University Of Tx Md Anderson Can Ctr

NIH Research Projects · FY 2025 · 2025-04

Project summary/abstract Immune checkpoint inhibitors (ICI) transformed oncological care for multiple cancers. Yet, 80% of ICI patients will eventually fail therapy. Colossal efforts are invested in overcoming ICI resistance. A promising candidate is the gut microbiome which was associated with ICI clinical outcomes. I led a seminal clinical trial in which the gut microbiome of patients with ICI refractory metastatic melanoma was modulated via fecal microbiota transplantation (FMT). FMT and ICI re-induction resulted in increased intra-tumoral infiltration of CD8+ T-cells and objective clinical response rates of 30%. However, microbiome modulation remains far from wide clinical use. While FMT showed consistent clinical efficacy, it is not feasible outside of major academic centers; and some probiotics have been associated with a deleterious effect on ICI efficacy. Therapies that mimic the microbiome effect on the immune system can enhance ICI efficacy while omitting FMT obstacles. However, the development of such therapies is hindered since the mechanisms driving the gut microbiome's effect on anti-tumoral immunity remain unknown. In this proposal, I will test the hypothesis that an adverse microbiome induces a state of chronic inflammation that impedes ICI efficacy. FMT from donors with favorable microbiomes promotes anti-tumoral immunity by disrupting the net inflammatory signaling; hence, attenuating inflammation by direct immune re-programming can mimic the FMT effect. To test this, I propose the following research plan. In Aim 1, I will determine the effect of microbial-induced inflammation on anti-tumoral immunity by analyzing longitudinal stool, serum, gut, and tumor samples from a unique cohort of 33 patients with ICI- refractory melanoma (n=20) and microsatellite-instability high cancers (MSI-H, n=13) who participated in clinical trials of FMT and ICI re-induction (NCT03353402 and NCT04729322, respectively). Spatial transcriptomics of gut and tumor samples will be used to demonstrate FMT-induced immune dynamics and to test my sub-hypothesis that microbial inflammatory signals are mediated via myeloid antigen-presenting cells (APC). In Aim 2, I will determine the immune system's ability to override microbial signals. I will conduct FMT from cancer patients who responded and did not respond to ICI into CD11c-Cre+ Stat3f/f (Stat3Δ/Δ) mice that have dendritic cells with hyper-activated toll-like receptors (TLR) signaling. This experiment will test the ability of an immune system with a chronic inflamed state to overcome the beneficial effect of FMT from a donor with a favorable microbiome. To re-program the immune system to override the effect of adverse microbiome- mediated inflammation and hence overcome ICI resistance, I will compare the immune activity and tumor growth of mice undergoing FMT versus mice treated with a combination of ICI and interleukin (IL)-1b blockade; since IL-1b secretion can be a product of TLR activation and our previous work showed that an adverse microbiome induces IL-1-mediates gut inflammation. Overcoming ICI resistance by microbial-derived inflammatory signal blockade can enhance the clinical efficacy of ICI in patients with various cancer types.

NIH Research Projects · FY 2026 · 2025-03

ABSTRACT Soft-tissue sarcomas (STS) pose a substantial global health challenge with a low survival rate for advanced cases. Despite current treatments, there is a pressing need for effective therapeutic strategies. This proposal focuses on investigating the potential of Abemaciclib, a CDK4/6 inhibitor, alone or in combination with circRNA- silencing, to enhance anti-tumor immune responses in STS. The study aims to elucidate the interplay between Abemaciclib, circular RNAs (circRNAs), and immune responses in STS using newly developed immunocompetent mouse models. The research is structured around three specific aims: Aim 1 explores how circCsnk1g3 limits Abemaciclib-triggered interferon and inflammatory responses. Abemaciclib and circCsnk1g3 exhibit opposing effects on these responses in sarcoma cells, and the study aims to uncover the shared signaling pathway impacted by both. Experimental approaches include treating with Abemaciclib, manipulating circCsnk1g3 expression, and assessing the RIG-I/MDA5/MAVS pathway through co-immunoprecipitation assays and downstream effector evaluation. Aim 2 investigates whether circCsnk1g3 silencing enhances Abemaciclib's anti-tumor effects and shapes the tumor microenvironment (TME). The study hypothesizes that circCsnk1g3 targeting could serve as a therapeutic adjuvant to boost Abemaciclib-induced anti-tumor immune responses. Advanced techniques such as single-cell RNA-sequencing and flow cytometry will be employed to comprehensively assess tumor immune composition, including sub-types of tumor-associated macrophages (TAMs) and T cells. Aim 3 assesses the functional role of circCdyl in regulating TAM inflammatory responses. TAMs express higher levels of circCdyl and RIG-I than sarcoma cells, and the study aims to determine the impact of circCdyl on TAM activation and anti-tumor effects. Intervention with circCdyl expression in bone marrow- derived macrophages (BMDM) will be conducted, and in vivo experiments will assess the influence of circCdyl- manipulated BMDM on tumor growth. Overall, this research aims to deepen our understanding of the mechanisms underlying the potential synergy between Abemaciclib and circRNA-silencing in STS, with a focus on immune responses and the tumor microenvironment content.

NIH Research Projects · FY 2026 · 2025-03

Project Summary This project will address several important open issues related to transient multiphase flow and heat transfer in biological tissues, including formulation of a class of mathematical models that satisfy conservation laws of multi-constituent chemically reacting flow through porous tissue and stable time-stepping schemes for efficient solution to the highly nonlinear and degenerate coupled governing equations. Mathematical models of chemically reacting miscible fluid flow in living porous tissue will include all relevant phenomena: mass-momentum-energy conservation of multiple chemical species, exothermic chemical reactions during delivery and within the tissue, as well as liquid-gas phase changes induced by exothermic acid-base neutralization reactions. To focus mathematical model developments, research will develop a class of mathematical models toward understanding the fundamental thermal, hypoxic, and pH response of an exciting thermoembolization therapeutic approach for treating hepatocellular carcinoma (HCC). Mathematical predictions will be validated in an animal model of HCC. The validated models will be used to optimize delivery protocols. The goal of these mathematical sciences efforts is to provide fundamental understanding of mechanisms that define a successful treatment. Our high-fidelity mathematical approach will provide guidance toward the treatment extent that can be achieved for a given combination of patient anatomy, disease extent, chemistry, and injection parameters. Further, the computational methodology is cost effective and helps to reduce and refine animal experiments. A multi-disciplinary team with expertise in imaging physics, mathematical modeling, numerical algorithms, interventional radiology, and biochemistry has been assembled to accomplish project goals.

