University Of Iowa

NIH Research Projects · FY 2025 · 2023-08

ABSTRACT. Autism spectrum disorder (ASD) is one of the most common neurodevelopmental disabilities, adversely affecting an increasing number of families worldwide. Although its etiology is strongly linked to genetic factors, perinatal experience, including prenatal stress and post-natal social experience, may also contribute to deficits in social communication in ASD, potentially via epigenetic mechanisms. For example, the oxytocin receptor gene (OXTR) is epigenetically altered by early social experience, plays a crucial role in mammalian social and cognitive development, and is associated with both genetic and epigenetic risk for ASD. However, the relationship between perinatal experience and epigenetic change in ASD is unclear. Our central hypothesis is that prenatal stress and early social experience predicts epigenetic changes in specific genes, which are associated with social communication deficits in ASD. To achieve our overall goal of discovering modifiable pathways for intervention in children at risk for ASD, we will recruit over 7,200 pregnant women to use an innovative smartphone application, BabySteps, to collect prospective data from the 3rd trimester of pregnancy until 30 months post-delivery. Between ages 18 to 27 months, BabySteps will be used to screen for symptoms of ASD or developmental delay (DD) in the offspring, which will trigger a full diagnostic assessment at the Center for Disabilities and Development. Children with a range of social communication deficits (including those diagnosed with ASD or non-ASD DD [n=200]) will be compared with typically developing children (TD; n=200) who are matched on race, sex, and socioeconomic status. We will examine 1) differences in DNA methylation (DNAm), and change over time, in 27 specific ASD-associated loci and 3 OXTR loci, and 2) differences in biologic age acceleration using epigenetic clock algorithms, as a function of age, perinatal experience, and social communication outcomes. We will compare DNAm from stored newborn dried blood spots to samples collected around the time of diagnosis. We will calculate polygenic risk scores for social communication, repetitive behavior, and ASD, and assess the relative polygenic and epigenetic risk. The relationship between perinatal experience, DNAm, and social communication outcomes will be evaluated using 4 complementary measures: 1) ecological momentary assessments (EMAs) of prenatal stress and parental anxiety and depression, collected using BabySteps; 2) app-recorded free play between parent and child analyzed for dyadic synchrony and interactive behavior; 3) standardized assessments of child social communication skills; and 4) a Language ENvironment Analysis (LENA), using a LENA audio-recording device worn by the child at home and in daycare. We expect to identify epigenetic biomarkers that link prenatal stress and early social experience with social communication outcomes in ASD. A better understanding of how polygenic risk and perinatal experience—via epigenetic mechanisms—contribute to the ASD phenotype will help overcome a critical barrier to progress in the field, by identifying modifiable pathways for intervention.

NIH Research Projects · FY 2025 · 2023-08

Project Summary     SAPHO syndrome and chronic nonbacterial osteomyelitis (SAPHO-­CNO) is a painful and disabling  autoinflammatory disease primarily targeting bones and joints, with no FDA-­approved therapies. Severe sterile  inflammation of multiple bones (osteitis), driven by the interleukin-­1 (IL-­1) pathway, leads to irreversible bone  damage, chronic pain and disability in adult patients. Critical knowledge gaps remain about disease activity  assessments, risk factors for severe outcomes, and influence of variants in IL-­1 pathway genes on clinical  phenotypes in adults. This K23 proposal will propel our understanding of the longitudinal course of SAPHO-­ CNO in adults, garnering generalizable knowledge about this understudied and disabling autoinflammatory  disease. The proposed project will investigate clinician, patient and MRI-­assessed disease activity in a large  SAPHO-­CNO cohort (Aim 1), identify risk factors for bone damage in SAPHO-­CNO patients (Aim 2), and  discover IL-­1 signaling pathway gene variants and explore their correlation with clinical phenotypes in adults  with SAPHO-­CNO (Aim 3). The science resulting from this K23 award will lay the groundwork for a future R01  application. Dr. Aleksander Lenert is spearheading a unique prospective observational study in adult SAPHO-­ CNO (the SCS study) designed to address these knowledge gaps. His long-­term career goal is to develop into  an independent clinical investigator focused on patient-­oriented clinical and translational research in adults with  SAPHO-­CNO. Under direct mentorship from Dr. Polly Ferguson (world-­leading expert in CNO) and his  experienced mentoring team, Dr. Lenert will build on his foundational research skills to gain critical training and  hands-­on experience in agreement and psychometric analyses, latent trajectory modeling, genetic sequencing  analysis and interpretation, and prospective observational cohort study management. In addition to Dr.  Ferguson, his mentoring team includes Dr. Robyn T. Domsic (clinical investigator and observational cohort  study guru in systemic sclerosis), Dr. Daniel H. Solomon (leader in clinical science research in rheumatic  diseases), Dr. Mary Vaughan-­Sarrazin (experienced clinical outcomes researcher), and Dr. Jonathan Templin  (measurement science and applied psychometrics researcher). To further guide this scientific proposal,  develop focused training and aid his career development, Dr. Lenert has garnered the support of content area  experts in advanced imaging (Dr. T. Shawn Sato), and genetics and bioinformatics (Drs. Hatem El-­Shanti and  Benjamin Darbro). This proposal benefits from an exceptional scientific environment and established  infrastructure at the University of Iowa, including Dr. Polly Ferguson’s world-­renown center for the  management of patients with SAPHO-­CNO, and for clinical and translational research. Accomplishment of the  proposed Aims for this K23 award will directly benefit adults with SAPHO-­CNO, and lead to improved patient  outcomes. The K23 award will provide a framework for Dr. Lenert to acquire advanced methodologic research  skills and experiences necessary to become an independent clinical researcher in adult SAPHO-­CNO.

NIH Research Projects · FY 2025 · 2023-08

PROJECT SUMMARY/ABSTRACT Turner syndrome (TS) is a common genetic disorder caused by X chromosome (Xchr) abnormalities. Women with TS have a four-fold higher risk of developing diabetes mellitus (DM) than the general population, and DM contributes significantly to mortality. Despite the prevalence of DM in TS, the underlying mechanism(s) and specific Xchr contributions driving diabetes risk remain elusive. As such, there are no specific preventative strategies or treatments for DM in TS. The objective of the proposed project is to unravel the genetic and physiologic mechanism(s) that lead to hyperglycemia in TS, using glycemic phenotyping in the context of Xchr gene dosage, Xchr parent-of-origin, and genomic and epigenetic techniques. My central hypotheses are that TS-associated hyperglycemia is a consequence of altered Xchr gene dosage (e.g., by Xchr imprinting and/or structural Xchr variation) and that this contributes to a TS-specific phenotype of progressive beta cell functional impairments first detectable only in response to oral glucose but not mixed macronutrients. To test these hypotheses, we propose the following aims: (1) Identify Xchr contributions to the TS hyperglycemia phenotype and (2) Determine if beta cell function is impaired in response to mixed macronutrients in TS. We will perform multivariable analysis of data from National Institute of Child Health and Human Development’s Data and Specimen Hub, which includes frequently sampled oral glucose tolerance tests (fsOGTT) and Xchr parent-of- origin for 84 individuals with TS to determine if an Xchr parent-of-origin effect exists with respect to categorical glycemia. Additionally, we will enroll 30 individuals with TS to undergo long-read Xchr sequencing in conjunction with RNA sequencing. This will allow identification of candidate imprinted Xchr genes. This project also includes paired fsOGTT and mixed meal tolerance tests (MMTT) for 20 individuals with TS and 10 age-, sex-, and BMI- matched controls to further elucidate TS-specific impairments in beta cell function. Completion of the proposed project will add to understanding of Xchr contributions to the TS hyperglycemia phenotype and contribute toward identification of drug targets and/or new disease managements strategies. The project is also a vehicle for me to achieve my career goals and objectives by providing me with expertise in glycemic phenotyping, genomic and epigenetic techniques, multivariable statistics, and multisite study design and execution. The proposed integrated research, mentorship, and didactic training program combined with the collaborative research environment at the University of Iowa and off-site collaboration with faculty at the University of Minnesota and Indiana University will foster my long-term career goal of becoming an independent investigator leading a translational research program focused on isolating genomic and epigenetic contributions to diabetes risk.

