Sloan-Kettering Inst Can Research

NIH Research Projects · FY 2026 · 2026-06

PROJECT ABSTRACT The Philadelphia-chromosome negative myeloproliferative neoplasms (MPNs) are clonal hematopoietic stem cell disorders, which include polycythemia vera (PV), essential thrombocytosis (ET), and primary myelofibrosis (PMF). MPNs carry an inherent risk of progression to advanced MPN, consisting of accelerated- phase disease (AP; 10-19% blasts in the peripheral blood or bone marrow), as well as blast phase disease (BP; ≥ 20% blasts in the peripheral blood or bone marrow). The prognosis of patients with advanced MPN remains quite poor, with median survival of 2.6 months. Importantly, chemotherapy regimens used to treat Acute Myeloid Leukemia (AML) such as standard induction chemotherapy (which are often used in advanced MPN) appear to have limited efficacy in this setting. Thus, the treatment of advanced MPN is a major unmet clinical need. We recently carried out a phase I/II study to test the safety and efficacy of combination therapy with the JAK1/2 inhibitor Ruxolitinib and the hypomethylating agent Decitabine in patients with advanced MPN (MPD-RC 109 study; NCT02076191). This combination (RUX-DAC) was based on data demonstrating synergy between these drugs in in vitro preclinical studies. 46 patients were accrued to the phase I and II studies. 37 patients were response evaluable. Complete response (CR) occurred in 10%, Complete Response with incomplete count recovery (CRi) in 24%, Partial Response (PR) in 24%. 42% of patients had no response to therapy. Using samples available from the MPD-RC 109 study, as well as samples from a contemporaneous clinical trial of 28 patients with advanced MPN treated with the RUX-DAC regimen carried out at the MD Anderson Cancer Center (NCT02257138), and samples collected from advanced MPN patients treated with the RUX-DAC regimen as a standard of care at Memorial Sloan Kettering Cancer Center, we seek to assess and validate genetic and epigenetic determinants of response to RUX-DAC in this cohort of homogenously treated advanced MPN patients. Specifically, we seek to assess whether the mutational profile of advanced MPN patients explains and predicts response to therapy. We further seek to assess whether alterations in genomic architecture in advanced MPN occur in patients who respond to therapy. Finally, we seek to determine if the baseline global methylation profile correlates with response to therapy, as has been demonstrated for other myeloid malignancies. Data resulting from these studies could be used to guide therapeutic decisions and identify patients for whom combination RUX-DAC therapy has the highest likelihood of procuring a response, as well as to open new lines of biologic and therapeutic inquiry into this disease.

NIH Research Projects · FY 2026 · 2026-06

PROJECT SUMMARY The Reducing ReADmissions through Innovative ApplicatioNs of Telemedicine (RADIANT) trial aims to build the evidence base necessary to establish a scalable remote patient monitoring (RPM) and integrative medicine (IM) intervention delivered via telemedicine platform to medical oncology patients discharged to home after hospitalization. The 12-week readmission rate for patients with cancer ranges from 33%-55% and reducing these readmissions would alleviate the high psychosocial, physical, and financial costs for patients and caregivers. We developed and implemented an RPM program that identifies medical oncology patients at hospital discharge and monitors their symptoms using electronic patient-reported outcomes (ePROs). Extended from approaches in other high-risk areas of oncology, the system intervenes as necessary to help manage symptoms. However, oncology patients discharged from the hospital have additional complicated needs related to their lingering symptom burden. Clinical guidelines now include interventions such as exercise and mind-body therapies (eg, yoga, tai chi, meditation) for symptom management during cancer treatment. Yet few patients have access to these treatments due to barriers for patients (eg, time, costs, transportation) and at the system level (eg, resource allocation, staffing, space constraints). Recently, the investigators completed a pilot randomized controlled trial (RCT) using telemedicine for IM and found that the intervention not only improved symptom burden, but also reduced rates of hospitalizations relative to enhanced usual care. Each of these approaches—RPMs and telemedicine for IM—has shown effectiveness in reducing hospital admissions, but no single platform connects ePROs and symptom management with mind-body therapies. We will combine IM therapies with the existing RPM capacity, such that the RPM can recommend a live, synchronous IM class to a patient based on RPM symptom inputs. Our hypothesis is that patients engaged in this telemedicine intervention, Connected Care, will have reduced rates of 12-week readmissions, and these reductions will correlate with reduced symptom burden as compared with control group patients receiving enhanced usual care. To test this hypothesis, we bring together a multidisciplinary team, including Medical Oncology, IM, Informatics, Implementation Science, and Biostatistics. We will randomly assign 530 medical oncology patients recently discharged to home to either 12 weeks of Connected Care or enhanced usual care. Our specific aims are to: (1) determine the effect of Connected Care on rates of 12-week readmissions among medical oncology patients; (2) evaluate the effects of Connected Care on symptom burden; and 3) develop implementation strategies to address real-world barriers to implementation of Connected Care. By addressing critically important gaps in care delivery of symptom monitoring and IM therapies via telemedicine, RADIANT will have a practice-changing effect, providing an evidence-based, replicable model of supportive care for patients with cancer discharged from the hospital.

NIH Research Projects · FY 2026 · 2026-06

PROJECT SUMMARY/ABSTRACT This application seeks partial funding for the Lymphocyte Antigen Receptor Signaling Workshop (LARSW), to be held June 21-25, 2026, at the Certosa di Pontignano, in Tuscany, Italy. The major goal of this conference is to provide a comprehensive survey of recent advances in antigen receptor signaling and the implications of these advances for health and disease. This meeting will be the sixth occurrence of the LARSW, which has garnered widespread interest in research institutes, academia, and industry because of its outstanding speaker rosters, the cutting-edge nature of the work presented, and its translational relevance. Additionally, since most mainstream immunology meetings do not provide an in-depth focus on antigen receptor signaling mechanisms, the LARSW has attracted leaders in immune signal transduction worldwide, as well as new investigators and students. The particular emphasis of this iteration of the LARSW is autoimmunity, which will be the subject of three meeting sessions, including the Keynote address. Other topics will include antigen receptor structure, signal transduction from the membrane, metabolic regulation of lymphocyte function, lymphocyte mechanobiology, lymphocyte differentiation, and cancer immunology. These topics represent the technical and conceptual breadth of modern immunological research, and we anticipate that they will appeal to researchers in both basic and translational science. We have ensured that new ideas and research areas will be addressed in 2026 by featuring 26 new invited speakers (out of 28). We have also prioritized representation of women (15) among the invited speakers. In addition, most sessions will have space for two short talks (for a total of 14), which will be selected from abstracts. Priority for short talks will be given to new investigators, postdoctoral fellows and students from groups in which PIs are not presenting. This will ensure a wide ranging group of topics at the meeting. The overall objectives of the meeting are: 1) To provide a critical and intensive overview of the recent advances in antigen receptor signaling and related topics; 2) To bring together a varied group of senior scientists, young investigators, and trainees (including postdoctoral fellows and students), in a stimulating and supportive atmosphere involving formal presentations and informal discussions; and, 3) To advance rapidly research on the molecular mechanisms and translational implications of antigen receptor signaling by broadly disseminating information and recent breakthroughs. We anticipate that this LARSW will build upon the success of past conferences in charting the course of antigen receptor signaling research.

