University Of Chicago

NIH Research Projects · FY 2025 · 2022-08

Project Abstract This application to be a Pelvic Floor Disorders Network Clinical Site contains both an innovative randomized controlled trial and comprehensive description of Northwestern Medicine’s unique strengths, as a team and environment, to contribute to all PFDN trials. Our concept proposal draws on the collective experience of our team in exercise physiology, perioperative optimization, and postoperative recovery. The proposal describes a randomized controlled trial of prescriptive early exercise following prolapse surgery to reduce deconditioning and improve recovery without any negative impact on pelvic floor outcomes. Our proposed study will go beyond existent research and be the first to implement and quantitatively evaluate (using accelerometer data) a postoperative exercise regimen and its effects on recovery and pelvic floor symptoms. In addition, our proposal highlights the strengths of our large, high volume, multi- disciplinary team, which draws from a diverse patient population across several regional hospitals to ensure equity and inclusion within PFDN clinical trials. We can also leverage our resources and collaborations as part of two NIDDK cooperative networks related to urinary incontinence and bladder health to advance the PFDN’s goals. The NM team is a nationally recognized group of collaborative, productive, and established investigators well poised to lead the design, implementation, analysis and dissemination of this multicenter RCT as well as participate in and lead additional studies within the PFDN.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY There is increasing evidence that early intervention for psychosis in coordinated specialty care (CSC) services improves outcomes and lives. The outcome of early course psychosis (EP) is heterogeneous, ranging from early full recovery to treatment resistance and functional decline from the onset of illness. This heterogeneity limits our ability to predict individual level outcomes needed for treatment planning and for tailoring the type, duration and intensity of therapeutic interventions. Biomarkers as well as clinical and demographic features, early in the illness can predict outcome, but taken individually, their prognostic value is limited. Our Bipolar- Schizophrenia Network for Intermediate Phenotypes (BSNIP) consortium has recently developed, replicated and validated a biomarker (EEG, eye movement testing, and neurocognition) based categorization (Biotypes 1, 2 and 3) in a trans-diagnostic sample of cases with idiopathic psychosis (schizophrenia, schizoaffective disorder, or bipolar disorder with psychosis), ranging from 18-35 years of age. In this study, we will leverage this categorization, along with clinical and biomarker data to predict illness trajectory and outcome during follow-up at 1, 6 and 12 months in 320 EP patients across CSC clinics at the five B-SNIP sites. First, we will characterize outcome trajectories and Biotype structure in EP. Our available data indicate the Biotype structure will be the same in EP as in our large sample. Second, we will investigate the predictive value of the nine bio-factors and the three Biotypes identified by B-SNIP for symptomatic and functional outcome. We predict that the EP population will manifest distinct outcome clinical trajectories (good, intermediate and poor) and will have a Biotype structure similar to that seen in chronic psychosis subjects, i.e., Biotypes 1, 2 and 3) (hypothesis 1). Biotype-3, and Biotye-2 cases, will have the best outcomes (defined both categorically, and dimensionally, using symptomatic, cognitive and functional measures); Biotype-1 will have the worst outcomes to CSC treatment, across all target time points (hypothesis 2). Notably, Biotype-1 and Biotype-2 cases will have the same level of cognition function at baseline. Finally, we will investigate the predictive value of clinical (such as diagnosis, illness duration, substance abuse, and treatment adherence), and biomarker (including neuroimaging) features in a multi-variate model and will develop a feasible biomarker battery and predictive algorithm for application in community CSC sites nation-wide. We will thus provide to the field a means for predicting success of EP cases in CSC treatment to improve clinical practice and to enhance efficient use of available treatment resources.

NIH Research Projects · FY 2025 · 2022-08

Enter the text here that is the new abstract information for your application. The objective of the University of Chicago IRACDA Program is to provide Postdoctoral Scholars recruited to the University of Chicago with a high-quality mentored research experience, as well as the opportunity to gain in-depth teaching experience and training at our partner institutions, Chicago State University and Northeastern Illinois University. Two Scholars per year will be selected, through a formal application process, based on demonstrated commitment to scientific investigation, need for teaching experience and desire for an academic career. Inclusion in the IRACDA and the opportunity to teach will provide a critical impetus in establishing their academic careers by increasing competitiveness for teaching positions. In turn, students at the partner institutions will receive enhanced mentorship and career advice, research opportunities, and improved and expanded curricular offerings, all of which will make them better prepared and more competitive for graduate school. Faculty mentors from the University of Chicago will supervise the research experience, and Teaching mentors from the partner schools will direct their in-depth teaching experience and training at the partner institution. It is anticipated that mentor interactions mediated by Scholars will spawn faculty collaborations as well. In addition, a formal curriculum, based in the Institute for Future Academics, in career-enhancing skills such as grant- writing, communication, lab management, etc., will be provided. The Program and its components will be evaluated with both qualitative and quantitative measures at specific intervals. The ultimate goal is to train a cadre of biomedical and behavioral scientists with both research and teaching skills sufficient to be competitive for academic positions.

