University Of Chicago

NIH Research Projects · FY 2025 · 2022-09

Project Abstract: Small nucleolar RNA (snoRNA) are natural guide non-coding RNAs derived from over 900 annotated snoRNA genes in the human genome. The major known function of about one-third of snoRNAs is to install 2’O-methyl and pseudouridine modifications in the ribosomal RNA. These rRNA modifications guide ribosome assembly and maturation, and fine-tune translation in a cell type and cell state dependent manner. However, the majority of snoRNAs do not have a well described function; they are called orphans because their cellular RNA targets are not known. How snoRNA interacts with the human transcriptome and the functional consequences of these potential non-canonical snoRNA-RNA interactions in gene expression regulation and human diseases remain to be determined. We recently developed several new sequencing technologies that are directly relevant to studying snoRNA biology. They include methods to robustly identify inter-molecular RNA-RNA interactions in cells and transcriptome-wide sequencing of 2’O-methyl and pseudouridine modifications. These new tools will allow us to address mysteries of snoRNA biology. Aim 1 will identify the cellular RNA targets of the snoRNAome through an advanced version of kethoxal-assisted RNA-RNA interaction sequencing (KARR-seq) approach to enable comprehensive capture and identification of snoRNA-RNA interactions at the transcriptomic scale. These results will be used to identify the rules of snoRNA-guided targeting of mRNA sequences. Aim 2 will investigate two types of snoRNA-mRNA interactions transcriptome-wide and the consequences on regulating gene expression through the application of new sequencing methods to map 2’O-methyl and pseudouridine modifications in pre-mRNA and mature mRNA, and associate these results with the snoRNA-mRNA interactome. We will also selectively delete snoRNA genes or knockdown snoRNA levels, alter the expression of snoRNP components to investigate the consequence of specific snoRNA-mRNA interaction. All together these results will provide the first comprehensive snoRNA-RNA interactome and derive the guiding principles of snoRNA-mRNA interactions and the associated biological functions.

NIH Research Projects · FY 2025 · 2022-09

Project Summary The ability to sense dynamic changes in the cellular environment and translate that information into rewired biomolecular interactions forms the backbone of cellular signal transduction. Despite significant interest and investment in methods capable of detecting and quantifying protein-protein and other protein-biomolecule interactions, the most commonly employed methods solely map interactions in non-physiologic environments outside of cells where many important factors contributing to the interactions under study are lost. These methods are particularly poorly suited to study signaling events in cells that rely on the cellular architecture and chemical environment in order to form and function. Therefore, new methods are needed to quantitatively map protein “social networks” inside of living systems. Here we propose to develop and validate several complementary light- dependent proximity profiling platforms capable of detecting protein interaction dynamics in live cells with high spatial and temporal resolution, as well as minimal perturbation to the cellular environment. We will accomplish this goal through three interconnected aims that are supported by preliminary data and our previously published work with an intracellular photoproximity profiling platform. First, we will synthesize and test tunable photoproximity chemical probes to map protein complexes at nanometer scale inside of cells. In parallel, we propose to test potentially more efficient catalytic photoproximity profiling platforms for increased resolution of low abundance macromolecular complexes inside of cells. Finally, we propose to apply these platforms to study the dynamic sensing of altered metabolic and redox stress inside cells through the integrated antioxidant and unfolded protein response pathways. These proximity profiles will enable drafting of the first quantitative, comprehensive maps of the integrated stress response in cells, which will identify points of intervention for diseases such as cancer, aging and neurogenerative disorders. Furthermore, the methods and proximity profiles developed herein will also be widely useful to the biological community for application to diverse questions in intracellular signal transduction.

NIH Research Projects · FY 2024 · 2022-09

PROJECT SUMMARY / ABSTRACT Despite a steady rise in cure rates, cancer remains deadly for many children, especially those with relapsed or refractory disease. Precision medicine holds great promise for these kids, but matching children to available clinical trials remains a challenge due a lack of up-to-date information and highly complex eligibility criteria based on clinical information and genomic and immunophenotype biomarker data. In collaboration with The Leukemia & Lymphoma Society, the Pediatric Cancer Data Commons (PCDC) team has developed GEARBOx (Genomic Eligibility Algorithm at Relapse for Better Outcomes), a clinical trial matching tool to allow clinicians to quickly find potential matches for their patients with relapsed or refractory acute myelogenous leukemia (AML). We now endeavor to expand GEARBOx to include several more tumor types, including acute lymphoblastic leukemia, neuroblastoma, rhabdomyosarcoma, Ewing sarcoma, and osteosarcoma. Additionally, we will augment the often-manual abstraction of eligibility criteria from clinical trials with new automated methods. The information available to clinicians about trials will be supplemented to include critical data for how to quickly and efficiently enroll a child on a matched study. Finally, the PCDC team will partner with a third-party flow cytometry lab (Hematologics) to create ways to automatically pull and incorporate structured immunophenotype data directly into the GEARBOx tool. These enhancements will greatly enhance the process of finding appropriate clinical trials for patients and then getting them enrolled, thus improving access to critical precision therapy for these children.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY/ABSTRACT: Immune checkpoint inhibitors (ICI) are active in only 10-25% of metastatic, castrate-resistant prostate cancer (mCRPC) patients. Co-clinical immune profiling studies of the tumor microenvironment (TME) in mCRPC patients and murine PC models demonstrated sparse immune infiltrates, with predominance of immunosuppressive myeloid cells, particularly tumor-associated macrophages (TAM). PTEN loss-of-function (LOF) occurs in multiple cancers, and specifically in 50-75% of mCRPC. It is associated with poor prognosis, therapeutic outcomes and de novo/acquired resistance to ICI in preclinical and clinical studies in multiple tumor types. In addition to the predominance of TAM within the sparse immune infiltrate in PC, we observed a 2-fold increase of myeloid derived suppressor cells within the PTEN LOF TME, relative to isogenic PTEN-proficient counterparts. These data reinforced our project goal of elucidating mechanisms underlying altered cancer/myeloid cell cross-talk in PTEN LOF mCRPC, that are likely similar across PTEN-deleted malignancies and contribute to ICI resistance. We have demonstrated that cyclic GMP-AMP Synthase (c-GAS)/Stimulator of INterferon Genes (STING) pathway, typically activated in response to cytosolic DNA double strand breaks (DSB), is frequently silenced in cancer cells, and cGAS/STING activation within myeloid compartment of the TME is critical for generating a robust immune infiltrate. However, generation of DNA DSB is insufficient to enhance T cell infiltration, which is consistent with lack of response to PARP inhibition (PARPi) plus ICI observed in our murine models and clinical studies. Probing more deeply into this disconnect, we found that failed STING pathway activation within TAM was responsible for this resistance. Furthermore, PI3K activity was preventing STING pathway activation in TAM, and PI3K inhibition (PI3Ki) plus DNA damage with PARPi led to ICI responsiveness in PTEN-proficient, but not in isogenic PTEN-knockout PC, suggesting that additional immunosuppressive mechanisms are driven by PTEN LOF. The central hypothesis of this proposal is that PTEN LOF PC are de novo resistant to DNA DSB sensing c-GAS/STING pathway activation, which can be overcome by direct STING agonist-based combinations, leading to ICI sensitization. To test this hypothesis, we propose the following specific aims. First, we will dissect the TME in a completed investigator-initiated clinical trial of PARPi/ICI in mCRPC patients, to determine whether the immune inhibitory mechanisms identified in preclinical models are relevant to patients. Second, we will elucidate the cancer cell extrinsic mechanism(s) by which PTEN-deficient PC are de novo resistant to DNA-sensing STING pathway activation. Third, we will interrogate the anti-cancer mechanism and therapeutic potential of direct STING agonist/PI3Ki combination therapy in sensitizing PTEN-knockout murine CRPC to ICI. Collectively, these “co-clinical” studies will provide the mechanistic foundation for the next wave of immunotherapeutic strategies to eradicate PTEN LOF mCRPC.

