Fred Hutchinson Cancer Center

NIH Research Projects · FY 2025 · 2025-09

Project Summary Gene regulation is a fundamental biological process through which noncoding regulatory elements work interactively in a holistic model to determine traits and diseases. Regulatory elements (e.g., enhancers) recruit transcriptional factors (TFs) collectively and explicitly control gene expression to define phenotypic states. The epistatic interaction, in which the function of one enhancer depends on the presence or absence of another enhancer, has been recognized as fundamentally important to understand the complexity of gene regulation. Elucidating the principles of how enhancers coordinate to control gene transcription, and the TFs they utilize to get there, is a major challenge in the field. Perturbing combinatorial enhancers and measuring their epistatic effects on the gene regulatory contributions to traits and diseases is necessary. Recent advances in CRISPR-based genome engineering technologies have enabled new approaches for the multiplexed perturbation of regulatory elements. We recently demonstrated that multiplexed CRISPR interference (CRISPRi) systems enable the robust and accurate interrogation of the function of enhancer epistasis networks in gene regulation. Furthermore, the emergence of new technologies and datasets, including single-cell RNA sequencing, non-linear deep learning models, and large-scale genome-wide association studies (GWAS) datasets, provides unprecedented opportunities to uncover the mechanisms underlying enhancer epistatic interactions and how they relate to gene expression. My research program aims to exploit this enormous potential by developing analytic approaches that probe the enhancer epistatic interactions in gene regulation and model the interactive consequence of noncoding variants for functionality and ultimately pathogenicity. We will (i) map the epistatic interactions by establishing best practices in multiplexed perturbation assay design and analysis; (ii) dissect how inter-molecular TF interactions determine enhancer epistasis; (iii) develop novel mechanistic computational approaches to predict the functional consequence of interactive enhancer variants. Our studies will lead to novel insights into fully understanding the regulatory complexity that controls the expression of human genes. They will shift the paradigm in the interpretation of millions of noncoding disease variants from a locus-by-locus model to an epistasis-aware model. We anticipate that ability will be particularly powerful for translating genetic associations into disease mechanisms, thus creating a windfall of new knowledge about how genomic regulatory elements contribute to disease, and how to monitor and manipulate enhancers for diagnostic and therapeutic benefit. 1

NIH Research Projects · FY 2025 · 2025-09

Abstract In this proposal, we will determine the influence of oral pre-exposure prophylaxis (PrEP) on the pharmacokinetics (PK) of passively administered monoclonal antibodies (mAbs) and vaccine-induced polyclonal antibodies (Abs) in females vulnerable to HIV-1, using data and specimens from past HIV-1 prevention trials. This research will have a significant impact on global health because oral PrEP is currently the most accessible pharmaceutical HIV-1 prevention option, and Abs are critical for immune protection and therapeutic efficacy. Aim 1 focuses on determining whether oral PrEP affects the PK of VRC01, a broadly neutralizing HIV-1 mAb, in female participants from the recently completed Antibody Mediated Prevention (AMP) study. We will identify biomarkers of PrEP use that correlate with increased mAb clearance, with a specific emphasis on assessing PrEP’s effects on two intestinal Ab clearance mechanisms: disruption of the epithelial barrier and increased Fc receptor (FcR) mediated Ab degradation. Aim 2 extends this investigation by examining the impact of oral PrEP on the magnitude and durability of HIV-1 vaccine-induced antibodies (Abs) in female participants from two completed HIV-1 vaccine efficacy trials. To extend beyond HIV-1, we will also assess durability of Hepatitis B (HB) vaccine-induced Abs in female and male participants from AMP and the vaccine trials. Consistent with what was observed for VRC01 PK in males from the AMP trial, our preliminary data in two pre-efficacy vaccine trials suggest an association between PrEP use and faster decay of HIV-1 vaccine-induced Abs. We plan to identify PrEP biomarkers associated with vaccine Ab kinetics. In biopsy donors, we will also determine the association between HB vaccine Ab kinetics and identified biomarkers with the two potential intestinal mechanisms of Ab clearance. Characterizing any PrEP effects on Abs is crucial for people who take oral PrEP and rely on mAb immunotherapies and/or Ab-inducing vaccines for protection against pathogens. Aim 3 focuses on developing a pharmacokinetic and statistical modeling framework to rank and select mAb regimens for efficacy testing. This framework will account for PrEP use and mAb PK biomarkers identified in Aim 1. It will also incorporate mAb levels in serum and rectal tissue from both males and females, recognizing the importance of tissue levels in predicting protection against HIV-1 and intestinal PrEP effects on mAb PK. By building and validating advanced PK models and statistical methods for bridging differences in study populations, we seek to enhance the accuracy of selecting the most promising mAb regimens for future clinical trials, ultimately contributing to more effective HIV-1 prevention strategies.