NIH Research Projects · FY 2025 · 2023-08

Project Summary Teen drivers are three times more likely to be involved in a fatal crash than adult drivers. Several factors contribute to increased crash risk among novice teen drivers, including distracted driving, inexperience, heightened risk taking, and an underdeveloped ability to identify potential roadway hazards. Potential hazards refer to emerging threats on or near the roadway (e.g., the car in front of you braking suddenly due to a pedestrian darting into traffic) which may or may not evolve into an actual hazard or crash. Experienced drivers quickly identify and respond to potential hazards with little to no effortful cognition. Novice drivers need repeated experience in the perception of hazards to effectively identify and respond to potential hazards, yet fail to develop this skill during the learner phase of licensure. We hypothesize that this experience can be hastened with specific parental guidance. As primary supervisors and teachers during the learner phase of licensure, parents are well positioned to teach their children to identify latent hazards in the driving environment. However, research on driving supervision indicates this type of instruction is almost completely absent. The overall goal of the current project is to improve parental instruction and practice surrounding these events. The first aim of this proposal is to describe parent-teen conversations about hazard identification and mitigation while parents and teens jointly engage in a perceptual/adaptive learning module – a hazard anticipation training program delivered via video. We hypothesize that parents will vary in how they scaffold teens’ ability to correctly identify and perceive hazards according to individual differences in teen temperament, parenting style, and family communication pattern. The second aim seeks to develop a hazard anticipation training program to teach parents to better communicate with their children about identifying potential hazards on the roadway. To this end we will modify an existing training program, designed to help drivers anticipate hazards on the roadway, to help improve parents’ communication related to these events. For the third and final aim, we will test the impact of the intervention in a state-of-the-art driving simulator, the NADS-1. We hypothesize that compared to controls, parents exposed to the intervention will show improved high-order driving instruction - applicable to the current and future driving environment. We also hypothesize that teens of parents exposed to the intervention the will look to and respond to potential hazards on the roadway more quickly and reliably than those assigned to the control. My graduate training in parent-child communication, my MPH which trained me in population-level primary prevention, and my postdoctoral fellowship in simulation research have prepared me to begin this interdisciplinary research. This K99/R01 award will equip me with the necessary training and skills in intervention development, implementation, and evaluation to achieve the aims set forth in this proposal. Additionally, this proposal directly addresses goals set forth by the NICHD strategic plan by assessing and preventing the leading cause of traumatic injury in teens, motor-vehicle crashes.

NIH Research Projects · FY 2026 · 2023-07

Project Summary Formation and maintenance of synaptic connections between appropriate neuronal partners is essential for proper nervous system function. Indeed, impairments in either initial synapse formation or in subsequent developmental synapse elimination underlie many neurodevelopmental disorders. Synapse elimination that occurs outside of appropriate developmental contexts underlies synaptic loss associated with age-related cognitive decline and in neurodegenerative diseases. Thus, defining the mechanisms that underlie the regulation of synapse number will provide insight into how appropriate connections are formed during development, and these pathologies of synapse elimination. Despite its essential role in nervous system development and function throughout life, we still know little about the mechanisms underlying this process. We do know, however, that glia are required. In order to identify novel glial regulators of synapse development, I completed a forward genetic screen in Drosophila, and identified 91 molecules that, when knocked down in glia, alter synapse number. Among these molecules is the immune receptor Crq, which I found is required for glial elimination of synapses in development. This proposal will focus on understanding Crq’s role in synapse elimination, in order to gain insight into the larger questions of which synapses undergo developmental synapse elimination, the mechanisms underlying the specificity of this process, and whether these same mechanisms are re-used in pathological synapse loss associated with aging. Aim 1 will address the question of which synapses undergo developmental elimination across the nervous system and evaluate which of these are Crq-dependent. I have recently developed an inducible pre-synaptic label that makes this work possible, and will generate inducible postsynaptic labels as part of this aim. Aim 2 will use proximity labeling to identify the neuronal ligand(s) for Crq that act to specify which synapses undergo elimination, and will identify how expression and localization of these ligands are regulated. Aim 3 will define which synapses are lost with aging, and identify whether Crq acts as a common mediator of synaptic loss in development and aging. I will also perform a targeted screen based on a recent transcriptional profiling experiment I completed to identify additional glial regulators of age-related synaptic loss. Together, these studies will address the mechanisms by which synapses are targeted for elimination and how. This is a key question in achieving the larger goal of understanding how neurons and glia work together to create and maintain appropriate synaptic connections throughout life. Dissecting these mechanisms will also provide insight into the process of age-related synaptic loss that underlies age-related cognitive decline. In addition, performing this work will allow me to address existing gaps in my technical skills that will allow me to carry out my long-term research goals as an independent invesitigator.

NIH Research Projects · FY 2024 · 2023-07

Project Summary/Abstract The World Health Organization estimated that 2016 and 2017 each saw an increase of 2–4 million cases of malaria worldwide, rising to a total of 241 million cases and 627,000 deaths by 2020, mostly among small children. These resurging numbers signal that the effective treatment of malaria is under threat from the development of drug resistance in Plasmodium falciparum and related malaria parasite species. Consequently, combatting resistance is a critical priority and requires continued effort in discovery and development of new antimalarial drug candidates with novel mechanisms of action. Natural product chemistry has had a dramatic impact in treatment of infectious disease. Bastimolide A is a recently discovered natural product that shows noteworthy activity (IC50 80–270nm) against resistant strains of P. falciparum, and its polyketide structure is unique among current clinical and investigational antimalarial drugs, suggesting a novel mechanism of action. If confirmed, this would strongly impact the field of antimalarial drug discovery, offering a new avenue to address the critical priority of combatting drug resistance. Our specific aims in this proposal are (a) to synthesize bastimolide A and analogs, including chemoproteomics probes, and (b) to evaluate their antiplasmodial potency, improve pharmacological properties, and identify protein(s) and lifecycle stage(s) targeted. The synthetic aims will exploit efficient new synthetic methods developed in the Friestad labs, including further development of a novel asymmetric catalysis approach to 1,2-difunctional compounds, and further expansion of a programmed synthesis approach to access 1,5- polyols with complete control of challenging remote stereochemical relationships. The biological evaluation of bastimolide A and analogs will employ resistant strains of P. falciparum, and for this aim, the extensive experience with assessment and development of novel antimalarial drug leads in the Chakrabarti labs is ideally suited. Measurement of EC50 versus chloroquine-resistant P. falciparum Dd2 will identify hits and verify activity of chemoproteomics probes; the latter will allow isolation and identification of a biological target for bastimolide A. Further screens of analogs will entail cross-resistance profiling versus geographical isolates and evaluation of pharmacological properties such as aqueous solubility, LogD, permeability (PAMPA), plasma protein binding and microsomal stability. A reiterative approach will be used, with feedback from initial analogs guiding the selection of higher-priority analogs to prepare during the second year of the proposed two-year funding period. The R03 funding requested will permit access to the preliminary results needed to assess the viability of a more extensive project that would be competitive for funding via R21 or R01 mechanism.