NIH Research Projects · FY 2025 · 2022-08

Project Summary: Memory enables animals to acquire, store, and recall knowledge of the world through experience and use this knowledge to maximize reward and avoid danger. Understanding the circuit mechanisms within and between brain regions that underlie the formation and recall of memories is considered one of the great scientific challenges of our time, and has the potential to drastically influence the treatment of memory disorders. The hippocampus is both necessary and sufficient for the formation and recall of episodic memories—memories of experiences placed in time and space. These memories are encoded in the hippocampus by the firing activity of populations of neurons called place cells, which fire at specific locations as animals move around their environment, creating a cognitive map. Synaptic plasticity in the hippocampus is critical for forming cognitive maps, and in brain slices norepinergic and dopaminergic inputs from the Locus Coeruleus (LC) and the ventral tegmental area (VTA) to the hippocampus modulate synaptic plasticity, suggesting LC and VTA inputs to the hippocampus may influence cognitive map formation and plasticity. However, the activity of VTA and LC inputs to the hippocampus during learning, their synaptic connectivity, and their effect on hippocampal cognitive maps are unknown. Currently, a major technical obstacle in the field is measuring and manipulating the activity of LC and VTA axons during learning, and determining their synaptic connectivity, directly in the hippocampus. To solve this problem, we will implement an innovative approach to directly measure and manipulate the spiking activity of LC and VTA axons, and the spiking activity of large populations of place cells, in the hippocampus of mice during hippocampal-dependent learning tasks—changes in environment context and novel environment exposure. Optogenetic manipulation of LC and VTA axons in hippocampus and locally applied receptor antagonists will reveal the necessity, sufficiency, and mechanism of action of these hippocampal inputs on cognitive map formation and plasticity. Ex-vivo electron microscopy of the axons imaged during behavior will reveal their synaptic connectivity in the hippocampus. We hypothesize that LC and VTA axons in hippocampus will signal environment novelty and changes in context, respectively, with LC signals influencing cognitive map formation during novel environment exposure, and VTA signals reshaping cognitive maps during contextual changes. This will provide the first insight into the information being carried by these neuromodulatory circuits directly in the hippocampus during hippocampal-dependent learning, and will reveal how these signals form and alter memory representations and the synaptic circuitry through which this occurs.

NIH Research Projects · FY 2026 · 2022-08

Project Summary/Abstract Physical inactivity is associated with poor asthma control and quality of life, and greater health care utilization. Rates of physical inactivity, asthma, and asthma mortality among African American (AA) women are higher than those of their White counterparts. Our formative work identified barriers to PA among African American women with asthma including a lack of social support, self-efficacy, unsafe neighborhood and fear related to experiences with life-threatening asthma exacerbations. Given the unique barriers to PA and high rates of physical inactivity that are associated with poor asthma outcomes in African American women, there is an urgent need to optimize PA interventions for this population. The proposed study uses our theory-driven intervention (ACTION: A lifestyle physiCal acTivity Intervention for minOrity womeN with asthma) to deliver a 24-week lifestyle physical activity intervention designed for and by urban AA women with asthma. Participants will be recruited through two urban health care systems that care for a diverse urban AA population. Patients will be randomized to one of two groups: 1) ACTION intervention (group sessions, physical activity self-monitoring and text-based support for goal-setting), or 2) education control (an individual asthma education session and text messages related to asthma education). Participants will be followed for an additional 24-weeks after the intervention to assess for the maintenance of intervention effects on asthma health outcomes. We are proposing an efficacy study that focuses on asthma outcomes (Aim 1A/B), explores behavioral mechanisms of the intervention (Aim 2) and assesses factors that influence its reach and implementation potential (Aim 3). This trial will provide the first ever evidence of the efficacy of a lifestyle physical activity intervention among urban AA women with asthma, a population that is understudied yet plagued by low levels of PA and poor health outcomes. Our study has high potential to advance clinical treatment of asthma, and further the mechanistic understanding of physical activity interventions in minority populations living in low-resourced urban environments.

NIH Research Projects · FY 2025 · 2022-08

Microbial Engineering to Control the Structure and Function of the Gut Microbiome SUMMARY The human microbiota, the collection of microbes that live on and in the body, is fully integrated with human physiology and has been extensively implicated in health and disease. As with all microbial communities, the summation of environmental, interbacterial, and interkingdom interactions governs both the composition and function of the microbiota. To date, top-down approaches have been largely used to study microbiome function, using multi-omics techniques to draw correlations between microbial taxa, genes, and metabolites with functional properties in different environmental conditions. While these studies contribute a rich set of hypotheses, bottom-up approaches are required to causally pinpoint the molecular mechanisms through which microbes interact with their environment, one another, and the host. Synthesis of these mechanistic studies can further enable predictive models that can be leveraged to engineer microbiomes. Through the development and application of novel technologies, the research program described herein aims to predictively engineer ecological responses and metabolic functions in the gut microbiome. A defined microbial community that mirrors the phylogenetic and functional diversity of natural communities will be used as a testbed to model the emergent phenomena that arise as a result of interbacterial interactions. Using inspiration from natural microbial communities to fuel synthetic biology approaches, we will create new tools to allow for genetic manipulation and expression control in previously intractable gut symbionts. These genetic tools will be applied to link microbial genes and associated functions with emergent properties of microbial communities, including resilience to environment perturbations and metabolic networks in the mouse gut. These studies will provide an experimental framework to pursue investigations into the core functions that structure microbial communities and to establish design rules for rational microbiome engineering.