NIH Research Projects · FY 2024 · 2022-09

Diffuse characterized histone substitution levels and By profilying the epigenome of H3K27M mutant DIPG patient cells I found that H3K27M co-localizes with H3K27 acetylation (H3K27ac). In accordance with previous biochemical data, heterotypic H3K27M- K27ac nucleosomes co-localize with bromodomain proteins at actively transcribed genes, whereas PRC2 is excluded from these regions, suggesting that PRC2 is not sequestered at sites of incorporation of H3K27M. I also showed that the heterotypic nucleosomes H3K27M-K27ac co- localize with bromodomain proteins in DIPG, importantly treatment with BET bromodomain inhibitors in DIPG xenograft mouse models potently reduces tumor growth and extend animal survival. During my mentored phase (K99) I'm planning to study the molecular details of the formation of the heterotypic nucleosomes using in vitro biochemistry and molecular biology assays and gather further insights in the pathogenic mechanisms of aberrant acetylation and H3K27M deposition in DIPG. While transitioning toward the independent phase (R00) I'm planning to improve the BET inhibitors therapeutic strategy by identifying mechanisms of resistance and cooperative factors that can lead to an improved and durable therapy for children affected by DIPG. Altogether my plan is to perform experiments that push forward our knowledge of this incurable disease with the goal of finally having a standard-of-care option that can offer a reliable and efficacious treatment for DIPG patients. Intrinsic Glioma (DIP G) a highly aggressive pediatric brainstem tumor by rapid and nearly uniform patient demise. A heterozygous point mutation of H3 occurs in more than 80% of these tumors, and results in a lysine-to-methionine (H3K27M). Expression of this histone mutant is accompanied by a reduction in the of Polycomb Repressive Complex 2 (PRC2) mediated H3K27 trimethylation (H3K27me3) this is hypothesized to be a driving event of DIPG oncogenesis. Pontine is

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY In recent decades, bioimplants in human bodies have been more and more routinely used in almost every biomedical specialty, with the functions ranging from pathological and biological studies to medical treatments and restoration of body functions. Among all the different types of bioimplants, implantable electronic devices comprise a major category that provide highly accurate and programmed signal transductions. However, the longevity and stability of all types of bioimplants, including electronic devices, have been facing a common challenge, that is the excessive ingrowth of collagen and inflammation reactions around the device, which have been known as “foreign-body response (FBR)”—a type of immune-mediated reaction on foreign/synthetic material “invaders”. Even for the most successful, FDA-approved bioimplants that have been used for decades, excessive FBR can be provoked in many individuals, which is the primary cause of the device failure before their desired functional periods. For solving this commonly existing grand challenge, although a substantial amount of efforts has been made in the development of new biomaterial designs for suppressing FBR, the research has been almost exclusively focused on insulating-type polymers/hydrogels. To proceed to the next horizon of solving the immune-compatibility problem for implantable electronics using the most promising material family— electronic polymers, it is vitally important for us to develop a set of innovative material designs for electronic polymers for concurrently achieving superior immune compatibility and high electrical property. We propose to achieve this by intellectually addressing the extraordinary challenge of unprecedentedly interfacing immunology with semiconductor physics and polymer sciences, and experimentally combine the approaches of polymer synthesis, morphological engineering, device fabrication, electrical characterizations, in vitro cell tests, and in vivo animal tests. Specifically, the focuses of this research include four aspects: 1) developing new designs of semiconducting and conducting polymers for achieving immunocompatible chemical property; 2) developing “hydrogel-architecture” polymer semiconductors for realizing tissue-level elastic moduli for achieving immunocompatible physical property; 3) in vitro and in vivo study of the elicited FBR by these immunocompatible designs of electronic polymers; 4) combining the material and device developments to realize proof-of-concept immunocompatible devices, including electrophysiological devices, and transistor-based biochemical sensors. Based on the highly important uses of implantable electronics, we envision the realization of immunocompatible electronic devices from this research will create significant benefits and far-reaching impacts to a wide spectrum of biomedical areas.

NIH Research Projects · FY 2025 · 2022-09

The United States biomedical workforce is responsible for scientific discovery and advancement of our nation’s science. Early-career researchers bring new ideas, skills, and talents to support such innovation and impact. In 2024, the National Institutes of Health funded over 5,000 early-career researchers with career development awards, supporting the research pipeline that is critical for scientific discovery. Such funding is foundational in the early career stage, and researchers must transition to independence with continued funding to remain in the biomedical workforce and advance the research enterprise. Early-career faculty, including those at pivotal points in their trajectory such as transitioning to independence, are more vulnerable to challenges at the local and national levels due to fewer established funding sources and publishing opportunities. As such, interventions are needed to support early-career researchers to successfully transition to independence. Coaching, a practice commonly utilized in business and management, holds potential to be a high-impact intervention for early-career investigators. Coaching applies inquiry, encouragement, and accountability to increase self-awareness, motivation, and the capacity to take effective action. The current literature on coaching in medicine suggests benefits for clinicians and administrators in terms of process metrics largely. Few studies have focused on investigators, combined individual and group coaching with customized feedback, or examined productivity and advancement outcomes. This randomized controlled trial aims to evaluate a professional coaching intervention directed at early-career investigators, based on having a K-level or equivalent award. This novel intervention is based on principles of social cognitive career theory, and content is aligned with researcher competencies and informed by early-career researchers. Outcomes focus on established measures of success for faculty investigators, including self-efficacy, research productivity, and career advancement obtained through surveys (Aim 1 and 2). These data will be combined with interviews to fully capture the impact of the coaching program by understanding nuanced individual experiences (Aim 1) and experiential sampling method to examine the mechanism by which the program fosters research productivity and career persistence (Aim 3). Results from this study will provide rigorous evidence about the effect of a novel, theory-based coaching intervention on early-career investigators while offering a scalable approach that can be readily adopted by academic institutions and professional organizations. Dissemination will be supported by the development of a train-the-coach guide and coaching program toolkit. Such interventions are vital to maintain a skilled biomedical workforce and support scientific innovation in order to address the health needs of the nation’s population.

