Sloan-Kettering Inst Can Research

NIH Research Projects · FY 2026 · 2025-06

Project Summary: The goals of this research program are to understand the molecular mechanisms underlying proteins and protein complexes that facilitate intracellular ion transport and ensure genomic integrity by replicating and repairing the genome. For proteins involved in membrane transport, we aim to elucidate the mechanisms by which ions are recognized and transported across the membrane as well as how the activities of these proteins are regulated. For those involved in maintaining genomic integrity, we will address how genomic features are recognized to recruit the replication and repair machineries to specific genomic loci. We employ a highly collaborative approach, combining high-resolution structure determination, electrophysiology, in vitro reconstitution, cell biology, computational analysis and mouse models to establish a holistic understanding of these proteins and protein complexes at the molecular level and their how dysregulation can lead to disease. We are currently focused on investigating four families of ion transport proteins including the lysosomal potassium and proton channel TMEM175, the CLC family of chloride channels and transporters, the inositol trisphosphate receptors and CLN7. TMEM175 is a lysosomal channel responsible for maintaining lysosomal pH that is critical for lysosomal function and homeostasis. We are identifying novel inhibitors of TMEM175 to better understand its physiological roles and determining how diverse stimuli coordinate to regulate its activity. Humans express 5 CLC transporters in the endolysosomal system, where they regulate ion and pH homeostasis. We are elucidating how lipids, accessory subunits and other stumuli regulate the activity of CLCs. Inositol trisphosphate receptors are tetrameric channels that release Ca2+ stored in the endoplasmic reticulum to stimulate diverse cellular pathways including fertilization, cell death and cell division. We aim to understand how IP3Rs are regulated by their diverse stimuli and how these regulatory stimuli result in Ca2+ oscillations. CLN7 is a lysosomal chloride channel that more closely resembles transporters than channels. We are investigating how CLN7 can selectively permeate chloride ions in the lysosome. Genomic integrity requires that the genome be duplicated during each cell cycle without errors. We are investigating how DNA structures, such as a G4-quadreplexes act as impediments to the DNA replication machinery and how these impediments can be overcome to complete replication. Collectively, these studies will reveal insights into protein function that will improve understanding of their roles in critical physiological processes. As dysregulation of any of these components can lead to disease, these studies will also provide insights into the molecular basis of disease.

NIH Research Projects · FY 2025 · 2025-06

Project Summary/Abstract In eukaryotes, energy is stored primarily as highly reduced triacylglycerols (TG) in membrane-less organelles called lipid droplets (LD). A central question for the field is what protein machinery evolved to efficiently and reproducibly make these emulsion particles in cells for storing lipids. Starting with our screens to identify genetic components of this process, our work has helped to shape the current understanding of LD formation, including elucidating the molecular structure and mechanism for a TG-synthesis enzyme (DGAT1), the components and structural information for seipin and the ER-based LD assembly complex (LDAC), and molecular insights into ER enzymes that modify this process, such as FIT2. The current proposal builds on our progress and proposes to overcome key knowledge gaps for each of these aspects of LD formation. We will extend our studies of TG synthesis to elucidate the structure, biochemical function and cell biological functions of the DGAT2 enzyme, which is closely linked to de novo fatty acid synthesis and a drug target that is in phase 2 trials for fatty liver disease. We will obtain a structure of the complete LDAC, including the key protein LDAF1, and utilize biochemical and molecular dynamics simulations studies to test models of how the LDAC facilitates LD formation. Finally, we will study the LD modifier, FIT2, to test the hypothesis that this enzyme plays a key functional role in providing CoA for mitochondrial metabolism. Achieving our goals will provide leading edge data to unravel the molecular machinery that underlies lipid and energy storage in cells and will help to elucidate the pathogenesis of diseases with alterations in lipid storage.

NIH Research Projects · FY 2026 · 2025-05

ABSTRACT The risk of contralateral breast cancer (CBC) after a first breast cancer diagnosis is well-documented and substantial. Radiation therapy (RT) is an important component of treatment for over half of all women with primary breast cancer yet it is a potent carcinogen and an established risk factor for future CBC. Despite major advances in defining the genetic basis of breast cancer susceptibility, and the identification of multiple risk genes with key roles in the DNA damage response (DDR), the influence of inherited genetics in modifying risk of CBC in the setting of RT, a potent carcinogen, remains poorly understood. This critical knowledge gap has hindered the ability of providers and patients to select tailored treatment plans guided by the rapidly expanding germline and tumor DNA sequencing data available in the clinic. In this proposal, we seek to identify the genetic determinants of radiation-associated breast cancer and develop detailed CBC risk estimation, with the long-term goal of enabling informed therapeutic decisions that balance benefits and risks to optimize outcomes. We leverage the extensive resources of the WECARE Study, a multi-site population-based case-control study of 1233 CBC cases and 1746 individually-matched controls with unilateral breast cancer (UBC) all of whom provided a biospecimen and were interviewed using the same questionnaire; for those who received radiation therapy (RT) individual absorbed radiation dose was estimated. Specifically, we will screen for variants in all WECARE Study CBC cases and UBC controls using whole exome sequencing (WES), apply functional screening in the presence or absence of radiation to classify variants, and utilize these data to develop a comprehensive integrated model of CBC risk. Our goals are to provide detailed CBC risk estimation and define the genetic basis of radiation-associated breast cancer. In AIM 1 we will identify variants that confer risk for radiation associated CBC. In AIM 2 we will develop, and validate, a comprehensive integrative model of genetic predisposition to radiation-associated CBC. Research focused on genetic predisposition to radiation-associated CBC has been sparse. The proposed study in our large well characterized study population offers a unique opportunity to clarify the underlying genetics of radiation sensitivity, identify genetic variants that act jointly with RT to increase risk of CBC, and inform clinical decision-making related to RT and other treatment options. The potential impact of this novel study should be considered in the context of the over 3 million breast cancer survivors in the US alone, the high lifelong risk of CBC they incur, and the indications that women with genetic predisposition may be more susceptible to radiation- associated CBC.

NIH Research Projects · FY 2025 · 2025-05

Project Summary/Abstract Understanding the functional architecture of human diseases and traits at a cellular resolution is critical for informing follow-up functional characterization experiments and nominating genes and pathways for developing drug targets. Large scale omics data encompassing multiple modalities (RNA-seq, ATAC-seq, ChiP-seq), a broad range of tissues and cell types, and diverse biological contexts, such as disease stages, developmental trajectories, and gene perturbations, offer significant new resources to gain a deeper understanding of the genetic architecture of complex diseases. In this proposal, we plan to develop statistical and machine learning approaches that bridge the gaps between human genetics and single-cell omics data to decode the regulatory activity underlying disease variants, link variants to genes accurately in relevant cell types of action, and identify disease-critical co-operative programs of genes and genomic elements activated in specific biological contexts . The proposed aims are targeted at uncovering new insights into complex disease etiology by advancing our understanding of gene regulation and exploring the synergies and contrasts in epigenomic activity and downstream cellular processes or biological pathways. A key goal of this application is to produce a set of computational tools and workflows that can identify and rank functionally disease-critical variants, genes, and pathways, along with a detailed understanding of their putative cell type and biological context of action. This can greatly inform downstream disease-focused intervention strategies like drug perturbation, and single-guide or combinatorial CRISPR screening experiments. In the first aim of this proposal, we will leverage single-cell RNA+ATAC multiome data to learn improved strategies of linking enhancers to genes in a cell type, explore the co-operative effects of multiple enhancers on gene regulation, and identify sets of enhancers and linked genes that together constitute distinct disease-critical functional units. In the second aim, we will use quantitative trait loci (xQTL) data spanning a broad range of molecular phenotypes to map the cis and trans-regulatory architecture of GWAS variants, and better pinpoint causal variants for these phenotypes through integration with base-pair resolution variant function assays and models, such as sequence-based deep learning models. In the third aim, we will leverage multimodal omics data observed across multiple biological contexts to identify programs of genes and elements activated under specific contexts and assess their impact on complex disease GWAS signals. We will also demonstrate how disease-related benchmarking of gene programs activated upon enhancer and gene perturbations can inform a cost-efficient experimental plan of a downstream perturbation experiment with multi-omics readouts. All variant- level functional annotations, variant-gene links, and gene programs, together with a quantitative and qualitative assessment of their impact on human diseases, and all relevant computational software and pipelines will be shared publicly with the scientific community.