NIH Research Projects · FY 2026 · 2026-06

PROJECT SUMMARY Anaplastic thyroid cancer (ATC) primarily affects elderly individuals and has a dismal prognosis compared to other thyroid cancer subtypes. One of the hallmarks of ATCs is their admixture with myeloid cells, primarily macrophages. The recent development of combinatorial treatment with BRAF and MEK inhibitors led to improved outcomes in Class 1 BRAF-mutant ATC patients. Although their initial response to MAPK inhibition is substantive, responses are not durable, leading to a median overall survival (OS) of ~15 months7. With aging, somatic mutations in hematopoietic stem and progenitor cells (HSPCs) promote clonal expansion over non- mutant HSPCs. When this is present in the absence of malignant transformation it is termed clonal hematopoiesis (CH). CH mutations arise most frequently in epigenetic modifier genes, such as DNMT3A and TET2. CH is associated with an increased risk of atherosclerotic cardiovascular disease and other diseases associated with aging. We showed in a pan-cancer analysis that CH, in particular CH with putative driver mutations (CH-PD), is associated with adverse outcomes in solid tumor patients, including those with ATC. The specific interactions between CH leukocytes and tumor cells in the TME and their impact on therapeutic response remain uncharted. We find that TET2-mutant CH is enriched in the TME of patients with ATC and other solid tumors. We developed syngeneic immunocompetent mouse models of concurrent Tet2-mutant CH and orthotopically implanted BrafV600E-driven ATC to explore the mechanisms involved. Using single cell-CITE-RNASeq we found that Tet2- mutant macrophages selectively infiltrate mouse BrafV600E-mutant ATC and cause resistance to BRAF-MEK inhibition through overexpression of Tgfβ-family ligands. Importantly, inhibition of the effects of Tgfβ at three distinct nodes restores sensitivity to MAPK pathway inhibition, opening a path for synergistic strategies to improve outcomes of patients with ATCs and concurrent CH. The mechanisms by which Tgfβ activation render ATCs insensitive to MAPK inhibition remain to be defined. We will investigate whether macrophage Tgfβ ligand overproduction induces resistance to MAPK inhibitors through cancer cell autonomous mechanisms and/or by its immune suppressive effects and use genetic approaches to nominate the key Tgfβ ligands responsible for treatment resistance. The mechanisms delineating how DNMT3A CH leads to worse outcomes in solid cancers in general, and ATC in particular, have eluded explanation. We will determine whether Dnmt3a-CH affects ATC biology and response to therapy in mice and test the hypothesis that this is driven by the infiltrating mutant myeloid population. Finally, we found that CH-PD is associated with worse OS in patients with ATC, but the effect of individual CH genes has not been established. We will determine whether specific CH genotypes impact OS in ATC and if this manifests at low CH variant allelic fractions (VAF) using a high sensitivity assay. We will also investigate whether advanced thyroid cancers of any type with a high tumor-to-blood CH VAFratio (i.e. CH mutant cell enrichment in the tumor as compared to blood) have worse clinical outcomes.

NIH Research Projects · FY 2026 · 2026-06

PROJECT ABSTRACT In recent years, structural maintenance of chromosomes (SMC) complexes have emerged as critical ring-shaped and ATP-dependent DNA tethers and loop extruders. The most well-known SMC complex, cohesin, has vital importance in nearly all aspects of chromosome metabolism, including gene expression, nuclear architecture, DNA replication and repair, and mitotic chromosome segregation. Against this backdrop, large-scale cancer sequencing projects revealed frequent mutations in cohesin subunits in tumors at multiple organ sites. How these mutations promote cancer, and whether they create collateral vulnerabilities that could be targeted therapeutically, are important unsolved problems. Building on our previous studies of cohesin and DNA replication, we analyzed cells that lacked STAG2, the most frequently mutated cohesin subunit and a TCGA-designated pan-cancer driver. We discovered that STAG2-deficient cells are prone to accumulation of R-loops and experience all the hallmarks of replication stress. They are also “addicted” to R-loop mitigating factors, including RNAse H2 and the Fanconi Anemia pathway. Via NER endonucleases, STAG2-deficient cells produce cytoplasmic R-loop fragments that trigger innate immune signaling. We propose studies that will dissect the mechanisms that underlie R-loop homeostasis, gene regulation, and avoidance of replication-transcription conflicts. This information will expand and deepen our understanding of how STAG2 regulates the genome under normal conditions and how its loss impacts cancer cells. This information is needed to develop more effective and less toxic cancer therapies.