NIH Research Projects · FY 2025 · 2025-03

ABSTRACT/SUMMARY The majority of lung cancer patients do not respond to treatment effectively or develop the resistance quickly. To increase the response rate and minimize the drug resistance, it is critical to develop novel treatment strategies based on molecularly matched preclinical models. Currently, mapping preclinical models relies mainly on genomic and transcriptomic data, which, according to our analysis, fails to match >30% patients to representative preclinical models. Given that proteins are key functional units responsible for major cellular activities and therapeutic targets, we hypothesize that proteomic data are more informative to identify suitable preclinical models. Reverse-phase protein arrays (RPPAs) offer a powerful functional proteomic approach to identifying biomarkers, targets, and biological mechanisms, enabling the evaluation of numerous protein markers in hundreds of samples in a cost-effective, sensitive, and high-throughput manner. Our team has been a leader in implementing this platform and disseminating our RPPA data to the biomedical research community. Our current objective is to develop a functional proteomics approach to accurately mapping tumor samples with the preclinical models. To accomplish our goal, we have assembled a highly productive team with a long collaboration history and diverse expertise, and will pursue two specific aims, Aim #1: Expand the proteomics profiling of lung cancer PDX models using the RPPA platform. Our platform has recently been upgraded to cover ~500 cancer-related proteins and has characterized ~9,000 TCGA patient and CCLE cell line samples. This includes ~700 non-small cell lung cancer tumor samples and 175 lung cancer cell lines. Using this platform, we will expand this dataset to include both small cell and non-small cell lung cancer PDX models. Aim #2: Build a comprehensive correspondence map linking lung cancer tumors with preclinical models. Leveraging the RPPA data generated from patient, cell line, and PDX samples, along with other omics data, we will systematically assess their pairwise associations. We will develop deep-learning models based on both RPPA data and functional response data, to identify and validate novel lung cancer vulnerabilities and potent drug combinations. The expected outcome is (i) a well-characterized and harmonized cohort of lung cancer preclinical models as well as patient samples coupled with high-quality RPPA profiling data; (ii) a mechanistically interpretable correspondence map linking individual patient tumors to preclinical models; (iii) a shortlist of novel lung cancer vulnerabilities through our state-of-the-art computational framework that are ready for clinical evaluation. Our proposed research is innovative because it offers a fundamental, mechanistic view on proteome- guided associations between multi-platform preclinical models and patient tumors. This project will have a lasting, positive impact by: i) generating a unique lung cancer proteome resource for preclinical models; ii) establishing a highly accurate, comprehensive multi-omics molecular mapping between lung cancer tumors and preclinical models; and iii) developing novel therapeutic strategies based on RPPA-guided molecular mappings.

NIH Research Projects · FY 2026 · 2025-03

PROJECT SUMMARY Brain metastasis is a major clinical challenge associated with high morbidity and mortality. Growing evidence suggests a critical role for the immune system in the pathophysiology of brain metastasis. Our group and others have demonstrated that microbiota, i.e. the assembly of microbes residing within the human body, plays a major role in shaping immune responses and tumor immunity. However, the impact of different microbial communities on brain metastasis remains poorly understood, limiting our ability to harness the power of accessible and cost- effective microbiome modulation strategies to enhance clinical care and improve the outcome of brain metastasis patients. My postdoctoral studies demonstrated, for the first time, that the brain metastasis tumor microenvironment harbors intracellular bacterial signals, confirming the existence of a tumor microbiome in brain metastasis tumors. Importantly, this tumor microbiome was enriched in oral bacteria, suggesting that the oral microbiota plays a role in the formation of the tumor microbiome in brain metastases. Furthermore, spatial transcriptomic analysis of patient and murine samples demonstrated that the oral microbiota and the orally derived tumor microbiome can be associated with transcriptional alterations in the brain, involving both resident microglial cells at early stages and infiltrated innate immune cells at later stages. Building on these studies, this proposal pioneers the investigation of the impact of the oral microbiota in brain metastasis development and progression. In Specific Aim 1 (K99 phase), I will elucidate the mechanisms underlying the formation of the orally derived tumor microbiome in brain metastases. In Specific Aim 2 (K99/R00 phase), I will use longitudinal clinical studies and spontaneous mouse models of brain metastasis to determine the local and systemic contribution of the oral microbiota in brain metastasis development and progression. Insights gained from these studies can inform the development of novel diagnostic, preventive, and therapeutic strategies for metastatic brain tumors. The mentored phase of this project will be conducted under the supervision of Drs. Jennifer Wargo, James Allison, and Michael Davies, at the University of Texas MD Anderson Cancer Center, who are world-renowned experts in microbiome, cancer immunology, and brain metastasis research. An outstanding advisory team will also provide guidance on the various aspects of this proposal and training activities. My exceptional mentoring and advisory teams and the rich intellectual environment at the MD Anderson Cancer Center offer valuable opportunities for successful completion of the proposed research and career development plan. Completion of the mentored phase of this award will set the stage for a smooth transition to an independent career where I can integrate the emerging fields of microbiome and brain metastasis research to tackle outstanding questions in cancer research.

NIH Research Projects · FY 2026 · 2025-03

Project Summary The existence of asymptomatic precursor lesions that are known to predate invasive pancreatic ductal adenocarcinoma (PDAC) by years provides a compelling “window of opportunity” for cancer interception efforts. One such precursor is intraductal papillary mucinous neoplasm (IPMN). Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) imaging of metabolites in tissue sections from resected patient IPMN cases and from a KrasG12D/GnasR201C mouse model of IPMN, we have made a discovery in identifying long chain hydroxylated sulfatide species that are selectively enriched in IPMN. Targeting of sulfatide metabolism via small molecule inhibition of ceramide galactosyltransferase (UGT8), a key enzyme in the synthesis of the sulfatide precursor galactosylceramide, suppressed sulfatide synthesis and induced ceramide-mediated compensatory mitophagy, and subsequent apoptosis in Kras;Gnas IPMN cells and suppressed tumor growth in an allograft mouse model of IPMN. The primary objectives of this proposal are to 1) define the biological role(s) of sulfatide in the development and progression of pancreatic cancer precursor lesions, 2) test whether small molecule inhibition of sulfatide metabolism is a viable cancer interception strategy, and 3) conduct a ‘proof-of-concept’ study that MALDI-MS imaging-based assessment of sulfatides can identify positive margins and malignant nodules in challenging intraoperative frozen tissues from PDAC surgical resections. In Aim 1A, we will use an unique cohort of patient-derived organoids (PDOs) established from resected IPMN samples as well as murine-derived organoids (MDOs) and cell lines derived from Kras;Gnas mice. Using CRISPR/Cas9 technology, we will establish UGT8-/-, galactose-3-O-sulfotransferase (Gal3St1-/-), and double UGT8-/-/Gal3St1-/- knockouts to define the cell autonomous effects of sulfatide and sulfatide precursors on mitochondria lipid composition, function, dynamics, and quality control. Findings will be further integrated with transcriptomics, proteomics, and metabolomics data. In Aim 1B, we will investigate the role(s) of sulfatide in promoting the initiation and progression of pancreatic precursor lesions and evaluate its impact on the nascent tumor microenvironment and immunophenotype using orthotopic mouse models of parental and isogenic (e.g. UGT8 KO) model systems established in Aim 1A. To assess for clinical potential, in Aim 2, we will test whether targeting of sulfatide metabolism using an selective small molecule inhibitor of UGT8 attenuates the development of precursor lesions and invasive carcinoma in Kras;Gnas mice. Given the observed specificity of sulfatide to pancreatic precursor lesions and carcinomas, in Aim 3, we will collect intraoperative surgical margins and suspicious metastatic nodules from patients undergoing PDAC surgical resections at MD Anderson Cancer Center, and we will test the extent to which MALDI-MS imaging of sulfatides can identify involvement by cancer cells. Potential findings from our studies may lead to cancer interception strategies and imaging-based diagnostic applications for PDAC.