NIH Research Projects · FY 2025 · 2022-09

We propose to conduct research that will determine the impact of relevant behaviors on HIV prevention among young people, such as heavy cannabis use. Data from our group and others demonstrate heavy cannabis use as prevalent and increasing in young people is associated with HIV acquisition, use as a sex-drug, greater likelihood of membership in an HIV transmission cluster, and decreased HIV testing. We propose to explore mechanisms, specifically neurocognitive impacts of heavy cannabis use, linking heavy cannabis use to HIV prevention outcomes, and whether motivations for cannabis use, amidst a changing cannabis regulatory, social acceptance and legal landscape, modify its effects on HIV prevention. In the proposed study, we will rigorously examine links between heavy cannabis use, neurocognition, sex behavior and PrEP care engagement. First, we will elucidate the effects of cannabis use on neurocognition - specifically, brain systems supporting risk/reward (RR) processing, as well as higher order organizational functions collectively referred to as executive function (EF) in young people. Second, we will explore how cannabis use, directly and via neurocognitive impacts, is associated with HIV prevention, and particularly PrEP care engagement (primary outcome). The proposed study will integrate and expand these lines of research within the context of traditional health department and CDC supported HIV prevention programs that engage young people in the South Side of Chicago and adjacent suburbs. We will use rigorous objective measures to assess cannabis use (e.g., quantification of cannabis metabolites in plasma), neurocognition (e.g., neuroimaging) and PrEP outcomes (e.g., EMR measured persistence), and triangulate that data using validated survey measures. We will also rigorously account for other substance use, as a proportion of young people who use cannabis also use other substances (e.g., alcohol), and there is increasing recognition of the need to study substance use as it occurs in real-world settings, including polysubstance use. We will assess these factors longitudinally over 1.5 years (3 times 9 months apart) in a cohort of 280 young people living with and living without HIV, to permit examination of within-individual biological changes and the dynamic nature of cannabis use and its association with prevention care outcomes. We propose to conduct research that will determine the impact of relevant behaviors on HIV prevention among young people, such as heavy cannabis use. We propose to explore mechanisms, specifically neurocognitive impacts of heavy cannabis use, linking heavy cannabis use to HIV prevention outcomes (and particularly PrEP use), and whether motivations for cannabis use, amidst a changing cannabis regulatory, social acceptance and legal landscape, modify its effects on HIV prevention. Identifying neurocognitive mechanisms through which cannabis use affects HIV prevention and the importance of motivations for cannabis use in understanding clinical outcomes will provide targets for future HIV prevention efforts.

NIH Research Projects · FY 2025 · 2022-09

ABSTRACT Mounting evidence shows the microbial communities living in (and on) the human body play a key role in the etiology of disease. A major obstacle in the field is the dearth of reliable methods for extracting meaningful signals from small, noisy, intercorrelated, and highly variable microbiome datasets. Enhancing the ability of researchers to generate robust characterizations of the complex relationship between microbiota and their hosts will support novel, more reliable diagnosis of disease and bring the field one step closer to finding the causal links underlying microbiome-based therapeutics. Until now, however, researchers have not had the huge volume of data required to draw these conclusions. Although microbiome data from hundreds of thousands of samples is available in the NCBI Sequence Read Archive (SRA), these datasets have not been leveraged at a large scale. To bridge this gap, we will build an automated pipeline to process and aggregate more than 750,000 samples of amplicon and shotgun metagenomics sequencing data from all publicly available human microbiome samples. We will build a platform, which we call "The Human Microbiome Compendium," for compiling collections of relevant samples that can be used by researchers to find ecological dynamics that have until now been hidden in the noise. The compendium will allow users to see relative abundances of microbial taxa in every sample, which will also be linked to NCBI metadata and annotations generated by a new tool that imputes a uniform set of descriptors for sample type, body site, and host traits. We will also use the compendium to train machine learning models for dimensionality reduction, which will improve the power of independent microbiome studies by incorporating insights from the compendium's collection of hundreds of thousands of samples. These data and tools will be distributed across multiple channels, including a web application where users will be able to upload data to be processed in real time by the dimensionality reduction tools. The proposed studies will generate the first comprehensive aggregation of the microbiome datasets available via the SRA, which will be used to provide characterizations of the human microbiome in unprecedented detail. The resulting compendium will encourage the use of publicly available data and inform new microbiome analysis tools that will help extract important associations in studies where it's impractical to acquire the sample sizes required by conventional techniques. Results from this study will be a starting point to identification of microbiome biomarkers for disease and the development of novel therapeutic approaches.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY Celiac disease (CeD) is a complex T cell-mediated enteropathy induced by dietary gluten in HLA-DQ2+ and/or HLA-DQ8+ individuals, which currently affects 1% of the global population. A gluten-free diet (GFD) is, to this date, the treatment of choice for CeD. However, 50% of CeD patients are unable to effectively adhere to a diet that sustainably excludes gluten, with many patients suffering from inadvertent gluten exposure. Moreover, over 30% of CeD patients have persistent high symptom burdens, resulting from continued mucosal damage, despite adhering to a GFD. Persistent mucosal damage on a GFD is associated with several severe complications, including malignancies, especially lymphomas and bone diseases. In addition, patients with active CeD display a wide range of clinical presentations, including metabolic defects (vitamins, iron, and cholesterol) that are not correlated to the degree of tissue damage. Although much progress has been made in understanding CeD, major gaps remain, notably regarding the biological mechanisms involved in different clinical presentations and the inconsistent healing process. For instance, it is poorly understood why, independently from the degree of villous atrophy, certain patients display nutrient and lipid deficiencies, whereas others have normal levels of vitamins, cholesterol, and iron. Furthermore, while there is evidence for a role of the microbiome in CeD, we lack information on small-intestinal mucosal microbiota in human CeD (which is more likely to have metabolic effects and directly interact with the immune system). Finally, we have little knowledge about interactions between gluten, intestinal epithelial cells (IECs), immune cells, and the microbiota, and how they are linked to the different CeD clinical phenotypes. Our RC2 proposal will test the hypothesis that CeD is a heterogeneous disorder, while attempting to define interactions between IECs, microbiota, immune system, and genetics that underlie differences in clinical presentation, severity of tissue destruction, and the ability to heal. It will also address critical gaps in our understanding of CeD pathogenesis and clinical presentations, and develop tools for non-invasive monitoring of CeD patients. We have assembled a team of internationally recognized experts in the field of CeD, epithelial cell biology, mucosal immunology, microbiome, and chemistry. The RC2 proposal is anchored around multi-omics studies performed in the context of cross-sectional and interventional gluten challenge and de-challenge studies, on 445 well-characterized adult and pediatric patients. The proposed specific aims are: 1) Developing an approach to precision medicine in CeD; 2) Deciphering the mechanisms associated with tissue destruction and healing in CeD, 3) Developing non-invasive tools for monitoring CeD patients, and 4) Developing research resources for the scientific and medical community to advance patient care as well as discovery-based and hypothesis-generating science. This application aims to generate the much- needed knowledge base and resources to further our understanding of CeD pathogenesis and its heterogeneity, improve individualized patient care and follow-up, and develop new therapeutic and preventive targets.