NIH Research Projects · FY 2025 · 2025-09

ABSTRACT Highly effective HIV pre- and post-exposure prophylaxis (PrEP and PEP) have been available at public HIV clinics in Kenya for almost a decade; however, limited opening hours, long wait times, and HIV stigma at clinics have hindered uptake and consistent use of these interventions, thus attenuating their impact on population- level HIV incidence. To increase PrEP/PEP use, the Kenya Ministry of Health (MOH) is interested in expanding delivery to new settings, including private community pharmacies. Our research team recently completed two prospective pilot studies in Kenya to test a novel delivery model in which trained pharmacy providers initiate and manage clients on PrEP and PEP under remote clinician supervision (NIH R34 MH120106, PI: Ortblad; BMGF INV-033052, MPIs: Ortblad/Bukusi/Ngure). This model reached PrEP- and PEP-eligible individuals and was highly acceptable to providers and clients; however, two key implementation challenges emerged: the heavy time burden on pharmacy providers and suboptimal continuation among clients. To understand whether introducing a remote nurse to assist with delivery and provide client support improves clinical and implementation outcomes, we propose conducting a hybrid effectiveness-implementation cluster-randomized controlled trial at 20 pharmacies in Kisumu and Homa Bay Counties (Western Kenya). In Aim 1, we will 1:1 randomize 20 pharmacies (n=1,580 clients ≥15 years) to either: 1) telehealth support, where a remote nurse screens, counsels, and guides clients through HIV self-testing (HIVST) and, between visits, communicates with interested clients via 2-way SMS, or 2) standard delivery, where the pharmacy provider performs all delivery tasks and clients are not given additional support. Our primary outcomes will be PrEP/PEP initiations and continuation by 6 months; secondary outcomes will include reach, visit duration, product mix, product switching, and PrEP adherence. In Aim 2, we will evaluate intervention acceptability and feasibility and identify implementation barriers and facilitators using a sequential explanatory mixed methods approach that integrates Aim 1 quantitative findings with qualitative data from routine technical assistance reports, de-identified SMS transcripts, and in-depth interviews (n=81) with clients, pharmacy providers, remote nurses, and key stakeholders. In Aim 3, we will estimate the intervention’s cost-effectiveness and budget impact. In line with recent World Health Organization recommendations, this study will use HIVST to support PrEP delivery and enable client choice by offering multiple types of biomedical HIV prevention products (e.g., daily oral PrEP; on-demand PrEP; PEP). This study will be the first to leverage telehealth for PrEP/PEP delivery in brick-and-mortar pharmacies in Kenya; if found effective, this model has high potential to inform PrEP delivery guidelines in Kenya and other settings where private pharmacies are numerous and highly accessed, but staff typically do not offer services beyond dispensing. Our teams’ extensive experience conducting HIV implementation research in collaboration with the Kenya MOH and our support from national pharmaceutical organizations will ensure the success of this project.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY/ABSTRACT Patient-oriented research of infection prevention strategies in chimeric antigen receptor T cell therapy (CARTx) recipients will facilitate improvement in clinical outcomes and a wealth of opportunities for trainees. This award will provide protected time for Dr. Hill to mentor trainees in clinical research related to mitigating the immune-related adverse effects from CARTx, thereby reducing infectious complications. This proposal will study the use of passive and active immunotherapeutic strategies to prevent infections after CARTx, including immunoglobulin replacement therapy (IGRT) and vaccination. In Aim 1, Dr. Hill will conduct the first randomized, controlled, multicenter trial of IGRT in 150 adult CARTx recipients with serum total IgG ≤400 mg/dL at five cancer centers. These data will provide critical insights into the potential risks and benefits of IGRT in this patient population. The key objectives of this study are to evaluate whether IGRT in CARTx recipients reduces infection rates compared to placebo, and to understand the impact of IGRT on cytokine release syndrome, immune effector cell-associated neurotoxicity syndrome, and healthcare resource utilization. As part of new research supported by this award, patients will be administered a validated survey to evaluate whether IGRT is associated with improvements in health-related quality of life (Aim 3), which will enable future cost-effectiveness research. In Aim 2, Dr. Hill will conduct an open-label clinical trial using an inactivated rabies vaccine in 28 CARTx recipients with relapse-free survival for ≥6 months, in addition to 10 healthy controls. Vaccination after CARTx cell therapy may provide a more durable and cost-effective approach to infection prevention than IGRT, but there are limited data to guide vaccination strategies after CARTx. The objectives of this study are to determine antibody responses, and clinical correlates of vaccine responsiveness, using a rabies virus vaccine as a neoantigen challenge. The rabies vaccine provides a unique tool to assess immune responses while patients are receiving prophylactic immunoglobulin given no or low anti-rabies immunoglobulin in these products. Dr. Hill will build on this infrastructure to study innovative vaccination strategies to improve immunogenicity in immunocompromised patients in Aim 4. He will conduct a pilot study in 20 CARTx recipients using a ‘fractional escalating dose’ delivery for the initial vaccine dose, followed by a booster ‘bolus’ dose. The objectives of this study are to determine whether the fractional escalating dose strategy improves the proportion of patients who develop protective antibody responses, which could shift the paradigm for vaccinating immunocompromised individuals. These aims address critical knowledge gaps in CARTx recipients, provide a robust infrastructure for POR training of physician scientists, and will provide the groundwork for future studies to refine infection prevention strategies in the growing population of CARTx recipients.