NIH Research Projects · FY 2026 · 2025-04

Modified Project Summary/Abstract Section Family COMIDA (Consumo de Opciones Más Ideales De Alimentos) (Eating More Ideal Food Options) targets the obesity epidemic in the U.S., and was developed for the Hispanic population, a community at increased risk for obesity and its associated adverse health outcomes. Hispanics, the largest U.S. ethnic minority group, reached 62.1 million in 2020 (19% of the population); the Mexican-origin population is the largest subgroup (62%). Hispanic adults are 1.2 times more likely to be obese than non-Hispanic whites (NHWs), and Hispanic children are 1.8 times more likely to be obese than NHW children. Childhood obesity is a significant predictor of obesity in adulthood. Parental obesity more than doubles the risk of future adult obesity among obese and nonobese children under age 10. This is in part due to genetics but also due to parent modeling of health behaviors, and the home environment. In our prior work to address adult obesity in the NYC Mexican community, up to 19% met the target 5% weight loss, and in focus groups, participants were particularly concerned about obesity in their children. Participants described family as a primary motivator for behavior change, desire for group-based motivation, belief in short-term goal-setting, and time constraints as barriers to intervention adoption. In Family COMIDA, we aim to address these findings and answer the question - What is the optimal family-centered intervention (FCI) to address both adult and childhood obesity among Mexican American families? FCIs, in which mutually influencing interactions within the family can support and model healthy behaviors, are considered to be the ‘gold standard’ for childhood obesity. FCIs that jointly address both adult and childhood obesity, however, are limited, and recent systematic and scoping reviews revealed a dearth of literature describing culturally tailored FCIs for Hispanics. There are gaps in understanding the optimal combination of parent- and/or child-focused intervention components, and in understanding family-level contextual factors that may impact weight related behaviors, though family functioning is known to be associated with youth obesity. To address these gaps, build upon our prior work, and answer our question of what is the optimal obesity FCI for Mexican American families, we are proposing Family COMIDA, the first study to use the Multiphase Optimization Strategy (MOST), an innovative methodological framework, to guide assembly of an optimized, scalable, culturally and linguistically tailored, weight loss (parents)/obesity prevention (children) FCI for Mexican American families. Family COMIDA is grounded in Social Cognitive Theory (SCT) (including, e.g. goal-setting, etc.) and Family Systems Theory (FST), will address parents and children in tandem, includes group-based motivation, and utilizes mHealth to address time constraints. We will also assess family functioning as a potential mediator, and SCT constructs. We will recruit parent-child dyads (overweight/ obese parent + child aged 8-12 regardless of child’s weight) (‘parents’ includes non-parental caregivers).

NIH Research Projects · FY 2026 · 2025-04

PROJECT SUMMARY/ABSTRACT Dietary flavonoid ingestion has been linked with a reduction in cardiovascular events. We previously made the serendipitous finding that a specific class of flavonoid quercetins inhibits protein disulfide isomerase (PDI). PDI is an oxidoreductase that is important for protein folding in the endoplasmic reticulum. However, when released into the extracellular environment, PDI promotes thrombus formation. Over the past decade, we studied the use of flavonoid quercetins to target PDI in the context of thrombosis. Our experiments have spanned atomic resolution studies evaluating structural elements of the flavonoid-PDI interactions to cell-based assays to preclinical models to human studies. Recognizing the unmet need to develop an antithrombotic agent that is well tolerated and does not increase the risk of hemorrhage, we focused the clinical development of isoquercetin in patients with cancer at high risk for developing venous thromboembolism. We previously conducted a phase 2 trial in patients with advanced cancer and observed a significant reduction in circulating plasma D-dimer consistent with antithrombotic activity. However, before proceeding with a definitive phase 3 trial, we acknowledge critical gaps in the data package. Importantly, based on recent pharmacodynamic modeling, we remain uncertain of the optimal dosing schedule, as we currently believe that isoquercetin 1000 mg twice daily is preferred rather than the previous phase 2 dosing schedule of 1000 mg once daily. We also identified different prothrombotic mechanisms specifically in cancer, which we believe can identify patients with cancer who are likely to benefit most from primary thromboprophylaxis with isoquercetin. Our aims in this study are 1) to determine the optimal isoquercetin dosing based on target PDI inhibition utilizing a PDI-sensitive thrombin generation assay in patients with ovarian cancer, a group particularly at risk for thrombosis; and 2) to identify which hypercoagulable phenotypes of cancer are most amenable to PDI inhibition, and thus aiming to tailor treatment more effectively and advance a personalized approach to thromboprophylaxis in cancer care. In summary, this study seeks not only to refine isoquercetin therapeutic dosing schedule but also explore function- activity relationships of isoquercetin in specific hypercoagulable contexts, thereby enabling a phase 3 trial to develop a more targeted, safe, and effective approach toward prevention of cancer-associated thrombosis.