NIH Research Projects · FY 2024 · 2022-08

PROJECT SUMMARY Obesity and atherosclerosis are frequently comorbid conditions contributing to substantial morbidity and mortality worldwide. The processes are characterized by inflammation in the adipose tissue and vasculature, respectively, that share many pathophysiologic pathways. Although processes underlying obesity and atherosclerosis-related inflammation are well studied, the signals that promote disease resolution and remission are largely unknown, especially in the context of concomitant inflammation resolution. As a postdoctoral fellow, I investigated how resolution of obesity-related inflammation influences cardiovascular disease and found that caloric-restriction- induced weight loss in obese mice promotes resolution of atherosclerosis. Building upon these exciting findings, I propose in Aim 1 to evaluate the impact of caloric-restriction on obese adipose tissue and hematopoietic progenitors and whether the pro-resolving phenotype produced by to caloric-restriction can be transferred through adipose or hematopoietic cell transplantation. In Aim 2, I propose to investigate the mechanisms by which caloric-restriction influences the content and composition of atherosclerotic lesions and promotes atherosclerosis resolution. This work will reveal novel functions of cells and tissues that influence the atherosclerotic process in weight loss. Additionally, these studies will identify novel molecular pathways that may be targeted for the concomitant treatment of adipose tissue and atherosclerosis-related inflammation.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY Overdose deaths related to synthetic opioids have increased six-fold over the past 20 years. Repeated opioid users, such as individuals suffering from substance use disorder, are at the greatest risk for opioid induced respiratory depression, the hallmark of overdose. Although extensive understanding into the cellular, circuit and pharmacological basis by which opioids suppress breathing exists, how repeated opioid use impacts the control of breathing has been largely understudied. This is despite the clinical and laboratory evidence indicating that repeated opioid use significantly changes the control of breathing. This knowledge gap contributes to the limited ability to address opioid overdose among repeat opioid users—the population most vulnerable to overdose death. Even among repeat opioid users, tolerance to opioid induced respiratory depression can be labile. It is well-recognized that tolerance to the analgesic and euphoric effects of opioids has context-dependence. Similarly, the susceptibility to opioid overdose can be influenced by the context in which these drugs are used. Yet, the contribution of context-dependent mechanisms to the susceptibility of opioid induced respiratory depression is unknown. We developed a model of repeated fentanyl use that produces changes in breathing consistent with the breathing phenotype observed in repeated opioid users—including a form of tolerance dependent on context. The primary objective of this proposal is to examine the mechanisms involved with repeated opioid use-dependent remodeling in the control of breathing. We hypothesize that repeated opioid use remodels the control of breathing through direct cellular changes in the respiratory network and through the emergence of a labile form of tolerance dependent on behavioral conditioning and neuromodulation within the respiratory network. This work will examine: (1) the cellular and the neurophysiological mechanisms that underlie the remodeling of the control of breathing after repeated opioid use; (2) the contribution that learned behavior has in producing state-dependent breathing and influencing opioid susceptibility; and (3) the role that neuromodulation plays in influencing the stability of inspiratory drive prior to and after repeated opioid use. Thus, this work provides a much-needed mechanistic framework for understanding how repeated opioid use remodels the control of breathing. Such a framework can serve as a foundation for novel approaches and therapies to address the risk of opioid overdose in individuals most vulnerable to overdose-death and respiratory-associated co-morbidities.

NIH Research Projects · FY 2025 · 2022-08

Non-equilibrium activity is crucial for maintain and modulating tissue shape, development and morphogenesis, lysosome dynamics, cell membrane remodeling during cell division or membrane fusion and fission events. Importantly many of these processes play a significant role in human health helping regulate for instance immune system function and ensuring accurate developmental morphogenesis. However, there is a major gap in our understanding of how microscopic non-equilibrium biophysical driving forces give rise to a desired molecular response, function, or control. Indeed, while the theoretical and computational frameworks for the study of equilibrium biological processes are very well developed, there are very limited analogous tools for the study of complex far-from-equilibrium biological systems. Further, the large length and time scales of biological systems and processes make explicit computational simulations impractical. Addressing this problem requires the development of a range of multiscale non-equilibrium statistical mechanics techniques in combination with tools from machine learning and artificial intelligence so that the large length and time scales associated with the above-mentioned biological processes can be appropriately captured. The work outlined in this proposal builds towards these long-term goals by focusing on three paradigmatic example systems 1) Understanding and predicting non-equilibrium lysosomal dynamics and morphologies 2) Understanding and modelling cytoskeletal processes responsible for developmental patterning, cell-cell communication, and force generation 3) Developing frameworks for determining drivers of cell fate and differentiation from single cell RNA sequencing data. Each of these paradigmatic examples has implications for diseases. These paradigmatic examples build on the recent foundational non-equilibrium statistical mechanics frameworks developed by my group and expand them so that they can be utilized in biological contexts.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY The gut microbiome comprises hundreds of microbial species that inhabit the human gastrointestinal tract and impact host health in a myriad of ways. Diverse microbes coexist in the gut by specializing in distinct colonization strategies which collectively give rise to a complex microbial ecosystem with emergent functional properties. Despite the critical nature of the specialized ecological roles in explaining the composition and function of the microbiome, colonization strategies employed by the majority of gut microbes remains poorly defined. The proposed research will take two approaches to broadly assign colonization strategies to diverse gut microbes. A first part of the proposed project will employ comparative genome analyses to determine the distribution of established microbial functions across the gut microbiome and to guide the discovery of novel colonization strategies. A second part of the project will utilize unbiased growth assays to identify members of the microbial community adapted for diverse colonization strategies. The molecular basis of identified colonization strategies will be further interrogated through the application of genetic and biochemical approaches. By assigning ecological context to diverse members of the gut microbiota, these studies will advance a basic understanding of the gut ecosystem that could benefit the development of diagnostic and therapeutic microbiome-based technologies.

NIH Research Projects · FY 2025 · 2022-08

ABSTRACT Cancer is a disease mostly caused by accumulation of somatic alterations on DNA. These alterations can disrupt tumor suppressors, activate oncogenes, and create new genes with novel functions. Many alterations and genes can serve as biomarkers for diagnosis and prognosis, and some can be targeted by drugs. High-throughput sequencing technologies have enabled rapid discovery of genes which contribute to disease progression and drug response. The past few years have seen an explosion in the rate of genome sequencing. The main focus of cancer research has been on detecting point mutations, copy number changes and expression changes of protein- coding genes. In addition to the protein-coding genes, there are tens of thousands of non-coding RNAs (ncRNAs) in the human genome that are less well-understood. Some of them are known to play important roles in normal cellular processes, and a small subset can promote tumor growth, metastasis and drug resistance. More importantly, some ncRNAs are of clinical significance as they can be used as biomarkers and/or drug targets. However, the vast majority of ncRNAs have unknown functions and their contributions to cancer remain unclear. In this study, we will perform a genome-wide screen for novel cancer-driving ncRNAs leveraging existing large-scale data from several national and international cancer-genome-sequencing consortia. In tumor tissue, the normal functions of ncRNAs can be perturbed by different types of somatic alterations, for instance point mutations, DNA copy changes, genomic rearrangements, epigenetic changes, etc. Investigation of each of these diverse types of alterations requires specialized analytic approaches. To identify novel cancer-driving ncRNAs, we will specifically focus on a less well-studied type of alterations—genomic rearrangements. They include deletions, duplications, inversions, translocations and other more complex forms. A main consequence of genomic rearrangements is that they can shuffle the DNA content in the genome. We hypothesize that tumor-specific somatic genome rearrangements can reorganize ncRNAs and contribute to tumorigenesis. For example, we will systematically screen for new regulatory functions operating upon ncRNAs by relocation of regulatory elements in the genome due to somatic genome rearrangements. We will also screen for new ncRNA species created by shuffling of DNA fragments, which carry novel functions and contribute to tumorigenesis. Evolutionarily, exon shuffling has been an important mechanism to form new genes. Multiple complementary strategies will be implemented to overcome various scientific and technical challenges. Our study can lead to the discoveries of novel oncogenic ncRNAs, new biomarkers and potential drug targets, and reveal novel cellular process regulations in both normal and diseased conditions.