NIH Research Projects · FY 2025 · 2025-09

Project Summary/Abstract An accurate tumor classification is pivotal to clinical cancer care and precision oncology. Treatment options are often informed by the pathology or diagnostic from the tumor tissue. A major challenge for patients with metastatic cancer is the limited access to tumor tissue because surgical biopsies are not routinely nor repeatedly collected throughout the course of therapy. However, tumors can undergo drastic molecular changes during metastatic progression and resistance to therapies. Circulating tumor DNA (ctDNA) released from tumor cells into the blood is a non-invasive solution for addressing challenges in tissue accessibility. Current research and clinical efforts have focused on detecting genome alterations in ctDNA, but they do not always explain treatment failure. Treatment-resistant phenotypes are defined by distinct changes in the genetic and epigenetic regulatory landscape, which collectively form the tumor regulome. Currently, it is not possible to comprehensively portray the tumor regulome in patients during the course of therapy. We propose to overcome these limitations by developing innovative computational methods and epigenetic assays that will be employed to profile the tumor regulome and survey the regulation of resistant phenotypes directly from ctDNA. Our methods will integrate the analysis of genome alterations, chromatin accessibility, transcriptional regulation, and DNA methylation from the same ctDNA sample. This cost-effective strategy provides a temporal window into the patient’s disease by monitoring the tumor epigenetic regulation and its clinical phenotype. The innovative aspects of this project include the development of deep neural networks and machine learning methods to integrate the multi-omic data extracted from a single ctDNA assay. We will employ unique systems and resources to develop our methods and advance our understanding of tumor molecular heterogeneity and treatment response. (1) From rapid autopsy studies, we will assess the contribution of DNA from multiple metastatic lesions to determine the key source of ctDNA. (2) From patient-derived xenograft (PDX) mouse models, we will establish a repository of human ctDNA from mouse plasma to support development activities and studies under PDX treatment conditions using novel therapies. This framework is generalizable to address research questions related to tumor biology and treatment response, including monitoring cancer-associated pathways and the effectiveness of targeted therapies. Successful innovations made in this project will establish a paradigm shift in cancer research and accelerate translation of new clinical applications to advance precision oncology.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY/ABSTRACT Engagement in advance care planning (ACP), which includes having end-of-life (EoL) conversations and completing advance directives (ADs) (e.g., living will, health care proxy), has been shown to improve the quality of care and reduce suffering at the end of life. However, less than half of advanced cancer patients engage in ACP or complete ADs. One commonly overlooked barrier to ACP engagement and AD completion is a lack of acknowledgment that the majority of cancer patients report ACP as a social process in which they want to engage multiple loved ones and family members in their decision-making process. Dr. Shen's prior work suggests that patients frequently report involvement of family members as a critical concern and need for engaging in ACP and that 70.7% report their EoL care treatment preferences being shaped around concerns about their family members. Based on this pilot work and prior work indicating a patient preference to engage in ACP as a social process, this study aims to develop and pilot test a website [Planning Advance Care Together (PACT)] designed to improve advanced cancer patients' and caregivers' engagement in patients' ACP, presence of ACP discussions, completion of ADs, and receipt of goal-concordant care. The goals of this study are to: (1) refine and field-test a mobile application intervention (PACT) using an iterative design approach, “Think Aloud” exercises, and usability protocols; (2) evaluate the feasibility, acceptability, usability, satisfaction, and user engagement of the intervention among advanced cancer patients and their caregivers; (3) test the preliminary efficacy of the intervention on patients' and caregivers' level of engagement in ACP, documented ACP conversations, and patients' completion of ADs (primary outcomes); and patients' and caregivers' perceived social support and family functioning as well as patients' receipt of goal-concordant care (secondary outcomes); and (4) evaluate process measures in a post-intervention interview. An added proposed extension aim is to conduct a process evaluation to identify multi-level barriers and facilitators as well as best pathways to implementation of PACT. To achieve this newly proposed aim, we will conduct 16 focus groups (5 participants each) with patients with advanced cancer (n=20), caregivers/support persons of patients with advanced cancer (n=20), providers (oncologists, nurses, palliative care, psychologists, social workers) (n=20), and healthcare system leaders (n=20) to identify barriers, facilitators, and best pathway(s) for implementation (embedding within EPIC/MyChart, direct referral from providers, and/or direct-to-consumer marketing). Grounded in established theories of decision-making science, the proposed project takes the novel approach of utilizing web-based health technology to integrate loved ones into patients' ACP decision-making.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY Translation initiation determines the identity and amount of a synthesized protein. Dysregulated initiation occurs broadly in disease, including cancers, inflammatory diseases, and developmental and neurological disorders. The process requires a dozen factors and involves multiple coordinated steps that occur in under a minute. A key commitment step occurs when the initiation machinery selects a translation start site on an mRNA, which canonically is an AUG codon. Proper selection requires single-nucleotide precision to maintain the reading frame and avoid synthesis of truncated and potentially toxic peptides. Yet, genetic, biochemical, and genome-wide studies indicate that translation initiation also occurs at non-AUG start sites. These alternative start sites have critical roles during stress responses. Their differential usage becomes dysregulated in cancers and other human diseases. While we know eIF1, eIF5, and eIF1A play key roles, the molecular mechanisms that not only ensure high-fidelity recognition of the start site, but also enable flexible use of non-AUG start sites remain unclear. A major roadblock has been the inability to monitor the three proteins as they interact and rearrange in real time during initiation. In my postdoctoral research, I pioneered in vitro single-molecule spectroscopy approaches to analyze human translation initiation as it occurs in real time. During the ESI MIRA phase, we will use my versatile and powerful system to examine the molecular events that underlie tunable recognition of the translation start site. In Project 1, we will examine how the initiation machinery flexibly discriminates AUG and non-AUG start sites by developing new FRET-based single-molecule assays to monitor eIF1 and a key conformational rearrangement. In Project 2, we will define how initiation complexes commit to a start site by developing a new FRET-based single-molecule assay to directly monitor eIF5. In both projects, we will combine our single-molecule assays with synergistic biophysical, biochemical, cellular, and structural approaches. Collectively, we should define the kinetics that underlie start site recognition and reveal transient molecular branchpoints that proofread start site selection. We also should uncover the timing of molecular rearrangements that control the progression of initiation and define how cancer-linked mutations in eIF1A disrupt the dynamics. As my research program evolves, our discoveries and innovations will set the stage for us to examine non-canonical initiation modes and how human regulatory proteins control initiation. Our findings thus should illuminate key knowledge gaps in translation and may highlight new interactions or molecular interfaces that could be targeted with therapeutics to treat human disease.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY Cigarette smoking is responsible for over 480,000 deaths annually in the US—nearly double the number of drug overdose and alcohol-related deaths combined—making cigarettes the most deadly drug of abuse. Although smoking rates have declined over the past 50 years, tobacco use remains a critical public health problem, and more effective cessation interventions are needed. Depressive symptoms are a key barrier to cessation for many and reduce the odds of cessation by as much as 50-60%. Despite this, standard cessation treatments do not focus on reducing depressive symptoms as a means of supporting cessation. Doing so, however, could increase treatment effectiveness. Behavioral activation (BA) is a proven intervention for depression. Research suggests combining BA and standard cessation treatment may increase quit rates. Delivering this intervention through a mobile health application (mHealth app) would also make the treatment more accessible (smoking cessation apps are downloaded over 1 million times per year in the US alone), thereby increasing its impact. To test this hypothesis, we developed Actify!, the first app-based cessation intervention to combine BA with standard cessation support. In a rigorous, pilot randomized trial (n = 242), Actify! had descriptively higher user satisfaction and quit rates than the National Cancer Institute’s (NCI) QuitGuide app (e.g., 18.5% vs. 12.2% abstinence at 6 months). We now propose to conduct a fully-powered, randomized controlled trial to evaluate the efficacy of Actify! relative to QuitGuide at 6 months post- randomization (Aim 1), examine the moderating effects of pre-quit depression on 6-month cessation outcomes (Aim 2), and evaluate the extent to which changes in behavioral activation and depressive symptoms mediate these outcomes (Aim 3). This work is highly significant and innovative: (1) Actify! is the first standalone mHealth intervention of any kind to actively target reducing depression and promoting smoking cessation simultaneously; (2) strong preliminary evidence supports Actify!’s acceptability and efficacy relative to an active standard care comparator, the NCI QuitGuide app; and, (3) mHealth apps offer a promising and cost-effective modality for disseminating the intervention, if it is found to be effective. This project will also provide a definitive test of whether Actify! is superior to QuitGuide and, therefore, warrants future dissemination. It will also provide critical insights into our premise that addressing depressive symptoms with app-based BA can enhance cessation for people with and without a history of depressive symptoms at treatment initiation.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY The human body constantly replenishes blood and immune cells from stem cells in bone marrow through a differentiation process termed hematopoiesis. Disruptions in this process can lead to hematologic malignancies. Classically, hematopoietic fate decisions were modeled as discrete steps, but recent single-cell RNA sequencing studies demonstrate that hematopoiesis is continuous and that fate restriction occurs even within the hematopoietic stem cell population. These early fate decisions and the prevalence of epigenetic regulator mutations in hematologic malignancies highlight the essential role of the epigenome in hematopoietic fate commitment and the necessity of understanding these mechanisms at a fundamental level. Previous studies have demonstrated that epigenetic priming occurs in hematopoietic stem cells, but techniques capable of measuring these states in single cells have only recently become available. Utilizing single-cell measurements of gene expression, chromatin accessibility, and histone post-translational modifications in healthy hematopoiesis, I will develop computational tools to identify regulatory dynamics of cell fate gain and loss unique to single lineages. To characterize dysregulation of regulatory dynamics in disease, I will knock in a clinically relevant nonsense mutation in ASXL1, a regulator of histone H3 lysine 27 trimethylation, in human hematopoietic stem cells, differentiate them in vitro, and assay gene expression, chromatin accessibility, and multiple histone modifications in single-cell experiments to identify how these regulatory programs are disrupted and where in the developmental trajectory this disruption occurs. This research will unravel the complex regulatory landscape of priming and lineage biases in healthy hematopoiesis and improve the mechanistic understanding of hematologic malignancies in need of improved therapies.

