Fred Hutchinson Cancer Center

NIH Research Projects · FY 2026 · 2026-06

Abstract PROJECT SUMMARY/ABSTRACT In the US, vaginitis accounts for greater than 10 million medical office visits each year. Vaginal discharge syndrome is often indicative of bacterial vaginosis (BV), vulvovaginal candidiasis (VVC), or trichomoniasis. Each condition is associated with adverse reproductive and sexual health sequelae; annual costs for managing vaginitis exceed several billion dollars. Accurate diagnosis of vaginal discharge is critical for providing appropriate therapy. Some diagnostic tests are rapid and inexpensive, but insensitive, such as saline wet mount with microscopy to diagnose trichomoniasis. Other tests are highly sensitive and specific, such as nucleic acid amplification tests, but are expensive and may delay the diagnosis if sent offsite to a reference lab. A substantial number of women with vaginitis are misdiagnosed and receive inappropriate treatment. Syndromic management is common and there is an unmet need for new approaches of diagnosing infectious causes of vaginitis. Small molecule metabolites in vaginal fluid, products of microbial and host metabolism, have great potential to serve as diagnostic biomarkers for vaginitis. We have shown that metabolic profiles are dramatically different in women with and without BV and have identified several individual metabolites that have diagnostic potential. These molecules may also be useful for early detection, prediction of recurrence, and evaluation of test-of-cure. We propose to identify and validate vaginal fluid metabolites that may be diagnostic of BV, trichomoniasis and WC (Aim 1). We will also evaluate changes in concentrations of metabolites prior to the onset of symptoms to assess early predictors of disease and determine if changes in metabolites after treatment of vaginitis predict subsequent relapse (Aim 2). We will use vaginal fluid samples from two study populations for the training set. The first set includes samples previously collected from 251 women with >100 episodes of vaginitis. A unique feature is that daily samples were collected both prior to diagnosis of vaginitis and post-treatment. The second set will comprise prospectively collected vaginal fluid samples from 105 women with and without vaginal symptoms from a different geographical site to ensure selection of representative biomarkers. A sequential metabolomics approach will be used. First, a global untargeted metabolomics screen will provide >4000 metabolite features. A subset of metabolites will be selected using machine learning approaches that accurately classify each vaginitis condition. Absolute concentrations of this subset will be measured, and diagnostic performance will be assessed when compared with gold standard tests. High-performing metabolites will be used to develop a diagnostic algorithm that will combine metabolites for optimal diagnostic performance. The diagnostic algorithms will be independently validated using vaginal fluid samples from 720 women with and without vaginal discharge attending 26 sites in 18 US Metropolitan Statistical Areas. We will also determine the value of these metabolites for test-of-cure and ear1y diagnosis. We expect that this study could result in a simple, streamlined diagnostic algorithm for vaginitis based on metabolites produced by vaginal pathogens.

NIH Research Projects · FY 2026 · 2026-06

Project Summary/Abstract This application is focused on the MYC network, a group of conserved transcription factors that regulate gene expression programs linked to cell growth and proliferation. The MYC family of transcription factors (TFs) are the “founding” members of the network. While known to be essential for normal development, the expression of MYC family TFs is dysregulated in a wide range of cancers and drives growth-related changes that support tumor initiation, progression, immune escape and chemoresistance. We have shown that critical aspects of MYC’s oncogenic activity occur within the context of the MYC network, which is comprised of related, yet functionally distinct, TFs. We have found that these factors can promote and/or antagonize MYC’s normal and oncogenic activity. The individual network proteins are expressed and regulated in response to different signals (mitogenic, differentiation, growth arrest, metabolic flux) and possess different subcellular localizations and stabilities. Evidence indicates that the network is dynamic and that its effects on cell behavior are affected by changes in the abundance and activity of individual network members. This proposal builds on our findings, using genetically engineered mouse models, that two members of the MYC-network, MAX and MGA, each function as potent tumor suppressors. First, MAX is the obligate dimerization partner of MYC and is required for its transcriptional activity. Surprisingly however, MAX deletion acts to broadly induce neuroendocrine neoplasms in which MYC-MAX genomic binding is abolished, but the MYC proliferative expression signature is reconstituted by multiple shifts in genome occupancy of other network members. Second, deletion of MGA dramatically accelerates tumor progression in a lung adenocarcinoma model. Our goals involve elucidating how perturbation of the MYC network through MAX or MGA loss of function lead to oncogenesis. We hypothesize that significant alterations in enhancer-promoter interactions and chromatin architecture, as well as shifts in protein-protein interactions among network members underlie a more rapid evolution of neoplasia. Moreover, we will determine whether the derepression of meiotic cohesins observed in MGA-deleted tumors contributes to genomic damage and instability. We will also identify functional regions within the large (>3000 residue) MGA protein and screen for specific dependencies and vulnerabilities acquired by both the mutant MAX and MGA cancers. Our work identifies two different ways by which the balance among MYC network TFs can be perturbed. Because MAX and MGA alterations/mutations appear to be pervasive among a wide range of human cancers, the impact of this study lies in its potential to harness our knowledge of the dynamics of this essential gene regulatory network in order to develop novel genetic and chemical avenues to control cancer. Our use of mice in part of this study permits us to recapitulate cancer initiation, progression and metastasis under normal mammalian physiological constraints in an efficient and cost-effective manner.

NIH Research Projects · FY 2026 · 2026-06

PROJECT SUMMARY/ABSTRACT Herpes simplex virus type-2 (HSV-2) is one of the most prevalent sexually transmitted infections, affecting over 400 million people worldwide and nearly twice as many people with XX chromosomes as people with XY chromosomes. HSV-2 causes lifelong, recurrent lesions due to its ability to evade the adaptive immune system and establish latency. Understanding the immune response to early infection before the virus establishes latency can provide valuable insight into therapeutic and vaccine design. Early HSV-2-induced inflammation triggers the production of type I interferons (IFNs) which have broad effects on priming and enhancing the host response. Regulatory T cells (Tregs), an immunosuppressive subset of CD4+ T cells, have been shown to respond to IFN signaling in a systemic viral infection model, whereby IFNs attenuate Treg function to enable a functional, virus-specific effector T cell response. As HSV-2 causes a local infection in the vaginal mucosa, it is unknown how IFN signaling affects Treg function in a more nuanced infection model, especially since we have previously shown that vaginal Tregs are phenotypically distinct from the circulating Tregs that would be involved in a systemic infection. Preliminary data of murine vaginal tract Tregs shows that upon exposure to IFNs, Tregs have decreased expression of suppressive and activation markers. Using a conditional knockout mouse line where the IFNα receptor (IFNAR) is selectively deleted on Tregs, there is a decrease in cytokines and chemokines related to antigen presentation and T cell recruitment. This suggests that IFN signaling in Tregs is necessary to promote antigen-specific T cell activation. We hypothesize that IFN signaling in Tregs is responsible for attenuating Treg suppressive function during the early stages of HSV-2 infection to allow for appropriate antigen presentation and effector T cell priming. The proposed studies will use a combination of phenotypic, functional, and genomic sequencing assays to determine the mechanism by which IFN signaling in Tregs alters Treg suppressive function and the extent to which this impacts HSV-2 immunity in the vaginal mucosa.