NIH Research Projects · FY 2026 · 2025-04

Despite recent U.S. FDA approval of therapies for patients with acute myeloid leukemia (AML), clinical outcomes for AML patients continue to remain poor. Other than allogeneic stem cell transplant, there are no effective immunotherapies for AML, and this is, in part, due to a lack of known antigens which are unique to AML and not present on vital normal hematopoietic precursors. Hence, there is an urgent and critical need for novel therapies to improve outcomes in AML. To this end, we recently identified unique expression of the RNA helicase U5 snRNP200, on the surface of AML cells but not normal hematopoietic precursors. Anti-U5 snRNP200 therapeutic antibodies, originally isolated from AML patient in long term remission following allogeneic transplant, were efficacious across immunocompetent AML models. Genome-wide screens to identify regulators of AML cell surface U5 snRNP200 expression revealed that cell membrane localization of U5 snRNP200 required surface expression of the Fcγ receptor CD32A. Exhaustive evaluation of cell surface U5 snRNP200 expression on normal hematopoietic cells and non-hematopoietic tissues revealed that U5 snRNP200 expression was absent from the surface from normal cells except for robust expression on B-cells. The primary goals of this proposal are to develop novel cellular immunotherapies targeting U5 snRNP complex members and probe the mechanistic basis for their cell membrane localization in AML. Our preliminary data identify that the therapeutic anti-U5 snRNP200 antibodies which are most efficacious require engagement of activating Fcγ receptors and immune effector cells, factors often impaired in AML patients. We therefore have now developed novel chimeric antigen receptor (CAR) T cells targeting U5 snRNP200 and observed early evidence of their efficacy in preclinical models of AML. Importantly, CAR T cells which simultaneously target U5 snRNP200 and secrete IL-18, a cytokine known to upregulate CD32A (and consequently also cell surface U5 snRNP200) have augmented anti-tumor efficacy. We therefore hypothesize that IL-18 secreting CAR T cells targeting U5 snRNP200 will be a novel effective and safe cell therapy for AML. We further hypothesize that cell surface U5 snRNP200 expression may modulate CD32 signaling in a manner that provides mitogenic benefit to leukemia cells. Finally, we have found that additional U5 snRNP complex member EFTUD2, which physically interacts with U5 snRNP200 in the nucleus, is also translocated to the AML cell surface. This proposal will (1) test the efficacy and safety of CAR T cells directed against U5 snRNP200 in human and syngeneic mouse models of AML, (2) identify the mechanistic basis for cell surface U5 snRNP200 localization and potential requirement of this cell surface protein in AML, and (3) evaluate the cell surface distribution of additional U5 snRNP components and therapeutic potential of anti-EFTUD2 CAR T cells (either alone or in combination with anti-U5 snRNP200 CAR T cells).

NIH Research Projects · FY 2026 · 2025-04

PROJECT SUMMARY/ABSTRACT Cardiovascular disease (CVD) is the primary cause of late mortality (death ≥5 yrs from diagnosis) in early breast cancer (EBC). Effective treatment strategies that improve function across multiple systems are needed in order to reduce CVD in EBC. Aerobic exercise therapy (AT) is a multisystem intervention demonstrated to improve cardiorespiratory fitness (CRF), a strong, independent predictor of CVD and all-cause mortality in breast and other malignancies. However, in our prior AT trial in EBC, our group found that despite high AT adherence, CRF change ranged from -10% to +24%, and ~60% of participants were classified as CRF non-responders. These findings indicate that AT following the conventional volume (~150 min/wk) and / or length (~16 wks) is insufficient for improving CRF in a substantial proportion of EBC survivors. The objective of the parent trial is therefore to evaluate the effects of increasing AT program length and volume on CRF response rate and other pertinent outcomes in EBC. We hypothesize that results from the parent trial will show that higher volume and length of AT will improve CRF response rate compared to standard dosing. However, we expect critical knowledge gaps will remain. The proposed R37 extension will allow us to address these gaps by further investigating CRF response to AT, the long-term effects of AT, and explore facilitators and barriers to AT. For the proposed extension, we will build on the funded parent trial by extending the follow-up of participants to 1-year post- intervention, providing a long-term assessment of CRF in the post-treatment survivorship period. We will address 3 specific aims: AIM 1: Examine baseline factors associated with CRF response. AIM 2: Evaluate the long-term effects of AT dosing on CRF and patient reported outcomes. AIM 3: Explore AT implementation outcomes. IMPACT: A history of cancer treatment is not a qualifying condition for structured AT and, as such, AT is not currently considered a standard aspect of cancer management. The proposed study will fill significant exercise- oncology knowledge gaps and will support AT implementation in clinical cancer care.

NIH Research Projects · FY 2026 · 2025-03

PROJECT SUMMARY/ ABSTRACT Loss of chromosome 9p21.3 is the most common homozygous deletion across cancers, including pancreatic ductal adenocarcinoma (PDAC), and it is strongly linked to poor prognosis and increased resistance to immune checkpoint blockade (ICB). 9p21.3 deletions invariably affect the tumor suppressor genes CDKN2A/B, yet often include a linked cluster of type I interferon (IFN) genes, which encode cytokines with antiviral, antiproliferative, and immune modulatory effects. While often overlooked, our laboratory recently found that co-deletion of the entire type I IFN cluster contributes to an immunosuppressive microenvironment, leading to reduced immune surveillance, increased metastasis, and resistance to ICB in mouse models of PDAC. Preliminary data suggest that co-deletion of Ifne, the type I IFN gene closest to Cdkn2a/b, is sufficient to disrupt tumor immune surveillance and promote metastasis. The overall objective of this proposal is to understand the role, regulation, and therapeutic potential of Ifne in PDAC immune surveillance. Aim 1: Determine the specific contributions of IFNE to tumor immune surveillance. I will decisively assess if Ifne is a tumor suppressor in the context of Cdkn2a loss by evaluating the effects of Ifne deletion in orthotopic PDAC mouse models by measuring tumor growth, metastasis, and immune infiltrates. I will also test recombinant IFNE (rIFNE) as a potential therapy. Aim 2: Characterize the regulation of Ifne during PDAC tumor progression. I will profile Ifne expression in PDAC and the tumor microenvironment and will test the hypothesis that Ifne is induced early during tumor development by mutant Kras signaling. Training plan: I will work with an interdisciplinary team of mentors and collaborators to gain expertise in cancer biology, molecular and cell biology, and immunology. The skills that I will develop over the course of this project will prepare me for a career as an independent researcher.

NIH Research Projects · FY 2026 · 2025-03

PROJECT SUMMARY/ABSTRACT To reduce patient distress, combat rising healthcare costs, and improve overall patient outcomes, there is pressing need to minimize number needed to biopsy (NNB) and maintain our melanoma detection rate. The potential for curing melanoma through surgery alone, particularly at its earliest stages, underscores the importance of early detection to reduce morbidity and mortality. However, the clinical diagnosis of melanoma is challenging, resulting in dozens of unnecessary skin biopsies performed for every melanoma identified. Algorithms have shown the potential to outperform and enhance the competence of expert dermatologists in classifying dermoscopy photos by lesion diagnosis in controlled settings and pilot studies. Preliminary data from single-center studies at Memorial Sloan Kettering Cancer Center (MSK) and Stanford University (SU) indicate that utilization of artificial intelligence (AI) as a second opinion in lesions indicated for biopsy by the clinician can improve the NNB; however, prior to implementing AI in clinical practice, deployment to the clinical setting must be rigorously tested in order to assess and address potential risks of AI implicit biases. This proposal aims to close this evidence gap and build real-world data through 2 specific aims: (1) determine the potential benefits and barriers to technology adoption by performing a mixed qualitative and quantitative methods analysis of clinician surveys, followed by implementation of a mitigation framework to overcome potential barriers; and (2) determine the impact on NNB and melanoma detection rate with real time AI feedback by executing a dual center phase 2 randomized controlled trial (RCT) at MSK and SU, which will be the first RCT of dermoscopy-based AI in clinical practice. This trial will also maintain its focus on addressing potential AI biases by emphasizing diverse recruitment, measuring how the trial team is doing both in performance and in recruitment, and oversight through a steering committee of experts in AI bias with patient advocate engagement. The RCT will compare standard of care dermatology visits for skin checks of lesions suspicious for melanoma (control arm) to visits that are the same in every regard except for the addition of AI-assistance, representing an enhanced standard of care (intervention arm). Through our partnership with Canfield Scientific, the AI algorithm on study will be seamlessly integrated into clinics’ imaging process, enabling our research team to feasibly analyze a total of 18,000 lesions on the RCT, giving our study significant power and generalizability. We will also make all images acquired in the study public for future benchmarking. Our AI tool will be assessed for bias against Fitzpatrick Skin Type, which will be metadata that is also made public to the International Skin Imaging Collaboration (ISIC) Archive for future work. This project will lay the groundwork for the design and implementation of phase 3 multi-center clinical trials to strengthen the evidence base for this cutting-edge technology in a move toward widespread clinical adoption.