NIH Research Projects · FY 2025 · 2025-09

Project Summary Properly functioning cells must tightly regulate protein synthesis, folding and degradation: es- sential processes for gene expression collectively known as proteostasis. Proteostasis is a balanc- ing act between the activities of the ribosome and the proteasome, which respectively synthesize and degrade proteins. Dysregulated proteostasis may lead to or promote tumorigenesis, and cor- relates with age-related diseases like Parkinson’s and Alzheimer’s. The clinical use of proteasome inhibitors, particularly to treat multiple myeloma, further underscores the need to determine what stress responses and regulatory mechanisms they activate, and how they do so. Cells are known to respond to proteasome inhibition by invoking mechanisms of translational control that lead to the phosphorylation of translation initiation factor eIF2α, which attenuates protein synthesis. However, it is unclear which kinases phosphorylate eIF2α upon proteasome inhibition, and the mechanisms that regulate this translational response are not well understood. I propose to close gaps in our knowledge of the regulatory landscape between protein synthesis and protein degradation, by pursuing two primary objectives. First, I will investigate the factors that modulate eIF2α phosphorylation in response to proteasome inhibition, including determining which eIF2alpha kinases are activated by proteasome inhibition. I have also conducted pooled, RNA- linked CRISPR knockout and polysome profiling experiments that led to intriguing preliminary data. These data suggest that an E3 ligase, UBR1, plays a significant role in attenuating translation upon proteasome inhibition. Accordingly, my second objective is to determine how UBR1, and its substrates, are influenced by proteasome inhibition to regulate the ensuing translational response. Through a combination of innovative sequencing techniques and classic biochemical ap- proaches, my research will further elucidate the regulatory networks linking protein synthesis and degradation. The outcomes of my work could enhance our understanding of how proteasome inhibitors function as chemotherapies, and inform new therapeutic strategies for use against age- related diseases and cancers.

NIH Research Projects · FY 2025 · 2025-09

Title: Probing human HSC genesis in a flow-directed 3D hemogenic vascular niche model Project Summary/Abstract: Human induced pluripotent stem cells (PSCs) represent a promising and essentially limitless source of hematopoietic stem, progenitor, and terminally differentiated blood cells for a variety of “off-the-shelf” cellular therapies and disease modelling applications. However, a major obstacle to translating this promise to the clinic is that current protocols for differentiating blood cells from PSCs have not clearly defined the microenvironmental niche signals necessary to support the emergence of functionally transplantable and durably self-renewing hematopoietic stem cells (HSCs). We hypothesize that distinct biochemical signals and fluid mechanical forces specific to the aortic vascular niche, where HSCs first emerge, synergize to promote HSC fate from hemogenic endothelial cell (HEC) precursors. Our preliminary studies suggest a potential novel role for signals transduced downstream of hydrostatic pressure in establishing self-renewal programs essential to HSC fate. We have recently developed a 3D engineered hemogenic vascular niche which supports the induction of hematopoietic fates from PSC-derived endothelium. The primary objective of this proposal is to leverage this innovative platform to test how intrinsic arterial maturation, biomechanical forces, and mesoderm-derived growth factors synergize to promote HSC genesis ex vivo. We propose that replicating the temporal and spatial integration of synergistic biochemical and biomechanical factors will be critical to elucidating the mechanisms by which HSCs can efficiently and reproducibly be derived from PSCs. To accomplish the goals of this proposal, we will leverage the complementary expertise of MPIs Dr. Hadland and Dr. Zheng along with the state-of-the-art techniques available in their laboratories. We expect that success in these goals will accelerate the clinical translation of PSC technologies to advance cellular therapies and disease modelling applications for various blood and immune disorders.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY Pancreatic ductal adenocarcinoma (PDAC) is projected to become the second-most common cause of cancer- related death in the United States. Detecting PDAC early has been challenging due to its rapid progression and late presentation. Recent collaborative efforts among NCI, PanCAN, and NIDDK have resulted in multiple studies utilizing electronic medical records (EMRs). They provide opportunities to advance the early detection of PDAC, since the approach taken in the research setting is identical to what would be used in clinical practice. Future implementation in EMRs could lead to earlier diagnostic testing or interventions, enable the rapid identification of cancer trends or risk factors, and allow for quicker action. These studies, including our own, have demonstrated that individuals with glycemically-defined New Onset Hyperglycemia and Diabetes (NOD) have a significantly higher risk of being diagnosed with PDAC within 3 years of meeting diabetes mellitus criteria. The Enriching New-Onset Diabetes for Pancreatic Cancer (ENDPAC) score further stratifies individuals with NOD based on their PDAC risk, considering factors such as weight changes, blood glucose levels, and age at diabetes onset. However, several challenges need to be addressed to ensure the success of PDAC early detection. Firstly, it is important to better define the at-risk population for PDAC, as NOD alone may not be sufficient. Individuals with new-onset prediabetes and those with worsening long-standing diabetes mellitus may also be viable targets for early detection of PDAC. Secondly, more effective enrichment strategies leveraging biomarkers are critical, as directly applying existing biomarkers may not yield optimal results. For example, the ENDPAC score, which was developed primarily in a predominantly white NOD population, should be adapted for other high-risk groups, such as individuals with NOPD, LSDM, and diverse demographic populations to ensure broader applicability. We will develop a comprehensive set of methods to address these challenges, aimed at identifying high-risk populations, exploring promising biomarkers using EMR data, and integrating them with advanced biomarkers in an efficient manner. Given the expertise of our team and the strength of our collaborative partnerships, the advancements in methodologies, and the potential clinical applications, we anticipate that our efforts will yield tangible clinical benefits in the near term.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY Vaccination prevents millions of deaths each year by generating protective immunological memory against pathogens, mediated by long-lived memory B and plasma cells. Diverse B cell populations emerge after vaccination, including CD11c+CD21lo atypical B cells, which are primed for plasma cell differentiation and antigen presentation. However, the relationships between early vaccine-responsive B cell subsets and the long-lived memory B and plasma cells that provide durable immune protection have not been established in humans. Further, novel immunostimulatory adjuvants increase the durability and breadth of vaccine responses, but head-to-head comparisons of their effects on human B cell differentiation are lacking. Insufficient knowledge of the functional relevance and relationships among human B cell subsets and how they are modulated by adjuvants impedes the rational design of vaccines to induce protective immunological memory. Here, we will systematically interrogate human B cell, plasma cell, and antibody responses after HIV vaccination and dissect the mechanisms of their induction in a human immune organoid model. Our unique vaccine cohort is comprised of four groups receiving the same immunogen with a different adjuvant and includes sampling of lymph nodes, where memory B and plasma cells differentiate from germinal center B cells, and bone marrow, where long-lived plasma cells reside. I hypothesize that the adjuvant, 3M-052-AF, will direct atypical B cells towards a germinal center fate, yielding more potent and durable antibody responses. To test this hypothesis, I will leverage our team’s extensive expertise in human B cell biology, vaccinology, and the application of antigen-specific systems immunology tools. I aim to: (1) identify which vaccine-response B cell populations are clonally related to long-lived populations and predict durable immune responses; (2) evaluate the influence of four adjuvants on B cell and antibody responses; and (3) determine the impact of adjuvant on cell phenotype, germinal center organization, and B cell receptor repertoire in a human immune organoid model. To achieve these research aims and establish myself as an independent investigator, I have devised complementary career development goals: (1) expand B cell biology domain knowledge and scientific network; (2) develop expertise in human immune organoid experimentation; and (3) cultivate skills necessary to lead an independent research group. My mentors are Dr. Evan Newell, a systems immunologist, and Dr. Julie McElrath, Director of the HIV Vaccine Trials Network Laboratory, and my advisory committee is comprised of experts in B cell biology, immune organoids, vaccinology, and computational biology. This adept team will provide guidance on both research aims and career development goals, complementing a series of workshops and courses that I have identified to develop the skills and knowledge to lead my own research group.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY Kaposi sarcoma herpesvirus (KSHV) is the etiologic agent of Kaposi sarcoma (KS), which causes significant morbidity and mortality worldwide, particularly in people with HIV (PWH) 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. In our prospective KS cohort in Uganda (the “HIPPOS” study), we have observed that outcomes remain poor despite optimized treatment with antiretroviral therapy (ART) and chemotherapy, with an overall 1-year survival of 64% among the first 200 study participants. However, we have observed differential outcomes among participants, with 11% achieving a clinical complete response, 48% a partial response, 13% experiencing stable disease, and 25% progressive disease. Identifying the factors that contribute to these differences in outcome could inform the design of more effective KS therapies. Our ongoing studies of the HIPPOS KS cohort and findings from other investigators suggest that control of HIV is an important factor in KS response. First, among the initial 200 participants in our HIPPOS cohort, higher baseline plasma HIV viral loads were independently associated with increased mortality in HIV-associated KS. Second, RNA sequencing of pre-treatment KS tumors demonstrated high-level expression of HIV genes in KS tumors from PLWH. Third, transcriptionally active HIV and HIV Nef protein have been identified in treatment- refractory KS tumors, suggesting that KS tumors could be a reservoir for HIV that shapes the KS tumor microenvironment. Fourth, our studies of several KS cohorts have identified CD8+ T-cells specific for peptides derived from the HIV Gag/Pol, Vpr, and Nef gene products that persist in both KS tumors and peripheral blood of PWH with KS despite peripheral HIV suppression with ongoing ART. Collectively, these findings suggest that persistence of HIV in KS tumors of PWH might make an important contribution to treatment resistance. In this proposal we will test the hypothesis that intratumoral HIV persistence is associated with treatment resistance in PWH with KS through evaluation of: (i) HIV, KSHV, and host gene expression, and (ii) HIV and KSHV protein expression in serially acquired tumor biopsies from cohorts of PWH enrolled in three prospective KS therapeutic clinical trials. The first cohort comprises the HIPPOS study of newly diagnosed adults with KS treated with either bleomycin/vincristine or paclitaxel at the Uganda Cancer Institute in Kampala, Uganda. The second and third cohorts comprise adults with KS enrolled on two trials conducted by the NCI-sponsored Clinical Immunotherapy Trials Network (CITN) who were treated with a human IL-7 agonist (trial CITN-17) or with the PD-1-specific monoclonal antibody pembrolizumab (trial CITN-12). Central to all three clinical trials is the hypothesis that control of KSHV and HIV replication by KSHV- and HIV-specific T-cells combined with effective ART is essential for KS regression and resolution. The successful completion of these studies will contribute to improved outcomes for individuals with KS worldwide.