NIH Research Projects · FY 2024 · 2023-07

PROJECT SUMMARY: Craniofacial anomalies are the 2nd leading structural malformation to appear at birth, with the most common forms occurring in the mid- and upper-face regions. However, our limited understanding in the molecular mechanisms controlling their development has hindered strategies for effective treatment and prevention. Several studies have identified the pathways underlying lower face formation during embryonic development (e.g., jaw and teeth). Yet, less emphasis has been placed on the midface, and the unique mechanisms orchestrating the development of this region are poorly understood. The long-term goal of this study is to dissect the molecular underpinnings governing midface development and how their dysregulation causes dysplasia. We and others have independently uncovered key midface genes that function within the neural crest, an embryonic stem cell population that gives rise to facial bone and cartilage. For example, deletion of Alx1/3/4 (Alx), whose loss causes syndromic forms of Frontonasal Dysplasia, lead to a severe midfacial cleft in mice. Our lab has found that loss of Tfap2 in the neural crest compromises expression of Alx genes and presents the same midface cleft as the Alx knockout embryos. Thus, our overall objective in this research proposal is to leverage this new animal model for Frontonasal Dysplasia to uncover how TFAP2 transcription factors operate within the midface-unique gene regulatory networks (GRN’s). To approach this objective, we test the overall hypothesis that TFAP2 transcription factors directly regulate Alx gene expression for appropriate neural crest survival, midface fusion, and skeletal formation. In AIM 1, we will employ genome- and epigenome-wide assays (CUT&RUN, ATAC-seq) to decipher how TFAP2 targets Alx and shapes the genome landscape to regulate their expression levels. We will leverage zebrafish reporter strategies to test TFAP2-bound Alx noncoding enhancers for midface specificity. In AIM 2, we will couple sophisticated mouse genetics with immunofluorescence and skeletal analyses to characterize how Tfap2 and Alx genetically interact to control neural crest viability, behavior, and formation of the skeletal elements. Completion of these aims will fill a critical knowledge gap in our understanding for how these genes and pathways are linked to shape the developing midface. Such knowledge will contribute to the development of strategies in treating midfacial disorders or even preventing them. The principal investigator of this study, Mr. Nguyen, has extensive training in mouse genetics, embryology, and gene expression profiling techniques highlighted in this proposal. With combined mentorship from Drs. Van Otterloo and Amendt, Mr. Nguyen will develop skills in genome-wide molecular assays, next-generation sequencing approaches, bioinformatic techniques, and immunofluorescent and confocal microscopy methods; collectively, greatly advancing his doctoral training and expanding his research toolkit. The training plan, established team, and institutional environment outlined in this research proposal will not only pave the way to improving craniofacial treatment and health, but also catalyze his career towards becoming an independent researcher.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY / ABSTRACT Obesity results from an imbalance of energy that is driven by both environmental and genetic factors. While many genomic loci are associated with obesity, several non-coding single nucleotide polymorphisms (SNPs) in the first intron of the fat mass and obesity (FTO) gene have the strongest association with obesity in humans. The obesity-associated region containing these SNPs forms functional long-distance connections in the adult mouse brain with the promoter of a neighboring gene iroquois homeobox protein 3 (IRX3), but NOT FTO, suggesting that IRX3 may be a regulator of body weight gain. Interestingly, the obesity-associated SNP, rs1421085, is highly associated with increased IRX3 expression in human brain samples and has been proposed to increase IRX3 expression directly through interfering with the binding site of a transcriptional repressor of IRX3. However, the mechanism and relevant brain region(s) of IRX3 function have never been reported. Thus, there is a critical need to better understand the potential underlying mechanisms contributing to the obesity epidemic. The overall objective of this proposal is to investigate the central circuits and mechanisms by which IRX3, and by extension obesity-associated SNPs, influences body weight homeostasis. To accomplish this, we have developed a novel mouse model harboring the human rs1421085 SNP (OB-SNPrs142/rs142). Importantly, OB- SNPrs142/rs142 mice under humanized thermoneutral and high-fat diet conditions recapitulate phenotypes associated with humans possessing the rs1421085 SNP including increased fat mass percentage and an approximately 5% increase in bodyweight. Our preliminary data also reveals that OB-SNPrs142/rs142 mice exhibit increased Irx3 mRNA expression in the brain in a dose-dependent manner, similar to what was reported in the brain samples of humans harboring the risk-allele. Using a novel Irx3-CRE mouse crossed to a tdTomato reporter mouse, we have determined that IRX3 expression in the hypothalamus is primarily expressed in neurons in the ventral premammillary nucleus (vPM). This and additional preliminary data has led us to hypothesize that increased IRX3 expression in the vPM of the hypothalamus alters body weight homeostasis and increases body weight gain. This hypothesis will be evaluated through the following aims: In Aim 1, we will evaluate the contribution of vPM IRX3 to metabolic phenotypes, by utilizing a viral vector to increase IRX3 levels in the vPM and then monitor energy parameters. In addition, using chemogenetic activation of IRX3(+) neurons in the vPM, we will explore the role of IRX3 neurons to regulate metabolism. In Aim 2, we will investigate potential electrophysiological and transcriptional mechanisms through which increased expression of IRX3 in vPM IRX3(+) neurons impacts metabolism using patch-clamp recording, single cell RNA sequencing, and chromatin immunoprecipitation. This proposal is significant because it is the first to interrogate the physiological impact of increased IRX3 in the vPM as the driver of the metabolic effects of the obesity-associated SNPs.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY/ABSTRACT The integrity of the proteome is constantly being challenged. To maintain protein homeostasis, cells rely heavily on highly integrated protein networks to provide surveillance and ensure proteins do not become susceptible to aggregation, a driver of human neurological diseases and cancers. Paramount to these networks are molecular chaperones and their regulators, which assist in protein folding, transport, and degradation. As the diversity of proteins that require these chaperones increases, we have gained a broader understanding of the importance of these regulators across many cellular processes. Recently, we discovered molecular chaperones also influence cell metabolism by acting on key metabolic enzymes within glycolysis and purine biosynthesis to efficiently produce the necessary biomolecules critical for their survival and proliferation. However, our knowledge of how chaperones recognize and act on these enzymes remains largely elusive. The proposed studies combine super-resolution fluorescence microscopy, biochemical and molecular biology tools, and proteomic analyses to investigate the how chaperones regulate commonly observed phenomena across metabolic pathways including the formation of phase separated metabolic enzyme assemblies to facilitate substrate channeling, the folding of large multi-domain enzymes to drive tightly coupled activities, and the induced degradation of metabolic enzymes by chaperone-mediated autophagy. These findings will deepen our fundamental understanding of how cells respond to changes in nutrient availability to meet biomass demand, provide insights into the molecular mechanisms of dysregulation that drive disease, and inspire new therapeutic strategies targeting cell metabolism.