NIH Research Projects · FY 2026 · 2026-06

This application is responsive to Notice of Special Interest: Women’s Health Research, which seeks research to to extend healthy lifespan among older women. There are currently 1.4 million women in the U.S. ages 90 and older, which is expected to quadruple by 2050. While women’s lifespans are increasing, their healthspans, or years of healthy life, have not been rising. Identification of novel strategies to extend healthspan is important for older women, who live longer than men but experience a greater number of years lived with chronic diseases and physical impairment. Age is the strongest known risk factor for chronic diseases; yet, the mechanisms through which aging confers this risk are unknown. Evidence is emerging that clonal hematopoiesis of indeterminate potential (CHIP), an age-related phenomenon in which cells undergo somatic mutations that lead to overgrowth (“clones”) of a genetically distinct subpopulation of blood cells, is a risk factor for chronic diseases and mortality. However, several questions related to the epidemiology of CHIP and aging remain unanswered. In particular, the extent to which CHIP increases risk of multimorbidity and mobility impairment, conditions that are highly prevalent in older women, is unknown. Moreover, the impact of CHIP on exceptional longevity has been vastly understudied, as few cohorts have adequate numbers of long-lived survivors. Further, the mechanistic pathways through which CHIP influences disease and healthspan are unclear. We plan to use a large sample of ~10,000 older women from the deeply phenotyped Women’s Health Initiative (WHI) cohort who already have undergone deep targeted CHIP sequencing, including ~7,000 with longitudinal CHIP data at two time points 14-19 years apart. We will supplement the existing WHI CHIP resource by obtaining new baseline CHIP measures using our highly sensitive targeted gene sequencing method to study exceptional longevity prospectively in a total sample of 15,314 women (30% African American, 14% Hispanic, 11% Asian, and 38% White). In Aim 1, we will examine associations of baseline CHIP and longitudinal CHIP changes with multimorbidity and mobility impairment. In Aim 2, we will determine associations of CHIP with exceptional longevity (survival to ages 90, 95, and 100) and exceptionally healthy aging (survival to age 90 with intact mobility and free of cardiovascular disease, cancer, type 2 diabetes, and cognitive impairment/dementia). In Aim 3, we will use epigenomic and proteomic data to identify novel biological pathways that lie in the causal pathway between CHIP and outcomes from Aims 1 and 2. Our study will have a transformative impact by: (1) evaluating the potential for CHIP to be used as a novel, blood-based aging biomarker to predict risk of age-related diseases to advance precision medicine in older adults; and (2) identifying mechanistic pathways through which CHIP impacts disease risk and healthspan, which may identify novel therapeutic targets to concomitantly delay or prevent multiple chronic diseases and preserve mobility in older adults. Key findings will be replicated and extended to men in the extensively phenotyped UK Biobank and Jackson Heart Study.

NIH Research Projects · FY 2026 · 2026-06

SUMMARY Lung cancer screening (LCS) using low dose computed tomography (CT) can reduce mortality in individuals with high-risk smoking histories. However, there are critical limitations to current LCS approaches, which rely solely on interpretation of imaging findings, including: a) The mortality benefit is largely driven by patients with adenocarcinoma (AD) lung cancer, with limited benefit for squamous cell carcinoma (SCC) or small cell lung cancer (SCLC). b) CT screening frequently results in “indeterminate nodules” for which clinical management to determine malignancy is based on AD growth trajectories and often relies on repeat imaging. c) Current LCS protocols and resulting guidelines were created based on evidence from trial cohorts that do not reflect the most at-risk populations. The recent United States Preventive Services Task Force recommendations for LCS state, “Research to identify biomarkers that can accurately identify persons at high risk is needed to improve detection and minimize false-positive results.” Our biomarker data show lung cancer histological subtypes display distinct risk factors consistent with their different pathology, etiology and outcomes, leading our multi-disciplinary team to employ a novel lung subtype-specific approach to address the shortcomings of current LCS. Our methods include both detection of specific blood autoantibody levels and quantitative imaging features to assess the distinct risk of AD, SCC and SCLC lung cancer and will be used in concert with existing guidelines to recommend follow-up actions and lead to earlier diagnosis. While tissue analysis will still be used in diagnosis and treatment of lung cancer, our approach for screening will overcome critical limitations of current guidelines to better classify AD indeterminate nodules and increase SCLC and SCC detection sensitivity, thus identifying patients who benefit from immediate action. Our specific aims are to #1: Validate the performance of our subtype specific risk prediction models in existing LCS sample sets. #2: Evaluate the performance and real-world utility of our risk prediction models prospectively in patients undergoing LCS across multiple sites and populations.

NIH Research Projects · FY 2026 · 2026-06

PROJECT SUMMARY Microsimulation modeling is a powerful tool for using scientific evidence to inform health policy by projecting the long-term harms and benefits of interventions. Models are especially useful for estimating long-term effectiveness, harms, and costs of new cancer screening tests because gold-standard studies take decades to complete. Out of necessity, modeling has become an accepted way to generate evidence to aid in the creation of screening guidelines set by United States Preventive Services Task Force. The stakes are high: by informing policy, modeling affects the care offered to millions of Americans. Given the importance of simulation models, the lack of guidance on their development is both surprising and concerning. There are large gaps in our understanding of how to select model parameters so that model projections are consistent with statistics that describe the disease process, including results from clinical trials, findings from observational studies, and incidence and mortality rates from registries. This process, called calibration, is an essential step in developing a microsimulation model. Our proposed research directly addresses this knowledge gap by providing a flexible, publicly available tool for model calibration (Aim 1), developing a framework and tools for evaluating calibration methods (Aim 2), and developing and distributing guidelines for model calibration (Aim 3). This work is highly responsive to the notice of funding opportunity PA-25-172, which has a goal of supporting cancer research in statistical and analytic methods including “decision modeling using simulation or other methods to determine efficient or cost-effective strategies for the prevention, early detection, or treatment of cancer.” The tools we will create and distribute for evaluating calibration algorithms will be general and useful for assessing and comparing a wide range of calibration algorithms. Our proposed work will catalyze development of calibration methods that are sorely needed by the modeling community.