NIH Research Projects · FY 2026 · 2022-08

PROJECT SUMMARY RNA-binding small molecules have the potential to modulate the expression of genes whose protein products were previously considered “undruggable.” Risdiplam, targeting a precursor mRNA, was recently approved for the treatment of spinal muscular atrophy (SMA) and demonstrates the specificity and safety attainable by this approach. Although a variety of small-molecule scaffolds have been uncovered as RNA-binding ligands, their use is hampered by (1) lack of specificity and (2) unpredictable function. We propose a research program that will provide RNA-targeting chemical probes that will avoid these drawbacks. Inspired by Proteolysis Targeting Chimera (PROTAC) technology, we are designing chimeric molecules that will target RNA specifically and carry (deliver) the ability to induce RNA degradation or inhibit RNA translation, in a highly predictable manner. Our initial efforts towards an RNA-targeting chimera platform use a newly discovered RNA-binding coumarin derivative as a model and fine-tune its preferential binding properties through chemical modification. Through structural optimization, which includes using a “bidentate” RNA ligand strategy, we expect to achieve RNA-binding selectivity equal to or greater than that of oligonucleotides. At the same time, we propose to develop and optimize three novel effectors to precisely degrade RNA targets or inhibit the target RNA translation. These new effectors have shown promising results in inhibiting Zika virus (an RNA virus) gene expression. Ultimately, our proposed work will generate a top-down method for designing selective gene expression inhibitors that are independent of the gene's protein product. The long-term goal of our lab is to build a medicinal chemistry platform for making gene-specific and patient-specific therapies using RNA-binding small molecules. In this process, we will not only generate various tool compounds for studying important disease-modifying genes, but also combine computational and experimental technologies to understand the detailed mechanism of RNA-small molecule recognition.

NIH Research Projects · FY 2025 · 2022-07

PROJECT SUMMARY Syphilis rates in the U.S. have been increasing steadily since 2001, with more than 130,000 new cases reported in 2019. Left untreated, syphilis can lead to neurologic, psychiatric, cardiovascular, and other severe medical consequences, in addition to stillbirth or devastating congenital defects in infants of infected mothers. Syphilis disproportionately affects minority populations, in particular Black and Hispanic communities. Rates of congenital syphilis are also rising rapidly, paralleling an increase in rates among young women. Detection of syphilis among women of childbearing potential will be key to eliminating congenital syphilis. Current screening strategies rely on identification of symptoms or risk factors in patients attending ambulatory care, but this may result in many missed diagnoses, as syphilis can remain asymptomatic for years, patients may not perceive themselves as at risk or report relevant risk factors, and the patients most vulnerable to syphilis may also be the least likely to attend routine outpatient care. To address this issue, I created and pilot-tested an approach for universal syphilis screening in the emergency department (ED), where many vulnerable patients preferentially seek medical care. My long-term goal is to scale up this program and create a robust model that can eventually be scaled-out to other urban EDs in Chicago and across the country, and to accomplish this I will need additional data and training in implementation science. In this career development proposal, I will evaluate and improve my screening model and prepare for expansion to additional sites using implementation science strategies, informed by the Exploration, Preparation, Implementation, Sustainment (EPIS) model, a robust determinants framework in implementation science. The Exploration phase will consist of an assessment of the readiness of key stakeholders outside our institution to adopt a similar screening model. The Preparation phase will be developed concurrently to include an evaluation of the contextual factors that have contributed to successes and failures of the existing screening program, including specifically the costs associated with such programs. The Implementation and Sustainment phases represent future directions as the model is improved and sustained over time at our hospital and ultimately implemented at other institutions as part of future R01-level studies. The knowledge developed as a result of this proposal will fill important gaps in how to implement successful, context- specific ED screening programs with effective linkage to care plans, which may serve not only to increase syphilis diagnosis and treatment, but also could be applied to screening for other diseases affecting the most vulnerable populations. This K23 award will provide advanced training in implementation science, mixed methods research, and healthcare economics that will build on my background in public health and epidemiology. I will bring my research and clinical experience together with that of an experienced mentorship team to develop the skills necessary to become an independent investigator and eventually a leader in ED screening methodology and implementation science.