NIH Research Projects · FY 2025 · 2025-08

Project Summary/Abstract Vaccine efficacy (VE) trials are the gold standard to determine the VE, relative VE, and VE durability. In addition, VE trials generate rich data for characterizing and comparing vaccine-induced immune responses and correlating immune responses to the clinical outcome. An immune correlate of risk (CoR) is a biomarker predicting clinical endpoint risk within a single treatment arm, while a correlate of protection (CoP) builds on a CoR to reliably predict VE or relative VE. Established CoR/CoP analyses have deepened our understand- ing of the causal mechanism through which vaccine works and accelerate vaccine approval. Our extensive experience emphasizes three key aspects of recent and ongoing VE trials: First, these trials target di- verse populations with varying baseline immunity from prior exposures or vaccinations. Second, emerging variants can evade natural or vaccine-induced immunity, prompting the inclusion of variant-specific inserts in updated vaccines. Third, advanced diagnostic technologies, such as multiplex PCR tests used in the COVE trial, enable simultaneous detection of multiple pathogens triggering illness visits. This project aims to develop analytical tools to address these challenges by leveraging rick immune biomarker and clinical endpoint data. First, we will develop an immunogenicity model that seeks to make the best prediction of an individual’s post-vaccination immune biomarker given their baseline immune biomarker from the same im- munoassay and key demographic variables, and we will use this model to unpack how VE is modulated by baseline immunity. Second, we will develop scalable and efficient statistical tests for a “conditional variant- invariant model” across different vaccine platforms and develop robust estimators of relative VE for updated vaccines compared to approved ones against variant pathogens. Lastly, recognizing that vaccines have a null effect on vaccine-mismatched respiratory disease endpoints, we will create a statistical framework to mitigate bias in VE durability and immune correlates analyses using well-defined off-target endpoints from novel multiplex PCR tests. Successful completion will equip investigators with innovative tools to extract more knowledge from VE trials.