NIH Research Projects · FY 2024 · 2022-09

Project Abstract Most effective tumor treatments target multiple cellular mechanisms. This proposal will explore a previously under-appreciated cellular mechanism in cancer biology using a newly developed high throughput sequencing technology. Transfer RNAs (tRNAs) are adaptor molecules that read the genetic code for protein biosynthesis. tRNAs are essential for gene expression, an emerging source of cancer-related biomarkers, and a treasure trove of epitranscriptomic marks from both human and disease-associated microbes. tRNAs are dysregulated in many cancers. Due to technical difficulties, tRNA biology and its implications in clinical cancer care have lagged far behind other DNA and RNA-based approaches. We recently developed a new technology called Multiplex Small RNA-seq (MSR-seq) which makes feasible for the first time clinical-scale tRNA studies. Specific Aim 1 will further expand the capability and scope of MSR-seq for clinical samples. Colorectal cancer (CRC) is the second leading cause of cancer-related death in the US. Chemotherapy regimens have not substantively changed in a decade, are unnecessary for 50% of patients, and ineffective in another 30%. Currently there is no way to categorize patients ahead of time. Recent studies provide evidence that gut bacteria can influence growth and metastasis of colorectal tumors. Interactions between tumors and commensal gut microbes provide a new lens to understand the biology of CRC and a new opportunity to identify patients at risk for cancer recurrence and patients who have no need to endure chemotherapy. Specific Aim 2 will apply MSR- seq to screen a biobank of blood, biopsy, and stool samples from CRC patients, and to study a murine model of CRC recurrence. This combination of a unique biobank with a new technology has potential to transform how CRC is treated and explores the complex host-microbe interactions in a human disease.

NIH Research Projects · FY 2025 · 2022-09

Project Summary/Abstract Episodic memory impairment is a serious challenge for individuals with neurological and psychiatric disorders that impact the hippocampus, including epilepsy, brain injury, neurodegeneration, schizophrenia, and PTSD. The development of effective treatments will require better understanding of brain mechanisms that support memory formation, storage, and retrieval. The goal of this project is to improve such understanding by testing a hypothesis about the role of the human hippocampus and its interactions with large-scale brain networks in memory formation. Episodic memory formation is a temporally extended process whereby individuals actively sample information in the environment via saccadic eye movements (for visual information), bind this information into an evolving memory representation, and then use this memory representation to inform subsequent viewing of information, and so on. Although the necessary role of the hippocampus in episodic memory formation is well established, little is known regarding how it participates in the extended process of memory formation that occurs during active sampling. This represents a knowledge gap in mechanistic understanding of episodic memory formation, as active sampling is the dominant manner in which memories are created. This project tests the role of the human hippocampus in providing online representation of episodic content and providing the top-down signals to brain networks for visuospatial attention and visual processing needed to drive visual sampling for the formation of coherent episodic memories. This hypothesis will be tested in several experiments that measure and manipulate hippocampal activity within eye-tracking tasks designed to isolate the interplay between memory and visual sampling during memory formation. These experiments will be performed in individuals with epilepsy undergoing neurosurgical procedures as part of clinical care, as this provides invasive recordings of neural activity (iEEG) from the hippocampus and other regions of interest with temporal resolution that matches the rapid pace of eye movements. The temporal resolution of iEEG is key to addressing the hypotheses concerning how the hippocampus drives visual sampling, in addition to responding to it. Direct electrical stimulation through the iEEG electrodes will also be used to test the necessary role of hippocampal processing in driving active visual sampling. By rigorously testing the role of hippocampus in interaction with large-scale networks during the process of memory formation that occurs via active sampling, this project aims to better understand mechanisms relevant to the disruptions of memory formation that occur in neurological and psychiatric disorders. These findings could inform technological approaches to treat memory disorders.

NIH Research Projects · FY 2025 · 2022-09

Project Abstract: National trauma center verification relies on a commitment to injury prevention efforts, including against community-level violence. Hospital-Based Violence Recovery Programs (HVIPs) have expanded across the country as extensions of Level I and II trauma centers to address trauma recidivism with individual behavioral modification during the “teachable moment”. There is no evidence to date that has demonstrated effectiveness in this approach for HVIPs, despite proliferation across the country. A criticism of this approach to violence prevention is the difficulty for community-based violence prevention specialists from HVIP programs to address the larger inequities in the Structural and Social Determinants of Health (SSDOH) that lead to violence through individual behavior modification. Medical-Legal Partnerships have been one approach that has demonstrated evidence and success in improving health outcomes and reducing health-harming legal needs of patients, by connecting legal experts to medical experts for holistic care. This has yet to be done for trauma patients and has, to our knowledge, not been incorporated into any HVIP approach thus far, for a Medical-Legal Partnership (MLP). In our biphasic proposal, our UG3 aims are to clearly identify the types of health-harming legal needs of our patients and families affected by firearm violence and examine the population-level differences in types of legal needs by sociodemographic and geographic factors. We them aim to develop the HVIP-MLP model for implementation at our urban, Level I Trauma Center on the South Side of Chicago. Our UH3 aims would be to then examine implementation outcomes (acceptability and feasibility) of our novel MLP compared to standard of care with our HVIP. We would then examine health outcomes via a pragmatic clinical trial measuring primary health outcomes (stress and health-related quality of life) and secondary, validated SSDOH outcomes [improvements in income, housing & utilities, employment, legal needs and personal & family stability (I-HELP)]. As a developmental exploratory aim, we will also measure stress and health-related quality of life in our HVIP- affiliated violence recovery specialists that engage their patients in the MLP model, as well access the intervention themselves, as needed. Close coordination with the CLIP-VP Coordinating Center will be essential specifically for data handling, measurement, analytics support and consultation with future public/stakeholder engagement and dissemination to demonstrate our public health impact. This novel HVIP-MLP approach has the potential to broadly impact the HVIP model to include an MLP component to all trauma centers for verification to support patients, families and providers alike in this important public health work.