NIH Research Projects · FY 2026 · 2025-03

ABSTRACT Radiopharmaceuticals (RPs) are essential linchpins of cancer diagnosis, staging, and therapy. For diagnosis, the sensitivity and quantitative nature of positron emission tomography (PET) imaging, coupled with the ability to produce biologically active RPs bearing positron-emitting isotopes, renders PET uniquely capable of detecting tumors and quantifying their actionable molecular features. Moreover, recent successes in theranostics(1), which utilize targeted RP pairs for diagnosis and therapy, have led to improved outcomes in challenging clinical settings, such as neuroendocrine and prostate cancers(2, 3). Encouraged by these results and recent clinical approvals, pharma and academia alike are investing heavily in RP Research and Development (R&D) in pursuit of theranostics targeting other solid tumors, such as pancreatic(4, 5), breast(6), and lung cancer(7). Due to the immense infrastructure, resource, and logistical burdens associated with current strategies for radiopharmaceutical production (including PET imaging diagnostics and radionuclide therapeutics), the development and proliferation of radiopharmaceuticals beyond routine diagnostics such as [18F]FDG is challenging and expensive. The vast infrastructure required to develop, evaluate, and deliver radiopharmaceuticals, and even radioisotopes themselves, severely limits their deployment to the patients that need them(8). To address this critical hurdle, we will develop a rapid, inexpensive microfluidics-based approach for dose-on-demand production of human dosage quantities of ready-to-inject radiopharmaceuticals that can be adapted to a variety of radiopharmaceutical-related chemistries. In addition to facilitating end-user manufacturing and purification with a minimum of resources, the proposed platform will simplify raw isotope distribution logistics by using the chip itself as the shipping container and as the module for purifying (and eventually reacting) the desired radiometal. The objective of this proposal is to dramatically reduce barriers associated with RP production, rendering RP discovery and dissemination dramatically more accessible. To achieve these goals, we will build upon our prior development of the radiometal sub-family of simple, inexpensive, microfluidic ‘single dose-single device’ radiosynthesis platform RAPID-M (Radiopharmaceuticals As Precision Imaging Diagnostics-Metals). Based upon our published and preliminary studies, our Specific Aims are: To employ RAPID-M as a “ship-on-chip” device for simple isotope purification, transport and downstream, end-user application (Aim 1); to demonstrate RAPID-based synthesis of a theranostic pair for imaging and therapy (Aim 2); and to automate the RAPID concept to allow for production of RPs with minimal operator intervention (Aim 3).

NIH Research Projects · FY 2025 · 2025-03

Project Summary We aim to leverage machine learning to predict antigen-antibody interactions from massive sequencing data, for elucidating the roles of humoral immunity in various biological contexts, for discovery of antibodies of therapeutic values, and for development of diagnostic tools for immune-related diseases. Existing experimental methods for profiling antibody-antigen interactions are costly, time-consuming, and low-to-mid throughput, necessitating the need for AI-driven predictions. However, existing bioinformatics tools mainly optimize antibodies given antigen targets, whereas de novo detection of antibody-antigen interactions requires a different approach. Luckily, recent scientific developments have provided opportunities to solve this problem of fast, cheap and accurate detection of antigen-antibody interactions: (1) High-throughput sequencing technologies, like Libra-Seq, Beam-B and TRAPnSeq, have provided abundant antigen-antibody pairing data for training deep learning models. (2) The emergence of protein structure prediction models like AlphaFold3, RoseTTAFold and ESMFold have provided enabling weapons. (3) The introduction of multiplexed scRNA-seq/scBCR-seq data has provided another layer of complementary evidence to enhance the prediction of antigen-antibody interactions. We build on these new technologies/data, and our prior achievements and unique expertise in the relevant fields. We plan to develop and validate deep learning models to accurately identify antibody-antigen interactions and the binding epitopes on antigens from massive sequencing data (Aim 1). A complementary approach to integrate the transcriptomics of B cells with the BCR (B cell receptor, antibody) sequences is also taken to distill the gene expression information for enhancing the accuracy of antibody-antigen predictions (Aim 2). We seek to identify PD-L1-based PD-1 agonistic antibodies for autoimmune diseases, using the tools that we previously developed and those that are to be developed in this grant (Aim 3). This case study of PD-L1 antibodies has its own significance and innovation, but will also help validate and tune the tools to be developed in Aim 1 & 2. The multidisciplinary team includes experts in bioinformatics, computer science, and immunology, each responsible for different aspects of the research project. In particular, our prior research demonstrates expertise in deep learning of protein structures, development of novel therapeutic antibodies, and methodological development for single cell sequencing data analysis, which are essential for the success of this proposal. The impact of the research includes providing powerful tools for understanding the roles of B cells and BCRs in immune-related diseases, reducing the time and cost of identifying therapeutic antibodies (e.g. PD-L1-based PD-1 agonistic antibodies), aiding in vaccine development, and the derivation of BCR-based diagnostic and prognostic biomarkers for various diseases involving humoral immunity. We will disseminate our tools through workshops and webportals. Overall, the project addresses major unsolved problems in the field of B cell informatics that recently become solvable due to the advance of science and our latest works in this field.

NIH Research Projects · FY 2026 · 2025-02

Project Summary/Abstract Advanced gastric adenocarcinoma (GAC) presents significant treatment challenges due to frequent peritoneal metastases, leading to poor survival rates despite existing therapies. Understanding the mechanisms driving advanced GAC progression is crucial, with identified subsets like MSIH, Her2 positive, PDL-1 high, EBV, Claudin18.2 high, and FGFR2b+ tumors leading to patient stratification for customized treatments. We defined two advanced GAC subtypes: Type I, with CDH1/E-cadherin inactivation linked to SOX4 and EZH2 activation, and Type 11, marked by elevated RHOA activity. Unique immune profiles were elucidated for each subtype. We established murine organoid lines, including wild type (WT), KrasG120; Trp53Δ/Δ (KP), and Cdh1 knockout (KO); KrasG120 ; Trp53Δ/Δ (EKP), with EKP resembling Type I advanced GAG with EZH2 activation, inhibited by EZH2 blockade. SOX4 activation was confirmed in genetically engineered mouse models (Tff1-CreERT2; Cdh1MI; KrasG120; Trp5:t1'" [EKPTI), showing notably higher expression post-tamoxifen treatment compared to WT and Tff1-GreERT2; Cdh1MI; Trp5:t1'" (EPT). High SOX4 levels were evident in stage IV advanced GAG patients, correlating with poor prognosis. Functional studies, including SOX4 KO in GA0518 cells (GDH1-inactive human advanced GAG cell line), demonstrated suppressed tumor growth and improved survival rates, while SOX4 overexpression enhanced GDH1-inactive GAC aggressiveness. Further investigations will focus on SOX4 and EZH2-mediated transcriptional reprogramming in GDH1-inactivated advanced GAG. Additionally, we expanded our models to include six murine organoid lines (Trp53Δ/Δ [P], RHOAY420 [R], Cdh1 KO [E], Gdh1 KO; Trp53"" [EP], RHOAY42c; Trp53Δ/Δ [RP], RHOAY42c; KrasG120; Trp53Δ/Δ [RKP]) and three 2D cell lines (KP, EKP, and RKP) to explore subtype-specific responses to immune checkpoint blockade alongside EZH2 blockade for Type I and RHOA blockade for Type II advanced GAG. Herein, we hypothesized GDH1 loss promotes GAG progression via intrinsic (SOX4 and EZH2 mediated transcriptional reprogramming) and extrinsic (immune evasion) dysregulation. Two aims will be pursued: Aim 1. To determine the mechanisms of GDH1-inactivated advanced GAG progression; Aim 2. To determine the molecular subtype-based immune checkpoint blockade response. This study aims to uncover mechanisms of GDH1 loss-associated GAG progression, test molecular signature-based targeted therapy, and establish a new paradigm for GAG patient stratification.