NIH Research Projects · FY 2025 · 2025-08

Project Summary/Abstract Human immunodeficiency virus infects cells of the immune system and, if left untreated leads to the development of acquired immunodeficiency syndrome and death. With the advent of antiretrovirals, HIV infection has turned into a chronic infection. However, tools and therapeutics to dissect and deplete SIV/HIV latent reservoirs during combination antiretroviral therapy (ART) to interrogate their importance in defining reservoir dynamics are limited and are a focus of this application. Programmed cell death protein 1 (PD-1) is an immune checkpoint protein expressed on latently infected CD4 T cells and in particular T follicular helper (TFH) cells. TFH cells reside in the germinal centers and are enriched with replication-competent human immune deficiency virus 1 (HIV) provirus in people with HIV. Our proposal builds upon the pre-clinical work we performed in non-human primates in which we demonstrated that anti-PD1 chimeric antigen receptor T cells eliminated all detectable PD-1 expressing TFH cells; the first time the elimination of this reservoir of HIV has been reported. Moreover, it also depleted memory CD8+ T cells leading to accelerated disease progression. Here, we engineered novel CAR T cell modalities that are either controllable through an NS3 ON switch modulated by a small molecule inhibitor (Grazoprevir; GZV) or are a more specific CAR by integrating it into a LINK CAR platform that allows true Boolean AND gating by targeting CD4 and PD-1. Ultimately, we will combine these T-cell engineering strategies and build CAR T cells with higher safety and specificity, that are equally suitable for HIV cure interventions as wells as tools for CAR T cell-mediated depletion of cell subsets in the RM model. This will allow to deplete PD-1+ T cells or PD-1+ CD4+ T cell subsets temporarily and selectively. Initially, we will optimize these new CAR modalities in adoptive transfer experiment in uninfected rhesus macaques (RM). These experiments will show strong association of GZV plasma levels with expansion and collapse of the CAR T cell population, which will dovetail with depletion of PD- 1+ cells when CAR T cells are expanding. We will study whether immune reconstitution occurs after temporary PD-1- targeted deletion after cessation of GZV administration by following T cell dynamics and performing vaccination post-CAR T cell infusion. Subsequently, we will use these novel CAR T cells as tools to dissect the role of PD-1 in reservoir dynamics during ART. We will compare temporary and continuous depletion of total PD- 1+ as well as PD-1+ CD4+ T cells. Specifically, it is of interest how PD-1 depletion will affect the latent reservoir in terms of SIV intact proviral genomes. This project has the potential to substantially advance the utility of CAR T cells to dissect the pathology of SIV/HIV and reservoir dynamics in the nonhuman primate model to study the specific role of PD-1 during ART. It will inform and provide new strategies and targets for an HIV cure.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY Most patients with metastatic castration-resistant prostate cancer (mCRPC) are resistant to immune checkpoint inhibitors (ICIs), posing a significant clinical challenge that necessitates understanding the mechanisms behind this resistance. Immunosuppressive myeloid cells have been recognized in tumors, but their heterogeneity has made CSF1R inhibitors and other broad targeting approaches largely ineffective. My recent prostate cancer studies identified a distinct subset of tumor-associated macrophages, expressing high levels of SPP1 transcripts (SPP1hi-TAMs) that encode the osteogenic protein osteopontin (OPN). These cells become significantly more prevalent during disease progression and contribute to resistance to ICIs through adenosine signaling, particularly within the prostate. Despite bone being the most common site (>70%) of metastases in mCRPC patients and the poorer immunotherapy responses observed in patients with bone metastases, the role of bone- associated myeloid cells in resistance is unclear. My preliminary data identify granulocytes with high expression of CD62L and CXCR2 (CD62LhiCXCR2hi-gran) as key myeloid cells promoting immunosuppression through IL- 1R signaling in culture. I hypothesize that targeting CD62LhiCXCR2hi-gran and their corresponding molecular signals could enhance the efficacy of ICIs in mCRPC patients with bone metastases. I now propose to utilize intraosseous CRPC mouse models to determine whether CD62LhiCXCR2hi-gran are critical for immunotherapy resistance in vivo. By employing adaptive transfer experiments and pharmacologic interventions in mice and in situ hybridization imaging of patient bone biopsies, I expect to determine if these granulocytes mediate resistance to ICIs via the IL-1R pathway, consistent with our initial findings. Moreover, I aim to investigate whether this suppression mechanism is associated with spatial changes during disease progression by performing 10x Genomics Xenium in situ spatial transcriptomics analysis on formalin-fixed paraffin-embedded of patient and mouse tissues. I also plan to determine whether prostate-prevalent SPP1hi-TAMs can modulate the bone- associated myeloid landscape through long-range communication, particularly with OPN, during the progression of prostate cancer, and whether inhibiting these interactions can enhance the efficacy of ICIs for treating prostate cancer in bone. Preliminary results indicate that CD62LhiCXCR2hi-gran not only increase in abundance but also undergo transcriptional reprogramming during disease progression, with various soluble factors, including CCL5, being the most abundant drivers of myelopoiesis derived from CRPC cells. I now plan to determine whether signaling through these factors, particularly the CCR5-CCL5 axis, is necessary and/or sufficient for pathogenic myelopoiesis in mCRPC bone metastases, and whether it could serve as an immunotherapeutic target. Through these studies, my goal is to identify novel cellular and molecular therapeutic targets for mCRPC bone metastases, with the potential to translate into more effective immunotherapies.

NIH Research Projects · FY 2025 · 2025-08

Project Summary Many diseases arise from molecular alterations within cellular mechanisms, and our understanding of these processes is limited. Single-cell measurement technologies provide rich molecular data but current computational methods struggle with their complexity. Traditional approaches treat single-cell data as discrete sets, obscuring subtle continuous biological phenomena. To address this, we developed Mellon, an algorithm that offers a continuous representation of high-dimensional single-cell landscapes by inferring a continuous density function, effectively characterizing the distribution of cell states in a biological system. This proposal aims to develop robust tools for modeling and interpreting single-cell data using cell-state distribution representations (Aim 1) and novel specialized single-cell data representation (Aim 2). Our approach will uncover complex mechanisms of cell differentiation and analyze new modalities like perturb-seq in greater depth. We will demonstrate the utility of our methods with new datasets from collaborations, focusing on hematopoiesis, tissue regeneration and homeostasis in liver, and massive Perturb-seq assays. Aim 1 focuses on developing applications based on Mellon's cell-state distribution representation. This includes tools for differential cell-state abundance, massive relational analysis of Perturb-seq data, local co-regulatory mechanism analysis, and inferring cell-differentiation dynamics using partial differential equations. Aim 2 involves developing computational representation of tissue using cell-state distribution, enabling online learning, sampling strategies, and meaningful gradient estimates. We also aim to use hyperbolic spaces to reduce the computational footprint without sacrificing biologically meaningful signals. By addressing current limitations in data representation and analysis, this project will provide advanced computational tools for single-cell analysis, leading to a deeper understanding of cell differentiation, disease progression, and insights from large perturbation assays. The outcomes will significantly contribute to developmental biology, regenerative medicine, and disease modeling, paving the way for new therapeutic strategies.

NIH Research Projects · FY 2025 · 2025-08

Project Summary/Abstract Colorectal cancer (CRC) deaths have continuously decreased since the early 1990's, yet populations that receive care in safety-net healthcare systems, which represent 25% of all U.S. hospitals, have relatively poorer CRC-related outcomes compared to their counterparts. Safety-net healthcare systems disproportionately care for lower socioeconomic status individuals, minoritized groups, and other populations with high CRC-mortality due to lack of access to care. Fecal immunochemical test (FIT) is preferred for CRC screening in safety-net healthcare systems due to low-cost and ease of completion, however only 33% to 58% of patients in safety-net healthcare systems complete a follow-up colonoscopy within 1 year of an abnormal FIT. This failure to follow- up carries a 3-fold increased risk of advanced-stage CRC and a 2-fold increased risk of dying from CRC. Greater than 6-month delays in follow-up colonoscopy are associated with an increased risk of any CRC and advanced stage CRC. Previous research has shown that obtaining a follow-up colonoscopy is a complex process for safety-net patients due to multiple barriers at multiple levels of care, including lack of transportation, fear of colonoscopy, and fragmented care in a resource-constrained health system. To address these barriers, our project aims to evaluate a multilevel intervention for follow-up colonoscopy in a safety-net healthcare system compared to usual care. This study takes advantage of several single-level interventions that have been developed, tested and implemented at Harborview Medical Center (HMC) and Kent/Des Moines (KDM) clinic, safety net health settings in Seattle, WA. These interventions include: 1) a health system- level centralized CRC program aimed to improve screening and follow-up colonoscopy, 2) a health system- level navigation to follow-up colonoscopy program, 3) a patient-level rideshare program to address transportation barriers; and 4) a patient-level video to reduce fear of colonoscopy. We propose to evaluate these interventions together as a novel, multilevel intervention that addresses multiple barriers to follow-up colonoscopy at the patient- and health system-level versus usual care (centralized CRC screening and navigation to colonoscopy). Our central hypothesis is that a multilevel intervention that addresses multiple patient- and health system-level barriers simultaneously, will significantly increase the proportion of patients who receive a follow-up colonoscopy, compared to usual care, and will be possible to implement in a safety-net setting. To test our hypothesis, we will conduct a pragmatic randomized controlled trial of HMC and KDM safety-net patients with abnormal FIT results, randomized 1:1 to the multilevel intervention vs usual care. Our specific aims are: 1) Assess the effectiveness of the multilevel intervention at improving follow-up colonoscopy completion in a safety-net population compared to a health system-level only intervention (usual care); 2) Evaluate the facilitators and barriers to the reach, acceptability, fidelity and implementation of the multilevel intervention; and 3) Evaluate the cost of implementing the multilevel intervention in a safety-net population.