NIH Research Projects · FY 2025 · 2022-09

We will conduct a Hybrid Type II effectiveness-implementation randomized controlled trial of a Case Management Dyad (CM2) intervention, an evidence-based triadic social work intervention that uses a case manager dyad to engage patients in economic stability services. CM2 innovates on existing care continuum engagement models by (1) prioritizing resource counseling to improve care and prevention continuum outcomes, and (2) utilizing a triadic network approach where a client meets with a dyadic case management team in tandem–forming a triad with the client–which provides additional supports for the client and the case managers. CM2 is timely given that intensive interventions are critical for engaging community members most impacted by disease. CM2 will also test robust implementation strategies to support CM2 implementation and to enhance the professional development and prevent burnout in the front-line workforce. The CM2 intervention and associated implementation strategies emerge from prior work conducted by the Investigative Team. We will build upon these experiences, infrastructures, and relationships to evaluate the effectiveness and implementation of CM2 among N=180 patients. Data collection, at baseline, and every 6 months over 18 months, will include surveys and electronic medical record data. To study implementation, we will use the Consolidated Framework for Implementation Research as the determinant framework and RE-AIM as the evaluation framework. The specific aims are to: (Aim 1a) Evaluate the primary (financial well-being, food security) and secondary (care engagement) effectiveness of CM2 vs routine Non-Medical Case Management; (Aim 1b). Evaluate the effectiveness (time to successful resource referral completion, CM job satisfaction, CM burnout and CM-client relationship) of the CM2 intervention vs. routine Case Management among case manager study participants; (Aim 2a) Determine the extent to which financial well-being and food security mediate the relationship between CM2 and downstream 18-month integrated care continuum outcomes; (Aim 2b) Explore potential differential effects of CM2 on primary (resource) and secondary (care continuum) outcomes, based on mental health, substance use, housing and employment; and (Aim 3) Evaluate implementation strategies and outcomes at both patient and case manager levels using RE- AIM to study reach, adoption, implementation, and maintenance. Implementation strategies include individual and dyadic supervision, team consultation, and a train-the-trainer model, and implementation outcomes are acceptability, feasibility, appropriateness, feasibility, fidelity and cost. If successful, CM2 will intensify existing case management resource support systems, which will not only impact the lives and care continua of patients, but also fulfill a priority of revitalizing and sustaining the frontline workforce.

NIH Research Projects · FY 2024 · 2022-09

We will conduct a Hybrid Type II effectiveness-implementation randomized controlled trial of a Case Management Dyad (CM2) intervention, an evidence-based triadic social work intervention that uses a case manager dyad to engage younger Black sexual minority men (YBSMM) aged 18-35 in economic stability services. CM2 innovates on existing care continuum engagement models by (1) prioritizing resource counseling to improve HIV care and prevention continuum outcomes, and (2) utilizing a triadic network approach where a client meets with a dyadic case management team in tandem–forming a triad with the client–which provides additional supports for the client and the case managers. CM2 is timely given that intensive interventions are critical for engaging community members who have not benefited from existing Getting to Zero efforts. CM2 will also test robust implementation strategies to support CM2 implementation and to enhance the professional development and prevent burnout in the HIV front-line workforce, some of whom are directly impacted by HIV. The CM2 intervention and associated implementation strategies emerge from prior work conducted by the Investigative Team. We will build upon these experiences, infrastructures, and relationships to evaluate the effectiveness and implementation of CM2 among N=180 YBSMM. Data collection, at baseline, and every 6 months over 18 months, will include surveys and electronic medical record data. To study implementation, we will use the Consolidated Framework for Implementation Research as the determinant framework and RE-AIM as the evaluation framework. The specific aims are to: (Aim 1a) Evaluate the primary (financial well-being, food security) and secondary (integrated PrEP persistence/viral load suppression) effectiveness of CM2 vs routine Ryan White Non-Medical Case Management and PrEP Resource Counseling among YBSMM; (Aim 1b). Evaluate the effectiveness (time to successful resource referral completion, CM job satisfaction, CM burnout and CM-client relationship) of the CM2 intervention vs. routine Ryan White Case Management and/or PrEP Resource Counseling among case manager study participants; (Aim 2a) Determine the extent to which financial well-being and food security mediate the relationship between CM2 and downstream 18-month integrated care continuum outcomes; (Aim 2b) Explore potential differential effects of CM2 on primary (resource) and secondary (care continuum) outcomes, based on mental health, substance use, housing, employment and HIV serostatus; and (Aim 3) Evaluate implementation strategies and outcomes at both YBSMM and case manager levels using RE- AIM to study reach, adoption, implementation, and maintenance. Implementation strategies include individual and dyadic supervision, team consultation, and a train-the-trainer model, and implementation outcomes are acceptability, feasibility, appropriateness, feasibility, fidelity and cost. If successful, CM2 will intensify existing case management resource support systems, which will not only impact the lives and care continua of YBSMM, but also fulfill an ending the epidemic priority of revitalizing and sustaining the HIV frontline workforce.

NIH Research Projects · FY 2025 · 2022-09

Chromatin, the assemblage of protein, DNA and RNA that represents the physiologic form of the eukaryotic genome, imposes a million-fold length-scale compaction to fit DNA in the nucleus. Rather than serving as mere static packaging, chromatin structure acts as a dynamic regulator of underlying DNA function. Local chromatin structure may be stable for decades, yet is sufficiently dynamic to respond to signaling pathways, potentiating transcriptional program changes in development, disease, and environmental changes. Indeed, cellular identity and changes thereof are intimately connected to chromatin states-- keeping a neuron a neuron and not a liver cell. Apart from DNA sequence-specific transcription factors, the information carriers responsible for this structural variation are chemical modifications to the genome itself and attendant histone proteins involved in packaging (often referred to as “epigenetic” marks), as well as noncoding RNA acting at the chromatin interface. Although little known about these epigenetic information carriers, it is clear that they play crucial roles in development, cognition and disease. Elucidation of the molecular mechanisms by which epigenetic information carriers impact chromatin structure and function, particularly in the context of transcriptional activation is the unifying theme of the Ruthenburg lab. In the next four years, we will discover and characterize the detailed mechanisms of new epigenetic information carriers, focusing on nucleosome-level variation and orphaned histone modifications, defining binding partners for recently appreciated DNA modifications and their function, and performing detailed mechanistic characterization of a class of molecules we discovered--chromatin-enriched noncoding RNA that act as local transcriptional activators. In addition, we will biochemically define the function of RNA in the MLL/SET1 family of histone modification complexes and its functional consequences in cellular contexts. Our interdisciplinary work in these areas will require the development of new tools and experimental approaches—our outstanding track record of pioneering tool development with NIGMS funding makes the case that future efforts will meet with similar success. The fundamental mechanistic understanding of epigenetic information systems we will develop through these avenues will impact our understanding of nuclear function and its dysregulation in disease.