NIH Research Projects · FY 2026 · 2026-05

ABSTRACT Understanding the fundamental processes that underscore hematopoiesis is necessary to generate therapeutics that can correct hematopoiesis during disease or support hematopoietic regeneration during stress. The bone marrow microenvironment, or niche, supports hematopoiesis by providing cellular and acellular cues that influence hematopoietic differentiation, hematopoietic stem cell self-renewal, and the functional integrity of the bone marrow niche itself. Inadequate or inappropriate hematopoietic differentiation can lead to disease or death by depleting hematopoietic cell populations needed for organismal survival. Additionally, commonly used therapeutics like radiation and chemotherapy cause hematopoietic cell death and damage the bone marrow niche, leaving patients in a vulnerable state of hematopoietic insufficiency. The inability to restore hematopoietic homeostasis after radiation exposure puts patients at a heightened risk for developing deadly complications, such as infection or hemorrhage. Therefore, understanding how hematopoiesis is maintained and restored is of the utmost importance. Our previous studies showed that syndecan-2 (a specific heparan sulfate proteoglycan) expressed by hematopoietic stem cells promotes long-term hematopoietic stem cell self-renewal ability by supporting quiescence. The bone marrow niche is also a rich source of proteoglycans. Our preliminary data indicate that bone marrow mesenchymal stromal cells (MSCs) also highly express syndecan-2. Genetic depletion of syndecan-2 in MSCs using transgenic mouse models caused significant hematopoietic system imbalances in the peripheral blood at steady-state and after hematologic stress. In this application, we propose to elucidate how MSC-derived syndecan-2 regulates hematopoiesis in vivo. We will use a multi-scale approach to test the function of syndecan-2 at the molecular, cellular, and systemic scales by combining transgenic knockout mouse models and in vivo injury models with high-resolution bone marrow imaging and super- resolution imaging of MSCs. We will test the role of MSC syndecan-2 in hematopoietic differentiation, growth factor organization, and signaling. Because hematopoietic demands increase during states of hematopoietic stress, we will also test the function of syndecan-2 from MSCs in hematologic and niche regeneration from radiation injury. Successful completion of these aims will define the role of MSC-derived syndecan-2 in hematopoietic homeostasis and regeneration, providing foundational knowledge needed to leverage proteoglycans to correct or boost hematopoiesis during states of imbalance or stress.

NIH Research Projects · FY 2026 · 2026-05

PROJECT SUMMARY/ABSTRACT Over the last several decades, numerous healthcare practices achieved the status of evidence-based interven- tion (EBI) for cancer care when scientific evidence supported their use in clinical practice. Identifying the fac- tors preventing or facilitating, collectively called determinants, use of these interventions can bolster implemen- tation efforts to move these EBIs into practice and reduce the overall cancer burden. Determinants are often not assessed before implementing an EBI in clinical practice, although assessment in implementation research has increased. Several critical challenges to assessing determinants when implementing cancer care EBIs are: the lack of accessible, flexible, quantitative tools that are still comparable across time, settings and interven- tions; the use of different quantitative assessment tools; the use of quantitative tools with unestablished validity and reliability; the number of frameworks, models, and theories in implementation science without correspond- ing quantitative measures; and interpreting the results on quantitative measures of determinants. Scores on quantitative tools are continuous but deciding to address a determinant before implementing an EBI is a dichot- omous yes/no decision. This project will address all these critical challenges by using item response theory (IRT) to create flexible, tailorable, easy to interpret quantitative measures of intervention characteristic and pro- vider characteristic determinants that are still comparable across cancer care settings (community oncology, academic) and cancer care populations (treatment, survivorship, end of life) but most importantly can be used to track determinants over time. The measures will be item banks, which are collections of survey items that can be tailored to each individual setting, context, population and EBI. Our preliminary work (pilot studies) col- lected items to assess intervention and provider characteristic determinants of implementing cancer care EBIs. We have also established the content validity of the provider and intervention characteristic determinants item bank. Our pilot studies also initially tested the item banks in a sample of 170 healthcare personnel and 832 cli- nicians and personnel caring for people with small cell lung cancer. Our first aim is to create quantitative measures for each provider and intervention determinant using the item banks and map these to commonly used implementation frameworks and theories. We will use a survey of 750 healthcare personnel (physicians, nurses, advanced practice providers) implementing a cancer care EBI. Our last aim is to create the IRT scoring algorithm and interpretation guidelines for the provider and intervention characteristic determinant item banks. The item banks will be validated against use of the cancer care EBI. The provider and intervention characteris- tic item banks will increase measurement of determinants before implementing a cancer care EBI, helping im- plementation scientists and practitioners and quality improvement directors to address determinants before and during implementation.

NIH Research Projects · FY 2026 · 2026-05

SUMMARY SCLC is exquisitely sensitive to chemotherapy but rapid emergence of chemoresistance leads to extremely poor outcomes. We performed genetic screens in patient derived xenograft (PDX) models of SCLC that revealed KEAP1 as a gene for which deletion confers chemoresistance. KEAP1 is the negative regulator for NRF2 (NFE2L2), a transcription factor and master regulator of anti-oxidant responses. While this pathway has not been thought important for SCLC, interrogating genomic data from the IMpower133 clinical trial and mining mutation databases, we find that KEAP1 and NFE2L2 are indeed targets of pathogenic gene alterations in SCLC and that a subset of patients have activation of an NRF2 gene signature. Moreover, this signature strongly associated with worse survival in the chemotherapy arm of IMpower133. Like SCLC, large cell neuroendocrine carcinomas (LCNEC) are aggressive cancers with high recurrence rates and poor outcomes. More than 20% of LCNECs harbor NRF2 pathway activating mutations. We hypothesize that de novo and treatment-evolved mutations in KEAP1 or NFE2L2 drives chemoresistance in SCLC and LCNEC. We further hypothesize that small molecule inhibition of NRF2 will sensitize to cisplatin-etoposide (CIS-ETO) and immune checkpoint inhibitors, which is first-line therapy for SCLC. In Aim 1, we will leverage a panel of genetically perturbed PDX models of SCLC and LCNEC to determine if NRF2 activation or deletion governs CIS-ETO response in vivo. Cancer-derived mutations in KEAP1 and NRF2 will be tested. Unbiased molecular analyses will reveal pathways and ontologies controlled by NRF2, CIS-ETO and their combination in lung neuroendocrine cancers. A primary objective is to test NRF2 inhibitors as strategies to prevent or overcome chemoresistance in SCLC/LCNEC. Aim 2 will test a novel therapeutic approach to block NRF2. VVD-065 is an allosteric molecular glue that results in specific, potent, robust degradation of NRF2, including in cancers harboring select KEAP1 or NFE2L2 mutations. Using a bank of SCLC and LCNEC PDX models along with syngeneic models of SCLC, we will test if VVD-065 sensitizes to CIS-ETO and/or anti-PD1. We will elucidate the impact of NRF2 suppression together with ICI on tumor and immune cells. The results may support near-future clinical trials to overcome or prevent therapy resistance in SCLC/LCNEC. Last, we hypothesize that KEAP1/NFE2L2 mutations will be more prevalent in SCLC after treatment relapse and that new candidate drivers of chemoresistance could be identified using genomic analyses of SCLC samples from therapy treated patients. Currently available genomic data on chemotherapy treated SCLC is scant. The objective of Aim 3 is to perform deep genomic analyses to identify the mutational landscape of treatment-relapsed SCLC. We take advantage of the high fraction of ctDNA in the blood of SCLC patients to perform whole genome sequencing of cell free DNA before and following treatment with chemoimmunotherapy. Using longitudinally collected patient samples clonal analyses will reveal DNA mutations, deletions and gene amplifications associated with therapy resistance.