NIH Research Projects · FY 2026 · 2025-02

PROJECT SUMMARY/ABSTRACT: The proposed study seeks to use the established association of Fusobacterium nucleatum (Fn) with colorectal cancer (CRC) as a model to decipher critical determinants of microbial tumor niche colonization and examine mechanisms by which microbes contribute to CRC. Within the CRC tumor microenvironment (TME), malignant cells are surrounded by a complex range of non-transformed cells and a diverse collection of tumor-infiltrating microorganisms. Fusobacterium nucleatum (Fn), a member of the human oral microbiota, is found enriched in colorectal cancer (CRC) compared to non-cancer colon tissue, across patient cohorts worldwide. Previous work by our group and others has demonstrated that patients with CRC tumors harboring high levels of Fn have poorer survival, that Fn persists in metastatic disease, and that microbiome modulation targeting Fn could change the course of this disease. Additionally, our recent work has demonstrated that Fusobacterium exists within regions of oral and CRC tumors that are poorly vascularized and highly immunosuppressive; characterized by myeloid cell infiltration, upregulation of immune checkpoint proteins PD1, CTLA4 and Lag3, reduced T-cell infiltration - the same regions that are recalcitrant to immunotherapies and chemotherapeutics, thus supportive of cancer progression. However, mechanistic insights into how this microbe is homing to and colonizing the TME and how it is contributing to disease initiation or progression are severely lacking, which impedes prophylactic and therapeutic progress against Fn in cancer. Here, in preliminary studies, we isolated and characterized the genomes and epigenomes of >150 Fn strains from CRC tumors and the oral cavity and discovered that within Fn subspecies animalis, there are two distinct clades that differ in their enrichment in CRC, which we named Fna oral-clade and Fna CRC-clade. We show that Fna CRC-clade is the only Fn group significantly enriched in human tumors and fecal specimens. Pangenomic investigations of Fna clades revealed genetic factors whose putative functions are canonically associated with pathogenic colonization of the human gastrointestinal (GI) tract. These included operons for the metabolic utilization of the gastric substrates ethanolamine (EA) and 1,2-propanediol (1,2-PD), and a glutamate decarboxylase acid resistance (AR2) system (associated with extreme acid resistance) of relevance to survival during GI transit and immune-modulation in the TME. This proposal’s objective is to interrogate these genetic factors, enriched in Fna CRC-clade but absent in oral-clade, as critical determinants of gastrointestinal transit, colonization, and survival within CRC tumors. Our team brings together expertise in synthetic microbiology, pangenomics, and genetic engineering (PI Johnston), preclinical cancer models, and tumor-infiltrating microbiota (PI Bullman), in addition to metabolomics (Co-I Raftery). Thus, we are poised to provide mechanistic insights on the genetic basis of Fna’s pathoadaptation to CRC and could identify new therapeutic targets against this tumor-infiltrating microbe found enriched in CRC-patient cohorts worldwide.

NIH Research Projects · FY 2025 · 2025-02

Project Summary/Abstract Chemotherapy-induced peripheral neuropathy (CIPN) is a common dose-limiting side effect of cancer treatment. The lack of successful pain therapeutic development for CIPN is ascribed in part to the use of relatively young, healthy, naïve animals. Given the emerging role of cancer-driven disruptions to the immune system in nervous system function, we propose to develop and validate a mouse model of CIPN with several key refinements which we hypothesize will result in a model with face, construct and predictive validity. Our preliminary studies indicate that colorectal cancer growth in mice is associated with subtle signs of polyneuropathy, including myelin dysregulation, loss of intraepidermal nerve fibers, systemic inflammation, hypercoagulability and deficits in fine motor coordination. Many of these pathological features have been reported in patients with colorectal cancer. This is crucial because one of the main factors in an individuals’ risk of developing CIPN is the presence of pre-existing neuropathy. We contend that this largely subclinical neuropathy driven by colorectal cancer is a major contributor to the subsequent pain and neuropathy experienced as a consequence of chemotherapy, and one that pre- existing models of CIPN do not capture. Therefore, the overall goal of this project is to develop and validate a mouse model of CIPN that replicates tumor growth, surgical resection and treatment with an adjuvant oxaliplatin-based chemotherapy regimen as closely as possible. The first aim will assess the impact of surgery and tumor growth on the subsequent development of sustained pain hypersensitivity in response to a FOLFOX-like (fluorouracil, leucovorin, oxaliplatin) regimen, establishing face and construct validity of the model. The second aim will determine the predictive validity of this model, comparing the efficacy of drugs that are recommended and not recommended for treatment of CIPN in the clinic. Our multidisciplinary approach involves a number of reflexive and non-reflexive tests of tactile and thermal sensitivity, along with assessments of motor coordination. Our project will unambiguously establish the impact of prior tumor growth on the development of painful CIPN in colorectal cancer. Establishing such preclinical CIPN models with predictive validity is critical to the development of new- generation, efficacious analgesics.

NIH Research Projects · FY 2026 · 2025-01

Project Summary/Abstract The drug development process is an intricate and resource-intensive endeavor, particularly in the context of addressing complex diseases with unmet medical needs, such as cancer, serious rheumatic diseases, acute ischemic stroke, among others. There has been a surge in the development of new therapeutic agents and combination treatment strategies, driven by rapid advancements in biological knowledge. However, the conventional approach to clinical trials, where treatments are evaluated one at a time in a sequential manner, is fraught with several shortcomings, especially in the era of precision (personalized) medicine. This \one-treatment-at-a-time" paradigm in drug development is associated with notably low success rates. It not only consumes valuable time and resources between separate trials but also extends the overall drug development timeline. The discrete nature of these phases impedes the ecient exchange of information across di erent stages, potentially leading to a loss of overall eciency. Furthermore, the evaluation of multiple treatments individually presents challenges in accurately estimating and interpreting the relative treatment e ects of each drug due to the presence of \treatment{trial" confounding. Viewing the drug development process as a whole system, the multi-arm multi-stage platform trial provides an e ective way to eciently evaluate modern treatments. Platform trial can eciently evaluates treatment by quickly advancing promising ones and discarding ine ective or overly toxic ones. This reduces the time it takes to identify e ective treatments for patients in unmet medical need. Platform trials can easily add new treatment arms, enabling continuous adaptation and optimization. Additionally, they control family-wise false positives and increase eciency with methods like multiple testing procedures and adaptive randomization to allocate more patients to better treatment arms, among other prominent bene ts. During recent years, several well-known platform trials have been conducted to advance drug development. These trials include I-SPY2 for breast cancer, REMAP-CAP for pneumonia, and DIAN-TU for Alzheimer's disease, among others. Additionally, during the COVID-19 pandemic, more than 50 COVID-19 platform trials were registered globally between 2020 and 2021. In response to the growing prevalence of platform trials, this research aims to propose robust Bayesian adaptive designs and methods to address the practical challenges that arise in real-world platform trials. These challenges include optimizing sequential monitoring of multiple treatments and/or multiple endpoints, eciently establishing proof-of-concept and dose selection in multi-arm multi-dose platform trials, managing incompatibility issues due to non-concurrent controls, and addressing late-onset outcomes, among others. Each proposed method will be tailored to tackle a combination of these challenges in speci c platform trial settings. For each design, user-friendly software will be developed, which will include programs for trial simulation to establish design operating characteristics, facilitate trial conduct, and assist physicians in selecting optimal treatment for their patients. The overarching goal is to develop Bayesian adaptive methods to identify superior treatments or doses across various diseases and clinical settings, ultimately aiming to achieve greater anti-disease e ects, improved safety, and enhanced survival outcomes.