NIH Research Projects · FY 2024 · 2022-09

PROJECT SUMMARY In order to accurately store and retrieve memories, information about novel or salient experiences must be flexibly integrated into existing memory networks while maintaining the stability of previously stored memories. To accomplish these goals within the same circuit, the hippocampus must encode novel experiences and retrieve neural representations of familiar ones in parallel. Disruption of this balance between encoding and retrieval may underlie memory deficits observed in numerous neurological disorders that affect the hippocampus. The dentate gyrus (DG) and CA3 subfields of the hippocampus are often considered to be essential for memory encoding and retrieval, respectively. Encoding and retrieval in these regions rely on two complementary computational processes, pattern separation and pattern completion. Pattern completion in CA3 allows for a full memory to be retrieved despite incomplete inputs, while pattern separation in the DG prevents interference between similar memories during encoding. Mossy cells, a relatively understudied DG cell type, occupy a key node in the DG/CA3 circuit and mediate communication between these areas. Mossy cells, which receive extensive neuromodulatory inputs, may regulate DG/CA3 activity to enhance encoding of novel experiences and retrieval of familiar experiences. The central hypothesis of this proposal is that mossy cells promote encoding of novel environments by regulating the activity and neural computations of the DG/CA3 circuit. Technical limitations have prevented extensive study of mossy cells in vivo, and it is unknown how exploration of novel environments affects DG/CA3 circuit dynamics. I will perform two-photon calcium imaging in the dorsal hippocampus of mice as they explore novel and familiar virtual tracks to evaluate the role of mossy cells in encoding novel environments and regulating DG and CA3 activity. In aim 1, I will directly record activity from mossy cells to determine how their spatial activity differs in novel and familiar virtual environments. In aim 2, I will examine how mossy cells regulate communication between the DG and CA3 by recording granule cell and CA3 pyramidal cell population dynamics while optogenetically inhibiting mossy cell activity. Finally, in aim 3, I will generate a computational model of a combined DG/CA3 circuit to directly examine how pattern separation and pattern completion within this circuit are regulated by mossy cells. Understanding the neural basis of memory encoding and retrieval is an instrumental step toward lessening the burden of memory impairments observed in numerous cognitive disorders. The results of this proposal will provide fundamental insights into the role of mossy cells in regulating these essential memory processes.

NIH Research Projects · FY 2024 · 2022-09

PROJECT SUMMARY In sexually reproducing species males and females have divergent morphologies, behaviors, and reproductive strategies to reach their respective fitness optima while sharing a largely similar genome. These differences can cause sexual conflict, wherein the presence of a particular trait can result in opposite fitness effects in males and females. In intralocus sexual conflict (ISC) the presence of a single gene within a locus can increase the fitness of one sex while decreasing the fitness of the other. There is widespread evidence of ISC occurring in many animals, including humans, and the presence of sexual dimorphism suggests that some aspects of ISC can be resolved. While previous theoretical and gene association studies have helped predict ISC and strategies for its mitigation, we still have little empirical evidence of which genes are involved in ISC, their roles, and their direct impacts on sex-specific fitness in evolution. Recently, our laboratory published the first direct evidence implicating new gene evolution through gene duplication in the resolution of ISC. We found that a pair of recently duplicated genes in Drosophila had quickly accumulated sequence changes and acquired essential, sex-specific functions in male and female reproduction—supporting previous theoretical predictions. This was a groundbreaking finding as it suggests that ISC resolution can drive new gene evolution. However, the generality of this single case study remains unknown. The objective of this proposal is to define the generality of sexual conflict-driven new gene evolution. I hypothesize that intralocus sexual conflict resolution can drive the evolution of new genes through rapid acquisition of novel functions which contribute to sex-specific fitness. I will test my hypothesis in two major Aims. First, I will use a CRISPR-Cas9-aided reverse genetic approach to assess the genetic necessity of 36 newly duplicated genes through sex-specific fitness assays. Thus far I have knocked out seven new genes and found that loss-of-function mutations in three genes reduced the fertility of male or female flies, suggesting they may have contributed to the resolution of an ancestral sexual conflict. Second, I will conduct a deeper functional analysis on five genes examined in Aim 1, using RNA sequencing at both the tissue and single cell levels, to identify pathways and cell types that require new gene functions in resolving sexual conflict. My proposed research combines a CRISPR-Cas9-based reverse genetics approach with transcriptome profiling to define the generality of ISC-driven new gene evolution and how these new genes facilitate sex-specific functions to mediate or resolve sexual conflict.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY The long-term objective of this proposal is to build an electrochemical atlas of organelles to guide the rational manipulation of inter-organelle contacts in the context of neurodegenerative diseases. A new mode of intracellular communication is emerging at the level of organelles, whereby the membranes of two juxtaposed organelles are physically connected, via protein-protein interactions on their cytoplasmic faces, referred to as inter-organelle contacts. Ions and small molecules are actively transferred from one organelle to the other across these contacts, traversing two sealed membranes. Inter-organelle contacts are vital to cell function, tissue homeostasis and physiology because they regulate processes ranging from lipid metabolism to apoptosis. However, we still do not know what signals initiate contact formation or what switches on chemical transport across contacts, nor can we discriminate between functional and dysfunctional contacts. Hence, although we know of specific mutations in proteins that disrupt contact, leading to diverse neurodegenerative diseases, we still do not know how to restore these contacts and treat those diseases. I posit that the electrochemical states of organelles, alone and in contact, will inform which pathways and molecules should be targeted to rectify aberrant contacts in disease states. My rationale is that, if we abstract out the molecular details, inter-organelle contacts resemble neuronal synapses. Even in synapses, ions flow on cue across two sealed, abutting membranes. Just as ion-transport mechanisms across neuronal membranes were revealed by Hodgkin and Huxley’s electrochemical model, an analogous model of organelle membranes will reveal ion flow mechanisms across inter-organelle contacts and which specific flows are impacted in disease. I propose to build an electrochemical atlas of organelles as a universal reference to study contacts in health and disease. This atlas will be a compendium of equations comprising electrochemical models of major organelles, alone and in contact. By enabling us to discriminate normal and aberrant contacts, I envisage the atlas will reveal common pathways across diseases that can be targeted to restore contacts with impacted ion flows. The inability to assay ions or voltage in organelles has prevented the development of electrochemical models of their membranes. Over the last decade, my lab developed a chemical platform to quantify ions and voltage in organelles. By integrating electrophysiology to this platform, I propose to now map out the electrochemical characteristics of organelle membranes in isolation and in contact, and make an electrochemical atlas of organelles. We will apply the atlas to elucidate how Ca2+ flow across aberrant contacts between the endoplasmic reticulum and the lysosome can be rectified to restore lysosomal Ca2+ in parkinsonism. Dysregulated lysosomal Ca2+ is a common factor across many neurodegenerative diseases and the value of the electrochemical atlas is its pioneering ability to reveal common pathways that can be targeted for treatment in a disease cross-cutting manner.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY/ABSTRACT CANDIDATE: As a postdoctoral fellow in Dr. Scott Lowe's lab at Memorial Sloan Kettering Cancer Center (MSKCC), my research has focused on the contribution of recurrent genetic lesions to metastasis in pancreatic ductal adenocarcinoma (PDAC). My long-term goal is to establish an independent research program that aims to identify and mechanistically understand metastasis determinants in PDAC, with the ultimate goal of exploiting this knowledge for therapeutic benefit. The proposed research will form a solid foundation on which I can establish my own research group by the end of the mentored phase of this award. I have developed a detailed training plan to ensure my successful transition to independence, which focuses on four key areas: (1) scientific and career mentorship; (2) acquisition of additional knowledge and expertise; (3) professional development; and (4) launching a lab and separation from mentor. RESEARCH: Metastasis is the major cause for the high morbidity and mortality of PDAC, yet few determinants of this metastatic proclivity have been identified. Genomic studies have produced catalogs of recurrent mutations in PDAC, but the functional contribution of common genetic lesions to metastasis remains unclear. My early postdoctoral work has shown how two of these lesions, loss of Smad4 and deletions at the Cdkn2a locus, remove potent barriers to metastasis. By employing novel mouse models, I have discovered that restoration of Smad4 expression can disrupt established liver metastases, and a cluster of type I interferon (IFN) genes that are frequently co-deleted with Cdkn2a suppress metastasis by enforcing tumor immune surveillance. This proposal will test the hypothesis that Smad4, type I IFNs, and other recurrently deleted genes cooperate to inhibit PDAC metastasis through a combination of tumor cell autonomous and non- autonomous mechanisms. I will leverage innovative in vivo platforms to elucidate the mechanisms of metastasis suppression by Smad4 (Aim 1), and to identify genes that cooperate with type I IFNs to block metastasis (Aim 2). These studies will illuminate molecular and cellular programs that suppress metastasis in PDAC, which could inform new strategies for therapeutic intervention in advanced disease. ENVIRONMENT: MSKCC provides an ideal environment for me to accomplish my training and research goals, and successfully transition to an independent faculty position at an academic institution. My mentor Dr. Lowe is a world leader in cancer biology, with a particular expertise on tumor suppressor genes, mouse models, and functional genetics. In addition, I have assembled an advisory committee of three established scientists with relevant expertise and strong commitment to mentoring (Drs. Massagué, Rudensky, and Iacobuzio-Donahue), who will support my transition to independence by providing valuable research and career guidance. Together with the collaborative environment and broad spectrum of resources at MSKCC, this support network creates optimal conditions for the successful completion of the proposed research and career development plans.