NIH Research Projects · FY 2026 · 2026-06

Project Summary/Abstract: By 2040, 73% of cancer survivors will be ≥65 years old, with up to 35% of them developing clinically significant depression. Depression is problematic for many reasons, including its potential to interfere with the ability to engage in preventive and follow-up healthcare. National Comprehensive Cancer Network guidelines strongly recommend the management of depression among cancer survivors. However, older adults are the least likely age group to utilize mental health services, and Hispanic older adults are even less likely, despite being at higher risk for depression. Older adult cancer survivors (OACs; ≥65, post-cancer treatment) also have unique challenges relative to their peers without cancer (e.g., fatigue, cognitive changes, mobility issues, pain, social distancing and isolation). These issues often create additional barriers to benefitting from existing evidence-based depression treatment, which is ineffective for many OACs. Brief Behavioral Activation (BBA) is an evidence-based psychotherapy for healthy adults that has a strong theoretical rationale for use with OACs and the potential to overcome the limitations of conventional psychotherapies in this age group. It is adaptable for a range of functional statuses, and thus may be especially helpful for OACs given their typically faster rate of functional decline. Moreover, in OACs, BBA has the potential to promote cancer survivorship self-efficacy and improve health behaviors. We developed a BBA manual for OACs (BBA-OACs) with cancer-specific psychoeducation and modified worksheets with a focus on cancer survivorship, self-efficacy, and American Cancer Society (ACS)-recommended preventive health behaviors (i.e., healthy weight, exercise, healthy eating, avoiding alcohol and tobacco). In a fully remote (i.e., recruitment, intervention, and assessment) pilot RCT of telehealth BBA-OACs (N=81) we demonstrated its excellent feasibility, acceptability, and initial superiority to an active control, Supportive Psychotherapy, for improving OACs’ depression, anxiety, and coping. While this demonstrates the promise of BBA-OACs for reducing depression in this medically vulnerable group, we need to ensure its efficacy in a fully powered trial with a diverse sample that will have the ability to identify mediators and moderators of change. For this NIH Stage II RCT of telehealth BBA-OACs (N=502) with 4-month follow-up, we will partner with Cancer Support Community to recruit a diverse nationwide sample of English- and Spanish-speaking OACs with three aims: 1) Determine the efficacy of BBA-OACs for improving depressive symptoms; 2) Determine the efficacy of BBA- OACs for improving anxiety, loneliness, coping, and cancer-related health behaviors; 3) Determine the extent to which behavioral activation, general self-efficacy, and cancer-survivorship self-efficacy mediate the relationship between BBA-OACs and depressive symptoms. By expanding viable, evidence-based telehealth treatment options for depression, these results will ultimately improve the quality of life and cancer survivorship trajectories of OACs.

NIH Research Projects · FY 2026 · 2026-05

Project Summary Cell death plays important roles in normal biology and disease. Among various modalities of cell death, ferroptosis is a form of cell death driven by iron-dependent (thus the name) phospholipid peroxidation. Mounting evidence indicates that ferroptosis is highly relevant to cancer and contributes to the anticancer function of multiple tumor suppressors. Interestingly, altered metabolism, while providing growth advantage, often makes cancer cells more sensitive to ferroptosis. Further, we and others discovered that various signal transduction pathways impact ferroptosis through their role in modulating cellular metabolism. As these signaling pathways are frequently mutated in human cancer, these studies have provided strong evidence supporting that ferroptosis induction, either as a single-agent therapy or in combination with other regimens, might be an effective therapeutic approach for the treatment of cancers harboring specific oncogenic mutations. Hypoxia exerts profound effect on both normal biology and cancer via altering, among others, cellular redox and metabolic status. The oxidative and metabolic nature of ferroptosis prompted us to investigate how hypoxia might regulate ferroptosis. Our preliminary study revealed that prolonged hypoxia inhibits ferroptosis almost completely, and intriguingly, this effect is independent of the canonical oxygen-sensing mechanism mediated by prolyl hydroxylases (PHDs), the von Hippel–Lindau protein (VHL), and hypoxia inducing factors (HIFs). Instead, we found that histone demethylase KDM6A, which is a tumor suppressor frequently mutated in various cancers and which requires oxygen for its enzymatic activity, plays a central role in mediating the regulation of ferroptosis by hypoxia, i.e., KDM6A can function as a direct oxygen sensor for ferroptosis regulation. As sustained tumor hypoxia and loss-of-function mutation of KDM6A often exacerbate malignancy, we hypothesize that ferroptosis resistance is a contributor to the enhanced malignancy of KDM6A-defective cancer. In this proposal, we will investigate this central hypothesis by determining the mechanisms by which prolonged hypoxia and KDM6A regulate ferroptosis and the implication of the learned mechanisms in cancer progression and therapy. The innovative research proposed in this application will lead to important basic understanding of oxygen sensing and ferroptosis in cancer and shed light on novel strategy and biomarker identification for ferroptosis induction-based cancer therapy.

NIH Research Projects · FY 2026 · 2026-05

ABSTRACT Advances in cell therapies have drastically changed treatment algorithms for hematologic malignancies, broadening curative approaches from the previously singular option of allogeneic hematopoietic cell transplantation to now include the highly effective chimeric antigen receptor (CAR) T cell therapies. Despite the promise of CAR T cell therapies, which harness the patient’s own T cell compartment upon the direction of a transduced antigen-specific receptor, they are still accompanied by significant morbidity. Referred to as “cytokine release syndrome” (CRS) due to rapid increases in multiple cytokines, including IL-6, IFN-γ, IL-2, and TNF, the disordered inflammatory response accompanying CAR T-cell therapies manifests clinically as fever, hypotension, hypoxia, and dyspnea. Overall occurrence of CRS is 93% following CAR T-cell administration (23% severe, with potential for fatal outcome), resulting in use of costly antibody therapeutics and intensive monitoring and translating to a financial burden on the healthcare system. Despite its frequency, CRS lacks a widely accepted definition, a clear molecular mechanism, and reliable markers predictive of its occurrence. Most critically, it is known that the CAR itself is not sufficient to elicit CRS. Our central hypothesis is that the origins of CRS are both effector cell- and environment-intrinsic: critical differences between the CAR effector lymphocytes are what elicit CRS from myeloid cells that have become susceptible in certain patients and that absence of either the stimulus or the response mitigates the initiation and propagation of CRS. Natural killer (NK) cells endowed with the same CAR as T cells do not elicit CRS, despite being capable of achieving complete tumor remission. This crucial difference between the two effector lymphocytes is further highlighted by our own findings that NK-like T cells (TKLR), a lymphocyte population demonstrating features of each, also fail to cause CRS in a mouse model for CAR therapy despite robust anti-tumor efficacy. The overlapping spectrum of these three populations with different CRS outcomes permits a more focused dissection in Aim 1 of the features initiating, propagating or suppressing CRS, including differences in response kinetics. Using in vitro models, we will test combinations of cellular components for their ability to elicit cytokine production and transcriptional changes leading to CRS. CRS-associated cytokine and molecular candidates will then be validated in a murine xenograft CRS model. In addition, the toxicity profile of CAR T cell therapy ranges from no CRS to severe CRS, even when treating the same disease with the same CAR T product. Thus, patient-specific factors, particularly the myeloid cell population critical for the pathological feedback loop of CRS, will be analyzed. In Aim 2, we will identify the pre-treatment risk signatures (phenotypic functional, and transcriptional) in the myeloid cell population in matched CAR T recipients who did and did not develop CRS. This comprehensive profiling will reveal novel points of intervention and prevention for CRS and ultimately lead CAR therapies to greater safety.