NIH Research Projects · FY 2026 · 2025-01

Project summary/abstract Immune checkpoint inhibitors (ICI) transformed oncological care for multiple cancers. Yet, 80% of ICI patients will eventually fail therapy. Colossal efforts are invested in overcoming ICI resistance. A promising candidate is the gut microbiome which was associated with ICI clinical outcomes. I led a seminal clinical trial in which the gut microbiome of patients with ICI refractory metastatic melanoma was modulated via fecal microbiota transplantation (FMT). FMT and ICI re-induction resulted in increased intra-tumoral infiltration of CD8+ T-cells and objective clinical response rates of 30%. However, microbiome modulation remains far from wide clinical use. While FMT showed consistent clinical efficacy, it is not feasible outside of major academic centers; and some probiotics have been associated with a deleterious effect on ICI efficacy. Therapies that mimic the microbiome effect on the immune system can enhance ICI efficacy while omitting FMT obstacles. However, the development of such therapies is hindered since the mechanisms driving the gut microbiome's effect on anti-tumoral immunity remain unknown. In this proposal, I will test the hypothesis that an adverse microbiome induces a state of chronic inflammation that impedes ICI efficacy. FMT from donors with favorable microbiomes promotes anti-tumoral immunity by disrupting the net inflammatory signaling; hence, attenuating inflammation by direct immune re-programming can mimic the FMT effect. To test this, I propose the following research plan. In Aim 1, I will determine the effect of microbial-induced inflammation on anti-tumoral immunity by analyzing longitudinal stool, serum, gut, and tumor samples from a unique cohort of 33 patients with ICI- refractory melanoma (n=20) and microsatellite-instability high cancers (MSI-H, n=13) who participated in clinical trials of FMT and ICI re-induction (NCT03353402 and NCT04729322, respectively). Spatial transcriptomics of gut and tumor samples will be used to demonstrate FMT-induced immune dynamics and to test my sub-hypothesis that microbial inflammatory signals are mediated via myeloid antigen-presenting cells (APC). In Aim 2, I will determine the immune system's ability to override microbial signals. I will conduct FMT from cancer patients who responded and did not respond to ICI into CD11c-Cre+ Stat3f/f (Stat3Δ/Δ) mice that have dendritic cells with hyper-activated toll-like receptors (TLR) signaling. This experiment will test the ability of an immune system with a chronic inflamed state to overcome the beneficial effect of FMT from a donor with a favorable microbiome. To re-program the immune system to override the effect of adverse microbiome- mediated inflammation and hence overcome ICI resistance, I will compare the immune activity and tumor growth of mice undergoing FMT versus mice treated with a combination of ICI and interleukin (IL)-1b blockade; since IL-1b secretion can be a product of TLR activation and our previous work showed that an adverse microbiome induces IL-1-mediates gut inflammation. Overcoming ICI resistance by microbial-derived inflammatory signal blockade can enhance the clinical efficacy of ICI in patients with various cancer types.

NIH Research Projects · FY 2026 · 2025-01

ABSTRACT The advent of ribosome profiling (Ribo-seq) has enabled high-resolution measurement of translation at a genome-wide level, known as the translatome. Studies based on Ribo-seq have revealed a complex translational landscape in eukaryotic cells, uncovering translations beyond conventionally annotated events that may potentially yield thousands of new proteins and significantly expanding the known proteome. These unconventional translations involve alternative translation initiation sites (aTISs) within annotated protein- coding regions as well as occur in traditionally non-coding regions, such as 5' UTR, 3' UTR and long noncoding RNAs (lncRNAs). Certain lncRNA-encoded ORFs and novel translational isoforms of known protein-coding genes resulting from aTI have been shown to play significant developmental or physiological roles in evolutionarily diverse species. Despite an increasing appreciation of the importance of “dark” proteome produced by hidden ORF translation in development, physiology and disease, the functions of vast majority of hidden ORFs remain unknown . In addition, translation of hidden ORFs is often initiated at non-AUG start codons. The cis-regulatory elements and trans-acting factors that are important for regulating hidden ORF translation are yet to be elucidated. To address these gaps in knowledge, my overarching goal is to develop and apply advanced computational and high-throughput experimental approaches, in combination with in- depth mechanistic investigations, to systematically identify cryptic translation of hidden ORFs and to unravel their functions, mechanisms, as well as the cis-regulatory elements/trans-acting factors controlling their translation in development, physiology and disease. To achieve this long-term goal, I propose the following three research programs in the next five years: (i) Developing and employing machine learning based approaches for integrative modeling of translation initiation; (ii) Deciphering the trans-acting function uORFs in regulating estrogen- dependent cell proliferation; (iii) Decoding protein-protein interaction (PPI) networks between annotated proteins and the hidden proteins generated by cryptic translation. Collectively, these research programs aim not only  to contribute to novel computational tools for modeling translation initiations and for identifying new PPIs, but also to offer biological insights into the function and regulation of hidden ORF translation. My group has developed a computational toolkit, named Ribo-TISH that enables de novo prediction of hidden ORFs and/or identification/quantitative comparison of TIs from different types of Ribo-seq data (Nat Commun 2017). More recently, we have leveraged this tool and integrative approaches to decode the function and mechanism of lncRNA-encoded hidden ORFs (Nat Struct Mol Biol 2023; J Clin Invest, 2023). Given our expertise/track record in computational biology, functional genomics, and RNA biology as well as a diverse network of collaborators with complementary expertise, we are ideally situated to tackle the proposed research.

NIH Research Projects · FY 2026 · 2025-01

Project summary Lung cancer is a devastating disease that remains the top cause of cancer mortality. Despite improvements in targeted therapies against oncogenic kinases and immunotherapies for select patients, the majority of patients with lung cancer still lack effective therapeutics, underscoring the dire need for additional treatment approaches. Recent discovery of KRASG12C inhibitors (KRASG12Ci) has generated tremendous excitement and hope. Unfortunately, the duration of response to KRASG12Ci is very short with progression free survival of only 6-7 months due to primary and adaptive resistance. Further, a recent clinical observation showed that co-mutations in the tumor suppressor gene SMARCA4 predict even poorer response to KRASG12Ci, further increasing the urgency to understand and overcome resistance in this context. We have recently corroborated these clinical observations by various experimental approaches. As SMARCA2 is a known synthetic lethal genetic interaction partner to SMARCA4, we sought to study whether targeting SMARCA2 is a possible strategy to overcome resistance of SMARCA4 and KRAS co-mutant cells to KRASG12Ci. To this end, we have developed small molecules that degrade SMARCA2 based on PROTAC (proteolysis targeting chimera) technology. Our data indicates that SMARCA2 PROTACs, including our lead molecule YD23, induce robust SMARCA2 degradation, show promising combination effect with KRASG12Ci and are excellent chemical tools to determine the therapeutic potential of SMARCA2 targeting. In this proposal we first aim to investigate the mechanism of resistance of SMARCA4 mutant lung cancer to KRASG12Ci. We intend to utilize several orthogonal, genetically well-defined model systems and perform in depth molecular characterizations including unbiased transcriptomic, chromatin accessibility and SMARCA2/4 CUT&RUN to identify direct targets of SMARCA2/4 that are modulated by sotorasib, a prototypical KRASG12Ci. We also intend to experimentally develop cell lines resistant to the combination of YD23 and sotorasib that should help in understanding potential mechanisms of drug resistance that are expected in the future if used in patients. To aid our understanding of potential side effects of combination of YD23 and sotorasib, we aim to perform tolerability studies in mice. Importantly, we will determine the anti-tumor efficacy of YD23 and sotorasib using established lung cancer xenografts and novel PDX models. Finally, we will determine gene expression changes within tumors upon YD23, sotorasib as single agent or in combination to elucidate the molecular alterations underlying the in vivo biological effects of our novel combination strategy. In conclusion, these experiments are expected to elaborate the mechanism of resistance of SMARCA4 mutant lung cancer to KRASG12Ci and determine the potential utility of SMARCA2 PROTACs to overcome this resistance. Finally, as KRAS inhibitors are rapidly evolving beyond G12C into other genotypes, our work could have broader ramifications against multiple other cancer types.