NIH Research Projects · FY 2026 · 2023-07

PROJECT SUMMARY Sjögren’s disease is a chronic autoimmune disease characterized by immune-mediated destruction of salivary and lacrimal glands leading to profound dry mouth and associated oral health complications, vision-threatening dry eye disease, and decreased quality of life. The immunological mechanisms of Sjögren’s are poorly understood, and no disease-modifying therapies have been identified. There is a critical need to define the early immunological mechanisms to identify targets for earlier diagnostics and more effective therapies. Diagnosis occurs years after initiation of the autoimmune process making the study of early mechanisms impractical in humans. Nonobese diabetic (NOD) mice spontaneously develop salivary gland autoimmunity with features similar to Sjögren’s in humans including the characteristic focal lymphocytic sialadenitis that is a hallmark of Sjögren’s in humans. We have recently found that gene-editing to disrupt the Tyk2 gene in NOD mice prevents salivary gland inflammation in a lymphocyte-extrinsic manner. Tyk2 is a non-receptor tyrosine kinase associated with several inflammatory cytokines, and TYK2 gene variants are associated with Sjögren’s in humans. Our goals in this proposal are to define the specific innate immune cell subsets and the upstream cytokines that require Tyk2-mediated signaling for the development of autoimmune salivary gland disease. Our central hypothesis is that interleukin (IL)-12 and IL-23 signaling through Tyk2 in antigen presenting cells within the salivary glands are required to drive the focal lymphocytic sialadenitis. The specific aims to test this hypothesis are: (1) Identify cells that require Tyk2 signaling for salivary gland inflammation in NOD mice; (2) Define the requirements for IL-12 and IL-23 in the development of focal lymphocytic sialadenitis. We will use the NOD mouse-based spontaneous disease model, genetically edited NOD strains, our adoptive transfer model, bone marrow chimeras, in vitro cultures, and in vivo cytokine-blocking therapies to perform these studies. The significant positive impact of completing these studies include defining the mechanisms by which Tyk2 and associated cytokines drive salivary gland autoimmunity, which will lead to development of early diagnostic biomarkers and identification of immune proteins that can be targeted therapeutically in Sjögren’s. Notably, inhibitors of Tyk2 are in development, and IL-12 and IL-23 blocking therapies are already available to treat other autoimmune diseases. Identifying the roles of Tyk2 and associated cytokines in Sjögren’s will help guide future studies of Tyk2 and associated cytokine blocking therapies in subsets of individuals with Sjögren’s.

NIH Research Projects · FY 2025 · 2023-07

ABSTRACT As warm-blooded (endothermic) animals, our survival requires neurons that detect cold temperatures and initiate adaptive responses. These vital “cold-defense” adaptations allow us to inhabit diverse climates. Cold- defense responses are a set of motivated behaviors and autonomic changes that help us avoid the cold while generating and retaining heat. Often, however, these responses are impaired by aging, disease, drugs, or neurologic injury. Many patients suffer from chronic cold intolerance, and accidental hypothermia remains a significant public health concern, but our ability to investigate the underlying mechanisms is constrained by an inability to selectively target central cold-defense neurons. Closing this knowledge gap is the primary objective of this project. Successful completion of the proposed work will provide information that opens opportunities for progress in translational research on cold intolerance, as well as thermogenic treatments for obesity and improved protocols for therapeutic hypothermia. We begin by observing that cold-activated neurons in a specific region of the brainstem known as the parabrachial nucleus (PB) may represent a vulnerable bottleneck in this circuit. Neurons in this region collect input from the entire body surface, relayed via neurons at every level of the spinal cord, and they use this information to activate target sites in the forebrain. Cold-activated PB neurons are an accessible entry point, but they intermingle with other, diverse populations of PB neurons, and their molecular identity remains uncertain. We hypothesized that surviving at a cold ambient temperature requires a specific subset of neurons in this location, which promote cold-defense behaviors and activate autonomic responses. In our preliminary experiments, eliminating glutamatergic PB neurons did not alter body temperature or arousal at room temperature. However, cold exposure caused core body temperature to plummet in these PB-ablated mice, at ambient temperatures that do not cause decompensation in PB-intact control mice. These preliminary findings suggest that PB neurons are not only involved in, but necessary for cold-defense responses. In the proposed studies, we will use a rigorous and systematic approach to determine the identity of PB neurons required for cold defense. We will also determine the behavioral and autonomic changes produced by activating these neurons. Finally, we will determine which PB-activated behavioral and autonomic responses are required to sustain core body temperature during prolonged cold exposure. Successful completion of the proposed expeirments will determine the neurons and neural circuit mechanisms that allow mammals to survive in the cold. In addition to fundamentally advancing our understanding of this life- critical neural circuit, this work will improve our understanding of the genetically defined connections and functions of intermingled neuronal subpopulations in the PB. Our results will have broader impact by opening opportunities to engineer new methods of inducing and sustaining therapeutic hypothermia for critical care, field medicine, organ transplant, and someday, perhaps, spaceflight.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY/ABSTRACT Neurodevelopmental disorders (NDDs) such as Autism Spectrum Disorder, Attention Deficit Hyperactivity Disorder, and Intellectual Disability are a challenging set of conditions with large phenotypic overlap and predominantly unknown etiology. There is a lack of effective interventional strategies to target the most impairing aspects of NDDs, owing largely to a lack of knowledge about their underlying cellular and molecular mechanisms. Deletion of one copy of the 16p11.2 region results in a high penetrance of NDDs in humans, and because it can be faithfully modeled in mice, this deletion is a favored model for the neurobiological study of NDDs. Mice lacking one copy of the genomic region orthologous to the human 16p11.2 region (16p DEL) exhibit behavioral phenotypes with relevance to human NDDs including a male-specific deficit in reward learning. This deficit is recapitulated when 16p DEL is induced specifically in dopamine receptor D1-expressing medium spiny neurons (D1+ MSNs) of the striatum, implicating this neuronal population as critical to reward system dysfunction in NDDs. D1+ MSNs are known to play a critical role in signaling reward and learning action-reward associations, but little is known about how the function of these cells is altered in NDDs. Here, we propose to use the 16p DEL model to delineate how D1+ MSNs respond to reward in the context of NDDs. The ability of neurons to respond to experience and store information is known to require carefully regulated gene expression. During this process neuronal signals are transduced to the nucleus where molecular mechanisms facilitate the expression of specific genes whose products in turn alter neuronal function. Disruptions of these molecular mechanisms are strongly associated with the occurrence of NDDs, and multiple pieces of evidence suggest that the regulation of gene expression is disrupted in 16p DEL mice. The experiments outlined in this proposal will use state-of-the-art transgenic animals and analytical techniques to investigate the molecular mechanisms controlling the reward response of D1+ MSNs in the striatum of 16p DEL mice. In Specific Aim 1, we will characterize gene expression changes induced by reward in this neuronal population. In Specific Aim 2, reward-dependent histone post- translational modifications in 16p DEL D1+ MSNs will be characterized. Finally, in Specific Aim 3, we will outline alterations of calcium signaling in these neurons during a touchscreen operant task. This work promises to reveal the molecular mechanisms underlying reward system dysfunction in an NDD model, which will provide critical insight into the reward-related behavioral phenotypes observed throughout the spectrum of NDDs.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY The HIV/AIDS pandemic has claimed more than 36 million lives worldwide. Although effective antiretroviral drugs are widely available, virologic failure due to drug toxicity and poor adherence leading to the development of resistance is an increasingly serious problem. This highlights the need for continued development of novel HIV inhibitors and a strong commitment to basic research aimed at elucidating the mechanisms driving HIV replication, transmission, pathogenesis, and drug resistance. The cellular metabolite inositol hexakisphosphate (IP6) is an essential co-factor for HIV-1 replication. IP6 promotes particle production in HIV-1 producer cells by binding to and stabilizing the immature Gag lattice (IGL) and subsequently promotes particle infectivity by binding to and stabilizing the capsid, which is assembled during particle maturation. Importantly, these functions of IP6 suggest interplay between IP6 and two classes of HIV inhibitors: maturation inhibitors (MIs) and capsid inhibitors (CIs). During the mentored phase of this award, the applicant will investigate the separate roles of IP6 in each of these key steps in the HIV-1 replication cycle, informing the development of novel MIs and CIs. A forced evolution approach will be used in which replication-deficient mutant viruses will be propagated in T cell lines to determine how HIV-1 adapts to the loss of IP6 binding. In Aim 1, the role of IP6 during IGL assembly and particle production will be investigated. The interaction between IP6 and the IGL is hypothesized to ensure the packaging of IP6 into viral particles at levels required to promote capsid assembly during maturation. HIV-1 Gag mutant viruses that assemble independently of IP6 will be used to test this hypothesis. This work builds on the applicant’s recently published research showing that the replication of Gag mutants deficient for IP6 binding can be restored by IGL stabilization. In Aim 2, the role of IP6 binding to the HIV-1 capsid and the implications of this interaction for capsid assembly and virion infectivity will be investigated. The capsid, which assembles in the virion, must remain stable and intact during the post-entry steps of the virus replication cycle. Mutant viruses unable to interact with IP6 in the context of the assembled capsid are highly deficient in replication and particle infectivity due to an inability to assemble stable capsids. The mechanisms by which mutations within capsid that restore capsid assembly and particle infectivity to capsids unable to bind IP6 will be studied using cell-based assays and structural analyses via collaborations with expert investigators. In addition to research, the applicant will engage in a wide variety of career development activities including technical training and management, leadership, and diversity training. The applicant will also meet regularly with his advisory committee to discuss research progress and to receive advice on the academic job search. During the independent phase of this award, additional factors, including antiviral compounds, that affect capsid stability will be investigated. In Aim 3, the mechanisms of action of novel CIs and pathways of resistance to these compounds will be investigated. Additionally, host factors that affect capsid stability post-entry will be investigated in the context of CI activity and resistance.