NIH Research Projects · FY 2026 · 2026-05

ABSTRACT The importance of tumor microenvironment (TME) in regulating cancer progression and influencing therapeutic outcome is widely appreciated. Recent developments in multiplexed tissue imaging technology offer powerful platforms for dissecting the spatial biology of TME by enabling the simultaneous detection of multiple markers of interest on a single tissue slide. In this study, we will perform whole-slide multiplex immunofluorescence (mIF) tissue imaging analysis of 450 InterMEL Stage II/III primary invasive melanomas focusing on markers staining the immune cells and tumor vasculature. InterMEL is a case-control study that retrospectively enrolled pathological AJCC8 stage IIA-IIID cutaneous primary melanoma patients from 15 hospitals or treatment centers in the USA, Australia, and Spain. Cases were patients who had died of melanoma within 5 years of diagnosis; controls were patients who had survived for at least 5 years without evidence of melanoma recurrence. The outcome of the study will advance the field in several ways including a large mIF image data repository generated in primary melanoma; innovative computational methods and tools for spatial immuno-phenotyping and for identifying spatial TME signatures to distinguish aggressive versus indolent disease.

NIH Research Projects · FY 2026 · 2026-05

PROJECT SUMMARY Gastric cancer is the 5th most common cause of death worldwide with an incidence that is rising, particularly among adults younger than 40, underscoring the need to identify targetable drivers of gastric cancer development and progression. Chronic inflammation, due either to infectious or autoimmune etiologies, is amongst the strongest risk factors for the development of gastric cancer. Yet, despite high levels of inflammation, gastric cancers are marked by poor levels of T-cell surveillance. As such, most gastric tumors exhibit minimal or no response to immune checkpoint blockade. How persistent innate inflammation suppresses T-cell immunity in gastric cancer remains poorly understood. Our individual research groups have extensive experience in single cell genomics, cancer evolution, T-cell biology, and clinical outcomes in gastric cancer. We previously found that T-cell infiltration and differentiation within gastric tumors was significantly influenced by the relative success with which T-cells are primed in gastric tumor-draining lymph nodes. In exciting preliminary data, we profiled paired tumors and tumor-draining lymph nodes from patients with both early and advanced stage gastric cancer and found that chronic inflammation significant alters T-cell priming within tumor draining lymph nodes, through effects on both antigen presentation and stabilization of the quiescence-associated transcription factor KLF-2 in primed T-cells. Our findings raise the possibility that chronic inflammation promotes gastric tumorigenesis by inducing KLF-2- dependent T-cell sequestration and quiescence in tumor-draining lymph nodes. The goal of this project is to determine how chronic inflammation-dependent KLF-2 induction suppresses anti-tumor immunity in gastric cancer. We hypothesize that KLF-2 is preferentially induced in lymph node-resident T-cells from gastric cancers with high levels of innate inflammation, and this limits cytotoxic T-cell differentiation and tissue infiltration. To test this hypothesis, we will determine which gastric cancer-driven inflammatory factors drive KLF-2 expression in T-cells (Aim 1), define how KLF-2 stabilization alters T-cell differentiation and tissue residence in gastric cancer (Aim 2), and determine whether manipulating KLF-2 expression, either directly or by targeting myeloid inflammation, can restore anti-tumor immunity in gastric cancer (Aim 3). If successful, the proposed experiments will reveal the mechanism by which chronic inflammation leads to T-cell suppression during gastric tumorigenesis and nominate rational strategies to enhance anti-tumor immunity and response to immune checkpoint blockade in this increasingly prevalent malignancy.

NIH Research Projects · FY 2026 · 2026-05

Abstract Upon spinal cord injury, axons attempting to regenerate need to overcome the repulsive actions of myelin- associated inhibitors, including the myelin-associated glycoprotein, Nogo-A, and the oligodendrocyte myelin glycoprotein. These inhibitors bind and signal through a neuronal receptor/co-receptor/transducer complex comprised of NgR1, Lingo-1 and p75. Consequently, p75 is cleaved by alpha-secretase followed by gamma- secretase, triggering downstream signaling that inhibits axonal regrowth. ADAM10 and ADAM17 are both known to function as alpha secretases in neurons. We previously documented that the ganglioside GT1b mediates the assembly of neuronal receptor/co-receptor/transducer complex (NgR1/Lingo-1/p75) and this complex gains the ability to bind to the myelin ligands MAG or Nogo-A (a 5-component neuron-myelin signaling complex). Our preliminary studies also highlighted that that ADAM17, and not ADAM10, is the alpha secretase that recognizes and cleaves p75 when it is a part of a 5-component neuron-myelin signaling complex comprising of NgR1, Lingo- 1, p75, GT1b and a myelin inhibitor. Using a panel of anti-ADAM17 monoclonal antibodies (mAbs) generated in our laboratory, we were able to abrogate the cleavage of p75 in a neuroblastoma-glioma cell line (NG108-15) and to reverse the neurite outgrowth inhibition by the myelin-associated inhibitor MAG. Our studies, however, raise new questions that warrant further investigation. The molecular details of the interactions of the three myelin-based ligands with the neuronal receptor/co-receptor (NgR1/Lingo-1) complex and the specific role of p75 in mediating/stabilizing these interactions, resulting in the initiation downstream signaling, are still elusive. Likewise, the role of the three different myelin-based ligands in the activation of the alpha secretase ADAM17 and in stabilizing the ADAM17 interactions with the 5-component neuron-myelin signaling complex, ensuing regulated intramembrane proteolysis of p75, need to be elucidated. We now propose to carry out multi- disciplinary studies, encompassing biochemical, biophysical, structural and cell biological (using different neuronal cell lines and primary cortical neurons) approaches, that will address these questions and provide new mechanistic understanding of the neuron-myelin interactions and signaling upon spinal cord injury. Our studies will not only provide the first high-resolution structures of neuron-myelin signaling complexes but will also explore a new approach to promote neuronal regenerations via the use of novel, therapeutic alpha secretase-targeting monoclonal antibodies that reverse the myelin-induced neurite outgrowth inhibition.