NIH Research Projects · FY 2025 · 2022-09

Project Summary/Abstract Brain metastases (BMs) are a life-threatening disease, occurring in up to 40% of cancer patients. About 40% of BM patients have multiple (≥4) BMs (mBMs). Whole brain radiotherapy (WBRT), which has long been the standard of care for mBMs patients, has shown pronounced impairment of neurocognitive functions. Stereotactic radiosurgery (SRS) has improved tumor control and reduced negative effect on cognition function, compared to WBRT. However, it has been historically reserved only for patients with <4 BMs. Recently, several clinical trials reported strong evidence to support SRS for mBMs patients. National Comprehensive Cancer Network guidelines hence no longer restrict the number of BMs for SRS. However, the larger BM number in mBMs patients substantially increases the complexity of treatment planning. Conventional manual forward planning to manually determine plan parameters becomes cumbersome and impractical for mBMs. Modern inverse planning methods can determine plan parameters by solving an optimization problem that is composed of multiple objectives designed for various clinical or practical considerations, while the priorities among these objectives affect the resulting plan quality. The physician’s preferences for a particular patient can hardly be quantified and precisely conveyed to the planner, especially for mBMs patients due to the varying number, size, and locations of BMs. Hence, the best physician-preferred plan is often achieved through extensive trial-and-error priority tuning and several rounds of interactions between the planner and physician. Consequently, planning time can take up to hours, and plan quality may be suboptimal and can vary significantly, due to the varying levels of physician and planner’s skills and physician-planner communication and cooperation, leading to deteriorated clinical outcome. Inspired by the recent colossal advancements of artificial intelligence (AI), particularly deep reinforcement learning (DRL) and deep inverse reinforcement learning (DIRL), on intelligent decision-making in computer visions and robotics, we propose to develop an artificial intelligence driven automatic SRS treatment planning system for effective management of mBMs (Aid-mBMs), learning a human-level intelligence on treatment planning from human experts. We envision the system to have two deep neural networks: DNN-R that acts as an AI-physician to predict the physician’s preferences for each individual patient, and DNN-P that acts as an AI-planner to tune the priorities to achieve a plan of physician’s satisfaction. We will pursue two specific aims. Aim 1. System prototype development: We will collect human expert planners’ priority-tuning actions and develop DNN-R and DNN-P via interleaved DIRL-based reward function learning and DRL-based policy learning. Aim 2. System improvement and end-to-end evaluation: We will perform a prospective study to improve our system based on human expert’s further fine-tuning actions on the generated AI plans, and then evaluate the feasibility, effectiveness, and efficiency of our system. Upon completion, Aid-mBMs will provide high-quality and efficient SRS treatment planning to benefit mBMs patients, especially those in resource-limited regions.

NIH Research Projects · FY 2025 · 2022-09

Project Summary/Abstract: A fundamental problem in biology is to understand how the compendium of proteins in an organism (the ‘proteome’) cooperatively interact to create phenotype. Despite considerable experimental and computational advances with respect to defining and inferring protein-protein interactions (PPIs), no method currently exists to infer a hierarchy of protein interactions: that is, how proteins interact to create complexes, pathways, and phenotype. This proposal uses bacteria as a model to develop a novel statistical method that transforms a genome sequence into a hierarchy of protein interaction networks. Key to this approach is the advance that components of variation typically discarded as noise (harboring < 0.01% variance) in fact do contain biologically important information regarding PPIs. Preliminary results illustrate that our statistical method may be an effective multi-scale framework to describe emergent biological function arising from a ‘parts-list’ of proteins. We call our approach Spectral Correlation Analysis of Layered Evolutionary Signals (SCALES); the main thrust of our proposal is testing the experimental validity and robustness of our approach. With respect to validity, we will combine high-throughput molecular genetics with computation to test whether SCALES can accurately infer functions of uncharacterized proteins using P. aeruginosa as a model system. With respect to robustness, we will test whether our results are robust to the genomic feature used for measuring co-variation. Looking to the future of the laboratory, SCALES may be generally useful for understanding hierarchical architectures across different biological systems, spanning proteins to cells to ecosystems. Therefore, we believe this proposal will serve as a critical launching point to explore important concepts central to the focus of the post-genomic era, namely creating novel mathematical frameworks by which to convert the torrent of high- content, complex data being collected into useful and actionable biological knowledge. For defining the vision of the laboratory, natural systems are products of a generative process that is poorly understood—the evolutionary process. Though properly described as random variation and selection, evolution generates remarkably ordered, low-entropy biological systems that execute high-performance functions, are robust to perturbation, and have the capacity to adapt to new functions. It is therefore conceivable that quantitatively understanding design architectures of evolved systems, and how they come to be, may yield a new theoretical foundation of engineering for systems with natural-like properties; namely, the ability to dynamically interact with the environment. The broad vision of the Raman Lab is to elucidate organizational principles that govern the ability of evolved systems to work as well as maintain fitness. We hope to address this problem in a variety of systems subject to component variation and environmental selection. In doing so, our ultimate hope is to create rubrics for designing adaptive systems intelligently.