NIH Research Projects · FY 2025 · 2025-07

Project Summary/Abstract: Fred Hutchinson Cancer Center respectfully requests funds to replace its aging high-performance computing (HPC) cluster, aligning with technological advances and research computing trends from 2020 to 2025. The existing 212-node, 7,128-core HPC cluster, established in 2020 is reaching the end of its supported life and now requires replacement to facilitate biomedical research by integrating GPUs, leveraging their capabilities in artificial intelligence and machine learning. The proposed HPC system, slated for deployment in an updated space within Fred Hutch's datacenters, aims to replace this existing HPC system by adding 130 new nodes (totaling 7,799 cores). This system will culminate in a state-of-the-art 130-node, 7,799-core, 192 TB RAM HPC system with 1,753,088 CUDA cores, signifying a 9% surge in core count, an 97% boost in GPU processing power, and a 40% increase of memory capacity compared to the existing infrastructure. These enhanced computational capabilities are poised to catalyze deep and efficient analysis across a spectrum of biomedical research domains, facilitated by an increased emphasis on GPU-accelerated methodologies. Biomedical investigations, ranging from cancer eradication to infectious disease modeling, will benefit significantly from this computational enhancement. The core user group comprises no less than 38 NIH-funded research cohorts engaged in endeavors such as vaccine development, large-scale integrative analytics, and genomic studies, and are now increasingly reliant on GPU-accelerated algorithms for expedited insights. Furthermore, Fred Hutch acknowledges the imperative to meet these escalating computational demands of its user community and plans complimentary upgrades to the environment. Several major users are currently grappling with project delays, while others encounter hardware limitations with the incumbent infrastructure. This proposed upgrade not only addresses immediate needs but also anticipates future requirements, positioning Fred Hutch at the forefront of computational biomedical research. By embracing GPUs and contemporary computing paradigms, Fred Hutch endeavors to empower its researchers with the computational resources necessary for cutting-edge investigations spanning cancer biology, infectious diseases, and beyond, ultimately advancing scientific understanding and therapeutic innovation in the pursuit of improved human health.

NIH Research Projects · FY 2026 · 2025-07

Project Summary/Abstract Dramatic advances in artificial intelligence, single cell sequencing, spatial transcriptomics, and temporal data hold great potential for propelling biomedical understanding forward. However, access to training for these cutting-edge emerging technologies and data science best practices remains limited as researchers often struggle to find time to apply newly acquired skills to real-world data in a research context. To address these challenges, we propose expanding the Open Case Study (OCS) project to create Biomedical OCS (Bio-OCS), a comprehensive skills development program augmented by synchronous events and community support for research scientists and trainees. This initiative will focus on building bioinformatics skills using cutting-edge methodologies and tools, like AI and spatial transcriptomics, as the basis for case studies. Case studies demonstrating applications with real-world data have proven useful for teaching statistical thinking; the OCS project takes this model further by providing a free archive of case studies, guiding learners in working with data from start to finish and allowing them to demonstrate the necessary computational and problem-solving skills. To support uptake of these skills, the Bio-OCS program will also include virtual workshops for learners to work through our case studies with peers, launch a Slack workspace to facilitate a peer community, hold office hours and check-ins to assist in problem solving, and host in-person “Case-A-Thons” to support the application of case study lessons to participants' own data. Additionally, we will collaboratively adapt our current OCS Instructor Guide by hosting Reciprocal Instructor Summits where we assist instructors from other institutions to utilize case studies in their graduate courses. The new case studies, coupled with the supporting workshops, events, and resources, will enable us to better researchers and graduate students in building biomedical skills. Lessons learned through evaluation of our events and from Bio-OCS learner survey responses will be published in research papers to further support biomedical data science education.

NIH Research Projects · FY 2025 · 2025-07

PROJECT SUMMARY Prostate cancer is the second most common malignancy in the United States in men. Early-stage prostate cancer is androgen-dependent and relies on the androgen receptor (AR) signaling pathway for growth and proliferation. Following androgen deprivation therapy (ADT) and AR signaling inhibitors (ARSIs), the disease becomes refractory to AR-targeted therapies through a process known as phenotype switching. In prostate cancer, protein components of the translation apparatus have been shown to promote disease progression and even drug resistance. However, it remains elusive how prostate cancer utilizes RNA components of the protein synthesis machinery to support lineage plasticity and drug resistance. This represents a significant blind spot in our understanding of prostate cancer pathophysiology and an unmet need that has the potential to identify new biomarkers and therapeutic targets. Using state-of-the-art multiplex small RNA sequencing, I have found that lineage plasticity in prostate cancer is characterized by a significant decrease in a single tRNA, Arg-TCT-1-1. I have discovered that Arg-TCT-1-1 drives lineage plasticity through translation regulation of AR regulators enriched for AGA codons using a series of in vitro and in vivo models. In addition, I have conducted the first 5’ UTR tiled CRISPR dropout screen against all major oncogenic and tumor suppressive gene in prostate cancer treated with the ARSI enzalutamide and found that there are select regions within the 5’ UTRs of these genes such as CREBBP, EP300, CHD1, and RB1 which when targeted can drive a synthetic lethality with enzalutamide. Based on these preliminary data, I hypothesize that the RNA components of the translation apparatus (tRNA and 5’ UTRs) are critical in enabling aberrant mRNA specific translation which can drive lineage plasticity and drug resistance. In Aim 1, I will elucidate how Arg-TCT-1-1 tRNA impacts lineage plasticity in prostate cancer. In Aim 2, I will determine the mechanisms by which 5’ UTR-specific mRNA translation promotes treatment resistance in prostate cancer. To achieve these Aims, I will pursue additional training with my primary mentor Dr. Andrew Hsieh (mouse modeling and mRNA translation in prostate cancer), and co-mentors Dr. Tao Pan (tRNA biology), Dr. Michael Haffner (prostate cancer pathology and lineage plasticity), Dr. Alice Berger (functional genomics and computational biology), and Dr. Gabriele Varani (RNA structure biology). Fred Hutchinson Cancer Center is an ideal research environment providing cutting-edge research facilities and opportunities for further career development. With the proposed research and the training, I will be well-positioned to launch my independent research program at an academic institution.