NIH Research Projects · FY 2026 · 2026-04

Project Summary Metabolites profoundly influence cellular behavior by initiating signaling cascades and altering transcriptional programming. They can also directly react with and covalently modify cellular macromolecules, primarily proteins. These adducts, termed non-enzymatic covalent modifications (NECMs), alter protein structure and function and are linked to aging as well as an array of pathologies, including cancer, diabetes, and neurodegeneration. Due to their long half-lives and accessible tails rich in nucleophilic amino acids, histones are particularly prone to accumulating NECMs, which significantly impact chromatin structure and function. Although the landscape and function of enzymatically installed post-translational modifications (PTMs) are well understood, the study of NECMs has been limited by challenges in detection and manipulation. Our research has been at the forefront of discovering and characterizing the role of chromatin NECMs in cell fate, focusing on glycation through methylglyoxal (MGO), a reactive byproduct of glycolysis, which is upregulated under certain cell conditions. We have developed novel chemical probes and analytical tools to enhance the detection and study the biological roles of histone glycation in physiologically relevant models. We show significant endogenous glycation of histones in metabolically hyperactive cells, altering chromatin architecture and influencing gene expression. Importantly, we have identified several enzymatic mechanisms that regulate histone glycation and help maintain chromatin integrity, which are often misregulated in diseases. Despite these advancements, considerable gaps remain in our understanding of the specific sites where glycation accumulate on histones, their distribution within chromatin, the direct impact of glycation on transcription, the dynamics of these modifications, and the precise regulatory mechanisms they affect regarding cell fate and physiology. The inherent challenge of mimicking long-term exposure and tracking complex chemical adducts of glycation remains a significant obstacle. Moving forward, our research aims to deepen our understanding of the effects of histone glycation on transcriptional regulation and cell fate by developing tools targeting specific glycation mark and employing physiologically relevant models. Our integrated approach, combining chemical and cellular biology with cutting-edge high-throughput sequencing, aims to comprehensively address these complex biochemical phenomena. This work not only opens new avenues in epigenetic research but also establishes a detailed molecular mechanism linking a new class of metabolism-driven histone modifications and transcription regulation, thus providing essential insights into a fundamental biological problem and opening the door to new therapeutic avenues.

NIH Research Projects · FY 2026 · 2026-04

PROJECT SUMMARY Natural killer (NK) cells have been shown to play a dominant role in the immune-mediated control of viral infection in both humans and mice. Individuals lacking NK cells or NK cell function succumb to fatal viral infections, such as human cytomegalovirus (HCMV). Similarly neonatal mice, which lack mature peripheral NK cells, and adult mice with NK cell deficiencies are extremely susceptible to murine cytomegalovirus (MCMV) infection. Given the clinical significance of HCMV, MCMV infection in mice represents an appropriate model to study NK cell-mediated antiviral immunity. While NK cells are members of the innate immune system, it is now appreciated that NK cells share many characteristics with CD8+ T cells and can exhibit features of adaptive immunity. Although our understanding of the innate and adaptive features of NK cells has increased in the past decade, the molecular and dynamic genomic organization which underlies their development and optimal antiviral response remains unclear. Given the shared characteristics between NK cells and CD8+ T cells and that Arid1a chromatin remodeling in CD8+ T cells is instrumental for antigen-specific proliferation and mediating responses against pathogens, I postulate that Arid1a plays an essential role in NK cell development and antiviral function. However, the role of Arid1a signaling in NK cells is largely unexplored. Thus, this proposal seeks to explore 1) how Arid1a chromatin remodeling is mediated in NK cells for proper NK cell identity, 2) how Arid1a modulates dynamic chromatin organization in NK cells to sustain host antiviral defense. While profiling developing and mature NK cell subsets, I found that Arid1a is highly expressed. To investigate the role of Arid1a in NK cells, I generated a novel transgenic mouse containing NK cell-specific deletion of Arid1a. In preliminary data, one copy loss of Arid1a had diminished NK cell antigen-specific proliferation to MCMV. In Specific Aim 1 I will uncover the role of Arid1a in NK cell development. In Specific Aim 2 I will investigate the molecular mechanism of Arid1a signaling in NK cell antiviral responses. At the completion of this F31 we will gain key insights into the complex molecular networks that are induced by Arid1a. The mechanistic insights derived from this study will be instrumental in the development of novel therapies that enhance NK cell function and influence strategies aimed at improving antiviral therapies.

NIH Research Projects · FY 2026 · 2026-04

PROJECT SUMMARY/ABSTRACT The finely tuned generation and function of regulatory T (Treg) cells are essential for maintaining the balance that allows for protective immunity while preventing harmful autoimmunity. Treg cells are heterogeneous, comprising specialized subsets that contribute to tissue repair and mediate context-specific immune responses. Despite their critical roles in essential biological processes, it remains unknown whether the subset-specific functions of Treg cells are driven by their developmental origins, transcriptional programs, or a combination of both. This unresolved challenge largely stems from two issues: the lack of unbiased means to identify mutually exclusive Treg cell subsets with distinct functions, and the absence of tools to trace their ontogeny. However, my recent discoveries have opened promising avenues for overcoming these obstacles. Using colorectal cancer models and human patient specimens, I identified that interleukin-10 (Il10) expression distinguishes two subsets of Treg cells with opposing functions: IL-10+ Treg cells, which exhibit anti-tumor properties, and IL-10– Treg cells, which promote tumor growth. Furthermore, I identified Dapl1 as a gene uniquely expressed by naïve CD4 T cells, thereby providing a definitive marker for extrathymically generated Treg cells. The overarching goal of this research proposal is to determine whether the developmental origins of IL-10– vs IL-10+ Treg cells contribute to their distinct functions, and to identify the transcriptional programs underlying these differences. This proposal tests the hypothesis that both of these subsets are of mixed developmental origins, with their distinct functions driven by differentially expressed transcription factors. Specifically, in Aim 1, using a novel Dapl1-based lineage tracing model, I will determine whether IL-10+ and IL-10– Treg cells arise from thymic or extrathymic (peripheral) origins and elucidate how these developmental pathways shape their functions. Additionally, in Aim 2, I will define the transcriptional programs that drive their subset-specific activities, by inducing Treg cell specific deletion of key regulators such as Zeb2 and Nfil3. By employing genetic mouse models, advanced single-cell analyses, and CRISPR-based screening, the proposed studies will reveal the nature of Treg cell functional heterogeneity, ultimately guiding the development of more precise immunotherapeutic strategies with major implications for public health. The proposed career development plan complements my training in cellular and molecular immunology with single-cell analysis and computational biology. I will take advantage of the extensive resources of the Memorial Sloan Kettering Cancer Center, part of the Tri-Institutional network with the Rockefeller University and Weill Cornell, as well as benefit from the mentorship of Dr. Alexander Rudensky and guidance from Advisory Committee members Dr. Christina Leslie, Dr. Ming Li, and Dr. Steven Josefowicz. By the end of the mentored phase, I will have acquired the necessary tools to conduct comprehensive studies at the intersection of immune cell heterogeneity and immune communication with the environment as an independent investigator.