NIH Research Projects · FY 2025 · 2022-09

Innate lymphocytes include ILCs and innate-like NKT/MAIT/gamma-delta T lymphocytes that characteristically acquire Th1-, Th2- or Th17-like helper programs as well as tissue-resident properties during development in the bone marrow or thymus. In that respect, they differ fundamentally from their adaptive T cell counterparts, which are born naïve and recirculating, and only acquire tissue resident effector properties after exposure to pathogens and cytokines. Our research focuses on understanding the different mechanisms that control the parallel development of these populations in very different contexts. While we previously reported that the transcription factor (TF) PLZF was a common signature of innate lineages that directed their innate developmental fate, this project focuses on the layer of regulatory enhancers that differentially control the helper lineage-specific TFs Gata-3, T-bet and RORgt in innate and in adaptive lymphocytes, with emphasis on NK cells. We develop an epigenetic approach that identifies these enhancers and we generate enhancer reporter strains that are used to specifically manipulate innate and adaptive populations. The advantage of this approach is that epigenetic markers appear earlier and are more stable than the TF that they regulate. They also provide more complexity and specificity to dissect these developmental programs. In support of this approach, we recently identified a dedicated, ILC2- specific enhancer and generated mice lacking this enhancer to dissect the respective contribution of innate and adaptive type 2 responses in models of allergic airway inflammation. Here, we will apply this new approach to elucidate the issues of identity and relationship between NK cells and other group I lymphocytes, which express closely related properties and a degree of plasticity that have greatly confounded prior studies. The specific aims will (SA#1) identify candidate enhancers of the NK developmental pathway through a genome-wide bioinformatic search; (SA#2) validate these enhancers in vivo through CRISPR deletions; (SA#3) generate enhancer-reporter strains that specifically identify and manipulate NK cells. These studies will provide novel insights into the complexity and specificity of Group 1 Innate Lymphocytes, and generate new tools to probe their respective contributions in homeostasis and in tumor, infection and autoimmune conditions. RELEVANCE (See instructions): Our studies investigate a recently uncovered population of so-called innate lymphocytes. These cells act early in the immune response and provide major contributions in maintaining tissue health and in regulating the response in tumors, infections, allergy and autoimmune conditions. Specifically, we develop new genetic mouse models that will help define the differences between NK cells and ILC1s, two related subtypes that exert potent but distinct contributions against tumors and viral infections in mouse and human.

NIH Research Projects · FY 2025 · 2022-09

Triple negative breast cancer (TNBC), the most aggressive and metastatic subtype of breast cancer, is one of the major causes of cancer death in women. TNBC also has lower survival rates for primarily local cancers. Loss of hormone receptors and the lack of HER2 overexpression in TNBC limit treatments to cytotoxic therapies such as radiation, a key clinical strategy for 10-15% of breast cancer patients. Hypoxia is a major cause of resistance to radiotherapy, chemotherapy and even immunotherapy. Thus, identifying mechanisms to suppress the hypoxia stress response and increase the sensitivity of TNBC tumors to therapy remains a top clinical priority. Upon hypoxic stress, cancer cells initiate a transcriptional program that enables them to survive and migrate from an inhospitable microenvironment. While hypoxia-inducible factors (HIFs) are generally considered the main effectors, growing evidence suggests the hypoxia cellular response is much more complex and requires coordinated signaling with other stress response factors. One promising candidate is BACH1, a transcription factor that is induced by hypoxia and represses transcription of genes involved in heme oxidation and anti-oxidant production. Based on preliminary results, we now hypothesize that BACH1 is stabilized by hypoxia and functions as a key inducer of the cellular hypoxia response in TNBC cells leading to abnormal leaky vasculature that contributes to intratumoral hypoxia and radiation resistance. Specifically, we plan to: 1. Determine whether BACH1 is regulated by oxygen and induces a transcriptional hypoxic stress response in TNBC cells; 2. Determine whether BACH1 promotes angiogenesis, leaky vasculature and hypoxia in TNBC tumors; and 3. Determine whether BACH1 depletion sensitizes TNBC tumors to radiation. We propose that targeting BACH1 represents a unique strategy for increasing tumor oxygenation to improve the efficacy of cytotoxic, standard-of-care therapies such as radiation. Normalizing vasculature to suppress leakiness should also facilitate drug delivery to tumors. Since BACH1 can be targeted by an FDA approved drug either alone or in combination with HIF inhibitors, the proposed work could lead to a clinical trial in breast cancer and other cancer patients whose treatment involves radiation therapy.

NIH Research Projects · FY 2025 · 2022-08

The goals of this research project are to adapt elements of two existing career readiness interventions to the needs of young men, ages 18-29, living with HIV. Once adapted, a pilot study of the intervention will be conducted with 40 young men to determine intervention feasibility, acceptability, and efficacy for improving care engagement. To ensure this program can serve the needs of young men living with HIV, the research team will engage in a formative phase of adaptation, wherein quantitative and qualitative data will be collected from employers. A sample of potential employers (n=50) will complete a survey focused on challenges related to hiring and retaining individuals living with HIV. A second sample (n = 20) of potential employers will complete an interview with project staff, where they will respond to vignettes focused on successes and challenges a hiring manager could encounter when trying to hire and retain employees who are young men living with HIV. These data will inform the adaptation of the program. Next, a series of focus groups will be conducted with members of the population (n = 40) to identify what they most need in a career readiness intervention. More specifically, this phase will work to ensure the adapted intervention addresses the range of concerns associated with employment for young men irrespective of HIV status. Next, the research team will conduct a theater test with 8 young men aged 18-29 years old and 10 stakeholders serving the population, wherein stakeholders will observe the administration of content from the existing interventions to identify which content should be retained, adapted, or replaced. Next, 3 to 5 experts on employment and treatment barriers will be asked for additional feedback for intervention revision. The feedback will be used for additional revision of the program curriculum. Finally, a computerized readability test will ensure that language used in the revised intervention manual and activities is accessible to a 6th grade reading level. After the intervention manual and delivery procedures are finalized, 40 young men, ages 18-29, will be enrolled in a single arm pilot trial, with follow-up assessments at 6 and 12 months. The primary research outcomes for the pilot study are feasibility and acceptability. Additional outcomes include hours worked per week, job seeking self-efficacy, and proportion of missed HIV care visits. Further, we will use implementation science measures to identify the best approach for delivering the intervention in a community setting. Primary implementation outcomes are relative advantage of the intervention and implementation climate. Secondary outcome is readiness for implementation.