NIH Research Projects · FY 2026 · 2026-04

Summary: Childhood cancer survivors carry a high burden of morbidity resulting in a significant reduction in their lifespan. The chronic health conditions including congestive heart failure and coronary artery disease and frailty develop at an earlier age than would be expected in the general population and are thought to be indicators of accelerated aging in adult survivors of childhood cancer. It is important to note that while therapeutic exposures lead to initial tissue damage, modifiable risk factors are now recognized as a major contributor to the development of cardiovascular disease and frailty in childhood cancer survivors, providing a likely intervention to reduce long term morbidity in these individuals. The immune system undergoes several changes with physiologic aging in humans and has been implicated in the pathogenesis of heart disease. Strategies to modulate underlying inflammation are under active evaluation in the setting of heart disease. Our preliminary studies have combined several high-dimensional approaches to identify distinct alterations/dysfunction in immune cells and show that survivors of childhood B-lymphoblastic leukemia exhibit phenotypes consistent with advanced immune aging. Immune health in adult survivors of childhood hematologic malignancies remains unstudied and the magnitude of immune aging in long-term survivors compared with healthy comparison groups is unknown. Finally, it is not clear whether survivors with chronic health conditions are more likely to exhibit immune aging phenotypes when compared with those without such conditions. This application brings together investigators with expertise in immunology and survivorship to test the hypothesis that long-term survivors of childhood hematologic malignancies will exhibit distinct aging-associated immune phenotypes, and that these immune phenotypes will be associated with key chronic health conditions. It will leverage our access to well- annotated biospecimens linked to distinct health outcomes from the Childhood Cancer Survivor Study (CCSS), St Jude life as well as matched healthy controls (Emory University). Access to these resources and tools developed by our group will allow us to 1) compare aging-associated immune phenotypes in adult survivors of childhood hematologic malignancies vs. matched healthy controls and identify demographic, clinical, and therapeutic factors associated with aging-associated immune phenotypes. 2) characterize immune signatures in adult survivors of childhood hematologic malignancies with and without heart disease and physiologic frailty. Our application will not only identify distinct subpopulations of hematologic malignancy survivors at high-risk for immune aging, but also set the stage for future intervention studies to improve immune function in these cohorts and mitigate the risk of adverse outcomes.

NIH Research Projects · FY 2026 · 2026-04

Project summary Herpes simplex virus (HSV) establishes latency in ganglionic neurons of the peripheral nervous system. Latent HSV can later reactivate, causing recurrent disease and possible transmission to new hosts. Current anti-HSV therapy is inadequate, in that it does not eliminate latent HSV, and thus is only suppressive rather than curative. We developed a therapeutic approach based on gene editing using HSV-specific meganucleases. We showed that intravenous (IV) administration of adeno-associated virus (AAV) encoding anti-HSV-1 meganucleases can eliminate up to 97% of latent HSV DNA from dorsal root ganglia in mouse models of latent HSV-1 genital infection. We also demonstrated that this reduction in ganglionic viral load led to a corresponding reduction of viral shedding from treated vs. control mice. This approach offers the potential for a durable means of controlling latent HSV infection and subsequent reactivations, or even achieving a functional cure. In the R21 phase, we propose to extend our work to target HSV-2, and to determine whether IV or localized intrathecal (IT) administration is the optimal route. In the specific aims of the R33 phase we plan to address simultaneously several outstanding issues regarding both HSV biology and the safety and efficacy of in vivo gene therapy that are critical for clinical translation of our work. R21 Phase: Specific Aim 1. Evaluate IT vs. IV delivery of AAV/meganuclease therapy as a means to reduce AAV dose, minimize systemic exposure, and avoid pre-existing/induced anti-AAV immunity. We will evaluate the AAV biodistribution, antiviral efficacy, and dose response after IT vs. IV administration, and the doses at which toxicity occurs. We will also evaluate the ability of IT-delivered AAV to avoid neutralizing antibody present in serum, and whether IT administration will allow re-dosing of AAV. R33 Phase: Specific Aim 2. Compare the natural history of ganglionic HSV load and peripheral viral shedding in latently infected mice after IT or IV meganuclease therapy vs. untreated control animals. We will perform long-term studies of the ganglionic viral load and the frequency and quantity of peripheral shedding in control vs. AAV-meganuclease treated animals. These studies will shed light on the stability of reservoirs, the relationship of ganglionic viral load reductions with the frequency and quantity of viral shedding, and provide new insights into possible HSV re-seeding of ganglionic reservoirs after viral reactivations. R33 Phase: Specific Aim 3. Determine the host genomic consequences of AAV/meganuclease therapy, and compare to the effects after CRISPR/Cas9 exposure. We will perform an unbiased evaluation of genomic disruptions after our meganuclease therapy, and directly compare with CRISPR/Cas9 approaches, using the state-of-the-art techniques for the detection of off-target events, including GUIDE-seq, improved DISCOVER-Seq+, and analyses for the insertion of AAV vector (ITR-Seq) and HSV DNA (hybridization capture coupled with next generation sequencing) into the host genome.