NIH Research Projects · FY 2026 · 2023-07

PROJECT SUMMARY: Loss of teeth due to oral disease, trauma, aging or congenital defects is one of the most common organ failures. The first morphological sign of tooth development is the formation of the dental lamina (DL). How the DL—the critical structure for initiation of a tooth development program—is specified from naïve maxillary and mandibular ectoderm, remains poorly understood. We applied Laser Microdissection coupled spatiotemporal RNA-seq and single cell Multiome-seq to profile mouse mandibular ectoderm during DL specification and tooth initiation (E9.5-E12.5). In comparison to the non-DL epithelium (i.e., future skin), we identified a set of potential driver transcription factors (TFs) for DL specification including Pitx1, Pitx2, Sox2, and Foxe1. In contrast, another set of TFs was notably reduced in the DL, although enriched in aboral/ventral ectoderm, including Tfap2a, Tfap2b, Irx3, and Irx4. While single ectodermal knock-out (KO) of Tfap2a or Tfap2b resulted in normal DL and non-DL epithelial development we found that ectodermal double KO of both resulted in severe non-DL epithelial defects, a spatial expansion of DL specification, and an ectopic tooth. Similarly, we and other groups have found that the single KO of Pitx1, Pitx2 or Sox2 does not affect DL specification, despite expression of these genes prior to DL specification and tooth defects at later stages. Here, we propose that like the non-DL epithelium a redundant network exists to specify the DL epithelium. The long-term goal of this study is development of stem cell-based approaches for tooth repair and regeneration. The overall objective of the proposed research is to dissect the molecular and cellular mechanisms of tooth initiation, particularly the core transcriptional regulatory networks (TRNs) that drive specification of the DL within maxillary and mandibular ectoderm and initiation of a tooth development program. Our central hypothesis is that a few key TFs—including PITX1, PITX2, SOX2, FOXE1, etc.—redundantly drive the core TRNs that regulate DL formation and a tooth initiation program. Further, ectopic expression of a combination of these TFs could convert non-DL epithelium (e.g., skin) to DL epithelium and induce ectopic tooth development. In Aim 1, we will determine genetic redundancy and specificity of Pitx1, Pitx2 and Sox2 through double KO models and CUT&RUN-based TF target identification. In Aim 2, we will define the PITX1/PITX2-driven communication between DL epithelium and mesenchyme during tooth initiation using a Pitx1/Pitx2 KO mouse model. Finally, in Aim 3, we will determine the core set of TFs sufficient to drive DL lineage specification and non-DL epithelial reprogramming. Collectively, using a strong set of in vivo animal models, ex vivo explants, and genome-wide assays, these studies will fill a critical knowledge-gap in our current understanding of DL specification and its application to tooth regeneration. This experimental design and approach, along with PI’s/CoI’s with complementary expertise, and the strong environment outlined in this proposal provide the catalyst to improve oral and craniofacial health.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY Radiotherapy is the most effective nonsurgical treatment for glioblastoma; however, therapeutic efficacy is severely limited due to the development of radioresistance (RR). In the hope of overcoming this urgent clinical problem, significant research has focused on defining the molecular mechanisms underlying RR. The overall objective of this application is to confirm the assembly of the ETC into mitochondrial respiratory supercomplexes (SCs) as a novel mechanism of RR. The central hypothesis of this proposal is that RR in GBM is the result of a rearrangement of the ETC complexes into SCs triggered by the expression of COX4-1, which promotes reprograming of glioma cell bioenergetics from predominantly aerobic glycolysis to mitochondrial oxidative phosphorylation and, consequently, reduces the mitochondrial production of reactive oxygen species (ROS). The specific aims proposed will use established glioma cell lines, patient-derived xenograft lines, preclinical animal models, and patient tumor samples to rigorously assess the validity of this hypothesis. Aim 1 will determine the role of CcO in SC assembly and mitochondrial metabolism. Aim 2 will evaluated the effects of SC on the regulation of ROS. Aim 3 will evaluate the role of SCs in the response of IR. We expect that data generated will vertically advance our understanding of how respiratory SCs affect outcomes in GBM and reveal the therapeutic vulnerability in RR GBM than can be exploited by SC- disrupting agents.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY/ABSTRACT Women with a history of gestational diabetes mellitus (GDM) are at a ~2-fold greater risk for cardiovascular disease (CVD) and a ~7-fold greater risk for type II diabetes mellitus (T2DM) in the decade following pregnancy, but the underlying cause(s) of this association are relatively unstudied, and there is a paucity of trials evaluating preventive intervention to prevent or delay this onset of disease. Microvascular dysfunction precedes and contributes to the development of CVD and insulin resistance in humans, via reductions in endothelial-derived nitric oxide (NO) and insulin-mediated NO-dependent vascular responses, respectively. We have demonstrated that endothelium- and nitric oxide-dependent dilation are attenuated in the microvasculature of otherwise healthy women with a history of GDM and this reduction is mediated, in part, by increased oxidative stress. However, the degree to which this attenuation in dilation extends to microvascular insulin-mediated responses is unknown. Therefore, in aim 1, we propose a comprehensive examination of the role of oxidative stress in attenuated microvascular endothelial insulin sensitivity in otherwise healthy women who have had GDM. Our preliminary data suggest that nicotinamide adenine dinucleotide phosphate oxidase (NADPH oxidase) contributes significantly to elevated reactive oxygen species after GDM, and that inhibiting NADPH oxidase improves endothelial- and NO-dependent dilation, in vivo in these women. Therefore, in aim 2, we propose a comprehensive examination of the role of NADPH oxidase-derived reactive oxygen species -- which represent a future pharmacological target for the highly specific treatment and reversal of preclinical vascular dysfunction after GDM -- in attenuated microvascular endothelial function in these women. Metformin treatment improves vascular endothelial function and microvascular insulin sensitivity in patients at risk for T2DM, in part through reductions in oxidative stress, suggesting that metformin treatment applied before the onset of insulin resistance may improve microvascular endothelial responses in women with a history of GDM. Therefore, in aim 3, we propose to examine the acute and chronic effects of metformin treatment on oxidative stress-mediated mechanisms of microvascular dysfunction in otherwise healthy women with a history of GDM. Overall, using an innovative translational human approach that combines in vivo pharmaco-dissection of mechanisms of vascular function with the biochemical analysis of biopsied endothelial cells, the experiments proposed herein will provide novel understanding of 1) early vascular mechanisms preceding the development of overt cardiovascular and metabolic disease in women who have had GDM , and 2) mechanistically delineate the efficacy of a readily available, safe, and inexpensive treatment to restore microvascular function before the onset of disease in this high-risk cohort of women.

