University Of Chicago

NSF Awards · FY 2024 · 2024-07

The focus of this award is the development of a plan for the coexistence at the South Pole of transmissions to and from large communications satellite constellations like Starlink with instruments in the Antarctic Dark Sector vulnerable to these transmissions. This builds on extensive and varied experience in understanding and mitigating interference in precision CMB instruments. The proposed work would also continue ongoing efforts in understanding harmful interference thresholds and developing reasonable and well-justified plans for the inevitable existence of RF transmissions at some level within the Dark Sector. Historically, these efforts have addressed situations as they arise, or after data is discovered to be contaminated. The emerging threat of interference from large satellite constellations is too complex and potentially devastating to scientific datasets to address in the same ad hoc way. The project consists of coordination with the SpaceX network (Starlink) on a plan of coexistence; development of a prototype Starlink terminal suitable for long-term installation, including a winterized remote user terminal; development of an improved RFI monitoring system capable of detecting Starlink transmissions, with visualization tools and integration into scientific data streams; analysis of current data sets from the Dark Sector to characterize and understand RFI issues, and development of standardized RFI susceptibility tests to determine vulnerability of future instruments. The primary focus for this project is instruments (such as CMB-S4) designed to measure the cosmic microwave background with very long integrations. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-07

NON-TECHNICAL SUMMARY: The periplasm, a confined space inside bacteria, could be used as a platform for new technologies that combine bacteria with semiconductors. These biohybrid systems could have many uses, such as large-scale chemical production and controlling bacterial activities without changing their genetics. By adding light-sensitive semiconductor particles to the periplasm, chemical production can be increased by affecting key processes in bacteria. This approach uses the natural structures of bacteria and different combinations of semiconductor particles to advance microbial engineering. The principal investigator is developing methods to grow semiconductor particles within the periplasm in cells to study how they interact with bacteria. The goal is to design experiments that mimic photosynthesis to increase chemical production, for example in the production of malate, a valuable chemical precursor. This project will also provide valuable learning opportunities for students from all backgrounds. By offering interdisciplinary research experiences and international exchange programs, the project will increase participation in science and engineering. Educational initiatives will include summer research opportunities for high school and undergraduate students, as well as international symposia and partnerships with local art centers. The results will be shared widely through publications, seminars, conferences, and online platforms. TECHNICAL SUMMARY: The periplasmic space in bacteria offers a unique environment for creating semiconductor-based biointerfaces, which can be used for large-scale biosynthesis and modulation of bacterial processes without genetic modifications. Incorporating light-harvesting semiconductor nanoclusters into the periplasm can significantly enhance the efficiency of chemical production in biohybrid systems by modulating central metabolic processes. This approach leverages existing cellular structures and diverse nanocluster-cell combinations to innovate microbial engineering. The principal investigator aims to establish a robust protocol for biomineralizing semiconductor nanoclusters and their alloys within the periplasm. The study will probe the biomineralization mechanisms and the properties of the resulting biointerfaces using transcriptome, proteome, metabolome, and fluxome analyses to identify the molecular pathways and potential stress conditions involved. The optical properties of the semiconductor/bacteria composites will be examined with fluorescence microscopy and micro-spectrofluorometry, while transient absorption and time-resolved infrared spectroscopy will probe energy and charge transfer mechanisms at the biointerfaces. The research ultimately aims to conduct artificial photosynthesis experiments using a custom-built light emitting diode array for illumination and differential pulse voltammetry to measure chemical production, with a focus on improving malate bioproduction yield through a scalable bioreactor process. This research will also provide valuable interdisciplinary learning opportunities and foster broad participation in science and engineering through summer research experiences, international exchanges, and educational programs for high school and undergraduate students. The outcomes will be disseminated through publications, seminars, conferences, and online platforms. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-07

To pursue the promise of the big data revolution, the current project is concerned with a particular form of such data, high dimensional high frequency data (HD2), where series of high-dimensional observations can see new data updates in fractions of milliseconds. With technological advances in data collection, HD2 data occurs in medicine (from neuroscience to patient care), finance and economics, geosciences (such as earthquake data), marine science (fishing and shipping), and, of course, in internet data. This research project focuses on how to extract information from HD2 data, and how to turn this data into knowledge. As part of the process, the project develops cutting-edge mathematics and statistical methodology to uncover the dependence structure governing HD2 data. In addition to developing a general theory, the project is concerned with applications to financial data, including risk management, forecasting, and portfolio management. More precise estimators, with improved margins of error, will be useful in all these areas of finance. The results will be of interest to main-street investors, regulators and policymakers, and the results will be entirely in the public domain. The project will also provide research training opportunities for students. In more detail, the project will focus on four linked questions for HD2 data: contiguity, matrix decompositions, uncertainty quantification, and the estimation of spot quantities. The investigators will extend their contiguity theory to the common case where observations have noise, which also permits the use of longer local intervals. Under a contiguous probability, the structure of the observations is often more accessible (frequently Gaussian) in local neighborhoods, facilitating statistical analysis. This is achieved without altering the underlying models. Because the effect of the probability change is quite transparent, this approach also enables more direct uncertainty quantification. To model HD2 data, the investigators will explore time-varying matrix decompositions, including the development of a singular value decomposition (SVD) for high frequency data, as a more direct path to a factor model. Both SVD and principal component analysis (PCA) benefit from contiguity, which eases both the time-varying construction, and uncertainty quantification. The latter is of particular importance not only to set standard errors, but also to determine the trade-offs involved in estimation under longitudinal variation: for example, how many minutes or days are required to estimate a covariance matrix, or singular vectors? The investigators also plan to develop volatility matrices for the drift part of a financial process, and their PCAs. The work on matrix decompositions will also benefit from projected results on spot estimation, which also ties in with contiguity. It is expected that the consequences of the contiguity and the HD2 inference will be transformational, leading to more efficient estimators and better prediction, and that this approach will form a new paradigm for high frequency data. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-07