NIH Research Projects · FY 2026 · 2026-04

Project Summary/Abstract This proposal describes a five-year research training program that will facilitate my ongoing transition from an applied mathematician to an independent, quantitative, multidisciplinary biomedical researcher. I will work closely with clinicians, mathematical modelers, bioinformaticians, evolutionary biologists, virologists and immunologists to develop a suite of mathematical models which will be validated against viral, immune, phylogenetic and epidemiolocal datasets. The goals of my proposal will be to: 1) understand the mechanisms facilitating generation of SARS-CoV-2 variants of concern (VOC) during prolonged infections in immunocompromised (IC) individuals, and 2) identify key bottle necks that limit the number of VOCs that predominate in the general population. SARS-CoV-2 is the appropriate virus for which to develop this modeling framework due to the availability of data, and ongoing incidence, but the approach will be widely applicable to other pathogens. The training program includes an outstanding group of mentors and collaborators. My scientific advisory committee consists of experts in modeling infectious diseases (Dr Josh Schiffer and Dr Dan Reeves), clinical care for IC individuals (Dr Josh Schiffer and Dr. Alpana Wahgmare), epidemiology (Dr Cheryl Cohen and Dr Dobromir Dimitrov), viral evolution (Dr JT McCrone and Dr Mahan Ghafari), and biostatistics and machine learning (Dr Ollivier Hyrien). This group is dedicated to ensuring the success of my project, and my career development as an independent researcher. The specific learning goals required for my successful transition to biomedical research will be accomplished through didactic coursework in virology, immunology, epidemiology and phylogenetics as well as conferences and professional training in the skills of a successful mentor and group leader. The research plan addresses a critically important clinical and public health issue. Prolonged SARS-CoV- 2 infections in IC individuals are the most likely source of most novel VOC, which have extended and strongly exacerbated the impact of the pandemic. Though these infections have had an outsized public health impact, clear guidance regarding clinical management and safety measures is lacking. Understanding the within-host evolution of SARS-CoV-2 is paramount to addressing these issues. Through accomplishing the aims of this proposal, Dr Owens will address critical gaps in our knowledge of SARS-CoV-2 evolution and create an in silico framework to study SARS-CoV-2 interventions at both individual and population level. Ultimately, this proposal will allow Dr Owens to influence the future of pandemic response research as well as build a self-sustaining program at the interface of mathematical modeling, immunology, viral dynamics, and viral evolution.

NIH Research Projects · FY 2026 · 2026-04

PROJECT SUMMARY/ABSTRACT Herpes simplex virus types 1 and 2 (HSV-1/2) are major human viral pathogens that cause one of the most common, debilitating, stigmatized and lifelong infections of humankind with more than 143 million new infections every year and affecting more than 4 billion people around the world and more than 100 million Americans. Determining infection status is challenging, as viral latency makes PCR screening both ineffective and costly, while the inadequate specificity of serological IgG assays has led the CDC to recommend a two-step process that includes high throughput, sensitive but low specificity tests followed by more specific but unscalable and labor-intensive confirmatory assays. One of the two CDC-recommended confirmatory assays is the University of Washington (UW) Virology HSV Western Blot test (HSV-WB). The HSV-WB remains the FDA-recognized gold standard for confirmatory serological diagnosis of HSV-1 and HSV-2 infections and detects serum responses to multiple proteins within a viral lysate. This assay is highly sensitive and specific, but it is laborious, and thus costly and only available in the United States at one reference lab. Recurrent quality control problems with another confirmatory assay, biokit gG2-based membrane test, caused product recalls and lack of availability of the test in commercial reference labs. Therefore, making convenient, one-step, high-quality HSV serological testing more accessible is of compelling interest for national and global public health and a key component for development of a national HSV prevention program. In this project, we propose to create a new, high-throughput, one-step HSV serology test that combined the advantages of current FDA-authorized binding assays with the high-content, multiplex-driven specificity of the UW HSV-WB. Specifically, we propose to develop and clinically validate an HSV serologic multiplex bead-based binding antibody assay (HSV Sero-MBAA) that matches the performance characteristics of the HSV-WB, including high sensitivity, specificity, and differentiation of HSV type, on a scalable, inexpensive platform. HSV Sero-MBAA can be run both in central labs and can be kitted and licensed for future regulatory submissions that would allow it to be run in hundreds of clinical laboratories around the United States and world on already existing instrumentation.

NIH Research Projects · FY 2026 · 2026-03

PROJECT SUMMARY/ABSTRACT Dynamic interactions between intercellular membranes and the cortical cytoskeleton are critical for cell survival. During their normal functions, cells face physiological and environmental stresses that can lead to rupture of the plasma membrane and/or of the nuclear envelope. Rapid repair of such injuries, whether arising from daily activities or resulting from trauma, infection, or diseases such as cancer, is an active area of cell biology research. My lab has a long-standing track record in successfully identifying key molecules and elucidating their in vivo roles at the cell cortex necessary for the repair of plasma membrane and at the nuclear envelope necessary for repair of the nuclear cortex. The overall focus of the lab is to delineate how cells deal with such cell and/or nuclear cortex disruptions to efficiently and effectively repair the lesions. We have developed a robust inducible single cell repair model using the syncytial Drosophila embryo that has superb amenability for live imaging and genetic tractability that is unavailable in other cell wound repair models. We have also established a model for the newly appreciated nuclear export pathway (Nuclear Envelope budding) on the surface of Drosophila salivary gland and S2 cell nuclei that provides the same superb amenability for live imaging and genetic approaches. While both systems rely heavily on dynamic membrane and/or cytoskeleton/nucleoskeleton interactions, a major challenge in both of these systems is the absence of a molecular outline of the events occurring during the repair and/or export processes in any organism or system. Our goals during the proposed period are to establish the molecular framework underpinning these processes using a combination of state-of-the-art cell biological, genetic, developmental, biochemical, and high-resolution imaging approaches. Our studies are expected to be of significant medical relevance, as understanding the molecules, machineries, and pathways governing cell wound repair, NE-budding (nuclear export), and dynamic membrane-cytoskeleton/nucleoskeleton interactions will be extremely valuable for elucidating fundamental cellular mechanisms, as well as for developing new or enhancing existing strategies for treating conditions associated with cell/nuclear damage, and for disciplines such as regenerative medicine where cell based constructs are used to reconstruct tissues, clinical drug delivery systems where molecules cross cell membranes, and for virus nuclear egress.

NIH Research Projects · FY 2026 · 2026-03

PROJECT SUMMARY The putative oncogene DDX6 (RCK, p54) has critical roles in the nervous system, embryonic cells, and somatic cells. The importance of DDX6 is further emphasized by rare pathogenic missense mutations in DDX6 that are associated with developmental delays and intellectual disability in children. DDX6 is a member of the DEAD-box RNA helicase family, which are broadly involved in regulation of messenger RNA (mRNA) and translation. Despite its establishment as critical regulator of translation initiation, the molecular mechanisms that underlie DDX6 function remain unclear. Major roadblocks to this include that translation initiation is a heterogenous, multistep process that requires a dozen components and occurs within a minute. Further, the identity of interacting partners in a given DDX6 regulatory complex determines whether DDX6 promotes or inhibits protein synthesis. This complicates cellular study of DDX6, as DDX6 likely forms multiple distinct regulatory complexes on different mRNAs at any given time. To overcome these roadblocks, I will combine biochemical, single-molecule, and biophysical methods to examine my central hypothesis that DDX6 regulates the initial, rate-limiting step of translation initiation and global mRNA conformation in concert with its interaction partners. In Aim 1, I will identify the step of translation initiation that is regulated by DDX6 and its key partner proteins by using in vitro single molecule fluorescence microscopy and a reconstituted human translation initiation system. In Aim 2, I will examine how DDX6 assembles with partner proteins into distinct regulatory complexes and how this impacts mRNA dynamics. In each Aim, I will determine how pathogenic missense mutations in DDX6 disrupt its function. My proposed experiments will uniquely leverage my background in protein biochemistry and enzymology, the Lapointe lab’s expertise in human translation initiation and single molecule fluorescence microscopy, and the Stoddard lab’s expertise in structural biology and enzymology. My collective findings should elucidate which step of translation initiation is controlled by DDX6, how DDX6 assembles into translation inhibiting and translation stimulating complexes, how distinct DDX6 complex assemblies remodel mRNA, and how missense mutations alter DDX6 function. In parallel, my individualized training plan will provide me with opportunities to expand my research skillset into single molecule techniques and human translation initiation, to grow as a leader and mentor within the Lapointe lab, and prepare me for a career as an independent investigator.