NIH Research Projects · FY 2026 · 2023-06

PROJECT SUMMARY Chronic kidney disease (CKD) is a powerful mediator of morbidity and an independent predictor of death due to cardiovascular disease (CVD). Specifically, reduced glomerular filtration rate (GFR) is a powerful predictor of adverse outcomes. In this application we propose that the accumulation of Factor D (FD), which is filtered by the kidney and activates the alternative pathway (AP) of complement, represents an acquired dysregulation in the AP which then contributes to CVD and CKD progression. We compared the proteome of CKD patients to healthy controls. The strongest signal we observed was for components of the AP pathway. CKD patients had significantly higher levels of FD in circulating microparticles (sub-micrometer membrane vesicles that are shed from cells in response to activation or injury) and higher levels of Ba in the plasma (Ba is a biomarker of AP activation). FD activates the AP resulting in the generation of complement fragments including Ba. Factor H (FH) is the main inhibitor of the AP, but CKD was not associated with differences in the levels of FH. Our in vivo data indicate that even small increments in FD, if unopposed by adequate levels of FH, result in systemic AP activation. Furthermore, we found that plasma Ba levels are elevated in CKD and correlate with brachial artery flow-mediated dilation and with albuminuria, two indicators of endothelial dysfunction. Thus, increased levels of FD (as observed with reduced GFR in CKD) links CKD with systemic AP dysregulation, which may be an important mechanism of CVD and CKD progression in patients with CKD. Genetic variants in complement regulatory genes may also affect AP activation and may contribute to the risk of CVD and CKD progression in patients with CKD. Our group has identified several common CFH gene polymorphisms that associate with functional AP activation. Thus, our overall hypothesis is that CKD patients develop an acquired imbalance between FD and FH (high FD/FH ratio) leading to AP dysregulation (i.e., activation) such that biomarkers of the AP are predictive of CVD, CKD progression, and death in CKD. Secondarily, we hypothesize that individuals with a genetic propensity towards AP dysregulation will be the most susceptible to AP dysregulation in the setting of CKD. To test our hypothesis, we propose to utilize samples from two clinical trials: Veterans Affairs Nephropathy in Diabetes (VA NEPHRON-D) and the Systolic Blood Pressure Interventional Trial (SPRINT). In aim 1, if CKD is independently associated with AP activation and determine if high FD/FH ratio predicts AP activation in CKD. In aims 2a and 2b we will examine whether plasma Ba independently predicts CVD or CKD progression in CKD patients, respectively. In aim 3, we will determine if CKD subjects with the highest degree of AP activation are enriched for genetic variants in CFH and other genes of the AP vs those with the lowest degree of AP activation. The proposed experiments will help us understand the mechanisms that underlie AP dysregulation in CKD and may define new therapeutic targets in this high-risk patient population.

NIH Research Projects · FY 2026 · 2023-06

ABSTRACT An estimated 45,230 individuals were diagnosed with rectal cancer in the United States in 2021. Rectal cancer is primarily managed using a combination of chemotherapy, radiation, and surgery. Surgical resection of the rectum is associated with long-term functional deficits and decreased quality-of-life. Therefore, strategies to improve response to neoadjuvant chemoradiotherapy could increase non-surgical curative rates and enhance quality-of-life for rectal cancer patients. Carbon monoxide (CO) at low, non-toxic concentrations has been shown to provide paradoxical anti-tumor effects while inhibiting inflammation and oxidative-stress induced normal tissue injury that could serve as an adjuvant treatment to enhance chemo-radiotherapy efficacy. CO is a product of heme catabolism regulated by the Nrf2 transcription factor and the cytoprotective gene Heme Oxygenase-1 (HO- 1). The biochemical mechanisms by which CO simultaneously sensitizes tumor cells to die while preserving normal cell survival are unknown but likely involve fundamental differences in oxidative metabolism between cancer and normal cells. Identifying targetable redox sensitive mechanisms underlying the activity of CO in rectal cancer could rapidly lead to translational therapeutic approaches for improving radiation responses in cancers while limiting normal tissue injury. We have developed exciting new methods for CO delivery through the gastrointestinal (GI) tract to overcome the challenges of inhaled CO. Using these GI formulations to deliver CO, our central hypothesis is that CO, delivered as a safe biofoam, selectively chemo-radio-sensitizes rectal cancer while reducing normal tissue injury. Further that the mechanism involves differential effects on Nrf2/HO-1 signaling and modulation of mitochondrial oxidative metabolism. We will evaluate the impact of cytoprotective CO biofoams on normal rectal tissue responses and oxidative damage after exposure to chemoradiotherapy and determine the effects of CO as an adjunct to therapy for rectal cancer in mice.