NIH Research Projects · FY 2026 · 2024-12

PROJECT SUMMARY/ABSTRACT Despite major advances in cancer treatment over the last 20 years, metastatic pancreatic adenocarcinoma (PDAC) remains largely unresponsive to treatment. Signaling between cancer cells and the surrounding host tissue microenvironment (TME) is a critical regulator of tumor progression and metastasis, but an incomplete understanding of these interactions has hindered therapeutic targeting. Recent studies have identified extracellular vesicles (EVs) as potential mediators of intercellular communication to regulate cancer progression and metastasis. As a result, targeting EV transfer and/or the downstream effects of such transfer may provide therapeutic benefits; however, an understanding of the precise mechanisms of EV release and entry into target cells, and the functional consequences of EV exchange in vivo is urgently needed. Here, I will test the central hypothesis that cancer cell EVs modulate the tumor microenvironment to facilitate PDAC progression and metastasis. I will use novel genetically engineered mouse models to track and determine the functional impact of cancer cell EV (ccEV) transfer on the local and metastatic TMEs to alter PDAC initiation, progression, and metastasis. This will be accomplished through 3 Aims: (1) to investigate the functional contribution of ccEVs in PDAC initiation and progression, (2) to evaluate the functional contribution of ccEV release and CD47 on the surface of ccEVs in liver metastasis, and (3) to identify the role of mutant Trp53 and novel EV mediators of stromal reprogramming to facilitate liver metastasis. The proposed research program combined with additional research and career development skills training will enable me to launch my independent research career. I will be committed to expanding my networking, mentoring, leadership, lab management, and scientific communication skills, and I have assembled an advisory committee consisting of Dr. Ronald DePinho, Dr. Anirban Maitra, and Dr. Elizabeth Shpall to provide input and guidance on my career development. Altogether, this K22 award will help me accomplish my long-term goal of understanding the mechanisms of intercellular communication between cancer cells and the microenvironment to facilitate pancreatic cancer initiation, progression, and metastasis in order to identify novel therapeutic vulnerabilities.

NIH Research Projects · FY 2026 · 2024-12

PROJECT SUMMARY / ABSTRACT Recent clinical trials in adults and children with brain tumors from our group and others have shown that oncolytic viruses prolong the survival of a small percentage of patients (<20%). Importantly, these studies have also demonstrated that viroimmunotherapy induces Tcell infiltration into brain tumors. Such findings support the paradigm-shifting concept that complete tumor debulking by virotherapy requires the elicitation of antitumor immune responses following the initial oncolytic effect. Therefore, further enhancement of the immune arm of this treatment approach may be required to increase the percentage of positive responders. In a clinical trial developed by the MDACC team, 20% of GBM patients treated with the oncolytic adenovirus Delta-24-RGD showed complete response and survival longer than three years (NCT00805376). Although these studies have illustrated that robust immune responses can be invoked using oncolytic virotherapy, they have also shown that viruses are eliminated early during infection and thus preventing the development of an efficacious anti- tumor immune response in the majority of the patients. The first mechanism that is activated to eliminate the virus is the innate immune response. Mitigation of this response should result in the permanence of more viruses and during a longer period within the infected tumor, increasing the window of opportunity for the development of an anti-tumor immune response. During a screening of the factors regulating the anti- adenovirus innate immune response using RNA sequencing, we discovered that the NONO pathway, which was not previously connected with adenovirus infection, was significantly upregulated following infection. Based on this seminal information, we hypothesize that NONO pathway is an essential sensor of adenovirus DNA and capsid proteins in infected cells and that plays a key role in the modulation of an effective innate immune response against oncolytic viruses. To test this hypothesis and achieve the objectives of the project, we proposed the following two specific aims: Specific aim 1: To examine the NONO pathway in glioma cells treated with oncolytic adenoviruses. We hypothesize that NONO functions as a viral capsid sensor in response to adenoviral infection and interacts with players of the host’s innate immune response. Specific aim 2: To determine the immunomodulatory functions of NONO during oncolytic adenovirus treatment. We hypothesize that evading innate immune defenses allows for enhanced adenovirus replication and lysis, functionally tipping the scale towards anti-cancer immunity. Therefore, we will test the therapeutic efficacy of Delta-24-RGD oncolytic, as well as monitor the flux of cancer-specific T-cells and innate immune activation in the context of differential NONO expression. If successful, our project should propel the exploration of viral capsid-based recognition and NONO-cGAS crosstalk in the design of new oncolytic adenovirus strategies. This project is part of our long-term goal of legitimizing oncolytic adenoviruses as part of the conventional treatment for malignant gliomas and other solid tumors.

NIH Research Projects · FY 2026 · 2024-12

Summary Diverse exogenous and endogenous aldehydes produce aberrant adducts that, if left unrepaired, can promote genome instability and disease. Prevalent lifestyle choices as well as intrinsic metabolic dysfunctions and genetic exposures associated with cancer and aging have been linked to the accumulation of reactive aldehydes that produce persistent, genome-destabilizing DNA adducts. Inactivation of aldehyde clearance and DNA repair proteins leads to genome instability and cancer by rendering cells hypersensitive to formaldehyde- and acetaldehyde-induced DNA damage. Genotoxic DNA adducts are considered the de facto surrogates for aldehyde-related genome instability. However, another less studied mechanism of genome instability is defects in the folding of DNA repair proteins. In addition to damaging the DNA, aldehydes also modify proteins to produce aberrant protein adducts that cannot fold or function properly. Yet, the role of proteotoxic stress in aldehyde-induced genome instability remains enigmatic. Here, we hypothesize that aldehyde derived protein adducts target the central protein folding chaperone heat shock protein 90 (HSP90) in impairing the folding of critical DNA repair proteins that regulate genome stability. Our published finding that HSP90 can buffer (that is, mitigate) deleterious mutations in humans provided a system to compare side-by-side both the genotoxic and proteotoxic effects of aldehydes in cells and tumors. Using this system in preliminary work, we now show that mutations that HSP90-buffered mutations in DNA repair genes render genome instability conditional upon seemingly benign exposures to formaldehyde and acetaldehyde. The goal of the proposed research is to unravel mechanisms of HSP90-contingent genome instability elicited by reactive aldehydes. The rationale for this proposal is that understanding how aldehydes promote genome instability may reveal new universal approaches for risk stratification and management. This project will achieve this goal by employing innovative adductomics and functional genomics approaches strategically designed to 1) determine the mechanism of HSP90 impairment by formaldehyde and acetaldehyde, and 2) delineate the proteotoxic and genotoxic effects of aldehydes on genome instability in tumor xenografts. The successful completion of this project will define mechanisms linking genome instability, proteotoxic stress, and metabolic dysregulation, cellular hallmarks of disease that are traditionally studied in isolation. The proposed work will also evaluate protein adducts as comprehensive indicators of proteotoxicity and will probe the role of aldehydes as the ecological stressors that engage HSP90 function in driving genome instability in cells, tissues, and tumors. Achieving this will provide a framework and new tools for future studies to decipher gene-by-metabolite-by-environment relationships and to develop more efficacious individualized strategies for managing diverse aldehyde-related diseases, including many cancers.