NIH Research Projects · FY 2026 · 2026-02

Project Summary Chromatin organizes into distinct functional domains and regulates a wide range of biological processes, including gene expression, genome integrity maintenance, and DNA accessibility. Chromatin dynamically adapts its functional states by altering protein composition or introducing chemical modifications in response to various biological contexts, such as cell differentiation, the cell cycle, environmental stimuli, and disease states. To understand chromatin regulatory mechanisms, it is critical to elucidate how chromatin-associated complexes modulate their structures and functions in response to these alterations. However, traditional biochemical and structural approaches, which rely on in vitro reconstituted complexes of known chromatin proteins and modifications, are often inadequate for studying these dynamic regulatory processes, as they involve numerous biological context-dependent factors and modifications that have yet to be identified. My lab will address this gap by determining the structures of native chromatin-associated complexes within their physiological chromatin context, aiming to elucidate the structural mechanisms underlying key chromosomal processes. Leveraging the unique cryo-EM methods I have developed in conjunction with the distinctive capabilities of the Xenopus egg extract system—which can recapitulate complex biological processes such as cell cycle progression—my lab will focus on two primary research objectives over the next five years. [Project 1]: The first project aims to elucidate the structure and function of the stably bound FACT-nucleosome complex. FACT plays a critical role in various chromosomal processes, including transcription and replication. Although substantial amounts of the FACT-nucleosome complex formed in cellular or Xenopus egg extract chromatin, the purified FACT complex does not bind to an intact nucleosome in vitro. Consequently, the structure and function of the stably bound FACT-nucleosome complex were not well characterized. The cryo- EM structure of the native FACT-nucleosome complex will reveal novel protein-protein, protein-DNA, and protein-RNA interactions within the complex. These insights will facilitate the design of follow-up functional experiments in egg extract that will identify the structural features critical to their functions. [Project 2]: The second project will focus on methodological development to enable the visualization of telomeric chromatin. We will explore various approaches, including telomeric chromatin assembly in Xenopus egg extracts. By achieving direct visualization of telomeric chromatin, we aim to address fundamental questions such as: How do shelterin complexes and columnar nucleosomes cooperatively assemble to form telomeric chromatin? How does telomeric structure protect chromosome ends from DNA repair machinery while regulating telomerase activity? Together, these projects will establish a robust foundation for our long-term goal of bridging the knowledge gap between dynamic chromatin regulation and its structural mechanisms by enabling the visualization of native chromatin-associated complexes within their physiological chromatin context.

NIH Research Projects · FY 2026 · 2026-02

Project Summary/Abstract Immune correlates of protection (CoP) are biomarkers that predict vaccine-induced protection against dis- eases and play a crucial role in the design and development of effective vaccines. The U.S. government (USG)-led initiative to identify CoPs for COVID vaccines highlighted the importance of neutralizing antibody titers as surrogate endpoints, significantly impacting vaccine recommendations and approvals. To effec- tively measure these immune biomarkers, researchers utilize two-phase designs, such as case-cohort or case-control studies, to boost statistical power and enhance representation. This proposal aims to develop novel two-phase sampling designs that allow enrichment of longitudinal immune response marker mea- surements in immune correlates studies. The proposal also aims to develop advanced statistical methods for datasets collected under sampling designs that would introduce bias if analyzed using conventional in- verse probability-weighted methods. Aim 1 focuses on the analysis of the immune response biomarkers measured at the peak immunogenicity time point, while Aim 2 delves into the study of the decaying im- mune response biomarkers. The final product will feature a user-friendly software implementation of the proposed methods, along with its application to analyze COVID correlates datasets from past and ongoing USG-sponsored vaccine efficacy trials.

NIH Research Projects · FY 2026 · 2025-12

This proposal outlines the scientific agenda of the Leadership and Operations Center of the HIV Vaccine Trials Network (HVTN), which has pioneered immunological approaches to HIV prevention. One of the major accomplishments of the HVTN in this grant period has been the conduct of 3 vaccine and 2 monoclonal antibody (mAb) efficacy trials that have provided proof of principle that 1) broadly neutralizing antibodies (bnAbs) can prevent HIV acquisition and 2) vaccine approaches that elicit non-neutralizing antibodies, even cross-clade non-neutralizing antibodies, are not effective. These trials provide a new roadmap for HIV prevention: induction of bnAbs is the path to an effective HIV vaccine. This proposal describes a novel fast-track Discovery Medicine phase 1 program to assess, in an iterative fashion, candidate trimers, germline and lineage-based vaccines designed to elicit bnAbs in adults and HIV-1–exposed infants. This program integrates novel candidate immunogens using sequential immunizations with B-cell sequencing to elicit mature functional bnAbs. The HVTN utilizes 13 geographically diverse core sites and another 10-14 protocol specific sites for its studies in the US. International research sites are also critical to HVTN’s scientific strategy and directly advance public health goals to end the HIV epidemic in the U.S. Conducting trials in high-incidence international settings allows the HVTN to evaluate prevention strategies more rapidly with smaller sample sizes and substantially lower cost, thereby accelerating the advancement of prevention interventions for the U.S. population. The use of international sites also enables evaluation of diverse HIV subtypes and supports the identification of immune correlates of protection in locations with sufficient endpoint accrual. The HVTN 703 study showed the remarkable benefit of mAb therapy for preventing HIV in women; it enrolled 1,700 women in sub-Saharan Africa and followed them for two years to show bnAbs could prevent HIV. This contrasts with a proposed 11,000-women study requiring 4 years of follow-up if conducted only in the U.S. We are now designing a combination passive immunization bnAb study in the U.S. to begin in 2028 rather than a 2034 start date if past foundational studies could not be conducted efficiently with high prevalence international sites. Vaccine clinical trials involve a complex interplay between clinical trial sites, HVTN laboratories, computational scientists, and our operational, training, mentoring, and fiscal management teams; these interactions are described in the application. The clinical, laboratory and statistical infrastructure we have built for immune-based prevention of HIV will also be used to assist in tuberculosis vaccine development. Our network integrates community representatives and community advisory boards into all our research process and conduct. We will also continue to develop the next generation of vaccine scientists and expand our scientific collaborations to engage the scientific community to utilize the extensive specimen and data repositories we have established. The overall goal of the HVTN in this proposal is to develop immune-based preventive interventions that will reduce HIV acquisition in adults and infants by more than 80%.