NIH Research Projects · FY 2026 · 2025-03

PROJECT SUMMARY Leptomeningeal metastasis (LM) or spread of tumors into the spinal fluid-filled spaces that surround the brain and spinal cord represents an increasingly common, lethal complication of malignancy. A hallmark of LM is the robust inflammation that accompanies cancer cell growth in this space. Despite this inflammatory response to tumor, cancer cells invariably grow and overtake this space. We hypothesize that cancer within the leptomeningeal space derives benefit from this inflammatory signaling. Leveraging a collection of clinical samples obtained during the course of radiation treatment, we find that levels of CXCL1 increase in the spinal fluid in the setting of leptomeningeal metastasis, drop following radiation therapy, and return in concert with cancer cell growth in the space. In this proposal, we will investigate the relationship between leptomeningeal cancer cell growth and leptomeningeal-generated CXCL1. We have established immune-competent mouse models of LM, as well as craniospinal treatment techniques that faithfully replicate human disease and its treatment. We will leverage these mouse models to mechanistically dissect the CXCL1-CXCR2 signaling axis within the leptomeningeal space by first identifying cancer cell signals that provoke leptomeningeal CXCL1 generation. We will demonstrate the source of CXCL1, though single cell RNA sequencing, immunofluorescence, biochemical fractionation, in vitro coculture systems and immune-competent mouse models. To characterize and interrupt cancer cell responses to LM-generated cytokines, we will capture CXCR2 expression and downstream signaling in leptomeningeal cancer cell populations within leptomeningeal and extracranial microenvironments through flow cytometry and scRNASeq, interrupting the CXCR2-CXCL1 axis through CXCR2 blocking antibodies, inhibitors, and CRISPRi. Our comprehensive approach will capture the molecular call-and-response between cancer cells and the leptomeningeal microenvironment, focusing on the inflammatory signaling co- opted by cancer cells to support their own growth. Our unparalleled collection of human samples, facility with molecular interrogation of these samples, and innovative mouse modeling approaches enable thoughtful, mechanistic dissection of clinically-relevant targets against a destructive central nervous system malignancy with limited treatment options.

NIH Research Projects · FY 2026 · 2025-03

PROJECT SUMMARY/ABSTRACT Our cells possess multiple mechanisms for repairing DNA to safeguard our genomes. While predominantly error-free pathways such as homologous recombination (HR) are responsible for maintaining genomic integrity, low-fidelity repair mechanisms such as non-homologous end joining (NHEJ) contribute to genomic plasticity. When cells are under extreme stress, such as being exposed to anti-cancer drugs, they enter a state of persistence where low-fidelity DNA polymerases are upregulated and HR is downregulated, shifting dependence of DNA repair to error-prone mechanisms. If mutations occur in genes targeted by the anti-cancer drug, they can result in acquired drug resistance and lead to cancer relapse. In BRCA1/2-mutant cancers, which are HR-deficient, initial tumor response to DNA-damaging poly-ADP ribose polymerase (PARP) inhibitors is mitigated by reversion mutations that restore BRCA1/2 function and therefore HR. These resistance-conferring reversion mutations are often flanked by regions of microhomology, suggesting the involvement of the mutagenic DNA repair pathway, microhomology-mediated end joining (MMEJ). In colorectal cancer (CRC), initial tumor response to epidermal growth factor receptor (EGFR) blockade is mitigated by acquired resistance-conferring point mutations in EGFR, KRAS, and other genes. As such, understanding persistence and mutagenic DNA repair is critical for studying and treating cancer. However, the specific mechanisms that promote mutagenic DNA repair and drive acquired drug resistance in persister cancer cells remain unclear. We hypothesize that cellular stress induced by anti-cancer drugs rewires DNA repair pathways in persister cancer cells, increases their reliance on mutagenic DNA repair—by MMEJ—and drives the emergence of acquired resistance mutations. This proposal describes work to define the role of MMEJ in persistence-mediated acquired resistance in cancer cells by (1) investigating persistence in response to PARPi treatment of BRCA1/2 cancer cells; (2) examining mechanisms of mutagenic DNA repair in persister colorectal cancer cells; and (3) using high-content microscopy to determine a morphological signature of persistence. Given the clinical importance of persistence in cancer, this work has the potential to directly impact cancer treatment by identifying potential therapeutic targets, particularly regulators of MMEJ, that could reduce persistence-mediated relapse. Leveraging the sponsor’s, Agnel Sfeir’s, expertise in DNA damage repair and commitment to mentorship, Anne Carpenter’s support of the morphological profiling component, and the training institution’s, Sloan Kettering Institute’s, extensive network of core facilities, cancer-focused seminars, and commitment to supporting postdoctoral fellows, this trainee and project are well-positioned for success. Together, these investigations will provide a thorough and systematic evaluation of DNA repair and morphology in persistence while preparing the trainee for a career as an independent researcher.

NIH Research Projects · FY 2026 · 2025-03

PROJECT SUMMARY Therapies targeting oncogenic drivers have revolutionized the treatment of metastatic colorectal cancer (CRC) with new agents holding the potential to target most CRCs in the not-too-distant future. However, the impact of these new therapies has been limited by the short duration of response in the clinic; most patients with CRC progress within six months of starting targeted therapy. This proposal aims to address this problem of rapid resistance. Our analysis of acquired resistance to BRAF and KRAS G12C selective inhibitors indicates that gene amplification is a recurrent and often early mechanism of resistance in CRC. In our preliminary data, the development of gene amplifications at progression and the detection of amplifications at baseline prior to targeted therapy are both associated with shorter time on treatment. We hypothesize intrinsic tumor features enable a program of enhanced chromosomal instability that underlie rapid resistance to targeted therapy in CRC and that create a therapeutic vulnerability that can be exploited. Gene amplifications at resistance are often carried as extra-chromosomal DNA (ecDNA), which can be dynamically regulated in response to changes in drug levels. Beyond intrachromosomal amplifications, amplifications on ecDNA allow massive induction of expression of the amplified genes, while maintaining high intratumoral heterogeneity, enabling cancers to maximize their response to changing environments. These amplifications develop through chromothripsis, a process in which multiple rearrangements occur during a one-off cellular crisis, and require intact double- stranded DNA break repair pathways to form. In this proposal, we will evaluate how intrinsic tumor features modulate development of targeted therapy resistance and test a novel combination approach to prevent the development of resistance. Through deep analysis of clinical samples previously collected from patients with CRC who received targeted therapies, cell lines, and patient-derived xenograft (PDX) models, we will evaluate levels of markers of chromosomal instability, including amplifications, ecDNA, micronuclei, and fraction of genome altered. Cell lines will be used to map out the timing of increased chromosomal instability leading to resistance, and PDXs will be used to interrogate the effects of baseline tumor features on the time and nature of resistance that emerges in CRC. Using PDX models of BRAF V600E and KRAS G12C CRC, we will test a novel therapeutic strategy of combined DNA repair inhibition and targeted therapy to prevent resistance. We will specifically test DNA repair inhibitors against ATM, ATR, DNA-PK, and ecDNA given with matched targeted therapy from the start of treatment to prevent resistance. We believe this novel approach has the potential to transform targeted therapy for CRC and improve outcomes for patients.

