to combat zoonotic disease.

NIH Research Projects · FY 2025 · 2025-07

Project Summary Osteonecrosis (ON) of the femoral head (ONFH) is one of the most severe hip diseases affecting all ages with an estimated 20+ million affected people worldwide. ONFH has become a major cause of total hip arthroplasty resulting in great financial burdens. Currently, multiple high prevalence risk factors have been identified including trauma, glucocorticoid use, alcohol abuse and genetics, but none of these are certain and the etiology of ON is unclear. There are no gold standards for the treatment of ON. Most treatment are focused on delaying disease progression to preserve the joint using surgical techniques. No effective biological treatment has been identified due to that little is known about the molecular mechanisms associated with ON healing. ON is caused by a disruption of blood supply leading to necrotic bone cell death. An imbalanced osteogenesis and adipogenesis with impaired angiogenesis is often presented in the process of ON healing. It is thus critical to fully characterize the process of stem cell differentiation to repopulate necrotic bone and the mechanisms regulating revascularization in necrotic bone healing. Towards this end, we have successfully established a rodent model showing consistent human ON phenotype with ischemic tissue damage to the whole joint. Using non-biased scRNA sequencing, we showed that Osterix positive (OSX+) bone progenitors are significantly expanded in ON compared to other progenitor populations. Interestingly, these OSX+ cells demonstrate an expanded and sporadic marrow distribution that does not associate with vessels. Moreover, OSX+ cells in ON contain an increased progenitor subpopulation that co-expresses PPARγ which is absent in control. We also determined that enhanced adipogenesis in ON is accompanied by elevated LDL and oxidative stress resulting in increased levels of oxidized low-density lipoprotein (oxLDL). Importantly, using both in vivo and in vitro assays we show that oxLDL impairs angiogenesis by downregulating endothelial Notch signaling. Our long-term goal is to uncover the key mechanisms in ON healing, and thus provide a molecular basis for future biological treatment of ON. Our central hypothesis is that OSX+ cells are the critical cell population responsible for imbalanced osteogenesis and adipogenesis observed in ON, which negatively affects the revascularization of necrotic bone via an oxLDL-Notch signaling mediated mechanism. We will attest our hypothesis through two highly-related but independent specific aims: Aim 1: To identify and define the OSX+ population of progenitors that repopulate necrotic bone marrow in ON; and Aim 2: To determine the oxLDL-Notch mediated signaling mechanisms that regulate angiogenesis in ON. We will investigate the above listed aims by using single cell RNA sequencing technique, lineage tracing, metabolomics and Notch loss-of-function and gain-of-function models of genetically engineered mouse. Successful completion of this project will advance our understanding and identify key mechanisms that regulate bone progenitor cells differentiation and angiogenesis in ON. We believe that this work will lay the foundation for future investigation of biological treatment in ON.

NIH Research Projects · FY 2026 · 2025-07

PROJECT SUMMARY Systemic lupus erythematosus (SLE) is a highly morbid autoimmune disease. Despite recent advances, there is a critical unmet need to discover novel therapies that precisely target the pathophysiological basis of this disease. Emerging data suggest the importance of a relatively recently discovered cell type, the T peripheral helper (Tph) cell. It is pathologically expanded in lupus patients, highly correlated with disease activity, and produces factors that support autoantibody production. Our preliminary data suggest that one of the reasons why these cells are expanded in these patients is the high levels of circulating type I interferon, a cytokine. In this proposal, we will apply cutting-edge biochemical, epigenetic, and genetic approaches to human T cells (both healthy controls and patient samples). We will utilize these high-dimensional datasets to elucidate the molecular mechanisms by which IFN supports the production and expansion of this cell type. These data will likely reveal novel therapeutic approaches that can be leveraged for future therapies.