NIH Research Projects · FY 2026 · 2026-04

ABSTRACT The management of metastatic biliary tract cancer (BTC) has been transformed over the past 5 years, with FDA approval of anti-PD-1/PD-L1 antibodies and several molecularly targeted therapies. Despite these advances, most patients with metastatic BTC still die from their disease. The HER2 receptor tyrosine kinase (encoded by the ERBB2 gene) is implicated in the pathogenesis of several cancer types, and drugs that target HER2 have an established role in the management of breast, lung, colorectal, and esophagogastric cancers. While ERBB2 amplification and/or mutations are present in up to 30% of metastatic BTCs, older HER2-targeted antibodies and kinase inhibitors had only modest clinical activity in patients with BTCs. Unprecedented clinical activity was recently demonstrated with a new generation of HER2-targeted therapies in breast and lung cancers resistant to older HER2-targeted therapies, including HER2-low breast cancer and ERBB2-mutated lung cancer. The current proposal is based on 1) durable responses to next-generation HER2-directed therapies in a subset of patients with HER2-expressing BTC; 2) preliminary data indicating frequent mutational discordance of ERBB2 and heterogeneity of HER2 expression in paired primary and metastatic tumors collected from individual patients with BTCs; and 3) loss of ERBB2 expression at progression on HER2 targeted therapies in paired samples from patients with BTCs. Based on these preliminary data, we hypothesize that pre-existing HER2 expression heterogeneity will be a common mechanism of resistance to a novel HER2-targeted bispecific antibody in BTC and that molecular imaging can identify patients with biliary tract tumors most likely to achieve durable responses. To test this hypothesis, we will leverage a largest-of-its-kind prospective molecular characterization effort and a novel molecular imaging platform (89Zr-ss-pertuzumab PET) to define the prevalence of HER2 expression heterogeneity in BTC, its association with ERBB2 mutational status, and its impact on HER2-targeted bispecific antibody therapy response. We will accomplish these translational objectives through three broad approaches: 1) We will perform molecular analyses of paired primary and metastatic tumors collected from patients with BTC; 2) We will explore the extent of lesion-to-lesion HER2 heterogeneity in metastatic BTC using a bespoke HER2 PET imaging platform (89Zr-ss-pertuzumab PET); and 3) We will use 89Zr-ss-pertuzumab PET and tumors collected before treatment and at the time of disease progression on HER2-targeted bispecific antibody therapy to study the impact of HER2 genomic and expression heterogeneity on depth of response to this novel drug class. Mechanisms of HER2-targeted therapy resistance will be functionally explored using patient-derived BTC organoid and xenograft models. Given the promising clinical activity of novel HER2-directed therapies in patients with BTC, we predict that the studies proposed will directly influence the design of future clinical trials of HER2- targeted therapies and establish the clinical utility of HER2 PET as a predictive biomarker of response in patients.

NIH Research Projects · FY 2026 · 2026-04

PROJECT SUMMARY Locally advanced rectal cancer (LARC) is commonly treated with total neoadjuvant therapy (TNT), which consists of radiation therapy (RT), chemotherapy, and either total mesorectal excision (TME) or watch-and-wait based on tumor response. Most tumors treated with TNT show a spectrum of response ranging from minimal regression to complete tumor eradication, and some patients (~20%) with a clinical complete response (cCR) after TNT develop local tumor regrowth that may compromise their survival. Only ~50% of patients are able to forgo total mesorectal excision and achieve organ preservation. In addition, ~15% of patients develop distant metastatic recurrence, which is ultimately lethal. Given this data, there is an unmet need to understand mechanisms of resistance to TNT and local and distant metastatic tumor regeneration after therapy, and to develop strategies to improve local and distant disease control. Using genomic and transcriptomic analysis of pre-treatment LARC, mechanistic studies in patient-derived organoid and novel mouse models of LARC, and single cell transcriptomic analysis of metastatic colorectal cancer, we have identified that resistance to TNT and metastatic relapse are driven by a population of tumor regenerative cells (TRCs) that ectopically express the neuronal cell adhesion molecule L1CAM. L1CAM+ cells pre-existing in untreated rectal tumors are selected for during therapy, while L1CAM- cells can also dynamically enter into L1CAM+ TRC states through phenotypic plasticity. We have developed novel L1CAM targeting antibody drug conjugates (ADCs), and will test them in highly clinically relevant patient-derived organoid and organoid-derived orthotopic intraluminal rectal xenograft mouse models. The elimination of quiescence-capable tumor regenerative cells with an L1CAM targeting ADCs is expected to be complementary to chemotherapy and therapies that target rapidly proliferating cells. This represents a novel concept in cancer therapeutics that addresses the plasticity of cancer driving tumor relapse after therapy. We propose: (1) to interrogate the dynamics of clonal selection and phenotypic adaptation that govern entry into the L1CAM+ TRC state in rectal cancer. (2) Using novel L1CAM-targeting antibody drug conjugates (ADCs) that we have generated, we will determine the actionability of therapeutically targeting L1CAM+ TRCs before, during or after TNT to improve clinical outcomes. Together, these studies will inform the design of first- in human clinical trials to target tumor phenotypic plasticity using L1CAM-targeting ADCs, and define the optimal timing of targeting L1CAM+ TRCs during TNT for LARC. Through this work, our impact goals are two-fold: i) decrease the incidence of distant metastatic recurrence, and ii) increase organ preservation to maximize quality of life in patients with LARC.