NIH Research Projects · FY 2026 · 2025-03

Targeting the evolving immunopeptidome of metastatic colorectal cancer There has been limited success of chimeric antigen receptor (CAR) T cell therapies in solid tumors, in part, due to the inability to identify cancer-specific targets. Exploring the immunopeptidome, peptides presented by human leukocyte antigen (HLA) class I molecules, can expand the repertoire of targetable antigens. Our recent findings show that metastatic colorectal cancer (mCRC) cells adopt a highly stereotyped fetal-like phenotype, characterized by activating a developmental WNT-signaling signature as a mechanism of cell-fate reprogramming. This transcriptional signature is accentuated in metastasis initiating cells relative to the primary tumor and is highly conserved across diverse patients. Therefore, we hypothesize that these changes will translate into a cancer specific immunopeptidome and reveal a conserved and targetable sequence. Using our established integrated platform for the collection and multimodal analysis of resected normal colon, primary and metastatic lesions from patients undergoing CRC surgery, we have harnessed ex vivo patient-derived organoids (PDOs) that recapitulate patient- specific CRC cell states. Preliminary analysis using PDOs from HLA-A*02:01+ patients, the most common HLA allele, identified peptide targets derived from these fetal WNT-pathway gene states, specifically NKD1, that are both specific and prevalent in CRC and are lacking in healthy tissues. Furthermore, we showed that these peptides retain their immunogenicity based on healthy donor T cell reactivity. In Aim 1 (K99), we will systematically elucidate the evolving immunopeptidome from normal colon, primary tumor and metastatic lesion PDOs through mass-spectrometry and identify conserved intracellular targets for therapeutic interventions. In Aim 2 (K99), we will validate the biological role of NKD1 in CRC development, invasion, and metastasis by modulating its expression in metastatic lesion PDOs in an orthotopic xenograft mouse model. In Aim 3 (R00), we will identify NKD1-reactive T cell receptor (TCR) clones from HLA-A*02:01+ CRC patient’s peripheral blood to develop engineered TCR- T cell therapies. Drawing on my expertise in human immunology and medical oncology, along with the mentorship of prominent CRC biologist Dr. Karuna Ganesh and immunopeptidome-based therapy expert Dr. David Scheinberg at the outstanding Memorial Sloan Kettering Cancer Center, I am well- equipped to address these research questions. This foundation will enable me to master the necessary techniques, acquire knowledge, and develop the leadership skills required to emerge as a leading independent researcher and physician-scientist in the field of immuno-oncology.

NIH Research Projects · FY 2025 · 2025-03

PROJECT SUMMARY The Leukemia Translational Science Center (LTSC) aims to generate, coordinate and lead translational studies in leukemia within ECOG-ACRIN and within the National Clinical Trials Network (NCTN). The LTSC will serve as the central hub for studies of the Leukemia Laboratory Committee (LLC), with the support of the Leukemia Translational Laboratory (LTRL) and the Leukemia Tissue Bank (LTB), and a comprehensive Leukemia Data Warehouse. The LTSC is led by R. Levine and O Abdel-Wahab. They have developed an extensive track record in translational research leadership and implementation of state-of-the-art correlative studies in leukemia biology. The LTSC is further enhanced through its partnership with the MSK Centers for Molecular Oncology and Center for Hematologic Malignancies, which provide access to high-throughput genomics technologies, state-of-the-art genomic platforms, computational resources, and the capability to perform extensive, CLIA-certified, clinical genomics assays. In order to maximally accelerate high quality clinical trials based on the most important science, the LTSC will establish an interaction framework that will attract junior and senior clinical investigators, laboratory scientists, computational biologists, biostatisticians and others, and enable them to form synergistic research teams. The LTSC will provide pilot project funding for cross-disciplinary teams to jump-start these projects and an extensive suite of scientific resources, including access to patient samples and clinical/molecular data, genomic and epigenetic profiling capabilities and analytic platforms, scientific support, and a robust, productive collaborative leukemia research community. In this way, the LTSC will ensure that translational scientific studies are seamlessly integrated into leukemia clinical trials to identify predictors of response/outcome, identify and test novel therapies, and develop innovative correlative studies to assess response to anti-leukemia therapies. Through these activities, the LTSC aims to transform the standard practice of leukemia care with the development and implementation of personalized diagnostic methods, biomarkers and therapies.

NIH Research Projects · FY 2026 · 2025-03

PROJECT SUMMARY/ABSTRACT Tumors with different oncogenic mutations display diverse immunophenotypes that can affect CD8+ cytotoxic T lymphocyte (CTL)-mediated cancer immunosurveillance. Specifically, b-catenin activation leads to an “immune- desert” tumor microenvironment due to impairment of type 1 dendritic cell (DC1)-mediated CD8+ T cell priming, with mutations in the CTNNB1 gene among the most frequent oncogenic events in human hepatocellular carcinomas (HCCs). Of note, hepatic macrophages (hMfs) reside within a unique intra-vascular tissue niche with potential to act as antigen-presenting cells (APCs) to prime naïve T cells. Following our recent findings that monocyte-derived tumor-associated macrophages (TAMs) are capable of cross-presenting cancer cell antigens to CD8+ T cells and activation of the metabolic regulator mechanistic target of rapamycin complex 1 (mTORC1) potently affects macrophage differentiation and function, we will herein explore the effect of mTORC1 signaling on hMf APC functions in a murine model of b-catenin-driven HCC. Our preliminary data showed that hMfs lacking the mTORC1 suppressor TSC1 could correct the CD8+ T cell priming defects in the “immune-desert” HCC model and restore cancer immunity. Furthermore, TSC1-deficient hMfs display enhanced mitochondrial activities with the malate-aspartate shuttle playing a critical role to support macrophage reprogramming. Based on these observations, we hypothesize that hMfs can be reprogrammed via TSC1 deletion to overcome the “immune-desert” phenotype of b-catenin-driven HCC by acting as effective APCs to prime and activate CD8+ T cells, and this capability relies on their metabolic reprogramming. To test this hypothesis, I propose the following specific aims: 1) To determine whether and how TSC1-deficient TIM4- hMfs function as APCs to promote CD8+ T cell-mediated cancer immunity; 2) To define whether and how TSC1-deficient TIM4- hMfs are metabolically programmed to support CD8+ T cell-mediated cancer immunity. Completion of this project will generate mechanistic insights into the fundamental question of metabolic control of macrophage functions in cancer, and provide a novel therapeutic strategy to overcome immune evasion caused by defective DC-mediated T cell priming in “immune-desert” tumors. My long-term career goal is to become an independent investigator and lead a laboratory studying the metabolic function and mechanisms of tumor macrophages. To achieve this goal, I have devised a detailed career plan to gain skills in leadership, management, mentorship, grant writing, and scientific communication. I will work under the mentorship of Dr. Ming Li, a leader in the fields of cancer immunology and immunometabolism. Additionally, I have assembled an advisory committee comprised of Drs. Lionel Ivashkiv, Amaia Lujambio, Andrea Schietinger, and Hongbo Chi to provide me with complementary expertise and guidance in both scientific and career development. My research and career development plan, combined with the guidance of my mentor and advisors, as well as the outstanding academic environment at MSKCC, will serve as the bedrock for my independence in the field of tumor macrophage research.