Urban gangs are major security threats in many countries. Who joins these gangs and why? This project builds on a survey of 10,000 grade 7 and 8 boys in a setting characterized by hundreds of well-organized drug-selling gangs. The survey is designed to better understand their beliefs about gang versus legal careers. The project follows the subjects over time, tracking who stays in school, who drops out, who is arrested, and who joins a gang. It assesses what beliefs and circumstances drive gang entry, and how one may predict (and ultimately prevent) gang entry before it happens. After identifying the highest risk youth, the project develops and tests two programs to reduce gang entry. One improves children’s familiarity with and the attractiveness of higher education and legal careers and builds their planning and goal-achievement skills. The other provides financial incentives to avoid criminality. The project tests both approaches with randomized trials. Successful program models could be duplicated and implemented in cities around the world. The project builds on a longitudinal study in a single city charactered by high gang presence that attempted to survey 13- and 14-year-old boys in highest-risk schools. The survey focuses on subjective beliefs about a range of careers, including gangs. It elicits beliefs about financial and non-financial benefits and costs, plus interest in each career. The investigators use these data to estimate structural models of criminal occupational choice, assess which beliefs matter most to the decision, and simulate policies. Using rich administrative data, the project follows respondents long-term in school, arrest, and social security records to determine actual participation in legal and criminal careers. The investigators implement and evaluate several information and field experiments to test which misperceptions drive gang entry and if they can be corrected. Altogether, this is the first longitudinal panel study and experimental evaluations of armed group entry outside a high-income country. Compared to existing longitudinal studies of delinquency, the study has several advantages. The survey begins following youth before the age of recruitment and collects and follows their social network. It links all children to lifetime schooling, crime, and social security data. It is also the first panel to elicit beliefs about the financial and nonfinancial returns to criminal and legal careers (and hence estimate which beliefs matter). Findings from this project inform anti-dropout and anti-child recruitment interventions. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2026 · 2024-06

The United States ranks among the lowest of all developed countries in perinatal health, with high rates of maternal and infant mortality, particularly among women with lower socioeconomic status, those residing in rural regions, and across racial/ethnic backgrounds. Perinatal outcomes are influenced by an interplay of clinical, individual, and social factors, and there is growing interest in how place-based conditions affect maternal and child health (MCH) outcomes. The social, economic, and physical conditions outside the medical system that shape health, have been widely explored particularly through a multitude of place-based measures. However, many of these measures do not fully capture local housing, education, and employment conditions that shape health-related resources and risks. In addition, despite evidence that these place-based factors vary widely across regions in the US and some groups are more sensitive to their effects, the geospatial patterning of housing, education, and employment conditions and their association with MCH health is also poorly understood. Understanding the spatial patterning of housing, education, and work conditions and their association to MCH outcomes would inform the development of tailored, place- based, policies and multilevel interventions. The candidate, Dr. Martinez-Cardoso, is applying for this K01 award in order to develop advanced methodological training to address these research gaps. Dr. Martinez- Cardoso is a well-trained public health researcher with complementary expertise in quantitative data analysis and MCH. The training component of the award includes formal/informal training in big data science, geospatial analytics, and causal inference, paired with a high-caliber mentor and advisory committee. This training will be applied to research characterizing county-level typologies of housing, education, and employment conditions using data science and machine-learning approaches (Aim1). Aim 2 will investigate the association between these typologies and preconception health among women of reproductive age using causal inference methods and multilevel modeling. Aim 3 will explore associations between county-level housing, education, and employment typologies and perinatal health outcomes using spatial multilevel models. Ultimately, this research seeks to contribute to a comprehensive understanding of how local conditions shape MCH outcomes to improve MCH across the United States. The award will also catalyze the candidate’s long-term goal of becoming an independent investigator focused on improving MCH using novel data science tools and innovative multilevel interventions and policies.

NSF Awards · FY 2024 · 2024-06

Gen3 is an open-source software platform that enables researchers to manage, analyze, and share scientific data. There are over twenty Gen3 Data Commons around the world that, in aggregate, manage over 20 petabytes of data that includes 90 million data objects that are findable, accessible, interoperable, and reusable (FAIR). Today, Gen3 is typically used by larger organizations that have experience with setting up and operating large scale cloud computing applications. This project seeks to expand the reach of Gen3 to bring these same powerful data sharing and analytical solutions to smaller research organizations, so that they can achieve the same important benefits for scientific advancement and reproducibility. With funding from the Pathways to Enable Open-Source Ecosystems (POSE) program, the team will develop an open-source ecosystem around Gen3, which will allow them to more easily accept improvements to the code base from the community, learn about and develop new scientific use cases, and create a governance structure that brings community needs into the Gen3 development roadmap. As part of this project, the project will enable development and strengthen the community of users around the open-source data platform Gen3, which will make the product easier to set up and maintain, prioritize features needed by the research community, and make Gen3 more accessible to a broader community, including those with fewer technical or monetary resources. To accomplish these goals, the team will 1) create a governance structure with a steering committee and working groups that will advance the needs of the Gen3 community; 2) improve documentation and new user onboarding; and 3) manage external contributions to the Gen3 source code. With these structural improvements, Gen3 can leverage the expertise of its existing and future users to bring new data sharing solutions to a broad range of researchers. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2026 · 2024-06

Abstract Select humans and animals are able to control persistent viral infections via adaptive immune responses that include the development of neutralizing antibodies (Abs). However, the mechanisms underlying these exceptional protective responses remain largely unknown. Using a positional cloning approach, we identified a gene responsible for virus-neutralizing Ab responses in mice from the I/LnJ strain following infection with two distinct retroviruses, Mouse Mammary Tumor Virus (MMTV) and Murine Leukemia Virus (MuLV). This gene is H2-Ob (Ob), which encodes the b subunit (H2-Ob) of the ab obligate heterodimer H2-O. H2-O (DO in humans), is a non-classical Major Histocompatibility Class II (MHCII)-like molecule and a known negative regulator of the MHCII antigen presentation pathway. The recessive loss-of-function I/LnJ Ob allele allowed for the production of potent neutralizing Abs in infected mice. Subsequent bioinformatics and functional analyses of the human homologues (DOa and DOb) revealed both loss- and gain-of-function variants. Several of these variants were genetically linked to the differential outcomes of hepatitis B and C viral infections in humans which are controlled by neutralizing Ab responses. The process of loading of MHCII molecules with high-affinity, pathogen-derived peptides is mediated by the interaction of MHCII with another non-polymorphic MHCII-like molecule, H2-M (HLA-DM in humans). H2-M function is opposed by H2-O, which acts as an MHCII mimic, binding to H2-M and blocking its ability to catalyze MHCII peptide loading. Importantly, our studies showed that this accepted paradigm of direct competition between H2-O/DO and MHCII for interaction with H2-M/DM was incomplete, because at least 2 mouse Ob, as well as some human DOa and DOb variants result in H2-O/DO molecules, which bind to H2- M/DM but fail to inhibit its function. Clearly, there are gaps in our knowledge of the mechanism by which H2- O/DO negatively regulates MHCII presentation, a process that is central to controlling adaptive immune responses. Using positional cloning in the mouse and a biochemical approach, novel modulators of the MHCII pathway which have not been previously described were identified. We propose to study how these new modulators regulate Ag presentation by H2-O to direct potent virus-neutralizing antibody responses.