NIH Research Projects · FY 2025 · 2022-07

PROJECT SUMMARY The induction of protective immune responses through vaccination is central to the management of many pathogens. For antigenically variable pathogens such as influenza, protective immune responses impose a major selective pressure on viral populations and indirectly influence vaccine strain selection and vaccine effectiveness. Our poor understanding of the generation and maintenance of protective immunity to influenza hinders vaccine development and the accuracy of evolutionary forecasts. Antibody titers to the hemagglutinin (HA) surface protein were established as a correlate of protection 50 years ago, and more recent evidence shows many anti-HA antibodies directly and indirectly contribute to viral neutralization. However, HA titers remain only moderately predictive of an individual’s risk of infection on exposure, and the contributions of other immune responses are less well understood. Understanding the causes in addition to correlates of protection could increase the accuracy of forecasts of viral fitness and provide reliable endpoints for vaccine development. Here, we propose complementary approaches to identify the correlates and drivers underlying protection from infection and heterogeneity in vaccine responses. We will integrate diverse variables, including infection and vaccination history, baseline antigen-specific and antigen-agnostic immune states, intrinsic characteristics including age, sex, and body mass to predict responses to influenza vaccination and extract mechanistic insight. In order to address our specific aims, we will leverage data from existing, longitudinal studies of immune parameters following influenza virus infections and vaccination in humans. First we will use computational and multimodal single-cell approaches to investigate how vaccination and infection impact host immune status. Emerging evidence, including our own data, suggests that vaccination and infection can establish new antigen-agnostic immune set points that affect future vaccine responses. Next we propose to integrate complementary computational approaches, spanning machine learning, causal mediation analysis, and mechanistic modeling to predict and develop causal mechanistic insight into vaccine responsiveness and protection from severe and mild infection. We will develop and distribute a suite of accompanying tools to make these novel approaches accessible to bench and computational biologists. Improved prediction of immune responses, especially protective immune responses, could lead to more effective vaccination strategies that mitigate vaccine failure in different subpopulations and improve the public health impact of influenza vaccination. The methods and tools that we develop can provide foundational frameworks to dissect responses to other vaccines and pathogens.

NIH Research Projects · FY 2025 · 2022-07

Project Abstract Kidney stones are a major cause of morbidity and account for $11 billion in health care spending in the U.S. Low urine citrate and high urine oxalate both increase risk of stone formation. Mechanisms that regulate renal citrate and oxalate excretion affect kidney stone risk. Physicians use knowledge of mechanisms for stone prevention (e.g. potassium citrate to raise urine citrate, low oxalate diet to lower urine oxalate). The overall objective of this proposal is to expand our knowledge of mechanisms contributing to low urine citrate and high urine oxalate. This will advance scientific knowledge and improve kidney stone prevention strategies. The proposal will include study of mechanisms in two patient groups that are at high risk for kidney stones: obesity and Roux-en-Y gastric bypass (RYGB). Studying risk in these patient groups is important as obesity and bariatric surgery rates are on the rise in the U.S. This study will test the effect of diet on the association between higher urine oxalate and higher urine citrate in non-kidney stone patients that is disrupted in kidney stone patients. This will lead to future studies including testing the oxalate and citrate association under conditions of alkalosis. This may change clinical practice with new strategies such as providing alkali simultaneously with dietary oxalate to improve oxalate-citrate balance. It will also test the contribution of diet and paracellular gastrointestinal oxalate absorption to high urine oxalate in obese and RYGB kidney stone patients. This will lead to improved clinical care by focusing providers on higher yield strategies. Future studies will test these strategies. Furthermore, this study and support from the K23, will be vital to my career development. I will learn how to apply epidemiologic data to clinical research center (CRC) based human studies to investigate mechanisms responsible for the epidemiologic findings. I will learn how to design, implement, and conduct such studies, how to recruit and retain patients, and how to analyze repeated measures data. I will learn about management of kidney stone patients and high risk obese and bariatric surgery patients from a patient-centered perspective. I am in a rich research environment at the University of Chicago. I have developed a strong mentorship team with world experts in human based studies of kidney stone physiology and CRC study design and implementation. My advisory team includes world leaders in basic science, translational, and human studies related to citrate and oxalate and an expert in bariatric surgery. This team will support my scientific and professional development. At the end of the K23 award, I will be prepared to use the data collected to apply for an R01 in a follow up intervention study that I will lead as an independent investigator. My future studies will build on the data and skills I learned from this study. Therefore, through the research experience, training, and mentorship from this award, I will become a leader in kidney stones research and clinical management, including obese and bariatric surgery patients, with the ultimate goal to improve patient care.

NIH Research Projects · FY 2025 · 2022-07

PROJECT SUMMARY/ABSTRACT My group seeks to understand, in molecular detail, the steps taken by each of the major classes of membrane proteins to achieve their final assembled state. About one-quarter of all genes code for membrane proteins that are first inserted into the plasma membrane of prokaryotes or the endoplasmic reticulum (ER) of eukaryotes. These proteins perform many essential functions as receptors, channels, enzymes, anchors and transporters. Biosynthesis of membrane proteins is an inherently inefficient process, and numerous human diseases are linked to defective folding of membrane proteins. Thus, understanding how membrane proteins are made is a fundamental question in cell biology with important implications for the treatment of human diseases. Of the ~5,000 membrane proteins coded in the human genome, the majority have more than one transmembrane domain. Yet our understanding of how these “multi-pass” proteins are inserted, folded and assembled into functional entities is at an early stage. Work in my group over the past several years led us to discover a novel ~390 kDa translocon in the ER that is involved in the biogenesis of most multi-pass membrane proteins in human cells. We are now focused on defining the molecular mechanisms underlying this process, using an interdisciplinary set of biochemical, structural, cell biological, genetic and bioinformatic approaches. These studies promise new insight into the fundamental biological challenge of membrane protein biogenesis.