NIH Research Projects · FY 2026 · 2024-12

Project Summary Over 6 million Americans aged 65 and above currently suffer from Alzheimer's Disease (AD). This substantial prevalence among the elderly underscores aging as one of the most prominent risk factors contributing to the onset of AD. Microglia are cells that facilitate the clearance of cellular debris including protein aggregates through the process of phagocytosis. Notably, microglial phagocytic function is impaired in both aging and AD, however, the molecular mechanism that drives this dysfunction is not well characterized. My F99 work will delineate how the loss of the RNA-binding protein, Quaking (Qki), drives phagocytic dysfunction in AD. My K00 work will follow a similar path by focusing on how the dysregulation of an important phagocytic lipid, Phosphatidylinositol-3- phosphate (PI3P), can lead to impairment in microglial membrane dynamics in the context of AD. My sponsor's (Dr. Jian Hu) previous work has established the foundation to support the novel hypothesis that Qki promotes microglial phagocytosis to attenuate AD progression. For Aim 1 (F99), I will be utilizing the conditional deletion of Qki in microglia in an AD mouse model to 1) Assess the impact of Qki loss on the development of AD pathology. 2) Isolate primary microglia to directly test phagocytic activity. 3) Perform a rescue experiment with the agonist treatment of the Qki downstream transcription factor PPARβ. Published work indicating the downregulation of PI3P in AD and PI3P enrichment in the phagocytic cup along with data from Dr. Hu's lab indicating that PI3P synthesis is indirectly regulated by Qki has established the framework for my K00 research. My K00 work (Aim 2), will address the role of PI3P in the regulation of phagocytic membrane dynamic and eventual contribution to AD progression through 1) Validating the expression of the PI3P and its synthesizing enzyme Vps34 on the phagosome. 2) Utilizing conditional deletion of the Vps34 in microglia within AD mouse models to characterize the impact of PI3P loss on AD progression. Overall, this work will directly contribute to the NIA's priority of understanding the molecular mechanisms that contribute to AD which is one of the most prevalent age-related neurodegenerative diseases. To successfully complete my proposed aims, I will receive thorough training guided by an expert mentoring team in microglia culture, transcriptomic analysis, lipidomic analysis, and AD mouse pathology characterization. Together, this training will provide me with a well-equipped platform to succeed as an aging researcher with the establishment of an independent research laboratory focused on delineating microglial dysfunction in AD.

NIH Research Projects · FY 2023 · 2024-11

Hematopoietic stem cells (HSCs) maintain tissue homeostasis and replenish blood system upon stresses. HSCs have evolved unique mechanisms to maintain genome and proteome integrity throughout life. While the genome integrity safeguard mechanisms have been extensively studied, little is known about how proteome integrity is maintained in HSCs and how dormant HSCs are protected from protein damage during development and physiological stresses. This proposal will address this knowledge gap. We recently found that the Sel1L ER-associated degradation (ERAD) pathway plays an essential role in the maintenance of HSCs. ERAD is the principal protein quality control mechanism responsible for targeting misfolded proteins in the ER for cytosolic proteasomal degradation. The Sel1L-Hrd1 complex is the most conserved branch of ERAD. We found that Sel1L deletion in hematopoietic cells significantly reduced steady-state HSC frequency and led to complete loss of HSC reconstitution capacity in stress conditions including bone marrow transplantation and 5-fluorouracil (5-FU) mediated myeloablation. Interestingly, Sel1L deletion did not induce apoptosis or impair HSC engraftment. In contrast, we observed increased HSC cycling and reduced numbers of quiescent HSCs in Sel1L knockout mice. These data demonstrate the critical function of Sel1L ERAD in HSC maintenance and suggest a novel role for ER protein quality control machinery in regulating stem cell quiescence and self-renewal. ERAD monitors and regulates the maturation of transmembrane proteins. We found markedly decreased surface expression of CXCR4 and MPL, two master regulators of HSC quiescence and niche interaction, in Sel1L-knockout HSCs. Tracking HSC and niche cells at the single cell level in vivo showed aberrant localization of Sel1L-deficient HSCs in the bone marrow niche. We hypothesize that Sel1L ERAD governs HSC quiescence and self-renewal by regulating HSC transmembrane receptor maturation and HSC-niche interaction. We will establish the physiological significance of Sel1L ERAD in the maintenance of HSCs (Aim 1), determine the significance and mechanism of the ERAD- Unfolded Protein Response (UPR) crosstalk in HSCs (Aim 2), and elucidate the mechanism and significance of Sel1L ERAD in HSC-niche interactions (Aim 3). This study will provide significant insight into the post- translational regulation of HSC quiescence, self-renewal, and niche interaction by ER protein quality control mechanisms, and further identify novel determinants of HSC fates.

NIH Research Projects · FY 2025 · 2024-09

Metastasis is the major cause of cancer mortality. Effective therapies are urgently needed for patients with metastatic diseases. Increasing evidence suggests that interactions between cancer cells and tumor immune microenvironment drive metastatic progression. Although prior studies established the vital roles of immunosuppressive TME in metastatic progression, the epigenetic determinant in shaping the metastatic niche remains understudied. Absent, small or homeotic 1-like (ASH1L) is a histone lysine methyltransferase that induces methylations at H3K36 and . Although ASH1L was found to drive leukemogenesis, little is known about its biological function in solid tumors and metastatic disease. Our preliminary studies showed that ASH1L is genetically amplified and overexpressed in metastatic tumors and contributes to metastasis and immunosuppression. The goal of this application is to determine the role and mechanisms of action of ASH1L in the metastatic niche. The central hypothesis in this application is that histone H3K4 and activates gene transcription methyltransferase ASH1L contributes to the immunosuppressive metastatic niche and is a potential therapeutic target in metastatic cancers. In the proposed studies, we will 1) determine ASH1L’s role in reshaping the metastatic niche by combining a newly developed genetically engineered mouse model and cutting-edge single- cell transcriptomic technologies; 2) elucidate the mechanism by which ASH1L induces immunosuppressive metastatic niche by performing epigenetic profiling, proteomic approaches, and functional studies; 3) determine the anti-metastatic effects of genetically depleting or pharmacologically inhibiting ASH1L in combination with checkpoint immunotherapy in preclinical models, followed by profiling their impact on immune components in the metastatic niche. We expect to identify ASH1L as a key epigenetic determinant in priming immunosuppressive metastatic niche and develop effective targeted therapy and combinatorial immunotherapy for metastatic cancers. These studies are expected to have significant positive impacts, including bridging the knowledge gap on the role and mechanisms of action of an understudied epigenetic factor ASH1L in metastatic cancers, advancing our understanding of the crosstalk between invading cancer cells and immune components in the metastatic niche, and offering implications in regard to the biomarkers, therapeutic targets, and rational combinations for metastatic malignancies. 1