NIH Research Projects · FY 2025 · 2024-06

We, and others, have linked the increasing prevalence of non-communicable chronic diseases (NCCDs), to changes in the composition and function of resident intestinal microbes. To gain insight into the mechanisms responsible for a bacteria-induced barrier protective response, we have examined the roles of various Lachnospiraceae products, including the short chain fatty acid butyrate and tryptophan metabolites and commensal flagellins. In this proposal we explore the immunomodulatory capacity of Lachnospiraceae-derived secondary bile acids (SBAs). Bile acids (BAs) have long been known as emulsifying agents which facilitate the absorption of dietary lipids in the small intestine. Emerging evidence shows that BAs also potently regulate mucosal and systemic immunity. In collaboration with the Mimee laboratory at the University of Chicago, we have used a group II intron-based approach to target 3b-HSDH, a terminal enzyme in the biosynthesis of isoDCA, in the prominent Lachnospiraceae species [Ruminococcus] gnavus. R. gnavus is among a small group of gut bacteria which possess both the 3a- and 3b- HSDHs required to epimerize DCA into isoDCA. By pairing this novel mutant R. gnavus with the Clostridial strain P. hiranonis we have created a two-strain consortium that allows us to toggle isoDCA production on and off (while keeping other bacterial products and metabolites constant) in mice with a replete microbiome. This innovative approach will enable an interrogation of the mechanisms by which Lachnospiraceae-derived isoDCA modulates host immunity at homeostasis and an assessment of its immunomodulatory potential in well-established models of intestinal inflammation. We hypothesize that isoDCA has anti-inflammatory effects on all levels of the intestinal immune system including intestinal epithelial cells and CD11c+ antigen presenting cells through the Farnesoid X receptor (FXR) and the G-protein coupled bile acid receptor (GPBAR1/TGR5). In the first Aim we will identify key cell types and signaling mechanisms involved in the immunomodulatory activity of isoDCA. We will then examine the mechanisms by which isoDCA ameliorates intestinal inflammation in Aim 2.

NIH Research Projects · FY 2025 · 2024-06

Abstract The development of effective therapies for the treatment of T cell-dependent autoimmune diseases requires a lucid understanding of the mechanisms by which T cell tolerance is established and conferred. In mice and humans, the T cell repertoire harbors self-reactive conventional T cells with pathogenic potential, necessitating extrinsic regulation by Foxp3-expressing regulatory T cells and other mechanisms. In this regard, research over the past three decades has identified a unique CD4+ regulatory T cell population, termed “Tr1” cells, that is characterized by lack of Foxp3 expression, production of the suppressive cytokine IL-10, and potent regulatory activity capable of preventing or stifling autoimmune reactions in murine models. It has been proposed that Tr1 cells serve as a “failsafe” in scenarios in which tolerance mediated by Foxp3+ Treg cells is incomplete. Importantly, numerous studies have demonstrated that suppressive, antigen-specific Tr1-like cells can be generated in vitro and in vivo, galvanizing considerable interest in harnessing Tr1 cells for the clinical treatment of human autoimmune disease. Despite this great interest, there remain fundamental aspects of Tr1 biology that have evaded elucidation. In this study, we will perform clonal analysis of naturally occurring Tr1 (nTr1) cells in mice. We will utilize a two-tiered strategy pairing TCR repertoire profiling of Tr1-phenotype cells with clonal analyses of TCR “retrogenic” T cells expressing Tr1-biased TCRs. The objectives of this proposal are to define the nature of the TCR repertoire expressed by nTr1 cells and define the differentiation trajectory, reactivity, and transcriptional profile of these clones in vivo and in vitro. We will test the hypothesis that nTr1 cell differentiation is initiated in the thymus following the recognition of widespread self-antigens, leading to the establishment of a stable peripheral pool of nTr1 cells expressing a distinct TCR repertoire. In Aim 1, we will define the TCR repertoire expressed by naturally occurring Tr1 cells. This will provide key insights regarding the diversity and nature of antigens that direct nTr1 differentiation, the stability of nTr1 cells, and the clonal relationship between nTr1 cells and other T cells subsets. In Aim 2 we will determine whether nTr1 cells are reactive to widespread self-antigens, regional self-antigens, or antigens derived from commensal microbiota, and will define whether nTr1 cell differentiation is triggered in the thymus or periphery. In addition, we will use RNA sequencing to define unique signatures that distinguish nTr1 cells from other regulatory and conventional T cell subsets. Our studies will yield the first clonal analyses of naturally occurring IL-10-producing Tr1 cells – an important regulatory T cell population for which fundamental aspects of their antigen specificity, differentiation, lineage stability, and function remain undefined. Ultimately, these advances will be crucial for the development of new strategies to mobilize nTr1 cells for the treatment of human autoimmune disease.

NIH Research Projects · FY 2026 · 2024-06

Project Abstract: Circuit assembly, the collection of sequential developmental steps that ultimately lead to the formation of synapses, is a conserved process that determines organismal function and behavior. In humans, billions of neurons make trillions of synapses, and proper circuit function depends on correct synaptic partnerships. Perturbations in circuit assembly can lead to devastating neurodevelopmental diseases. While it is generally accepted that synaptic connectivity is determined by cell surface receptor interactions, only a relatively small number of these receptors have been identified, and the developmental signaling pathways downstream of these molecules remain mostly uncharacterized. Given the complexity of nervous systems, we need to expedite the discovery of neural receptor/ligand pairs and learn how they signal in order to understand brain development and the physiology of diseases where neural wiring is fundamental. Our labs leverage biochemical and genetic insights into cell surface protein interactions to identify new connectivity codes and corresponding signaling pathways. Previously, in an unbiased protein interaction biochemical screen, we identified two Drosophila interaction networks within the immunoglobulin superfamily – Dprs/DIPs and Beats/Sides. These “interaction codes” guide cell-cell interactions that underlie circuit assembly. Most members of these families bind each other in a complex yet specific manner; for example, each Dpr can interact with a specific subset of DIPs and vice versa. The expression patterns of these proteins are stereotyped, and combinatorial expression of Dprs, DIPs, Beats and/or Sides has been observed, likely serving as unique identity markers on cell surfaces. Deletion of these proteins lead to neural connectivity phenotypes, and specifically for Dpr11 and DIP-γ, misregulation of BMP signaling and neuronal death. Here, we propose to uncover the molecular pathways that are downstream of Dpr-DIP interactions and discover and study other cell surface receptors and secreted proteins that mediate Dpr/DIP function via direct interactions. Our exciting preliminary results already revealed new co-receptors, and follow-up experiments will include biophysical and structural characterization of these new interactions, followed by signaling assays in culture and genetic perturbations in vivo to establish functional roles for these interactions. Furthermore, we will reveal the structural basis of Beat-Side interactions, examine their complexes, manipulate the hetero and homodimeric binding abilities of these proteins and test them using established phenotypes in the embryonic and larval neuromuscular system.