NIH Research Projects · FY 2025 · 2025-09

Project Summary This project aims to develop a suite of advanced yet practical statistical tools with user-friendly interfaces to enhance the reliability and power of single-cell and spatial omics data analysis through experimental-data- based in silico data generation. Aim 1 focuses on developing statistical methods to generate in silico data that serve as negative controls and pseudo-replicates of experimental data. These digital alternatives will help uncover potential biases and variability in analysis results, which have become more common given the increasing complexity of single-cell and spatial omics data analysis. In silico negative controls and pseudo- replicates will enable sanity checks, bias correction, and variability analysis, addressing challenges such as double dipping, small sample sizes, and data sparsity. Aim 2 involves creating a power analysis suite leveraging experimental-data-based in silico data generation, covering multi-condition comparisons, temporal data analysis, and population-scale molecular quantitative trait loci analysis, with the goal of assisting experimental design considering the high cost of single-cell and spatial omics technologies. Aim 3 will develop interactive, modularized software packages with a website interface for the single-cell and spatial omics community to perform experimental-data-based in silico data generation. The software will integrate with state- of-the-art pipelines like R's Seurat and Python's Scanpy, enabling researchers to easily generate in silico data from experimental data and enhance the reproducibility of common analysis tasks in single-cell and spatial omics studies. Overall, this project will provide a new angle to extend the capabilities of computational genomic research, fostering more accurate and reproducible data-driven discoveries.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY Sleep deficiency is highly prevalent in the population and there are marked disparities in sleep health such as by non-clinical contributors. Factors driving sleep health disparities are not well understood. Thus, there remains a need to identify novel and potentially modifiable risk factors. There is emerging evidence for the role of solar jetlag and climate vulnerability as novel environmental risk factors in sleep health. Solar jetlag occurs from geographic variation in timing of environmental light exposure due to time zone position. People living in the western vs. eastern position of a time zone are exposed to light later in evening, suppressing melatonin, reducing sleep propensity, and reducing sleep duration due to early awakenings for work or social commitments. Climate vulnerability is characterized by exposure to extreme weather events such as high temperatures that increase the frequency, duration, and/or intensity of exposures to environmental factors (e.g., extreme heat, wildfire smoke). Environmental exposures exacerbated by climate vulnerability may affect sleep through mechanisms of disruptions in sleep thermoregulation and breathing. For this R21, we propose to apply geospatial analytics to conduct the first-ever epidemiologic study on solar jetlag and climate vulnerability to identify new risk factors for sleep health disparities. To date, epidemiologic studies on solar jetlag have used coarse-scale measures, and no sleep epidemiologic studies have examined a comprehensive measure of climate vulnerability. To address these research gaps, we propose to use our new high-resolution geospatial light exposure model for solar jetlag (developed by MPIs, Dr. Trang VoPham and Dr. Matthew Weaver) and the geospatial Climate Vulnerability Index (CVI). We will quantify the associations between solar jetlag and climate vulnerability and sleep duration (Aim 1); quantify the associations between solar jetlag and climate vulnerability and sleep quality (Aim 2); and will investigate the role of solar jetlag and climate vulnerability on sleep health disparities by non-clinical contributors (Aim 3). We will leverage a nationwide study population comprised of 5 waves of surveys among US adults in 2022 (n=24,908 total surveys) (Dr. Weaver was PI of these surveys). This valuable resource includes data on sleep outcomes using validated instruments, demographics, lifestyle, behaviors, comorbidities, and respondent geocoded addresses (latitude and longitude coordinates). We will conduct a state-of-the-science geospatial exposure assessment using a geographic information system (GIS), linking geocoded addresses with the MPIs’ new validated high-resolution geospatial light exposure model for solar jetlag and the geospatial CVI dataset. This innovative interdisciplinary research will contribute to the NHLBI mission through impactful science providing new insights into novel, modifiable, biologically plausible environmental risk factors for sleep health disparities. The study findings will have translational utility through informing targets for intervention to promote sleep health. This R21 holds great promise for advancing research on the environmental epidemiology of sleep health disparities.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY Kaposi sarcoma herpesvirus (KSHV) is the etiologic agent of Kaposi sarcoma (KS), primary effusion lymphoma, and multicentric Castleman’s disease. KS causes significant morbidity and mortality worldwide, particularly in people living with HIV (PLWH) and in sub-Saharan Africa (SSA) where KSHV seroprevalence is high. It is estimated that 80% of the KS burden in SSA, where the impact of KS is heaviest, is attributable to HIV infection. KS most often develops in the setting of T-cell deficiency or dysfunction, such as in KSHV-seropositive individuals with HIV infection or KSHV-seropositive recipients of solid organ or allogeneic hematopoietic cell transplants. In these settings KS can remit following initiation of antiretroviral therapy (ART) or withdrawal of immune suppression. In SSA, primary infection with KSHV is thought to occur in childhood, but most cases of KS and other KSHV-associated disease in both PLWH and people without HIV infection develop many years, often several decades, later. These observations suggest that loss or impairment of a T-cell component of pre- existing KSHV-specific immunity underlie the development of these diseases. Strategies that preserve or restore the T-cell component of KSHV-specific immunity in PLWH and others at risk should, therefore, have potential for the prevention or treatment of KSHV-associated disease. Our studies of tumor biopsies and blood samples from people in Uganda living with HIV and KS (epidemic KS) as well as adults with KS but no concurrent HIV infection (endemic KS) have identified a large repertoire of T- cells that are likely to be specific for KSHV. We have begun to identify the antigenic targets of these putative KSHV-specific T-cells and find that they demonstrate high avidity for KSHV-encoded peptides, recognize KSHV- infected cells, are detectable in KS tumors, circulate in blood, and persist across time. Additional preliminary data from whole exome sequencing and transcriptional profiling of KS tumors reveal a sparse mutational landscape but consistent expression of latent and lytic cycle KSHV genes, supporting the concept that immune interventions that preserve, enhance, or restore the T-cell response to KSHV could prove effective for the prevention or treatment of KS, particularly in PLWH who are at greatest risk. Comprehensive definition of the targets of the KSHV-specific T-cell response in KSHV-seropositive individuals and of how that T-cell response is impaired or disabled in individuals who develop KS will provide the blueprint for such immune interventions. The studies in this application will lay the foundation for specific immune therapy for KS by identifying the major targets of the T-cell response to KSHV, identifying those that are naturally presented by KSHV-infected cells, and defining mechanisms by which KSHV attempts to evade that response.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY / ABSTRACT Human endogenous retroviruses (HERVs) comprise roughly 8% of our genome. Originally considered “junk DNA”, we now know that HERVs play diverse roles relating to human health, innate immunity, and cancer. Repetitive elements have been notoriously difficult to study and quantify due to their repetitive nature and the lack of a standardized database. In this project, I will leverage a comprehensive database of HERV loci (HERVdb) created in the Blanco-Melo Lab to accurately measure the expression of HERVs and investigate their role in clear cell renal cell carcinoma (ccRCC), a common and aggressive form of kidney cancer that accounts for 80% of renal cancer cases. HERV expression in ccRCC has been linked to tumor immunogenicity and response to immunotherapy, making it a promising area of research. Our hypothesis is that HERVs are abnormally transcriptionally activated in tumor cells, where they are recognized by the immune system due to absence of expression in normal cells; HERV products (RNA or protein) can thus prime the anti-tumor immune response, resulting in a HERV specific immune response. To test this, I will pursue two main aims: Aim 1: Define the unique signature of HERVs in ccRCC (clear cell Renal Cell Carcinoma). Aim 2: Explore the role of HERV-derived tumor-associated antigens across ccRCC samples. The goal is to establish a clear baseline of HERV expression in ccRCC, identify tumor-specific HERVs, and explore relevant HERV-derived peptides that could serve as potential therapeutic targets. Ultimately, this project aims to demonstrate that HERVdb can be used to identify HERVs as targets for ccRCC treatments, and to establish a reproducible workflow for the interrogation of HERVs in other cancers.