NIH Research Projects · FY 2026 · 2026-04

PROJECT SUMMARY/ABSTRACT - There are no changes. Immunotherapy induces durable remissions in a subset of patients with highly mutated cancers. However, most cancers are modestly mutated and fail to respond to current immunotherapy treatments. This is especially true for malignancies caused by activating mutations in phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA), the most commonly mutated driver oncogene in humans. Mutant PIK3CA cancers exhibit resistance to conventional treatments, including chemotherapy, hormonal therapy, and antibodies. Innovative new approaches that bring the curative potential of immunotherapy to PIK3CA mutated cancers are therefore urgently needed. We and others previously performed detailed immune monitoring studies of exceptional patient responders to resolve the mechanisms of successful immunotherapy. These analyses revealed that T cells from responders often recognize neoantigens (NeoAgs) - peptides derived from the protein products of somatic mutations presented by a patient’s unique complement of human leukocyte antigen (HLA) molecules. In >99% of cases, NeoAgs are exclusive to an individual patient because they result from passenger mutations that do not contribute to cancer cell fitness and therefore are subject to clonal heterogeneity. NeoAg clonal heterogeneity has emerged as a major cause of immunotherapy resistance. We hypothesize that clonally expressed NeoAgs derived from hotspot mutations in mutant PIK3CA can be immunogenic and are amenable to therapeutic targeting using T cell receptors (TCRs). In support of our hypothesis, we discovered through a mass spectrometry (MS) screen that a shared NeoAg derived from mutant PIK3CA is naturally processed and presented in the context of a prevalent HLA allele. We have termed this unique subset of antigens “public” NeoAgs because they are cancer-specific yet expressed by groups of patients, enabling the use of off-the-shelf reagents. Using a novel TCR discovery platform, we successfully generated multiple T cell clones specific for this PIK3CA public NeoAg, retrieved their unique TCR gene sequences, and exogenously transferred public NeoAg reactivity to non-specific T cells. These results confirm the immunogenicity of MS-identified public NeoAgs and enable the development of TCR-based gene therapies. Building on these preliminary data, we propose in Aim 1 to develop a novel therapeutic approach for cancers expressing a PIK3CA public NeoAg using TCR gene transfer and adoptive immunotherapy. In Aim 2, we will establish in cancer patients the frequency, immune-compartmentalization, and potential pathways of resistance to T cells specific for a PIK3CA public NeoAg. In Aim 3, we will resolve the physical basis for PIK3CA public NeoAg immunogenicity by studying the physical and structural properties of public NeoAg/HLA molecules, their wild type counterparts, and the complexes they form with TCRs. Together, this work will elucidate the fundamental principles governing NeoAg immunogenicity in humans, enabling innovative new precision immune-genomic approaches for common epithelial cancers currently lacking curative treatments.

NIH Research Projects · FY 2026 · 2026-03

SUMMARY/ABSTRACT Gut-borne bloodstream infections are a significant cause of morbidity and mortality in immunocompromised patients, often leading to sepsis and poor clinical outcomes. Despite their severity, current clinical approaches rely on reactive antibiotic treatments, which fail to address the root cause—disruptions in the gut microbiome that allow opportunistic pathogens to expand and enter the bloodstream. This project will develop a proactive, microbiome-based strategy that leverages machine learning and ecological modeling to predict, prevent, and mitigate these infections before they occur. Our collaborative team has pioneered mathematical modeling and microbiome research, integrating longitudinal clinical data, ecological theory, and experimental validation to uncover the dynamics of microbiome resilience and infection risk. We have assembled a large clinical microbiome datasets, spanning over 1,000 immunocompromised patients, demonstrated that gut microbiome disruptions predict bloodstream infection risk, and conducted trials to restore microbiome composition for improving clinical outcomes. This application will translate these insights into actionable clinical tools by leveraging our expertise and data infrastructure. We will develop computational models to (1) forecast infection risk based on microbiome dynamics, (2) optimize antibiotic stewardship to minimize collateral damage to beneficial gut bacteria, and (3) design precision probiotics to restore microbiome defenses. This integrative approach combines large-scale clinical data analysis, computational modeling, and experimental validation using both in vitro and in vivo models to advance our mechanistic understanding of gut microbiome ecology and the molecular processes involved in protection against gut-borne pathogens. This work envisions a future where computational microbiome management becomes a standard tool for preventing gut-borne infections. By shifting the paradigm from reactive to proactive care, our approach can transform infection control, reduce the global burden of antibiotic resistance, and improve outcomes for immunocompromised patients.

NIH Research Projects · FY 2026 · 2026-02

PROJECT SUMMARY Establishing and maintaining immune tolerance to self-antigens is vital to prevent destructive autoimmune inflammation. Within the thymus, Aire plays a critical role in establishing self-tolerance, acting within medullary thymic epithelial cells (mTECs) to promote ectopic expression of tissue-restricted antigens which in turn leads to deletion of self-reactive T cells and generation of regulatory T (Treg) cells. However, a significant proportion of self-reactive T cells escape deletion in the thymus. A central unresolved question is how these self-reactive T cells are restrained within the periphery. To this end, we recently uncovered a novel lineage of antigen- presenting cells, named Thetis cells (TC), comprising four distinct subsets (TC I-IV). Our work thus far has demonstrated an essential role for TCs in extra-thymic Treg generation and tolerance to commensal and dietary antigens within the intestine. These studies established the tolerogenic potential of TCs. Whether and how TCs also regulate peripheral tolerance to self-antigens remain open questions. In a remarkable parallel, we found that TC I and Aire+ mTECs share a core transcriptional program that includes Aire and are critically dependent on the same transcription factors. These findings raise the tantalizing possibility that Aire+ TCs and Aire+ mTECs have shared immune regulatory functions. We hypothesize that Aire+ TCs restrain self-reactive T cells within the periphery through the expression of tissue-restricted self-antigens and immune-regulatory molecules. In the proposed project, we will determine i) the role of Aire+ TCs and extra-thymic Aire in peripheral immune tolerance, and ii) the molecular mechanisms by which Aire+ TCs mediate immune tolerance. Our preliminary data has established symmetry between Aire+ mTECs and Aire+ TCs and demonstrated the power of parallel analyses of these two cell types. In each aim, we will use novel genetic models and advanced computational approaches to address the Aire-dependent and independent functions of mTECs and TCs. In Aim 1 we will determine the role of Aire+ TC I in peripheral self-tolerance during steady- state and upon inflammation. In aims 2 and 3, we will address the mechanisms by which Aire+ TC I and mTECs regulate T cell tolerance, testing two non-mutually exclusive scenarios: expression of a ‘tolerogenic’ program that endows both Aire+ mTECs and TC I with the ability to induce T cell tolerance upon antigen presentation (Aim 2), and Aire-dependent regulation of tissue-restricted self-antigen expression (Aim 3). We anticipate that these studies will reveal fundamental mechanisms of immune tolerance and establish a new framework for self-tolerance. Elucidation of the role of TCs in peripheral immune tolerance will pave the way towards therapeutic manipulation of TCs with relevance to a broad range of autoimmune and inflammatory diseases.