NIH Research Projects · FY 2026 · 2024-06

Abstract: The activities of innate and adaptive immune cells need to be precisely coordinated for an effective immune response to a wide-range of pathogens. There are many similarities between immune responses in different species, but each species also has adapted to combat unique pathogenic insults. Mechanistically, structural variation in the genome between species plays a prominent role in the acquisition (or loss) of regulatory events involved in defining the functional activity of immune cells. Structural variation refers to genome rearrangements such as translocations, insertions, amplifications, and inversions. Structural variation in the genome between species has the potential to substantially alter the placement of genes and regulatory elements, including splitting apart clusters of genes with similar functions, relocating genes to different chromosomes, and changing the orientation of loci. The functional consequences for changes in the genome between species are based on how each change affects the regulatory events responsible for controlling gene expression. Therefore, it is important to define how structural variation between species affects regulatory principles to improve our ability to relate findings from mechanistic and preclinical studies in model organisms to the regulation of the human immune response. In this application, we will define how structural variation between the mouse and human genomes influences the regulatory events involved in controlling genes that are differentially expressed in mouse and human immune cells. We will determine how structural variation between the mouse and human genomes affects the 1) topology of the genome, 2) regulatory events that position topological domain boundaries, 3) enhancer landscape available to genes, and 4) long-range enhancer-promoter interactions for genes with differences in expression between mouse and human immune cells. We will test the functional consequences for divergent regulatory events between mouse and human immune cells, with a focus on defining the regulatory events contributing to differences in the LPS-inducible expression of Nos2 (encodes inducible nitric oxide synthase; iNOS) in mouse and human macrophages, and we will use this to build a mouse model reflecting human expression. The mouse is one of the most widely used preclinical models of the human immune response, and the studies in our proposal will aid in understanding how structural variation between the genomes of model organisms and the human genome contribute to species acquiring different cell-type and stimulation-dependent gene expression patterns and functions. It will also make it possible to predict how mechanisms defined in mice translate to human as well as build mouse models that better reflect human immune responses for pre-clinical studies.

NIH Research Projects · FY 2026 · 2024-06

Project Abstract Long-term success of transplantation and achieving transplant tolerance in the clinic is hindered by recipient sensitization and immunological memory, which predominantly arise as a result of graft rejection, pregnancy and blood transfusions. Paradoxically, semi-allogeneic pregnancy provides a unique example of allogeneic tolerance spontaneously induced in adults. Using preclinical mouse models, we showed that semi-allogeneic pregnancy simultaneously induces T cell tolerance to the semi-allogeneic fetus and to subsequent offspring-matched heart grafts. However, pregnancy also induces humoral sensitization to fetal antigens, and this sensitization overrides pregnancy-induced as well as co-stimulation-induced allograft acceptance. Our research aims to define the mechanisms underlying humoral sensitization by semi-allogeneic pregnancy, and how this sensitization over- rides pregnancy-induced and co-stimulation blockade-induced T cell tolerance of offspring-matched heart grafts. In Aim 1, we will test the hypothesis that at a cellular level, pregnancy enables the differentiation of CD4+ T cells into T follicular helper (Tfh) cells providing help to fetus-specific B cells and facilitating their differentiation into post-partum B cells and antibody-secreting cells. Simultaneously, pregnancy induceds a persistent state of cell- intrinsic hypofunction in fetus-specific non-Tfh cells. In Aim 2, we will test the hypothesis that pregnancy- sensitized Tfh, B cell and antibody responses synergize to constitute a barrier to the induction of transplantation tolerance by co-stimulation blockade. Completion of this project will provide an in-depth mechanistic understanding for the basis and consequence of humoral sensitization by semi-allogeneic pregnancy, and identify treatments capable of preventing and reversing this sensitization. The long-term goal of this project is to improve access to transplantation in historically-disadvantaged multiparous women and to optimize their post- transplant outcomes through the induction of transplant tolerance.

NIH Research Projects · FY 2026 · 2024-06

Project Summary: Tumor cells are exposed to a wide array of stressors ranging from hyperactive protein synthesis and metabolism to nutrient and oxygen starvation in the tumor microenvironment; these stimuli require tumor cells to activate protective transcriptional programs that promote tumor cell survival and growth. X-box binding protein 1 (XBP1) and hypoxia-inducible factor 1 alpha (HIF1a) are two of the most important stress- induced transcription factors (TFs), activate oncogenic and metastatic gene expression programs by assembling into complexes at unfolded protein response (UPRE) and hypoxia-induced response (HRE) elements, respectively. These target DNA sequence ‘motifs’ overlap in many target genes. Triple negative breast cancer (TNBC), the most aggressive and metastatic subtype of breast cancer, is heavily dependent on strong upregulation of XBP1s (the spliced, active form of XBP1), HIF1a and their downstream stress-responsive gene expression networks. Despite the profound need for targeted therapies against these and other oncogenic TFs, they remain largely untapped as drug targets due to the challenges of targeting protein-protein and protein-DNA interactions. Therefore, our team recently developed a modular strategy to create fully synthetic transcriptional repressors (STRs) to directly inhibit the oncogenic activity of TFs by blocking their ability to bind and regulate specific DNA sequences. Using this synthetic platform, we have designed potent (low nM), highly specific, cell permeable, and in vivo active inhibitors of HRE/UPRE-driven transcription. Our lead STRs directly antagonize XBP1/HIF1a for DNA binding in vitro and in cells, resulting in potent, global inhibition of hypoxia-induced gene expression programs, blockade of hypoxia-induced aggressive phenotypes, such as cell invasion, and anti- proliferative effects only under conditions of hypoxia. In animal studies, administration of lead STRs significantly inhibits tumor growth and hypoxia-induced gene expression, validating on-target activity in animals. The proposed project will test the hypothesis that XBP1/HIF1a transcriptional responses can be tightly controlled by optimized STRs that directly target their shared DNA binding sites. This will be accomplished through three complementary Aims: 1) Develop ultra-potent, pharmacologically stable STRs for cell based and animal studies; 2) Map STR-based reprogramming of hypoxia-induced, XBP1/HIF-dependent gene expression and oncogenic phenotypes in TNBC; 3) Test efficacy of optimized STRs in inhibiting TNBC growth, metastasis and chemoresistance using in vitro and in vivo models. These studies will provide fresh insight into the molecular underpinnings and pathogenesis of adaptive stress responses in TNBC, determine the effects of blocking XBP1/HIF1a -DNA binding at the level of chromatin and transcriptional dynamics and establish the efficacy of targeting hypoxia-dependent gene expression on TNBC tumor growth, metastasis and chemotherapeutic sensitivity.