NIH Research Projects · FY 2024 · 2023-06

PROJECT SUMMARY/ABSTRACT Preterm birth affects 1 in 10 infants born in the United States, resulting in significant morbidity and economic cost. Children who are born very preterm (VPT; gestational age<32 weeks) have increased risk for impaired neurodevelopment. VPT infants experience increased physiologic stress while their caregivers experience increased psychological distress—both are associated with impaired neurodevelopment. Epigenetic modifications are proposed as a possible mechanism linking physiologic stress and neurodevelopment in VPT infants. The main objective of the proposed research is to identify the mechanisms by which neonatal physiologic stress induces epigenetic modifications that contribute to impaired neurodevelopment, as well as how caregiver distress moderates the relationship between longitudinal neonatal physiologic stress and neurodevelopmental outcomes. Specifically, the proposed research aims to (1) create and validate novel indices of neonatal physiologic stress in VPT infants; (2) identify the effects of neonatal physiologic stress on epigenetic modifications and later neurodevelopment in VPT infants; and (3) determine the effects of caregiver distress on neurodevelopment in VPT infants. This aligns with the NICHD Strategic Plan 2020 scientific priority—to reduce the incidence of neurodevelopmental disorders by improving the understanding of their origins in the developmental process and identifying potential targets and optimal timing for intervention. The training plan includes several components necessary to reach the PI’s goal of becoming an independent clinical scientist, studying early life risk factors and etiological mechanisms in neurodevelopmental disorders. Specifically, the proposed training aims to enhance the PI’s molecular genetic expertise by adding training in epigenetic analyses via intensive workshops and laboratory experiences with an expert mentor and to expand the PI’s quantitative expertise to include complex longitudinal analyses. The new education and training on neonatal physiological stress will provide the PI with unique expertise that will lead to new avenues of investigation. Finally, the PI will develop professional development skills that will be critical for success as a tenure track assistant professor and independent clinical scientist. The academic environment at the University of Iowa is well-suited for the proposed research and training. Faculty members with expertise in advanced quantitative methods, epigenetics, and neonatal physiology are willing to provide expert mentorship to the PI. The Division of Neonatology conducts numerous research studies on preterm birth each year and has the infrastructure, including an outstanding team of clinical research nurses and a high-risk infant follow-up clinic, to support the proposed research. The Iowa Institute of Human Genetics provides researchers with a state-of-the-art, high-throughput genetic analysis facility and supports research focused on human genetics. Numerous institutional organizations provide a variety of opportunities to develop the skills necessary for success as an independent clinical scientist.

NIH Research Projects · FY 2025 · 2023-06

Significant deficits exist in the ability to translate findings from the bench to the bedside and to the community. One contributing factor is the shortage of trained professionals engaged in translational research and, especially those who understand the importance translational science is to improving health in rural states. To address this gap and strengthen the translational science workforce, we have developed a summer research experience for undergraduate students who have previously only considered careers as clinicians and have had little exposure to translational science. The University of Iowa, with its broad range of research across the translational spectrum, extensive resources, and distinctive position as the only academic medical center in a predominantly rural state, offers an ideal setting for this training. The goals of our program are to provide 1) enhanced short-term training in translational science, 2) sustained mentoring of future translational scientists, and 3) focused educational sessions related to clinical and translational science. To achieve these goals, the experiential educational opportunity for Beginning and Early Stage Translational (BEST) Researchers will embed students in teams actively conducting translational research. Participants will also engage in structured educational programming to build foundational skills for careers in translational science. This will include seminars and activities on topics such as bioethics, mentorship, wellness and resiliency, communication skills, self-advocacy, application and interview preparation, responsible conduct of research, data management and analysis, and community-engaged research. Incorporated into this training is how rural populations are impacted and role clinicians and translational science in our rural communities. The program incorporates the Stanton-Salazar Social Capital Framework to help students build effective relationships with mentors and institutional resources. Additionally, educational sessions are designed using the backward curriculum design framework to ensure alignment between learning goals and instructional activities. The Evaluation Program within the Institute for Clinical and Translational Science at the University of Iowa will oversee program assessment and continuous quality improvement. We will monitor both short- and long-term scholar outcomes, including skill development, ongoing research engagement, entry into graduate or professional training, and scholarly output such as abstracts and publications. In summary, our program will contribute to the development of a skilled translational science workforce and support broader efforts to improve translational science.

NIH Research Projects · FY 2026 · 2023-06

Project Summary Discrimination between threatening and non-threatening contexts is an adaptive neurobiological process, whereas traumatic stressors may shift responses toward generalization. From a translational perspective, the loss of discrimination, or over-generalization, from a stressful to neutral context is one of the core features of stress-related psychiatric diseases. To date, many studies have made inroads in understanding memory consolidation processes in terms of overall memory strength, yet the post-learning processes that underlie discrimination vs. generalization remain poorly understood. New data from our research team suggests that limbic forebrain influences over the anteroventral bed nuclei of the stria terminalis (avBST) are poised to differentially regulate memory strength and discrimination following an aversive learning paradigm. Interestingly, these data further suggest a role for the basomedial amygdala (BMA) and rostral prelimbic (rPL) subdivision of the medial prefrontal cortex in modulating memory strength and generalization, respectively, via direct influences through avBST. Notably, activation of limbic cortical inputs to avBST supports different aspects of memory modulation, whereas the disengagement of each input may exaggerate fear memory and generalization via diminished activation over distinct circuits within avBST. This proposed work will address the hypothesis that activity in BMA/rPL–avBST circuits play distinct roles over memory strength and discrimination with both glucocorticoid-dependent and independent components. Aim 1 will address the roles of the rPL–avBST and BMA–avBST pathways and the avBST itself in modulating precision and memory strength following inhibitory avoidance learning. Aim 2 will assess whether the effects of avBST and BMA-avBST inhibition on memory consolidation depends on their effects on circulating glucocorticoids in the posttraining period. Aim 3 will focus on the sites of action within specific circuits in which glucocorticoids are having their effects on memory strength and/or precision. These findings will be instrumental for improving our understanding of how these circuits influence memory strength vs. precision in the period following an aversive learning experience and determine the degree to which these effects depend on alterations in glucocorticoids vs. direct influences on neuronal processes within the brain.

NIH Research Projects · FY 2026 · 2023-06

PROJECT SUMMARY Patients who recover from the novel coronavirus disease 2019 (COVID-19) may experience a range of long- term health consequences. Since the lung is the primary site of viral infection, pulmonary sequelae may present persistently in COVID-19 survivors. Thus, clinical assessment of COVID-19 survivors in conjunction with chest X-ray (CXR) and computed tomography (CT) is recommended. CXR is more accessible, whereas CT provides more detailed information. Our long-term goal is to develop an integrated deep learning model that can assess lung images to assist with the management and treatment of long-term sequelae of post-COVID-19 subjects. The primary objective of the proposed research is to advance contrastive self-supervised learning models that take advantage of the accessibility of CXR scanners and the accuracy of CT images, identify the subtypes in patients with post-COVID-19, and characterize clinical, imaging and mechanistic biomarkers within subtypes. Our central hypothesis is that post-COVID-19 subtypes exist and they are characterized by distinct progression phenotypes. To test this hypothesis and achieve the primary objective, we will perform the following four specific aims. In Aim 1, we will advance contrastive learning methods to handle large-scale images with low training costs, and fine-tune the classifier and the encoder network on large-scale CXR images to detect post-COVID- 19 subjects. In Aim 2, we will advance contrastive learning methods that learn from CT images acquired at different volumes and different times to differentiate post-COVID-19 subjects from other cohorts and identify subtypes. In Aim 3, we will apply computational fluid and particle dynamics techniques to derive mechanistic biomarkers to explain the associations between clinical and imaging biomarkers in post-COVID-19 subtypes. In Aim 4, we will conduct a human subject study that examines post-COVID-19 subjects at 36-48 months after initial follow-up visits to assess the progression features of their clinical and imaging biomarkers. In summary, we will advance contrastive self-supervised learning algorithms based on CXR and CT images, respectively, for accessibility (Aim 1) and accuracy (Aim 2). We will generate in silico data for feature interpretability (Aim 3) and gather in vivo data for model training and validation (Aim 4). The pre-trained model from Aim 2 will be fine-tuned via transfer learning to input CXR images that are classified as post-COVID-19 by the model from Aim 1. An integrated deep learning model based on the two models from Aim 1 and 2 will take CXR images as inputs to provide CT-based detailed phenotypic information together with mechanistically and clinically meaningful interpretation. If successful, our study will not only advance contrastive learning algorithms, but also elucidate the pulmonary sequelae of post-COVID-19 patients in subtypes and associated clinical, imaging and mechanistic biomarkers. The ability to identify progression subtypes and associated phenotypic biomarkers will have a positive impact on the management and treatment of patients with post-COVID-19.