NIH Research Projects · FY 2025 · 2022-07

ABSTRACT Research and training on motor control at UChicago have a unique history of combining neurobiology and neuromechanics research with computational approaches. In the past few years, the University has significantly expanded its neuroscience community with the establishment of the new Neuroscience Institute. The significant investments have created exciting new opportunities for research and training in the area of motor control and movement and related disorders, especially in addressing questions by integrating experimental and computational approaches. Our training program will take advantage of the existing breadth and depth of motor control and movement research on campus. We have 15 Trainers whose research is focused on motor control and movement, covering a broad range from genetic, molecular and cellular studies to circuit, systems, biomechanics and computational approaches. Our research interests have a broad anatomic scope, from neuromuscular junction and spinal cord to cerebellum, basal ganglia and cerebral cortex. We employ a broad range of model organisms including invertebrates, insects, zebrafish and mice to non-human primates and human subjects. In evaluating candidates for the Training Program, a criterion will be their demonstrated interest in bridging experimental and computational work as an element of their dissertations. Trainees will complete the following Program Elements. 1. The “Experimental Design in Motor Control Research” course. 2. One or two rotations that broaden exposure to approaches. 3. Annual problem-solving workshop. 4. Journal club that emphasizes statistical methods. With the activities, we will bring together faculty and students whose work is mainly experimental and those whose work is computational. We will explore as a community how fundamental questions in motor control can be addressed at a range of levels of approach. In addition to the trainees supported by the T32, we will add Associate Members so that any trainee who is working on motor control research or is interested in motor control research could participate in T32 sponsored activities. All trainees will gain key skills in statistics methods. Writing and presentation skills will be emphasized throughout the training. Faculty in our Training Program have primary appointments in five departments (Neurology, Neurobiology, Organismal Biology and Anatomy, Molecular Genetics and Cell Biology, Anesthesia and Critical Care), and appointments in one or more than one of the five participating Graduate Programs (Neurobiology; Computational Neuroscience; Genetics, Genomics and Systems Biology; Integrative Biology; Medical Scientist Training Program). We propose to support 6 predoctoral trainees (starting with 3 slots in year 1). Students will be supported for 2 years during years 3 and 4 of their graduate training. We will appoint 3 new trainees every year.

NIH Research Projects · FY 2024 · 2022-07

Project Summary Mechanisms of Mechanotransduction by LIM Domain Proteins Mechanical forces are essential to controlling the shape, movement and even many aspects of cell physiology. Changes in the environment mechanics or defects in cellular mechanoresponse are implicated in a plethora of diseases including atherosclerosis, heart failure and cancer. A major challenge is to understand mechanotransduction - the mechanisms by which mechanical information is detected and communicated to pathways that control cell behavior. The LIM super family of proteins, which contain one or more LIM domains, represents a large number of putative mechanosensitive cellular proteins that are involved in physiological mechanotransduction pathways. Understanding how the LIM domains function to detect and transmit information about mechanical stress will result in a deeper understanding of mechanotransduction-based signaling, which is important for developing strategies of disease treatment and organ regeneration. This proposal leverages an innovative combination of cell biophysics, biochemistry molecular cell biology, live cell imaging and mathematical modeling to investigate the mechanism by which LIM domains sense mechanical stimuli in the actin cytoskeleton and, in turn, initiate YAP/TAZ mechanotransduction signaling. We recently discovered that a large number of LIM domains exhibit force-sensitive binding to actin filaments. Here we propose to: (1) identify the mechanism by which LIM proteins are recruited to mechanically stressed actin filaments, (2) determine how the LIM sequence enables specificity in force-dependent recruitment within the actin cytoskeleton and (3) elucidate how the mechanosensing by LIM protein LIMD1 initiates the YAP/TAZ mechanotransduction pathway. These studies have the potential to demonstrate a highly conserved mechanism of cell mechanosensing, and the methodologies will establish a novel strategy for tackling cell mechanotransduction.

NIH Research Projects · FY 2024 · 2022-07

Project Summary Altered metabolism is a hallmark of malignancy. Metabolic pathway changes contribute to cancer cell growth, transformation and survival. These differences can be exploited to image tumor tissue and provide predictive information to patients. Importantly, these metabolic differences can also be exploited therapeutically. Thus, understanding cancer metabolism has important implications for pathophysiology and clinical oncology. Progress in translating these studies into new therapies is limited by the fact that much of knowledge in tumor metabolism is derived from studies in cultured cells with unknown relevance to disease biology. Similarly, cell line xenografts may not accurately recapitulate the cellular heterogeneity of a primary tumor. For these reasons, little is known about tumor metabolism in vivo, and the factors that regulate this behavior. My proposal utilizes clinical samples wherein the metabolic behavior of the primary human tumor is evaluated and characterized. These tissues are translated to mouse models, where I will evaluate what metabolic phenotypes are retained, as well as test what intrinsic and extrinsic factors promote metabolic behavior. During the mentored phase of the grant, I will focus on identifying retained/intrinsic metabolic phenotypes, as well as extrinsic factors such as the role of tumor perfusion on nutrient preference. With these insights, I will continue independent research focusing on the molecular details of these factors, to identify combinations of factors influencing cancer metabolism in vivo.

NIH Research Projects · FY 2025 · 2022-07

My lab develops and applies new approaches at the interface of molecular evolution and protein biochemistry . We have played a lead role in developing ancestral protein reconstruction (APR) with molecular experiments as a powerful strategy to decisively identify the genetic, biophysical, and evolutionary mechanisms by which extant proteins evolved new functions. We recently expanded this approach by conducting the first studies to use deep mutational scanning of massive protein libraries to characterize the distribution of functions in the sequence space around ancestral proteins; this allows us to compare the trajectories taken during history to the vast number of alternative paths that could have been taken, thus providing insight into the roles of functional optimization, neutral chance, epistasis, and historical contingency in shaping the trajectories and outcomes of protein evolution. In the next 5 years, we will further develop these approaches and apply them to two major problem areas: 1) Evolution of complex protein features. Many proteins assemble into specific multimeric complexes and are functionally regulated by binding to allosteric effectors. These features usually many interacting residues, so it has been difficult to identify the evolutionary genetic and biochemical mechanisms by which they originate during evolution. We will use APR and vertebrate hemoglobin as an ideal model system to dissect the particular historical mutations and consequent changes in physical properties that cause this essential protein to acquire multimerization and allostery from a simpler precursor. 2) Comprehensive assessment of the functional, fitness, and epistatic effects of substitutions during long-term protein evolution. Targeted experiments have shown that mutations often epistatically modify the effects of other mutations in the same protein; theory and case studies suggest these dependencies can make evolutionary paths and outcomes contingent on chance events. There have been no comprehensive studies, however, to characterize the extent of epistasis among the full set of substitutions that occurred during history, their effects on evolutionary processes, or the temporal dynamics by which these effects emerge. We will use high-throughput protein library assays on ancestral proteins to measure the functional and fitness effects and epistatic interactions of all substitution that occurred across long, well-resolved historical trajectories, determine how shifts in these effects over time affected evolutionary processes, and analyze how underlying biophysical mechanisms mediated these effects. As in our past work, we expect these new strategies to generate strongly supported new knowledge concerning the mechanisms and forces that drive protein evolution, and that our approaches will be adopted by other groups to deepen our evolutionary and biochemical understanding of other protein families.