NIH Research Projects · FY 2025 · 2024-09

PROJECT SUMMARY Dysregulated activity within the neural networks that underlie reward and executive functions can increase vulnerability to compulsive drug use. Repetitive transcranial magnetic stimulation (rTMS) can selectively modulate neural activity within both the reward and the executive control networks. Empirical evidence indicates that both inhibitory rTMS to the ventromedial prefrontal cortex (VMPFC, a key node in the reward circuits) and excitatory rTMS to the dorsolateral prefrontal cortex (DLPFC, a key node of the executive control network) can be therapeutic in individuals with SUDs. However, responses to both treatments are highly variable and rTMS’ therapeutic utility for SUDs remains limited. Personalizing rTMS interventions targeting neuromarkers of dysregulated activity within the reward and cognitive control networks is likely to reduce treatment response variability and improve treatment outcomes. We have recently identified two robust neuromarkers of reward responses to drug-related cues and cognitive control during drug-related decisions that reliably predict nicotine self-administration. The goal of this application is to determine the extent to which these neuromarkers moderate responses to rTMS. Our central hypothesis is that smokers with high reactivity to drug-related cues will be more likely to reduce nicotine self-administration after inhibitory rTMS to the VMPFC, whereas smokers with low cognitive control during drug-related decisions will be more likely to reduce nicotine self-administration after excitatory rTMS to the DLPFC. In line with the scope of PAR-19-282 (Exploratory Clinical Neuroscience Research on SUDs), we will use a phased research approach to test our hypothesis. In the R61 phase, we will determine the extent to which the reward reactivity neuromarker (Aim 1) and the cognitive control (Aim 2) neuromarker moderate rTMS treatment effects. To test our milestones (i.e., observing a medium or higher effect size in at least one of the two aims), we will use Bayesian statistical methods. Using a Bayesian approach will allow us to obtain calibrated probabilities of treatment outcomes and make a principled go/no-go decision in moving forward to the R33 phase. In the R33 phase, we will determine the synergistic effect of the two neuromarkers in moderating rTMS treatment effects (Aim 3) and we will create a Bayesian classifier to personalize future rTMS interventions for SUDs (Aim 4). We anticipate that upon its successful conclusion, this Phase II trial will contribute to illuminate the psychophysiological mechanisms that drive compulsive drug use and will yield the fundamental knowledge needed to efficiently develop new personalized rTMS interventions for SUDs and other disorders characterized by poor impulse control.

NIH Research Projects · FY 2025 · 2024-09

Abstract/Project Summary Germline genetics research often relies heavily on large-scale hypothesis testing to detect associations between complex traits and their risk mutations. Traditionally, the statistical methods that we and others have developed for these settings have focused on powerful approaches that test global null hypotheses - identifying the existence of any signal in a set of individual tests. In recent years though, researchers have also increasingly emphasized novel study designs that are more suitable for another class of tests known as composite null hypothesis tests. Roughly speaking, the goal of a composite null hypothesis test is to identify the existence of multiple, as opposed to at least one, signal in a set of individual tests. However, the lack of validated variants identified by composite null analyses belies the high popularity of such studies, suggesting a lack of suitable quantitative approaches. The central goal of this proposal is to develop high-dimensional composite null hypothesis testing approaches that (a) provide interpretable results addressing the scientific question of interest and (b) offer robust performance over varied genome-wide settings. Specifically, one study design of interest is (i) pleiotropy studies. A common goal in performing pleiotropy analysis is to identify variants linked to multiple diseases simultaneously, which may, for example, suggest new indications for existing therapies. Many existing pleiotropy approaches test global nulls, which are still applicable but often less pertinent. Another related study type is (ii) mediation analysis. When testing for genetic mediation, interest lies in the simultaneous associations of a variant to a mediator and the mediator to an outcome. Thus, a composite null approach that identifies at least two associations is more suitable for this type of investigation. Additionally, (iii) replication studies are ubiquitous in genetics research and require more than one association to declare a successful replicated effect. We will develop approaches that leverage our existing empirical Bayes tools to perform composite null inference in (i)-(iii). Different models will be proposed to address unique statistical challenges such as the within-set correlation that arises in (ii) and directionality restrictions in (iii). Extensive simulation studies and real data examples will be used to illustrate (a) and (b), as well as demonstrate advantages over global null interpretations. Successful completion of this work will result in novel, interpretable, and robust strategies to perform large-scale pleiotropy, mediation, replication, and other translational genetics studies across a variety of phenotypes. We will also develop well-documented, publicly available software packages to share this methodology with the research community. Summary data from analysis of varied phenotypes will be released.

NIH Research Projects · FY 2026 · 2024-09

Project Summary The world’s population is aging, which brings about huge scientific challenges. Since the biological process of aging is by far the greatest risk factor for most chronic diseases, understanding the molecular and cellular mechanisms by which aging leads to these conditions is of vital importance to increase the health span of older adults. Aging results in several structural and functional changes in the immune system and is clinically associated with increases in the frequency and severity of infectious diseases and incidences of cancer, chronic in inflammatory disorders, and autoimmunity. This general dysregulation in immune system function is referred to as immunesenescence. Immunosenescence is a multifactorial and dynamic complex phenomenon, which is shown as a lengthy adjusting and remodeled process existing in immune system during lifespan. However, the mechanisms under-lying age-associated dysregulated immunity are still incompletely understood. This proposal investigates a new perspective on immune cell markers and function with age across NHP species with differing lifespans. In addition, we will examine the relationship between immune aging and neurodegenerative biomarkers and cognition and compare these relationships across the NHP species. These studies will help determine the role the immune system plays in longevity, neurodegeneration and cognitive decline, which may allow researchers to develop and test immuno-restorative approaches with the goal of improving longevity in humans.

NIH Research Projects · FY 2025 · 2024-09

My long term goal as a clinical scientist at MD Anderson Cancer Center is to lead clinical trials that improve survival for patients with gastrointestinal malignancies, particularly colorectal and anal cancer. To accomplish this, I have integrated novel testing techniques and promising immunotherapy combinations into the design of NCI-supported clinical trials. I am the overall Principal Investigator for the NRG-GI005 phase II/III trial evaluating circulating tumor DNA (ctDNA) as a predictive biomarker for adjuvant chemotherapy benefit in patients with stage IIA colon cancer. NRG-GI005 is the first NCI-supported trial for any solid tumor type to incorporate ctDNA as an integral biomarker for treatment assignment as part of a clinical trial design. Planned analysis of optional blood collected on this study will compare head-to-head different methodologies for detecting minimal residual disease (MRD) performed on the same samples and provide missing insights into optimal ctDNA assay selection needed for future NCI trials evaluating ctDNA as a surrogate for the presence of MRD. I have also written and led, as overall PI, two immunotherapy trials across NCTN (SWOG S2107) and ETCTN (NCI 9673) sites. Promising clinical activity for the triple therapy of encorafenib, cetuximab, and nivolumab for patients with microsatellite stable BRAFV600E metastatic colorectal cancer from a pilot trial at MD Anderson were applied for the subsequent SWOG S2107 randomized phase II trial, now activated across the NCTN. The ETCTN-sponsored NCI 9673 trial demonstrated antitumor activity of nivolumab metastatic anal cancer and led to this treatment as a recommended option on the NCCN Guidelines for anal cancer. As an R50 funded clinical scientist, I propose to combine these clinical trial leadership experiences and expand on the role of blood-based biomarkers to generate novel combination immunotherapy trials. I have utilized extravesicle RNA (evRNA) isolated from plasma to characterize changes in RNA signatures associated with treatment response to encorafenib, cetuximab, and nivolumab in patients with BRAFV600E metastatic colorectal cancer. With R50 protected effort, I will expand plasma evRNA analysis in evaluating response using samples collected from SWOG S2107, with >90% yield from patients enrolled thus far. During the funding period, I also propose to develop my leadership institutionally in my role as SWOG PI for the NCTN LAPS grant Executive Committee, where I will expand enrollment at new affiliate sites for MD Anderson, prioritizing SWOG/NCTN trials first, with the goal of improving enrollment on NCI trials conducted under MD Anderson umbrage. If successful, these efforts collectively could serve as justification to expand the utility of liquid biopsy beyond ctDNA, with the goal of applying translational studies to identify effective therapeutic strategies for all patients with gastrointestinal malignancies on future NCI-supported clinical trials.