NIH Research Projects · FY 2025 · 2025-07

Project Summary Campylobacter jejuni is both a pathogen that is the leading cause of bacterial diarrheal disease in humans in the US and throughout the world and a commensal of the intestinal tract of many animals and avian species. As such, sporadic cases of diarrheal disease in humans are most often attributed to handling or consuming contaminated poultry meat. For both the susceptible human host and the natural avian host, C. jejuni must identify lower intestinal niches that support growth for infection. We observed that C. jejuni senses and responds to specific metabolites generated by the intestinal microbiota of both avian and human hosts. We discovered that the C. jejuni BumSR two-component signal transduction system (TCS) is required to sense and respond to exogenous butyrate (a short-chain fatty acid; SCFA) and specific branched short-chain fatty acids (BSCFAs). Sensing these metabolites is important for host interactions as the BumSR TCS is required for C. jejuni to infect humans for diarrheal disease and promote optimal commensal colonization of chickens. We discovered that upon sensing butyrate and specific BSCFAs, the BumSR TCS mediates an unusual mode of signal transduction to alter expression of specific C. jejuni genes required for in vivo growth. We observed that BumS functions as a sensor phosphatase, rather than a sensor kinase, whose activity is altered upon sensing its specific cues. Instead of contributing to phosphorylation of a response regulator like most other bacterial TCS sensors, BumS dephosphorylates its cognate BumR response regulator to control its activity in altering gene transcription. Specific BSCFAs are direct cues sensed by BumS to inhibit its dephosphorylation of BumR. However, butyrate did not inhibit BumS phosphatase activity, suggesting that butyrate is indirectly sensed by BumS. Because BumS does not function as a kinase, BumR must use a non-cognate phosphodonor in C. jejuni to form P-BumR. Consequently, the design of this system in employing a sensor that exclusively functions as a phosphatase rather than a kinase requires the BumSR TCS to integrate multiple input cues to properly control transcription of its regulon. Molecular mechanisms for understanding how this unusual TCS senses intestinal metabolites and mediates sensor phosphatase-driven signal transduction remain to be discovered. In Aim 1, we will determine how BumS senses specific BSCFAs as direct cues and functions as a sensor phosphatase in a non-canonical mechanism of signal transduction for a bacterial TCS. In Aim 2, we will examine leading endogenous phosphodonor candidates for BumR and understand how these additional inputs inform the bacterium about conditions in intestinal niches. Completion of goals will establish new molecular mechanisms for how bacterial TCSs execute signal transduction by exclusively employing a sensor phosphatase and reveal how intestinal bacteria sense SCFA or BSCFA metabolites.

NIH Research Projects · FY 2025 · 2025-07

Project Summary The thymic tissue is the only organ supporting the development of the T cells of the immune system. The quintessential stromal cell type in this tissue needed for thymopoiesis is the thymic epithelial cell (TEC). TECs govern the positive and negative selection of T cells in the thymus. The master transcriptional regulator of TECs is the Forkhead Box N1 (FOXN1) gene. Three distinct autosomal recessive FOXN1 mutations were identified several decades ago, resulting in a nude and T-B+NK+ severe combined immunodeficiency phenotype. The T cell lymphopenia resulted from an athymia. In such cases, an allogeneic thymic tissue transplant, depleted of hematopoietic cells, remains the best clinical strategy for restoring some T cell development. Recent widespread use of genome sequencing for patients who have low T cell receptor excision circles (TRECs), which is a measure of low T cell output from the thymus, has increased the number of human FOXN1 variants to >500. As described in our prior JCI and JACI publications, we categorized the diverse FOXN1 variants based on their impact on protein function and thymopoiesis. Interestingly, most patients with low TRECs who had single allelic FOXN1 variants normalize their peripheral T cell numbers over time. This presents a major conundrum as to how such patients should be managed clinically. Thus, a serious scientific gap exists in our understanding as to why most single allelic FOXN1 variants result in a transient T cell lymphopenia. In this exploratory grant, we will determine if a previously unconsidered mechanism involving monoallelic FOXN1 expression accounts for the transient T cell lymphopenia. This will be done with mouse models genocopying selected human FOXN1 variants. Comparing the allelic expression of Foxn1 in TECs at embryonic, postnatal, and aged stages will establish whether monoallelic gene expression predominates at specific developmental stages. Since certain human FOXN1 mutations are more damaging than others, understanding their impact on thymopoiesis is also needed for appropriate clinical management. Our proposed studies will include modifications to thymus organoid procedures that enable a comparison of different epithelial cells for their capacity to support tissue growth. This will include the use TAT-FOXN1 fusion proteins that can be transduced into Foxn1-deficient TECs, prior to reaggregate thymic organ culture assembly, to compare the different human variants. With our strong expertise in thymus tissue specification and organ cultures, we will identify novel strategies to improve thymus functionality.