NIH Research Projects · FY 2026 · 2023-05

PROJECT SUMMARY The University of Iowa (UI) Health Care strategic plan for 2022-2027 expressly challenges the institution to (1) further expand clinical and translational science and research throughout our health care system, 2) build a diverse clinical and scientific workforce and to (3) enhance healthcare across the state through innovations in the systems of clinical and translational science (CTS) as well as clinical care. The Institute for Clinical and Translational Science (ICTS) is the scientific home for the CTS infrastructure and many of the training programs that support the university and is the entity charged with integrating CTS into the health care and research environments at the UI. As we envisioned the K12 program, we used the UI Health Care strategic goals to design a program that meets the needs of our state and that trains a CTS workforce to accelerate the pace of scientific discovery driving science from the bench to the bedside and into the community. Nearly 40% of Iowa's population lives in rural regions of the state where access to health care is challenged and many disease outcomes are inferior to those seen in urban populations. Resolving these rural disparities requires scientific and health care approaches that can adapt to geographic distance and make use of the existing systems of care that are in place in sparsely populated areas. Health delivery in rural Iowa is dependent on team-based care that incorporates allied health providers such as pharmacists, physical therapists, mid-level practitioners, dentists and importantly, community services. Our research agenda addresses the need to engage rural populations in practical ways closer to their homes and to train our scientists to work in multidisciplinary teams that include and value integration of community and allied health providers into research. Accordingly, our K12 program intentionally solicits Scholars from all health professions. The Objectives of our K12 Program are 1) Recruit and train outstanding Scholars (currently junior faculty or postdoctoral fellows with a pending faculty appointment) who will engage in an individualized curriculum and in mentored health care research during a three-year period in this multidisciplinary, multicultural K12 program. 2) Enhance the mentoring environment for translational research Scholars through a robust program for both mentors and mentees built on the NRMN training platform. 3) Provide a highly focused mentored research experience that fosters Scholars' successful transition to independence and continued engagement as leaders of translational health care teams. Meeting these objectives will require continued campus-wide, multidisciplinary participation of faculty as members of mentoring teams for K12 Scholars. Additionally, the ICTS, home of the only CTSA in the State of Iowa, will collaborate with CTSA hubs across the United States to enhance the learning environment and increase the opportunities for our K12 Scholars to build successful careers in translational science.

NIH Research Projects · FY 2026 · 2023-05

Since its origins nearly 60 years ago, the Iowa Medical Student Summer Research Program has continuously improved to sustain its mission of enveloping medical students in mentored research opportunities that foster their development into accomplished physician-scientists that positively impact human health. The last six years have demonstrated unprecedented success in the level of student engagement and productivity. It is against this backdrop of accelerated growth that we propose to sharpen our focus and deepen our students’ engagement with an exceptional cadre of enthusiastic mentors performing scientifically rigorous trans-NIDDK research focused on digestive and liver diseases; endocrine and metabolic diseases; obesity and nutritional disorders; or kidney and urologic diseases. Those four areas of investigation are long-standing institutional strengths, and with seed funding from our College of Medicine, we have begun transitioning our historically successful campus-wide single-stream funding model into a re-envisioned program with the same high level administrative infrastructure now leveraged to enhance support for a cohort of M1 students that are committed to a summer of immersive research with our curated roster of 42 outstanding and experienced Participating Faculty on a project within the research mission of the NIDDK. This training grant proposal seeks funding for 16 students to participate in 12-week summer fellowships, and the funds provided through this training grant would be matched by the College of Medicine, amplifying the impact of the award. In synergy with extensive opportunities provided through relevant Centers and Institutes, scholars will receive Instruction in Methods for Enhancing Reproducibility and the Responsible Conduct of Research, as well as mentor-guided journal clubs and research seminars. In the years that follow, students enroll in our research skills course, year-long research opportunities, the Research Distinction Track, and dual degree programs. We closely monitor students alongside their mentors as they continue their pathway towards a research career with incremental advancement through the continuity of support that is available at our institution, including funding during residency, fellowship, and junior faculty appointments. We critically evaluate every aspect of our extensive programing each year through a combination of anonymous surveys and collaborative discussions to continuously enhance the exposure of our students to the entire research process, from writing a proposal to analyzing data, presenting at local and national meetings, and ultimately disseminating the results in peer reviewed journals. The long-term impact of this program is the development of a cohort of physicians that are equipped to extend their discoveries into real-life applications that improve human health through prevention and improved treatment for gastrointestinal, endocrine, metabolic, nutritional, renal and urologic disease.

NIH Research Projects · FY 2026 · 2023-04

Project summary Antiretroviral agents reduce morbidity and mortality in HIV-infected individuals; however, mutations in the viral genome often result in clinical resistance to their effects. Due to the random nature of the mutations, the emergence of therapy-resistant mutants is mostly considered unpredictable. Consequently, antiviral treatment strategies are mainly empiric. The premise of this proposal is that the emergence rate of therapy-resistant mutants in each patient is largely predictable. Our published and preliminary studies suggest that changes in virus proteins can be accurately forecasted based their sequence properties before initiation of treatment. In the proposed study, we will use the example of the HIV-1 envelope glycoproteins (Envs). Several broadly neutralizing antibody (BNAb) therapeutics that target Env have shown great promise in clinical trials. However, escape from these agents often occurs after treatment, at different rates for different patients. The goal of this work is to advance our ability to personalize BNAb therapeutics to people living with HIV, by establishing the tools to determine the likelihood of each patient to develop resistance to each agent. The central hypothesis of this proposal is that each swarm of HIV-1 that infects a patient has an inherent and measurable likelihood to escape from each therapeutic. This likelihood is shared by the viruses that circulate in the blood and the reservoir of latent viruses, which is often the source of resistant mutants that emerge after therapy. To test the above hypothesis, we will first determine if the rate of HIV-1 escape from BNAbs is specific for each swarm of the virus that infects a patient. To this end, we will test in vitro the escape of strains from different patients that were isolated from samples collected at different time points. We will then test the ability of our models to forecast the rate and site of escape for each strain. Based on these studies, our models will be refined and applied to determine their ability to forecast resistance rates in four clinical trials of BNAbs in humans. Next, we will determine whether the appearance of resistant mutants is driven by their fitness (i.e., higher likelihood to appear before treatment) or by their resistance (i.e., higher replicative capacity after treatment). Such knowledge is critical for our ability to use patient samples before treatment, which inform of the viral fitness profiles, to predict escape from the treatment. We will then examine whether the fitness profile of BNAb escape sites is a persistent property of each virus swarm by measuring the changes that occur over time in patients. Finally, we will induce outgrowth of latent HIV-1 from peripheral blood cells and compare their fitness profiles at BNAb escape sites with those of viruses that circulate in the blood. The models to be developed have the potential to make important contributions to the treatment of patients by antiviral agents. They will lay the foundations for personalized antiviral medicine that is based on the likelihood of each virus swarm in a patient to develop resistance to each agent.