NIH Research Projects · FY 2026 · 2022-07

PROJECT SUMMARY/ABSTRACT Hypothesis: Diseases of the pancreas are life-threatening, including pancreatic cancer (PDAC), affecting exocrine cells, and autoimmune diabetes (T1D), destroying insulin-producing β cells. External factors like infections and diet are implicated as triggers, but the disease origins remain elusive and cures are lacking. The immune system strongly contributes to disease progression, but what governs pancreatic adaptive immune tone is understudied, preventing effective immune-targeting therapy. Lymph nodes (LNs) are key sites for the initiation of tissue specific adaptive immunity, and here we hypothesize that LN sharing between pancreas and duodenum and liver influences the nature of pancreatic immunity. We postulate that both, the major lymph output from these co-drained organs and their more direct exposure to environmental perturbation, allow them to dictate LN environments, thus impacting pancreatic adaptive immune cell fate both during homeostasis and upon intestinal or hepatic insults. Finally, we propose that migratory dendritic cells (DCs) presenting pancreatic antigen are the key cellular target for such immune cross talk. This hypothesis will be tested in our Specific Aims (SA): SA #1 will characterize the phenotype of pancreatic antigen loaded DC and consequences for exocrine or endocrine pancreas specific T cell polarization in the co-drained LNs during homeostasis. SA #2 will test to what extent LN DCs and T cell fates change upon intestinal versus hepatic perturbation such as infections. SA #3 will assess the relative importance of sharing LNs with liver versus gut for the T cell landscape back in the exocrine and endocrine pancreatic tissue and, as a proof of principle, will investigate how duodenal infection, through LN sharing, affects pancreatic tissue T cells and the progression of T1D. Unique approach: 1. We will identify LN DCs loaded with pancreatic antigen by virtue of tracking tissue specific antigen biotinylation or fluorescent protein uptake. 2. We have generated novel mice that permit expression of the model antigen OVA from exocrine or endocrine pancreas, liver or gut, allowing for monitoring OVA specific T cell fate. This method permits the systematic comparison of tissue-specific T cell responses in the LNs shared with the liver versus the duodenum. Impact: This project will provide fundamental insights into how pancreatic immunity may be shaped by environmental fluctuations. While potential sources of pancreatic perturbation through LN sharing, liver and duodenum could turn out as anatomical routes for therapeutic intervention in the pancreas. Mechanistically the research will increase our understanding of DC imprinting in tissue versus LN and the impact of this “plasticity” on dictating T cell responses. More broadly, the proposal features LN sharing between organs as a previously unrecognized force shaping tissue specific immunity.

NIH Research Projects · FY 2024 · 2022-07

Project Summary The cerebellum optimizes motor and non-motor performance by integrating input signals encoding prediction error with input relaying a spectrum of multisensory and contextual information. These input pathways–carried by climbing fiber axons (CFs) from the inferior olive and parallel fiber axons (PFs) of cerebellar granule cells, respectively–converge on the elaborate dendritic arbor of Purkinje cells (PCs), the primary cell type and sole output of the cerebellar cortex. Theories of cerebellar function are centered around PC-mediated integration and rely on the principles that each PC: 1) is a structurally and functionally redundant unit in the cerebellar cortex, 2) receives olivary ‘teaching’ signal input from only one CF, and 3) exhibits homogenous signaling across the entire dendritic tree. The specific aims of this proposal are designed to challenge the universality of these principles by revealing a ‘super-integrator’ PC subpopulation characterized by input from multiple CFs and non-homogenous signaling across dendrites. These PCs are defined morphologically by segregated dendritic compartments from either the early bifurcation of their primary dendrite (‘Split’) or multiple primary dendrites emerging from the soma (‘Poly’). ‘Super-integrator’ PCs are defined functionally by the presence of non-homogenous dendritic signaling produced by independent input to each compartment, such as from multi-CF innervation. This study will examine the anatomical CF→PC connection, describe signal heterogeneity in PC dendritic compartments, and examine how these functional elements affect integration during multisensory processing. To comprehensively assess these anatomical and functional features of PCs, experiments will be balanced between tightly controlled in vitro preparations and physiologically relevant in vivo conditions and will combine electrophysiology, Ca2+ imaging, and tracer immunolabeling methods. A central training goal of this proposal is to learn and apply a range of techniques, especially by pairing Ca2+ imaging and electrophysiology, and data analysis methods toward my development as an independent researcher. The final results of this work will provide a significant update to our current understanding of fundamental cerebellar anatomy and function. This update will introduce a panel of new research questions to better understand task-dependent cerebellar computations, expansion and compression of information as it flows through cerebellar circuits, and sources of dysfunction in disease as putative targets for therapy. Some features of ‘super-integrator’ PCs in wildtype animals (e.g. abnormal CF inputs and multi-compartment morphology) overlap with features that are overexpressed in mouse models of autism spectrum disorder. It is possible that, in addition to conferring normal cerebellar function, an overabundance of ‘super-integrator’ PCs may underlie some characteristics of cerebellar dysfunction in autism.