NIH Research Projects · FY 2024 · 2024-05

ABSTRACT RESUBMISSION 1R21 HL164436-01 IN RESPONSE TO NHLBI “NOT-HL-21-024 BOLD AND NEW BIOENGINEERING RESEARCH” In contrast with other organs, preservation times of lung grafts for transplantation are limited to no more than 8 hours with standard cold preservation. Declining quality with extending preservation times increases the risk of primary graft dysfunction, a risk factor for developing chronic rejection, which could account for the low 5-year survival rate (50%) following lung transplantation (LTx). Ex Vivo Lung Perfusion (EVLP) is expected to improve lung preservation and transplant outcomes by providing normothermic circulation and ventilation. A problem is that current EVLP is self-limited by normothermia-activated lung metabolism. The accumulation of toxic metabolites leads to a proinflammatory state, activating Receptor of Advanced Glycation End-Products (RAGE) and nuclear factor (NF)-B mechanisms, which in turn upregulate proinflammatory cytokine signaling. Experimentally, cross-circulation of a whole swine with EVLP by others demonstrated improved lung resuscitation, but the exact contributors to this improvement remain unclear. Own in vitro preliminary data suggest a role for hepatic function in enhancing endothelial preservation. In previous work, we have maintained normal hepatic detoxification, synthesis, and regulation in in vitro circuits using liver cell bioreactors (BRx). We hypothesize first that the liver function in the swine cross-circulation model played a major role in enhancing EVLP and tissue viability. We also hypothesize that a hepatocyte BRx can partly substitute for whole-swine liver function on EVLP and maintain the observed improvements lung preservation and LTx outcomes. Our Specific Aim is to provide proof-of-principle for the ability of hepatocyte BRx to enhance lung graft preservation. We will incorporate a hepatic BRx in our established EVLP circuits and demonstrate its effect on short-term LTx in experimental rat models. We will repeat these experiments using a cadaveric human EVLP model. We will conduct comprehensive phenotypic, transcriptional, and functional endpoint assessments on lung tissue and hepatic cells in BRx, such as RAGE and NF-B. If successful, our technology will provide the means to change the current state of EVLP for lung preservation and allow lungs to be maintained longer outside the donor body with less cellular injury. Ultimately, our work will address current limitations in LTx, including increasing viable donor organ transportation time and distance, helping reduce LTx waiting lists, and improving post-transplant patient survival.

NIH Research Projects · FY 2025 · 2024-05

PROJECT SUMMARY/ABSTRACT Physical inactivity is associated with poor asthma control and lower quality of life. Rates of physical inactivity, asthma, and asthma mortality among Black girls are higher than their White counterparts. Our formative work identified barriers to physical activity among Black women with asthma and led to the development of a culturally tailored physical activity intervention for Black women with asthma (ACTION: A lifestyle physical activity intervention for minority women with asthma). The goal of this study is to adapt the intervention for Black girls with asthma using a dyad approach. We will engage urban Black girls (8-12 years) with asthma and their mothers in interviews to understand how the ACTION intervention should be modified to fit the needs of urban Black girls with asthma. We will modify and then pilot test the intervention (Mothers and Daughters in ACTION). This study will provide the first ever evidence of a family-based lifestyle physical activity intervention culturally tailored for urban Black girls with asthma, a population that is understudied yet plagued by low levels of physical activity and poor health outcomes. We have assembled a multidisciplinary team that has the necessary expertise to carry out the proposed study, including in asthma, physical activity, dyad interventions, program development, qualitative methods, as well as observational and randomized studies. This award will provide the infrastructure and data about feasibility and preliminary efficacy to apply for funding (NIMHD R01 RFA-MD-22-007) to rigorously test the efficacy of the Mothers and Daughters in ACTION and advance management of asthma in minority populations living in low-resourced urban environments.

NIH Research Projects · FY 2025 · 2024-05

PROJECT SUMMARY/ABSTRACT Adversity, economic deprivation, poverty-induced stress, prolonged exposure to trauma and parental distress increase the risk of child maltreatment and may severely undermine the mental health functioning of children. While there are efficacious interventions targeting individual, family, and structural-level factors associated with children’s emotional and behavioral well-being, it is unknown how these interventions interact and complement each other and whether their effects can be synergistic (i.e., if the interventions’ combined effects are greater than the sum of the individual effects). To improve mental health outcomes among children aged 7–14 from low-income families in Azerbaijan, the proposed study will refine and test three evidence-based intervention approaches: (a) family-strengthening intervention; b) trauma-focused mental health care for parents; and c) economic empowerment in the form of Child Savings Accounts. These interventions have been adapted to the context of Azerbaijan. The adapted interventions will be tested with 600 child-caregiver dyads in a trial using the Multiphase Optimization Strategy (MOST) to compare different intervention components and identify the most optimal combination. Given the limited human and financial resources in the LMICs, it will be important to identify whether each of these interventions is necessary and/or sufficient for improving the mental health of children. The study will test the effects of each intervention component on children’s clinical mental health outcomes (symptoms of depression, anxiety; disruptive behaviors; post-traumatic symptoms;) and on cognitive and social processes associated with these outcomes (e.g., attention, inhibitory control, working memory, emotion recognition bias). The study will also examine the mediating pathways associated with each intervention component. If successful, the study results could inform the National Mental Health Care reforms implemented by the Ministry of Health, WHO, UNICEF and other organizations in Azerbaijan and other post-Soviet countries. The proposed study addresses the NIMH’s Strategic Plan Objective 3.2.A by tailoring existing interventions to optimize outcomes, and targets two top challenges within the NIMH Grand Challenges in Global Mental Health Goal B (Advance prevention and implementation of early interventions): 1) to develop locally appropriate strategies to eliminate childhood abuse and enhance child protection and 2) to develop interventions to reduce the long-term negative impact of low childhood socioeconomic status on mental health. Through training, mentoring and collaborative research, the project also aims to strengthen local research expertise in: 1) the core components and mechanisms of change of psychosocial mental health interventions for children and families living in conditions of chronic adversity; 2) the adaptation of multilevel evidence-based interventions and measurement tools to the new socio-cultural context of a post-Soviet country; and 3) methodological and statistical techniques for evaluating complex interventions with multiple components.