NIH Research Projects · FY 2025 · 2025-07

Down syndrome (DS) is caused by complete or partial trisomy of human chromosome 21 (Hsa21). It comprises a complex phenotype of over 80 features including metabolic dysregulation and a marked reduction in both neurogenesis and brain size. The specific molecular mechanisms by which trisomy of Hsa21 gives rise to DS pathologies remain unknown. Identifying the dominant genes or molecular pathways involved would open the possibility for developing targeted therapies to improve the lives of affected individuals. Here, we propose combining CRISPR interference (CRISPRi) technology with induced pluripotent stem cells (iPSCs) derived from individuals with DS (3S-iPSCs) to develop a selectable screen for Hsa21 genes that contribute to DS pathologies. The complexity of the DS phenotype has been a roadblock to definitive identification of genes that play prominent roles in the syndrome. Our preliminary data show evidence of two important, fundamental differences between DS cells and isogenic, euploid controls that can be detected and quantified at the single-cell level, thereby opening the door widely for the development of high through-put screens for gene identification. One of these key differences, elevated mitochondrial membrane potential (∆ψm), is evident in 3S-iPSCs in the pluripotent state; the other, reduced ability to commitment to a neuroectodermal (NE) lineage, is directly relevant to what is arguably the most prominent feature of DS, that of intellectual disability. The goal of this R21 proposal is to build the tools necessary to carry out CRISPRi-based, high throughput screens to identify genes on Hsa21 that contribute to DS pathologies at the earliest stages of development. Aim 1 will use TALEN-nuclease directed editing to integrate a transgene expressing dCAS9-KRAB into a safe-harbor locus in 3S-iPSCs. Aim 2 will focus on designing guide RNAs that achieve graded repression to more closely model a reduction in gene dosage from the trisomic three copies to the normal two copies. Successful completion of our proposed studies will provide proof-of-concept for our approach to functional gene identification in DS and lay the foundation for expanding to comprehensive and combinatorial screens of the full coding and non-coding content of Hsa21. It will also make a powerful and flexible tool available to the DS research community due to the totipotency of iPSCs.

NIH Research Projects · FY 2026 · 2025-07

PROJECT SUMMARY. Neurodegenerative disorders represent major sources of human suffering, yet the factors influencing disease severity remain poorly understood. Sex has been implicated as one such factor, yet there remains a considerable gap in our understanding of how sex hormones affect neurodegenerative processes. Retinitis pigmentosa (RP) is a retinal neurodegeneration in which photoreceptors undergo a progressive and irreversible degeneration leading to blindness. We recently discovered that females have a worse outcome than males in a mouse model of RP caused by the rhodopsin P23H mutation (Rho P23H), the most common cause of autosomal dominant RP in humans. Further, we showed that this association is caused by an adverse effect of circulating female sex hormones on retinal neurons, which can be ameliorated by depletion of these female hormones. RP can be caused by a wide diversity of genetic mutations, which creates a daunting obstacle to therapeutic targeting of each individual mutation. However, many of these mutations result in similar phenotypes and converge on shared downstream pathways leading to photoreceptor neurodegeneration. The objective of this proposal is to determine the molecular mechanisms by which female sex hormones adversely impact the severity of photoreceptor neurodegeneration. To investigate how the female sex hormones play a role in this common pathway of photoreceptor neurodegeneration, we propose to expand on our work in the Rho P23H RP mouse. We hypothesize that female sex hormones interact with key cell death and cell stress pathways downstream of the genetic mutation, to worsen photoreceptor degeneration. The findings from these aims will provide novel insights into how sex hormones modulate the pathogenesis and severity of neurogenerative disease. Results from these aims will identify the precise female hormones and any interconversions of these hormones driving advanced retinal degeneration in RP, and the mechanism by which this occurs. These findings have far-reaching implications for clinical trial design, such as sex stratification, hormonal medications, consideration of pre-, peri- , and post-menopausal states, and the use of hormonal therapy in females with certain neurogenerative disorders such as RP.

NIH Research Projects · FY 2025 · 2025-07

The mission of the UT Southwestern Perot Family Scholars Medical Scientist Training Program is to train the next generation of physician-scientists for a variety of medical and scientific careers that use the unique perspective of their combined MD and PhD training. The objectives are to provide integrated training leading to both MD and PhD degrees in eight years, with a high proportion of students who enter the program completing both degrees. The rationale for the program is that physician-scientists are uniquely positioned to translate laboratory discoveries to clinical practice (“bench to bedside”) and to use clinical observations to identify knowledge gaps and research opportunities (“bedside to bench”). Yet despite their widely acknowledged importance for bidirectional translation of biomedical research, clinician-scientists make up a decreasing proportion of the physician workforce. Additionally, MD-PhD graduates are needed to replenish the aging physician-scientist workforce. Program activities that promote skills development include rigorous didactic and experiential clinical and research training, emphasizing active learning in the clinic and the laboratory rather than passive learning in the classroom; extensive horizontal and vertical mentorship to foster physician-scientist identity, reinforced by abundant peer- and near-peer interactions to promote a sense of community among trainees; and robust training in scientific rigor and reproducibility as well as the responsible conduct of research. Interactions with role-model physician-scientist mentors at different career stages prepare trainees for transitions to a variety of MD-PhD careers. Twenty-four trainees out of a total of 96 training grant-eligible students will be appointed for 24 months during the first two years of medical school, with rare exceptions. Intended outcomes include timely completion of both MD and PhD degrees by a high proportion of trainees, who will continue to pursue research-related biomedical careers in academia and industry following their MD-PhD training, with continued research training during residency where applicable.