NIH Research Projects · FY 2025 · 2022-07

Project Summary/Abstract The rapid emergence of novel ideas and technologies is transforming molecular and cellular biology into an increasingly quantitative and interdisciplinary science, opening additional avenues for research, and creating new career paths for PhD scientists. To embrace these new challenges and opportunities, we propose a new implementation of the Molecular and Cellular Biology (MCB) training program at the University of Chicago. The primary goals are to train a new generation of interdisciplinary molecular and cellular biologists, to arm them with the modern quantitative and computational skills needed to carry out rigorous and reproducible science, and to prepare them for success in academia, industry, and other research-related careers. The new MCB program will unite an exceptional group of 55 faculty trainers who span a range of relevant fields and share a deep commitment to graduate training. We request 20 slots to support trainees from a large pool of highly qualified students belonging mainly to four core graduate programs: (1) Biochemistry and Molecular Biophysics, (2) Cell and Molecular Biology, (3) Development, Regeneration and Stem Cell Biology, and (4) Microbiology. The new MCB program will play a unique role by integrating interdisciplinary research and training in molecular and cellular biology across these graduate programs. Building on the success of the previous MCB program, which ends this year, the new MCB program will serve as an institution-leading driver of innovation and excellence in graduate training. MCB trainees will be supported primarily in Years 2 and 3, but they will participate in program activities from matriculation to graduation. A new quantitative curriculum will provide them with robust, rigorous, and customizable instruction in statistical and computational data analysis and modeling. Expansion and enhancement of a previous Research in Progress series will provide MCB trainees with team-mentored training in scientific communication and extend this opportunity to additional trainees in MCB trainers’ labs. A division-wide career development program, and a student-run MCB Symposium featuring MCB alumni, will help students to explore different career paths. The MCB program will promote excellence in mentorship through required activities that include mentoring compacts and annual faculty mentorship training. Additional guidance for MCB trainees will be provided by annual meetings with the MCB program directors. Professionally implemented evaluation tools will guide iterative improvements to the MCB program.

NIH Research Projects · FY 2025 · 2022-07

PROJECT ABSTRACT Despite declines in combustible cigarette smoking among young adults, use of electronic nicotine delivery systems (ENDS), such as e-cigarettes, continues to rise. Young adulthood marks a particularly susceptible time for the experimentation and initiation of substance use behaviors, including tobacco. Further, some who initiate tobacco use with ENDS transition to combustible products, such as cigarettes or marijuana, or become users of multiple products (dual/poly users). Despite the addiction potential of ENDS and high interest in quitting among young adults , there are few resources available to help individuals quit or reduce their use of ENDS. The aim of the proposed research is to develop an evidence-based mobile health (mHealth) text- message based intervention for young adult ENDS and dual (ENDS and cigarette) users (K99 phase 1), and determine whether the intervention is effective in reducing ENDS use (primary outcome) and increasing cessation , quit attempts, and use of nicotine replacement therapy (NRT; secondary outcomes; R00 phase 2). In phase 1 (K99), we will determine intervention content and delivery schedule based on existing evidence- based smoking cessation materials as well as utilize focus groups with young adult ENDS users (both ENDS- only and dual users) to adapt content to an mHealth ENDS-specific intervention. We will then run an initial pilot study with 45 participants to determine intervention feasibility and acceptability. After the pilot intervention, we will conduct additional focus groups with individuals who participated in the pilot to further refine the intervention. In phase 2 (R00), we will conduct a randomized control trial to determine the intervention’s effect on ENDS outcomes. Young adult ENDS and dual users will be randomized to one of three conditions: 1) mHealth ENDS intervention, 2) standard ENDS advice+NRT, or 3) standard advice alone . Standard advice will include a website that will be updated with information on products/safety and strategies for ENDS cessation as information evolves over the course of the study. Participants in the mHealth condition will complete a 6- week text-message based intervention with content tailored based on 1) motivation to quit ENDS, 2) whether an individual uses ENDS only or is a dual user of tobacco products, and 3) target quit date. Participants will complete an assessment of ENDS behaviors, quit attempts, and use of NRT at 3-month follow-up. ENDS use frequency will be the primary outcome , while biochemically verified 7-day point prevalence abstinence, NRT use, and quit attempts will be the secondary outcomes of interest. This study’s findings will inform emerging ENDS intervention literature, an area where a clear evidence base is currently lacking, and whether a mHealth intervention can impact young adults’ ENDS cessation, behaviors, and barriers to NRT use. This project will serve to provide valuable mentorship and training complementary to the proposed research to facilitate Dr. Brett’s transition to an independently-funded investigator and clinical addiction and tobacco control scientist.

NIH Research Projects · FY 2026 · 2022-07

Project Summary/Abstract Cytokine signaling is essential to the initiation of the immune response against microbial infection and cancer. The immune system is composed of two mechanisms of defense defined as the innate and adaptive immune systems, both of which critically rely on cytokine signaling to function. The innate immune system acts early during an infection or cancer and includes the type I IFN response. The adaptive immune system becomes fully active after approximately seven days. Although this response is delayed relative to the innate system, the time is needed to mount a T-cell response that is potent and specific. Interleukin-2 and interferon gamma are examples of cytokines that shape the response of the adaptive immune system. There are dozens of other cytokine families that each play an important role in the immune system including hematopoiesis, inflammation, apoptosis as well as many others. Understanding how cytokines signal, the genes they induce, and their functions are critical to understanding human health and disease. Recent examples of engineered cytokines demonstrate that tuning of cytokine signaling can drastically alter a cytokine’s response and may offer promising new therapeutic approaches. In this proposal, we aim to use protein engineering technologies to fill the large gaps in knowledge of cytokine signaling which may reveal new targets and approaches for therapeutic intervention. The paradigm of cytokine signaling is that cytokines drive the dimerization of cytokine receptors. Janus kinases (JAKs) are believed to be constitutively bound to the cytokine receptors. Upon receptor dimerization, the JAKs cross phosphorylate each other as well as the receptors. Signal transducers and activators of transcription (STATs) bind to the phosphorylated receptors, are then phosphorylated, dimerize, and translocate to the nucleus to elicit gene and functional responses. Recent tool development in our lab provides a streamlined approach to characterize protein-protein interactions which occur intracellularly, challenge assumptions in the field, and provide an opportunity to understand how every step in cytokine signaling contributes to cytokine signaling. We aim to show how altering these interactions tune cytokine signaling and response gene and functional signature.