NIH Research Projects · FY 2025 · 2024-04

PROJECT SUMMARY Multiple myeloma (MM), the 2nd most common hematologic malignancy, remains incurable with high rates of relapse and drug resistance despite recent advances in treatment options such as autologous stem cell transplantation, novel immunomodulatory agents, and proteasome inhibitors. Shorter duration of initial response predicts poor prognosis even in the modern era of novel agents. Several clinical features and high- risk cytogenetics are currently in use for stratifying patients by severity of disease. However, a substantial number of patients continue to have poor outcomes without known negative prognostic factors. Aberrant epigenetic modifications have been linked with more aggressive types and progression of MM. In addition to DNA methylation and histone modifications, accumulating evidence suggests that post-transcriptional regulation involving RNA modifications, particularly N6-methyladenosine (m6A), is associated with initiation and progression hematological malignancies. Emerging evidence suggests that m6A is also involved in the development and prognosis of MM. However, the role of m6A in outcomes of MM remains largely unknown due partly to the lack of quantitative methods to map whole-transcriptome m6A at high resolution. Some notable challenges of existing m6A profiling approaches include 1) low resolution; 2) not quantitative; and 3) the requirement of a large amount of input materials that are typically not feasible in clinical settings. To address these clinical and technical needs, we designed the m6A-selective allyl chemical labeling and sequencing (m6A-SAC-seq), which features transcriptome-wide profiling of m6A at single-nucleotide resolution with modification fraction information. The objective of this application is to use the m6A-SAC-seq to map transcriptome-wide m6A in CD138+ tumor cells from MM patients to identify m6A modifications associated with treatment outcomes. We will apply this novel technology in banked CD138+ cells collected at the time of diagnosis for ~100 newly diagnosed patients with MM enrolled in our NCI-funded clinic-based survivorship study as well as ~30 samples from a Phase II clinical trial. Our central hypothesis is that specific m6A signatures in CD138+ tumor cells at the time of diagnosis correlate with outcomes in patients with MM. We will identify altered m6A in transcripts associated with early relapse and response to first-line therapy (Aim 1) as well as minimal residual disease (Aim 2). With respect to outcomes, we expect to 1) identify specific m6A signatures and involved pathways that are associated with treatment outcomes among patients with MM; and 2) establish the m6A-SAC-seq for broader clinical applications. The proposed research is highly significant, because it is expected to vertically advance understanding of the biological basis for treatment outcomes of MM and promote the development of a new paradigm for prognostic risk stratification based on m6A modifications that has broad translational importance in the personalized management of high-risk patients.

NIH Research Projects · FY 2026 · 2024-04

ABSTRACT Oxygen is administered to unconscious, mechanically ventilated patients following successful cardiopulmonary resuscitation (CPR) from sudden cardiac arrest to ensure adequate oxygenation and to avoid potential worsening tissue hypoxia. The liberal use of oxygen is near universal because it is regarded as benign and to be of potential benefit. This dogma is being challenged by growing evidence that oxygen contributes to multi-organ injury and decreased neurologically intact survival. Understanding the role of oxygen toxicity on post-CA outcomes represents a major knowledge gap and barrier to improving outcomes. Antioxidants have not been found to be beneficial and the patterns of injury and mechanism underlying its effects are poorly understood. This project attempts to address these barriers by testing the effects of restricting oxygen availability through the administration of hypoxia with a fractional inspired oxygen (FiO2) of 10% between the first- and 7-hours following CA. We term this therapy oxygen restriction therapy (O2RT). Paradoxically, O2RT increased oxygen consumption, lowered biomarkers of glycolysis, decreased cellular injury and improved physiological recovery of the heart and brain resulting in improved survival. In contrast, hyperoxia (FiO2 30%) or room air (FiO2 21%) had the opposite effects. Both hyperoxia and normoxia following CA stabilized the hypoxia inducible factor 1a (HIF1a) while O2RT lowered HIF1a. This finding is relevant because HIF1a regulates changes glycolysis and inflammation. Our findings of HIF1a stabilization suggest potential worsening of tissue hypoxia by hyperoxia or alternatively aberrant HIF1a stabilization resulting in aerobic glycolysis and inflammation that occurs in pathologies like cancer. Aim1 further investigates the effects of O2RT vs. hyperoxia on post-CA injury during a critical 6-hour window of injury. Aim 2 tests the influence of O2RT and hyperoxia on changing patterns of breathing, blood flow, and metabolism in the heart and brain and Aim 3 interrogates the role of HIF1a in the brain and heart using cell specific knock out mice. Success of this research will establish the role of oxygen in mediating post-CA secondary injury while identifying a critical window of injury that can be targeted for therapeutic benefit and identifying HIF1a as a new therapeutic target for limiting oxygen toxicity.

NIH Research Projects · FY 2025 · 2024-04

PROJECT SUMMARY Non-Alcoholic Fatty Liver Disease (NAFLD) and the more severe Non-Alcoholic Steatohepatitis (NASH) are driving increased rates of cirrhosis and hepatocellular carcinoma in the USA. Though obesity is a known risk factor, the overlap between patients with obesity and NAFLD is incomplete, and a full understanding of the mechanisms that govern onset and progression of NAFLD is critically lacking. In this proposal, I will probe the role of the mitophagy receptor BNIP3 in the onset and progression of lipid accumulation in the liver to inform future disease treatment. BNIP3 is a known mediator of selective mitochondrial autophagy (mitophagy), and we showed previously that hepatic BNIP3 expression is highly induced by fasting and has a marked effect on metabolic homeostasis by decreasing mitochondrial mass. We have also shown that a liver-specific deletion of BNIP3 causes spontaneous lipid accumulation in adult mouse liver. BNIP3 is more highly expressed around the central vein of the liver, which is also the region where most lipid accumulates in Bnip3 null liver and in human and mouse NAFLD. Our findings indicate that BNIP3 is a critical regulator of hepatic lipid homeostasis, and the goal of this proposal is to define the mechanism of this regulation. My central hypothesis is that BNIP3 decreases lipid droplet (LD) content by promoting both mitophagy and LD autophagy (lipophagy) in pericentral regions of the liver. I propose that it does so indirectly by facilitating the engulfment of small LDs that are tethered to mitochondria targeted by BNIP3 for degradation at the lysosome. I have shown for the first time that isolated primary hepatocytes retain their patterns of zonal gene expression for over 24 hours following culture outside their hepatic nutrient microenvironment. This allows me to define for the first time the cellular processes modulating lipid metabolism in distinct zonal populations of hepatocytes ex vivo. In Aim 1, I will use this finding to determine whether BNIP3 drives lipophagy to clear LDs predominantly in pericentral hepatocytes. I will exploit machine-learning image analysis tools for unbiased quantification of rates of mitophagic and lipophagic flux in discrete populations of primary hepatocytes, sorted by their zone of origin, to test whether BNIP3 drives lipophagy more highly in pericentral vs. periportal hepatocytes. I will test this finding in vivo by assessing whether exogenous re-expression of BNIP3 is sufficient to clear lipid from pericentral regions of the liver in vivo. In Aim 2, I will test the hypothesis that BNIP3 promotes small LD turnover by targeting small LDs “hitchhiking” on mitochondria to the autolysosome. I propose that knockdown of well characterized LD-mitochondrial tethering proteins, such as PLIN5, will ablate the LD clearance capabilities of BNIP3 by disrupting LD-mitochondrial contacts. My work elucidating the mechanisms that lead to lipid accumulation in the liver may suggest novel ways to prevent NAFLD and NASH in the future.