NIH Research Projects · FY 2025 · 2025-07

PROJECT SUMMARY The study of differentiation and development is in many ways the study of how cells change over time. As cells differentiate and mature, they must change their state by changing their gene expression, chromatin accessibility, morphology, and other characteristics. These changes both describe and define the steps a cell must pass through as it differentiates and matures. This proposal seeks to develop computational models that can identify this sequence of changes that a cell must undergo to mature and transform from one type to another and compare changes in a cell’s gene expression and chromatin accessibility state in order to see how these modalities coordinate to drive the maturation and differentiation of a cell. This will be done by modeling the sequence of cell state changes over time as movement, inferring both the rate of change within each modality as well as the direction of change, i.e., peaks and genes that define these changes. Together the rate and direction of change describe a velocity for each cell, showing how the cell changes as it matures. Recent advances in single cell assay development now allow for the measurement of both the gene expression and chromatin accessibility modalities from single cells, giving a higher resolution view into the maturation of a cell. However, current approaches for inferring the dynamics of cell state change either reveal only the direction of change or cannot be applied equally to each modality. The methods proposed in this application seek to use the distribution of cells in the cell state space to infer both the rate and direction of cell state change, allowing these methods to be equally applicable to the gene expression and chromatin accessibility modalities. This velocity will be inferred with two approaches: (1) For single timepoint datasets, psuedotime will be used to define the direction of cell state change while the density of cells in each state will be related to their rate of change; (2) For time series data the change in density over time will be used to describe the flow of cells down developmental trajectories over time and will be related to a velocity using the drift diffusion equation. The algorithms proposed in this application aim to deepen our understanding of development by detailing how cells change their gene expression and chromatin accessibility as they mature down differentiation trajectories, by modeling the dynamics of these changes over time in single cell multimodal data. Further, these algorithms will provide a toolkit to explore the coordination between the epigenome and transcriptome, offering insights into cell fate priming and plasticity. This will lead to a better understanding of cell fate specification and will enhance our ability to design therapies for developmental diseases and uncover new targets for human reprogramming and regeneration.

NIH Research Projects · FY 2025 · 2025-07

PROJECT SUMMARY The purpose of this NIH/NCI Pathway to Independence Award for Early-Stage Postdoctoral Researchers (K99/R00) is to provide research training during the K99 Phase for Karl Cristie Figuracion, PhD, ARNP, a first- year postdoctoral research fellow at the Fred Hutchinson Cancer Center (Fred Hutch)/University of Washington (UW), and to become a productive, independent scientist during the R00 Phase with a research program focused on interventions to reduce symptom burden, improve quality of life (QoL), and return-to-work (RTW) outcomes in brain tumor survivors. This K99/R00 proposal outlines a training and career development plan that builds on and expands Dr. Figuracion's research skills to become a competitive applicant for a tenure-track faculty position at a research-intensive institution. Training Plan: To expand her research toolkit and advance her transition to independence, Dr. Figuracion assembled a multidisciplinary team of expert mentors from Fred Hutch and UW. Together with her mentors, they designed a robust training plan that includes regular mentored meetings and relevant advanced coursework, seminars, workshops, and research activities. The specific Learn the fundamental methods to develop a symptom management education intervention; 2) Receive didactic and hands-on training in qualitative study designs and analysis; 3) Gain didactic and hands-on training in analysis; and 4) Tra training goals of the K99 phase are to: 1) intervention design and implementation, clinical trial design, and nsition to an independent scientist by building a publication record in cancer survivorship and neuro-oncology survivorship research. Research plan: Isocitrate dehydrogenase (IDH) mutant glioma BT survivors experience significant symptom burden that impacts their overall QoL and RTW outcomes after radiation therapy (RT). However, there are limited symptom management interventions to improve self- management skills and health outcomes after RT. During the K99 Phase, Dr. Figuracion will refine a novel 5- session intervention, Symptom Management Education to Living Fully (SELF), which she developed in collaboration with subject matter experts. Specific Aim: 1) Refine SELF curriculum content through focus groups with IDH mutant glioma BT survivors (n=6-8), caregivers (n=6-8), and clinical care team (n=6-8). During the R00 Phase, she will test the feasibility and preliminary efficacy of SELF on reducing symptom burden and improving QoL, and RTW outcomes in IDH mutant glioma BT survivors (n=40). Specific Aims: 2) Test the study design feasibility as assessed via recruitment, adherence, retention, fidelity, and acceptability; 3) Examine the preliminary efficacy of SELF on self-efficacy, symptom burden, QoL, and RTW outcomes; and 4) Explore the preliminary effects of SELF on health promoting behaviors. Data generated in the R00 will serve as preliminary data for a future R01 efficacy trial to test the effects of SELF on increasing self-efficacy, reducing symptom burden, and improving QoL and RTW outcomes in BT survivors. The research generated from this K99/R00 will advance symptom management interventions to improve health outcomes in BT survivors.

NIH Research Projects · FY 2025 · 2025-06

Prostate cancer is the most common solid tumor in men and the second most common cause of cancer death in the United States. The Cancer Intervention and Surveillance Modeling Network (CISNET) Prostate Working Group (PWG) was formed in the year 2000 to address a wide range of questions about effective prostate cancer control. The PWG studied the rapid increase in prostate cancer diagnoses after PSA screening started in the late 1980s to estimate lead time and overdiagnosis associated with the test. The PWG studied the decline in prostate cancer mortality that began in the early 1990s to quantify the plausible contributions of PSA screening and changes in primary treatments. The PWG also studied how to interpret variations in incidence and survival across demographic groups, how to manage men with low-risk disease on active surveillance, and how to reconcile apparently discordant randomized trials of PSA screening and radical prostatectomy. In recent years, technologies surrounding prostate cancer screening and treatment have evolved rapidly, and opportunities to improve patient care using patient-specific data abound. Genetic testing can identify men at increased risk for developing aggressive disease, new biomarkers and imaging tools can help men avoid unnecessary biopsies, and new hormonal treatments can lengthen survival for men with advanced disease. The objective of this application is to extend PWG models to evaluate optimal ways to utilize data-driven approaches to improve patient care while limiting harms and costs. We will determine whether we can improve early detection using novel stratification approaches and whether we can safely limit overtreatment and other harms by optimized, strategic choices of primary and secondary therapies. These approaches will be applied in multiple cancer control settings with different resources and priorities.