NIH Research Projects · FY 2026 · 2025-02

Endometrial cancer (EC) incidence and mortality are rising rapidly in the U.S. Black women are experiencing the sharpest increase, with incidence and mortality rising 46% and 29%, respectively, from 1999–2015. While the 5-year survival for EC overall is 80%, for Black patients it is only 63%. This is due, in part, to the more frequent diagnosis of aggressive non-endometrioid tumor subtypes in Black women (~35% vs ~17% non-Black). Primary staging and treatment for EC is surgical hysterectomy with bilateral salpingo-oophorectomy; several adjuvant therapies allow for the tailoring of post-surgical treatment, requiring careful balancing of prognosis/recurrence risks with adverse effects of therapy to improve outcomes and avoid mistreatment. Black women are more commonly diagnosed with these aggressive histologic subtypes not amenable to surgical resection alone. There are no prognostic tools to inform discussion of adjuvant therapies for Black women diagnosed with EC. This Early K99/R00 application leverages years of NIH funding and collaboration to develop and externally validate prognostic tools for Black women with EC post-hysterectomy. This research will inform discussion of tailored adjuvant therapies in clinical settings. It is foundational for Dr. Peeri to achieve research independence focused on creating clinical decision-making tools for all populations. Our specific aims are to: 1A) build a robust prognostic tool tailored for Black EC patients using readily available clinical and epidemiologic factors to predict survival 3- and 5-years post-hysterectomy, and to externally validate this tool in the MSK Cohort; 1B) compare model performance for Black patients with an established model developed primarily in White women; 1C) develop an easy-to-use survival nomogram web-based tool for clinician and patient use; 2A) assess the utility of adding existing TCGA molecular subtypes to our prognostic tool for Black women and externally validate in the MSK cohort; and 2B) use established clinical tools in our population as a point of reference for evaluating the performance of our model; 3) build biomarker-based prognostic tools to predict overall survival at 3- and 5-years post-hysterectomy in 3A) Black women, expanding upon the prognostic tools developed in Aim 1, and 3B) White women, expanding on an established tool. The training goals are to: 1) receive training in rigorous prognostic model development and validation methods; 2) receive training in cancer genomics including advanced methods for whole-exome sequence data; 3) expand knowledge of biomarkers of clinical significance and machine-learning methods for model development; and 4) lay a foundation to support an independent research career in cancer health disparities. Ultimately, this proposal will advance the career of a young investigator with a strong research background from postdoctoral fellow to independence.

NIH Research Projects · FY 2026 · 2025-02

ABSTRACT The research program described in this proposal focuses on an in-depth exploration of the ubiquitin and autophagy pathways, which partake in a process called proteome homeostasis, or proteostasis, and is an essential cellular process. Over the course of this proposal, our team aims to uncover novel aspects of molecular intricacies of ubiquitin regulation and to explore the mechanisms underlying selective autophagy in response to various cellular stimuli. Regarding the ubiquitin machinery aspect of our work, our goal is to identify and understand the cellular relevance of recently discovered regulatory switches for ubiquitin signaling. For the autophagy facet of our work, we aim to enhance our comprehension of singular regulatory factors we’ve identified, which are involved in this complex biological process. This program combines our expertise in quantitative mass spectrometry, biochemistry, and cell biology to investigate the different aspects of proteostasis dynamics and its disruption in proteostasis-related diseases. Our investigation aims not only to advance scientific knowledge but also to have a substantial impact on healthcare by reducing our current limitations in understanding disease mechanisms.

NIH Research Projects · FY 2025 · 2025-02

TITLE: Myeloma Defining Genomic Events to Differentiate Benign and Malignant Myeloma Precursor Conditions Cancer genetic study section: https://public.csr.nih.gov/StudySections/DBIB/OBT/CG ABSTRACT Multiple myeloma (MM) is the second most frequent hematological cancer, and its life-history is characterized by a progressive evolution from asymptomatic precursor stages (i.e., monoclonal gammopathy of undetermined significance and smoldering myeloma) to symptomatic disease. While these myeloma precursor conditions (MPC) are found in 3-5% of the adult population, only a small fraction will ultimately progress to MM. The ability to identify high-risk patients before major clonal expansion and symptoms arise has the potential to enable strategies of early prevention, which currently represents one of the most important unmet clinical needs. In the last four years, our group has shown for the first time that bulk whole genome sequencing (WGS) is the only technology able to comprehensively identify the key MM defining genomic events such as chromothripsis, APOBEC mutational activity, mutations in distinct driver genes. These events are emerging as critical to differentiate progressive from stable MPC. Despite its comprehensive resolution, bulk WGS has intrinsic limitations in defining small subclones, which often drive the MPC progression into MM. This limitation also affects our understanding of the early disease life-history and the early identification of MPC destined to progress. To overcome this, we have successfully explored a novel single-cell WGS platform (direct library preparation; DLP+) to fully characterize the subclonal genomic complexity and plasticity in each phase of MM evolution. Thanks to this unprecedent resolution combined with single cell RNA of the immune microenvironment, this study will allow to comprehensively define the clinical impact of MM defining genomic and immune events among MPC, allowing to differentiate benign from malignant entities. Among the key MM defining genomic events APOBEC mutational activity is the most prevalent and its presence is emerging as one of the most sensitive prognostic features for MPC progression, being detectable by bulk WGS in virtually all MM and in 80% of progressive patients, but absent among the stable ones. Despite its importance, it remains unclear whether APOBEC mutagenesis represents a genuine driver that promotes genomic instability and mutations in driver genes, or if it is merely an epiphenomenon of genomic instability and transformation. Considering that MM evolution is spread across decades, it is impossible to define when APOBEC starts its aberrant mutational activity during MM and MPC pathogenesis. To overcome this limitation, our group has interrogated the genomic landscape of the immunocompetent Vk*MYC mouse model known to spontaneously develop MM over 12-18 months. Spontaneous APOBEC mutational activity was detected in ~50% of the mice, making the Vk*MYC mouse the first immunocompetent model of cancer where it is possible to investigate the spontaneous APOBEC mutational activation. Exploring longitudinally with scWGS DLP+ the progressive expansion of clonal plasma cells in the Vk*MYC mouse model and combining the Vk*MYC mouse with mouse models with constitutive and inducible APOBEC activity will allow to define the role of APOBEC activation in MPC progression into MM.