NIH Research Projects · FY 2026 · 2024-04

Project Abstract Autologous fat grafting (AFG) is a procedure whereby adipose tissue is processed and transferred from one part of the body to another to add volume and address contour irregularity in soft tissue reconstruction. Anecdotally, we see improvement in tissue fibrosis and pain with standard grafting after radiation treatment indicating more than just a volume benefit of AFG. We have recently discovered that the transferred fat or adipose brings in healthy progenitor cells, growth factors and immune cells helpful in tissue regeneration and repair. Thus, purified graft is effectively a biological scaffold which can be modified to direct tissue healing or targeted therapies. One of the hurdles to clinical translation is the variability in graft retention and our ability to follow the graft over time. The long-term goal of our research is to investigate the capacity of engineered adipose grafts to improve clinical outcomes by mitigating inflammation and promoting graft retention. We propose a feasibility study investigating a novel imaging platform to quantitatively assess the overall volume and three-dimensional (3D) shape of the breast after fat grafting in cancer treatment.

NIH Research Projects · FY 2026 · 2024-04

PROJECT SUMMARY/ABSTRACT Organ shape is vital for proper function. Malformations in the looping and folding of the heart, for instance, represent the leading cause of birth defect mortality in humans. Visceral organs rely on the coordinated activity of multiple laminar tissue layers to fold and coil into targeted shapes. While the community has learned much about the genetic signals governing cell fates during development, less is understood about the mechanical stresses and tissue dynamics that translate gene expression into the shapes of organs. This proposal aims to link hox gene expression to physical forces driving 3D multilayer organ shape change using the D. melanogaster midgut as a model system. The midgut begins as a tube of two concentric tissue layers that undergoes a sequence of constrictions to fold into chambers. Hox genes — conserved master regulators of patterning during development — have long been known to govern the final shape of this organ, but the mechanical stresses and tissue dynamics translating hox expression into organ shape have remained elusive. We recently found that organ constrictions proceed through a mechanical program mediated by calcium pulses in the outer layer, under the control of hox genes. Advances in light-sheet microscopy now enable live visualization of the whole organ at sub-cellular resolution during development. Integrating these imaging methods with physics approaches provides the ability to follow cell dynamics across tissue layers throughout morphogenesis and quantitatively relate genetic patterning in the tissue to the tissue mechanics and dynamic cellular behaviors driving 3D shape change. The proposed work aims to first (1) decode the relationship between the hox gene expression pattern to the downstream pattern of calcium pulses in the midgut. (2) Secondly, a physical model will relate calcium pulses to tissue-scale mechanical stress, using spatiotemporal maps of calcium activity to constrain an in silico model of the morphing tissue. Together, these aims will reveal how genetic patterning controls a mechanical process to sculpt complex shapes in a bilayer organ. (3) Finally, this proposal will address how the midgut model visceral organ coils into a chiral tube later during development. Recent discoveries of `cell intrinsic' chirality, in which cytoskeletal machinery breaks left-right symmetry, have proven to provide a major role in determining organ-scale chirality. The mechanical process by which cell chirality translates into 3D organ-scale shape change, however, remains largely unknown. By combining the in toto imaging toolkit and molecular biology approaches mastered during the K99 phase with my expertise in chiral mechanics from my PhD, this aim will link cellular chirality to the dynamics of organ-scale coiling. Together, these research aims and the training in biology, microscopy, and modeling during the K99 phase will ensure I am equipped to begin an independent research lab revealing the physical mechanisms harnessed by biology to sculpt complex shapes of visceral organs.

NIH Research Projects · FY 2026 · 2024-04

Project summary One of the primary goals of the primate brain is to learn about structure in the world, and to shape neural representations such that they encode this structure in an efficient, generalizable format. An important behavior that relies upon the formation of these abstract neural representations is categorization, the process by which objects that may differ in their basic sensory features are assigned to the same behavioral output. Decades of research on the neural basis of categorization has contributed substantially to our understanding of the mechanisms underlying the representation of learned categories, and has led to the identification of a widely-distributed network of brain areas that may be involved, such as the lateral intraparietal region (LIP), prefrontal cortex (PFC), and superior colliculus (SC). However, prior work has almost exclusively relied on tasks that involve teaching non-human primates (NHPs) to assign stimuli to categories using a single visual feature, such as motion direction or color. Natural categorization, in contrast, often requires the integration of multiple features in order to determine to which category an object belongs (multi-feature integration categorization). Categorization and category-learning are disrupted in a number of neurological disorders, such as Alzheimer’s Disease, Parkinson’s, and ADHD, and multi-feature integration categorization seems to show a different pattern of deficits in these disorders than simpler category structures. This suggests that the circuit mechanisms mediating categorization or category learning may differ, depending on task demands. However, little is currently known about mechanisms of stimulus categorization when assignment to the correct category first requires the integration of disparate sensory features. A greater understanding of the neural mechanisms that support feature-integration for categorization will enhance our ability to provide targeted treatment for disorders that disrupt the categorization system. This work will involve conducting large-scale simultaneous electrophysiological recordings in two regions that have been implicated in mediating categorization; LIP and PFC. In Aim 1, neural activity in areas LIP and PFC will be recorded while NHPs switch between performing a multi-feature integration categorization task in which the direction of motion and the color of a moving-dot stimulus must be combined to determine the category, and a motion-direction categorization task in which only the direction of motion is relevant. In Aim 2, paired recording-inactivation experiments will be performed in which LIP (or PFC) will be reversibly inactivated while recording in PFC (or LIP). The results from this study will reveal what computations are necessary to perform categorization tasks of complex structure in which multiple sensory features must be combined or integrated, and how these demands shape the neural mechanism the brain uses to perform these tasks. Further, this work will elucidate the circuit mechanisms underlying categorization behavior through the use of simultaneous multi-area recordings and paired inactivation-recording experiments.