NIH Research Projects · FY 2025 · 2025-09

Project Summary/Abstract: The Fred Hutchinson Cancer Center (Fred Hutch) proposes the construction of an Enhanced Biosafety Level 3 (BSL-3)/Animal BSL-3 facility to address critical gaps in regional capacity for high-containment research on pathogens of significant public health concern, particularly Highly Pathogenic Avian Influenza (HPAI) and other emerging infectious agents. Despite Fred Hutch’s leadership in infectious disease research, the absence of an on-site BSL-3 facility limits the institution’s ability to fully support multidisciplinary biomedical research and respond rapidly to outbreaks. Notably, Seattle Children’s Research Institute lacks shower-out and effluent decontamination systems, and the University of Washington’s BSL-3 facility also lacks an effluent decontamination system. The proposed 5,145-square-foot facility, located on the Fred Hutch campus in Seattle, Washington, will incorporate next-generation biosafety features, including a shower-out system, an Effluent Decontamination System (EDS), and dedicated containment zones. The design includes flexible laboratory spaces, specialized areas for pathogen-specific research, and advanced facilities for automation, flow cytometry and waste processing. These features ensure compliance with NIH, CDC and USDA biosafety standards, further enabling cutting-edge research. This next-generation BSL-3 facility will serve as a regional hub for collaboration, leveraging expertise from Seattle Children’s Research Institute, the University of Washington, and other stakeholders. By applying lessons from the COVID-19 pandemic and expanding research capacity for high-priority pathogens, the facility will strengthen public health preparedness, support sustainable infrastructure, and bolster the Seattle area’s leadership in infectious disease research. The project directly aligns with Fred Hutch’s mission to advance global health and biomedical innovation by providing critical infrastructure to address pathogens which cause severe disease in our immunocompromised transplant patients as well as emerging infectious disease challenges. Its construction will position Fred Hutch and its partners as leaders in collaborative and high-impact research, driving long-term scientific and public health advancements.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY The long-term objective is to elucidate the mechanisms of adipocyte-brain communication and their impact on glial function, neuroprotection, and brain aging, with potential implications for preventing dementia and age- related cognitive decline. We will do this my executing two specific Aims: i) Investigate the role of adipocyte- derived lipoproteins in glial phagocytosis, neuroprotection, and senescence. ii) Examine how adipocyte mitochondrial oxidative phosphorylation impacts glial function and senescence. To achieve these aims, using Drosophila as a model organism, we will explore how adipocyte-derived signals influence glial cell function, particularly phagocytic activity. We will focus on two key adipocyte-derived signals: lipoproteins and mitochondrial components. For Aim 1, we will investigate how lipoproteins and their receptors modulate glial phagocytic activity through various molecular and cellular approaches, including knockdown studies, signaling pathway analyses, and lipidomics. For Aim 2, we will examine the impact of adipocyte mitochondrial function on glial cells using similar techniques, as well as targeted proteomics and Translating Ribosome Affinity Purification (TRAP). Our research will employ genetic manipulation, confocal microscopy, biochemical assays, and high-throughput sequencing to analyze glial function, lipid metabolism, and gene expression changes in response to altered adipocyte signaling. We will assess the effects of these signals on glial senescence, lipid accumulation, and neuroprotective capabilities under various metabolic conditions and during aging. This study aims to uncover novel mechanisms of adipocyte-brain communication and their roles in neuroprotection and age-related cognitive decline. The high degree of evolutionary conservation between Drosophila and mammals in adipocyte-brain signaling and glial biology suggests that our findings may have broad translatable implications for human health, potentially leading to new therapeutic strategies for improving age-related conditions impacted by diet-induced obesity.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY Facioscapulohumeral muscular dystrophy (FSHD) is the third most common form of muscular dystrophy that is caused by mis-expression of an early embryonic transcription factor DUX4 in skeletal muscle. DUX4 induces an early embryonic transcriptional program and activates transcription of LTR-retrotransposons, endogenous retrovirus elements and repetitive sequences. A major mechanism driving DUX4-mediated cellular toxicity in FSHD muscle is transcription of pericentric human satellite II (HSATII) repeats and subsequent formation of HSATII-derived ribonucleoprotein (RNP) complexes. The long-term goal of this proposal is to provide a new mechanistic understanding of DUX4-driven pathogenesis of FSHD and identify new disease biomarkers that will aid in the diagnosis of FSHD and design of promising therapeutics. The significance of this proposal is that it addresses a currently unexplored area in FSHD research – the impact of HSATII RNA expression in FSHD pathogenesis and disease. The overall hypothesis is that transcriptional activation of HSATII and subsequent RNA aggregation act as a molecular sink to sequester nuclear regulatory proteins exacerbating DUX4- mediated cellular dysregulation. The specific aims of this proposal are: Determine the composition of HSATII- derived ribonucleoprotein complexes and the consequence of their formation on cell function (Aim 1) and elucidate the molecular mechanisms regulating HSATII regions (Aim 2). With the use of state-of-the-art molecular biology approaches and generation of new targeting strategies this proposal will be the first to dissect the mechanism(s) of FSHD disease pathology mediated by HSATII RNA aggregation and subsequent RNP formation. Moreover, this work provides the basis for future studies of HSATII genome biology and function in human development and disease.