NIH Research Projects · FY 2026 · 2025-01

PROJECT SUMMARY/ABSTRACT The management of metastatic bladder and upper tract urothelial cancer has been transformed over the past five years with the FDA approval of anti-PD-1/PD-L1 antibodies, antibody-drug conjugates targeting Nectin-4 and Trop-2, and the fibroblast growth factor receptor (FGFR) inhibitor erdafitinib. Despite these clinical advances, urothelial cancer remains fatal for most patients with metastatic disease. Nearly all urothelial cancers harbor one or more mutations in chromatin modifying genes, with mutations in KDM6A, KMT2D, ARID1A, CREBBP, and EP300 being the most common. The role of mutations in these genes in urothelial cancer pathogenesis remains poorly understood, as does their impact on systemic therapy response. In preliminary studies, we find that EP300 gene knockout or loss-of-function mutation results in IL-6-JAK1-mediated STAT3 activation and resistance to erdafitinib. Based on these findings, we hypothesize that EP300 loss-of-function mutations are a mechanism of erdafitinib resistance in patients with urothelial cancer and that co-targeting IL-6-JAK1-STAT3 signaling could delay or overcome resistance to FGFR inhibitors. We will pursue three aims to investigate the phenotypic consequences of EP300 loss-of-function mutations and their role in mediating resistance to erdafitinib in patients with urothelial cancer. These aims will utilize unique resources assembled by our investigative team, including: 1) a large prospective cohort of genomically profiled urothelial cancers for which we are collecting detailed patient demographic and treatment response data, and 2) a large biobank of patient-derived organoid models of urothelial cancer. In Aim 1, we will study the role of EP300 loss-of-function mutations in mediating kinase inhibitor resistance using a large panel of patient-derived models, including FGFR3 mutant and wildtype models. We will also identify mechanism(s) of p300-independent STAT3 activation and the impact of p300- dependent and independent STAT3 activation on FGFR3 dependence. In Aim 2, we will identify genomic alterations associated with intrinsic resistance to FGFR3 inhibition using pre-treatment tumors collected from patients with urothelial cancer, with an initial focus on EP300 co-mutation as a basis for intrinsic resistance to erdafitinib. Finally, in Aim 3, we will identify mechanisms of acquired erdafitinib resistance using paired pre- and disease progression tumor and cell-free DNA samples and employ patient-derived models to test combinatorial strategies designed to overcome or delay erdafitinib resistance. The long-term translational objective of the studies proposed is to define the mechanism(s) through which EP300 mutations promote urothelial cancer pathogenesis and the impact of EP300 mutation on systemic therapy response, with the goal of using the resulting insights to develop mechanistically based combination strategies designed to prevent or delay FGFR3 inhibitor resistance. As EP300 mutations have been identified in other cancer types, the studies outlined in this proposal will also provide insights into the functional and clinical significance of EP300 mutations in cancer more broadly.

NIH Research Projects · FY 2026 · 2025-01

PROJECT SUMMARY Less than 8% of pancreatic ductal adenocarcinoma (PDAC) patients are alive 5 years after diagnosis. PDAC is typically diagnosed at an advanced stage, limiting treatment options. Chemotherapies are the mainstay for advanced PDAC, though they produce incomplete responses. Thus, development of novel therapies for PDAC patients is urgently needed. A possible explanation for failure of standard chemotherapies in PDAC is cellular phenotypic heterogeneity within tumors. Heterogeneity may enable subpopulations of cells to survive therapy and repopulate the tumor. Cancer stem-like cells (CSCs) have been described in multiple solid tumor types. CSCs have robust proliferative potential and are typically resistant to cancer therapies. Elimination or re- differentiation of cancer stem-like cells is an attractive strategy: By homogenizing cancer cell phenotypes within tumors, such therapies may suppress tumor progression and lead to improved responses to conventional therapies. Our pilot data suggest that secreted Wnt ligands produced by one cancer cell subpopulation drive a stem-like state in another cancer cell subpopulation, in essence forming a specialized microenvironment, or niche, within pancreatic tumors that maintains CSCs. We found that highly plastic basal cells express Slc4a11+, whereas niche cells are marked by Porcupine and DLL1. Hypothesis: Disrupting CSC and niche cells can translate into novel therapeutic strategies for PDAC patients. We propose to identify mechanisms that drive basal niche cell states and to explore the potential of Wnt inhibitors in PDAC therapy. These studies have the potential to translate into new PDAC therapies. Aim 1. Interrogate function of stem-like PDAC cells. We will profile Slc4a11+ pancreatic cancer cells and evaluate ability to functionally contribute to PDAC progression, metastasis, and resistance to chemotherapy. We will perform lineage-tracing and -ablation, and gene expression and proteomic profiling of Slc4a11+ cells in genetically engineered mouse PDAC tumors. Results will reveal phenotypic shifts in PDAC cell populations, which may provide added means to target these cells. Aim 2. Elucidate biology of Porcupine+ PDAC niche cells. We will identify molecular mechanisms that drive the Porcupine+ niche cell state. We will use a Porcupine reporter allele to ablate these cells in PDAC to evaluate their role in tumor progression, and isolate niche cells for proteomic and gene expression profiling. Results will provide insights into role of Porcupine+ cells in PDAC progression and how to target them. Aim 3. Therapeutically target candidate drivers of the basal cell state in PDAC. We will interrogate SOX11, NRARP, and DLL1 alone and in combination with the MEK + HSP90 inhibitor combination, KRAS inhibitors, and chemotherapy agents. These therapies will be tested in orthotopic mouse and patient-derived xenograft models of PDAC. These efforts will test the therapeutic potential of basal state drivers in PDAC, which may sensitize pancreatic tumors to chemotherapy.

NIH Research Projects · FY 2026 · 2025-01

PROJECT SUMMARY/ABSTRACT Pancreatic cancer is one of the deadliest cancers while comprising only 3% of new cancer cases in the U.S. each year. This is due to its advanced stage at diagnosis and resistance to standard treatment approaches. Although population-based screening is not justified due to its low incidence, pancreatic cancer screening and surveillance is recommended for high-risk individuals (HRIs) who have specific genetic syndromes and familial predispositions that put them at risk for developing pancreatic cancer. The goal is to detect resectable, early- stage pancreatic ductal adenocarcinoma (PDAC) and high-risk precursor lesions before malignant progression. Magnetic resonance imaging and endoscopic ultrasonography (EUS) are the preferred screening modalities in HRIs. EUS is generally considered the most sensitive imaging modality to evaluate pancreatic lesions but has several limitations. EUS is highly operator-dependent and limited to qualitative assessment of pancreatic tissue based on B-mode features. There is an unmet clinical need for a more robust approach to EUS-based characterization of normal and abnormal pancreatic tissue. In this study, we will develop a system and methodology for multiparametric endoscopic ultrasound (mpEUS) imaging of pancreatic tissue using B-mode, ultrasensitive microvessel imaging (UMI), shear-wave elastography (SWE), and tissue microstructure characterization with pulse-echo quantitative ultrasound (PEQUS). We will implement real-time mpEUS in HRIs enrolled in our institution’s pancreatic screening program to determine the feasibility and benefits of mpEUS in a clinical setting. As a secondary objective, we will test the system in a clinical study with 30 PDAC patients to identify associations with current clinical assessments and mpEUS. We hypothesize that mpEUS will be sensitive to pathophysiological and microstructural characteristics of pancreatic cancer and its precursor lesions. There is increasing awareness of the benefits of pancreatic screening and surveillance in HRIs, and considerable effort has gone into identifying the target population, developing novel biomarkers, and improving imaging techniques. Multiparametric endoscopic ultrasound offers a non-subjective, quantitative approach for detection and characterization of pancreatic cancer. Ultimately, this approach could lead to mpEUS imaging biomarkers that clinicians could use for enhanced pancreatic cancer screening. It is expected that this research could introduce a safe, cost-effective imaging platform to improve outcomes and save lives of individuals at high-risk for developing pancreatic cancer.