NIH Research Projects · FY 2026 · 2024-04

PROJECT SUMMARY/ABSTRACT Epigenetic modifications play a crucial role in mammalian development, cellular differentiation, and disease, with 5-methylcytosine (5mC) being the most well-studied epigenetic modification. 5mC globally represses gene expression and has significant gene-regulatory importance in various diseases. The ten-eleven translocation (TET) family of enzymes can oxidize 5mC to 5-hydroxymethylcytosine (5hmC), which is a stable marker of global transcriptional activation. While previous studies have characterized the role of 5hmC modifications in healthy human tissues and evaluated plasma cell-free DNA (cfDNA) for its biomarker potential in various malignancies, urine cfDNA has not yet been studied. Urine represents a non-invasive, easily collectible, and proximal biofluid to a number of GU diseases. At present, it is unclear how urine cell-free DNA (cfDNA) 5hmC profiles reflect normal physiological conditions and mirror the composition of neighboring tissues. Researchers wonder whether urine cfDNA 5hmC profiles might offer a superior alternative to plasma cfDNA, the current gold standard in liquid biopsy, in the diagnosis of GU cancers like bladder cancer. To address these questions, this proposal seeks to characterize the genome-wide 5hmC landscape of healthy urine and develop biomarkers in the setting of localized bladder cancer. The proposal aims to achieve these objectives through two specific aims. The first aim focuses on identifying sources of unwanted variation, characterizing the genomic and epigenomic 5hmC landscape, and inferring the tissue-of-origin of cell-free DNA (cfDNA) derived from healthy urine samples. To accomplish this aim, a bioinformatic pipeline will be optimized for processing 5hmC profiles from urine cfDNA. The 5hmC regulation in urine cfDNA will be characterized by analyzing its activity on gene bodies, promoters, enhancers, and various regulatory epigenomic regions. This aim also proposes the creation of tools to determine the tissue-of-origin of urine cfDNA and confirm its enrichment for GU tissues compared to plasma cfDNA, highlighting the applicability of urine cfDNA in GU contexts. The insights gained from Aim 1 will provide a reference for evaluating the deviations in 5hmC distribution in urine cfDNA in various cancer and non-cancer disease states. The second aim focuses on developing robust diagnostic and predictive biomarkers for localized bladder cancer. The study will demonstrate the utility of urine cfDNA 5hmC-profiles in bladder cancer diagnosis and treatment surveillance and compare its performance to plasma cfDNA 5hmC profiles. Additionally, a multi- omics classifier model incorporating 5hmC, copy number, and targeted mutational data will be created and validated for predicting minimal residual disease in bladder cancer patients who underwent curative-intent bladder removal surgery. The results from Aim 2 will generate 5hmC signatures that can be used to predict the onset of localized bladder cancer and to predict minimal residual disease. Ultimately, the data from Aim 2 could deliver a set of new gene and enhancer targets that maybe serve as exciting therapeutic targets for prevenation and treatment of bladder cancer.

NIH Research Projects · FY 2026 · 2024-03

PROJECT SUMMARY/ABSTRACT A major hurdle in the clinical management of pancreatic adenocarcinomas (PDAC) is the profound resistance to chemotherapeutics exhibited by these tumors. PDAC chemoresistance is mediated by the tumor microenvironment (TME) as isolated PDAC cells cultured ex vivo readily respond to therapies while PDAC cells in tumors do not. Thus, identifying the TME factors and mechanisms by which the TME regulates drug response in PDAC is critical to being able to effectively treat this disease. Towards the goal of identifying TME factors regulating PDAC biology, we have taken the strategy of measuring physiological parameters in the PDAC TME and recreating these conditions ex vivo to study in mechanistic detail how PDAC cells are impacted by TME physiology. As part of this approach, we recently developed techniques to isolate interstitial fluid (the local perfusate) from PDAC tumors and quantitative metabolite profiling techniques to measure availability of ~150 major nutrients in the PDAC TME. This provided us with the first quantitative atlas of nutrient availability in PDAC and we found that local nutrient abundance in these tumors was strikingly different than in the bulk circulation or healthy tissues. To study how abnormal access to nutrients in the TME could impact PDAC cells, we developed a novel cell culture model in which PDAC cells are cultured with the precise levels of ~120 major vitamins and nutrients they encounter in the native TME. Using this model, we found that PDAC cells exposed to TME nutrition exhibit resistance to a wide array of clinically used chemotherapies, identifying abnormal tumor nutrient availability as a critical TME factor mediating chemoresistance in this disease. Further analysis of TME nutrient- induced chemoresistant phenotype indicated that: (1) increased availability of the amino acid glycine in the TME causes PDAC cells to become highly chemoresistance and (2) TME glycine does not endow PDAC cells with the ability to evade action of chemotherapies, but rather the ability to tolerate damage induced by therapeutic challenges. Based on these preliminary studies, we developed the hypothesis that TME glycine impairs the ability of PDAC cells to undergo cell death in response to chemotherapeutic insult, thus enabling PDAC cells to tolerate chemotherapeutic treatment. In this proposal, we will determine: (1) the metabolic basis for how glycine accumulates in the PDAC TME and if targeting TME glycine availability can sensitize PDAC tumors to chemotherapy and (2) the mechanism by which PDAC cells gain tolerance to chemotherapeutic stress and if targeting these tolerance mechanisms can synergize with chemotherapy. Therapy resistance is a major contributor to the poor prognosis of PDAC patients. Our work addresses this key therapeutic challenge in a disease with much unmet clinical need and could identify novel therapeutic options for PDAC patients.

NIH Research Projects · FY 2025 · 2024-03

PROJECT SUMMARY An organism’s response to environmental perturbations is a complex process that is influenced by the interplay between genetic and environmental factors. However, despite playing a critical role in health and survival, the gene-by-environment interactions (GxE) shaping disease susceptibility remain poorly understood. Understanding the genomic mechanisms underlying GxE is therefore essential for understanding the consequences of genetic variation on genomic function and complex traits. The immune response to infectious agents is a GxE interaction with clear consequences for health and survival. Mounting an appropriate immune response is essential, but substantial genetic variation in immune function exists within and between species. This makes immune responses an ideal system to understand how genetic and environmental variation interact to shape genome function. Specifically, comparative studies leveraging genetic variation within and between species can help reveal the genomic mechanisms for GxE, while also shedding light on the molecular basis for differences in susceptibility to infectious disease. The research questions driving this proposal are: How does genetic variation, both within and between primate species, influence the gene expression response to immunological perturbations? What are the gene regulatory mechanisms that mediate the relationship between gene expression and genetic variation? Which genetic variants are causally connected to variation in the gene expression response? To answer these questions, I will characterize the transcriptomic response to immune stimuli in peripheral blood cells using a powerful, in vitro assay and single-cell sequencing. This project will identify GxE interactions that are cell type, stimuli, and species-specific. I will then profile chromatin accessibility to identify key regulatory elements involved in the response to immune perturbation and use experimental assays to causally link genetic variation to differences in the response. This project is therefore an ambitious, novel integration of functional and population genetic approaches to study how the genome responds to environmental perturbations. At its conclusion, this study will reveal how immune GxE interactions have evolved among primates, improving our understanding of genome function and the genetic basis for complex traits.