NIH Research Projects · FY 2026 · 2025-01

Cancer remains a significant global health challenge, with an anticipated 611,240 deaths in 2024. Substantial strides in cancer research have enhanced our understanding of the mechanisms underlying its development, progression, and spread. While current treatments such as surgery, radiation, chemotherapy, targeted therapy, and immunotherapy have shown efficacy in certain cases, drug resistance poses a pervasive challenge. Resistance often leads to cancer cells regenerating into new tumors with altered molecular profiles that diminish drug effectiveness. Alternatively, cancer cells can adapt during treatment, acquiring genetic mutations that allow them to evade therapeutic effects. One approach to address this issue is combining different therapies to restore sensitivity in resistant cells. However, the molecular heterogeneity of cancer remains a significant barrier, contributing to treatment resistance and subsequent relapse. Therefore, it is crucial to comprehensively understand how various treatments induce specific molecular changes within both the tumor and its microenvironment, and how these changes influence the diverse outcomes observed in cancer therapy. In this proposal, I will evaluate the response of different cancer therapy modalities in various cancer types. I will employ high-dimensional single-cell approaches to identify differential gene expression driven by the different anticancer treatments and treatment-persistent cell subpopulations that possess regenerative potential when subjected to treatments, respectively. Further, I will develop analytical tools to identify ligand-receptor interactions between the tumor and its surrounding microenvironment that could be used as therapeutic targets, and to gain a unique insight into how tumors, their microenvironment, and the host respond to different treatments. Lastly, I will engineer ex vivo and in vitro culture systems that recapitulate the complexity of the tumor microenvironment, particularly to study the previously identified interactions, and establish them as 3D co-culture platforms for therapeutic target validation and high-throughput drug screening for my research program. Completion of this project will successfully prepare me to launch an NIH-funded research laboratory engineering cancer-oriented nano-systems to target interactions in the tumor microenvironment that contribute to cancer progression and resistance.

NIH Research Projects · FY 2026 · 2025-01

Project Summary/Abstract The overall objectives of this proposal are to elucidate novel mechanisms underlying the regulation of the transcription Factor EB (TFEB) and autophagy-lysosomal pathway (ALP), and to investigate their therapeutic potential as mechanism-based treatments for Alzheimer’s disease (AD). Genetic evidence indicates that dysfunction of ALP contributes to the pathogenesis of AD. Furthermore, TFEB, a master regulator for lysosomal and autophagic biogenesis, has been shown to mitigate AD progression in AD mouse models. Our preliminary studies demonstrate that two protein phosphatases, CDC25A and PP2A, regulate TFEB signaling and downstream ALP pathway and Tau clearance. Importantly, we found that inhibition of CDC25A activates TFEB in an AMPK-mediated manner; that inhibition of lysosomal acidic ceramidase (ASAH1) enhances PP2A activity, thus leading to TFEB activation; and that a combined inhibition of ASAH1 and CDC25A activates TFEB synergistically. Therefore, we hypothesize that CDC25A and PP2A play important roles in the regulation of endolysosomal and autophagic network via modulating TFEB, and that inhibition of CDC25A and ASAH1 can promote the clearance of Tau aggregates for AD treatment. In this proposal, we will elucidate the mechanisms underlying the regulation of TFEB and lysosomal autophagic function by CDC25A/AMPK and ASAH1/PP2A signaling. We will also examine the role and therapeutic implication of targeting CDC25A/AMPK and ASAH1/PP2A signaling axis in AD pathogenesis and treatment. Interdisciplinary techniques including chemical biology, proteomics, genomics, iPSC-based neuron differentiation, and mouse modeling for AD pathogenesis will be used for this mechanistic and preclinical investigation. Success of the proposed research will lead to an in-depth mechanistic understanding of the regulation of TFEB and ALP and achieve the proof-of principle of potential therapeutic strategies for AD treatment by targeting CDC25A and ASAH1, alone or in combination. Further, beyond Tau pathology, this study can be expanded in the future to APP/Aβ pathology in AD.

NIH Research Projects · FY 2026 · 2024-12

There are no effective countermeasures for the Gastrointestinal-Acute Radiation Syndrome (GI-ARS). Studies proposed here will support our ongoing effort to develop an anti-ceramide Ab as a mechanism-based approach to mitigate GI-ARS morbidity and mortality. GI-ARS results from destruction of crypt/villus units, loss of mucosal integrity, and infection by resident enterobacterial flora. GI-ARS pathophysiology involves depletion of a small pool of intestinal stem cells (ISCs) residing at the base of the Crypts of Lieberkühn termed crypt base columnar cells (CBCs). We showed CBC depletion post-ionizing radiation (IR) occurs over 24-48 h preceding physical crypt dissolution between Day 2.5-3.0 post IR. Further, CBC survival at Day 2 predicts crypt regeneration at Day 3.5, and GI-ARS lethality. Our lab has pioneered the concept that IR releases acid sphingomyelinase (ASMase) within min to outer endothelial plasma membranes, hydrolyzing sphingomyelin to generate pro-apoptotic second messenger ceramide therein, which couples to direct ISC damage to coordinately determine ISC fate. Further, our anti-ceramide Abs bind ceramide on the irradiated endothelial surface protecting mice against GI-ARS lethality. Recently we showed endothelial apoptosis increases 25-fold above background by 4 h post 15 Gy, the GI-ARS LD90 dose in C57BL/6J mice, remains elevated for 36 h, slowly returning to baseline by 84 h. Anti- ceramide delivery at 24 h post IR induces immediate cessation of endothelial apoptosis facilitating Lgr5+ ISC regeneration, preventing lethality. Full autopsies of mice surviving 90 days are nearly normal in 42 organs, including the GI tract. Based on these findings, we initiated studies that address impact of acute anti-ceramide protection on delayed effects of acute radiation exposure (DEARE) to small intestines. We show mice treated with 7-13 Gy whole body irradiation, sublethal GI-ARS doses, plus bone marrow transplantation (BMT) display acutely reversible weight loss and remain asymptomatic for extended periods. However, over time they develop dose-dependent weight loss and at high doses moribundity. Day 200 autopsies reveal dose-dependent villus- crypt blunting and crypt loss, which at high doses are marked, accompanied by vascular irregularities. Anti- ceramide single chain variable fragment treatment at 24 h post IR prevents endothelial apoptosis, facilitating crypt regeneration, preventing delayed weight loss and normalizing Day 200 crypt-villus architecture. Further, using a green fluorescent protein (GFP)-labeled BMT at 20 h post-IR, we discover within hours large numbers of GFP+ endothelial progenitors enter the damaged area, deposit exclusively at the crypt base juxtaposing the CBC compartment, and die by apoptosis. Anti-ceramide provision at 24 h post IR abrogates regenerative endothelial cell apoptosis. We propose protection of regenerative endothelial cells enhances ISC regeneration at 24-72 h post-IR, mitigating GI morbidity/mortality acutely and chronically, to be assessed in 3 Specific Aims. These studies, if successful, will show that acute protection of the microvasculature results in regeneration of the damaged Lgr5+ ISC compartment leading to acute and long-term preservation of small intestinal integrity.