NIH Research Projects · FY 2026 · 2026-01

PROJECT SUMMARY Chalkophore mediated respiratory oxidase flexibility and M. tuberculosis virulence Diisonitrile lipopeptides are a novel class of copper-chelating natural products that are biosynthesized by non- ribosomal peptide synthetases found in a variety of Actinobacteria, including Mycobacterium tuberculosis, the bacteria that cause tuberculosis. In multiple studies, genetic disruption of the M. tuberculosis diisonitrile biosynthetic gene cluster attenuates bacterial virulence in mouse models of tuberculosis. This copper-binding activity identifies the diisonitriles as `chalkophores', which are structurally distinct from the well-known methanobactin chalkophores in methanotrophs. Further, we have shown that M. tuberculosis mutants in which chalkophore biosynthesis is disrupted are defective for growth in low-copper or copper-chelated media, and that this defect can be rescued by treatment with exogenous, synthetic diisonitriles, consistent with a role for diisonitriles in copper uptake. We have also shown that the diisonitrile chalkophore system is required to maintain the function of the copper-containing respiratory oxidase in low-copper culture and in mouse infection, establishing a specific physiologic target for diisonitrile chalkophore function and defining chalkophore mediated respiratory oxidase flexibility as an important virulence determine of M. tuberculosis. Further, the host immune pressure that targets M. tuberculosis respiration is independent of adaptive immunity. Building upon this work, in this proposal we will discover and characterize components of the chalkophore biosynthetic and handling systems using genetic, chemical biologic, and proteomic approaches. We will define the metal responsive transcriptional switch that controls respiratory oxidase flexibility and define the host pathways that target Mtb respiration during infection. This project will be carried out through a multidisciplinary collaboration led by Michael Glickman and Derek Tan comprising combined expertise in organic synthesis, organometallic chemistry, chemical biology, molecular biology, proteomics and microbial pathogenesis. Our long-term goals are to elucidate the roles of chalkophore mediated respiratory oxidase flexibility in M. tuberculosis pathogenesis and to understand the host factors that target the metal centers of the bacterial respiratory chain.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY The overarching goal of this proposal is to transform Perturb-seq into a platform for rationally engineering cellular transcriptional states. We are motivated by ongoing cell atlas projects, which have revealed remarkable diversity in the form of hundreds of distinct cell types, but also highlighted that even greater heterogeneity exists at the level of transcriptional states within tissues and across disease contexts. However, these observational studies leave open the questions of how these diverse transcriptional states are established and whether they confer specific functional properties. Answering these questions in vivo is labor-intensive due to the rarity and number of states. To address this gap, we pursue a complementary approach, developing a combination of experimental and computational tools that extend Perturb-seq to enable systematic reconstruction of these states in vitro using combinatorial genetic perturbations. We will focus on fibroblasts, a cell type with extensive transcriptional heterogeneity linked to their diverse roles in tissue homeostasis, wound healing, and disease. Our preliminary data from CRISPRa Perturb-seq screens identified perturbations that induced physiological levels of relevant transcription factors and that elicited gene programs resembling in vivo fibroblast states, supporting the feasibility of our method. We will develop three complementary approaches to transform Perturb-seq into a tool for engineering cell states: Aim 1 will establish an iterative selection strategy suitable for reconstructing states when a cell surface marker is known. We apply it to realizing an interesting "universal" fibroblast state in vitro using ordered combinations of CRISPRi/a perturbations. Aim 2 will develop and apply multiomic Perturb-seq to test the hypothesis that perturbation-induced chromatin remodeling can predict synergistic gene combinations genome-wide, yielding a biologically grounded approach for choosing which combinations of perturbations to prioritize. Aim 3 will produce INNsight, an invertible neural network that learns the manifold of reachable fibroblast transcriptional states, removes technical confounders, and enables rational experiment design from Perturb-seq data. The innovation of our approach lies in the use of CRISPRa to perform nuanced perturbations, our development of novel technological extensions of Perturb-seq, our focus on developing principles for efficient, biased exploration of possible combinatorial perturbations, and the development of INNsight, a model that can provably disentangle independent sources of transcriptional variation. The project is significant because it will (1) enable in vitro models of in vivo transcriptional states, facilitating the study of their regulation and functional properties; (2) enhance our understanding of the transcriptional heterogeneity of fibroblasts, a major current area of research in cancer and autoimmune disease; and (3) establish principles for the rational engineering of transcriptional state in differentiated cell types that are directly relevant to engineering cell therapies.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY Malignant lymphomas are a leading cause of cancer death ranking 6th among malignancies resulting in mortality. Among these, mature T-cell lymphomas often exhibit an aggressive clinical course and their pathogenesis is poorly understood. ALK-negative anaplastic large cell lymphoma (ALK-negative ALCL) represents a poorly understood category of mature T-cell lymphomas. Unlike other hematopoietic malignancies, recurrent genetic alterations that have been exploited as rational therapeutic targets have not been described in these tumors. We discovered for the first time, recurrent translocations targeting the intracellular tyrosine kinase TYK2 in ALK- negative ALCL. In this regard, we identified a gene fusion juxtaposing the nucleophosmin (NPM1) gene (5q35) to the TYK2 gene (19p13). NPM1 is a nucleolar phosphoprotein involved in several oncogenic gene fusions and mutations in cancers. Notably, TYK2 was the first member of the Janus activating kinase (JAK) family described and propagates physiologic cytokine-driven signals and is critical for T-cell proliferation and differentiation. The signaling networks by which the NPM1::TYK2 fusion promotes lymphomagenesis are unknown. Based on our preliminary data, it is our central hypothesis that NPM1::TYK2 is an oncogenic driver that promotes the development of TCL, and that the kinase activity of NPM1::TYK2 is required for its oncogenicity. Our preliminary results demonstrate that expression of the recurrent NPM1::TYK2 fusion in conditional transgenic mice induces lymphomas that recapitulate the morphologic and genetic features of TCL, specifically ALCL. Thus, the main goal of this proposal is to investigate the in vivo oncogenicity of NPM1::TYK2 and the pathways of NPM1::TYK2- induced lymphomagenesis. The overall impact of this proposal is to advance understanding of the mechanisms by which oncogenic TYK2 causes lymphoma and identify currently unknown downstream signaling modules which may serve as vulnerability targets for novel precision therapy for oncogenic TYK2-driven cancers.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY/ABSTRACT Advancements in rare cancers can rarely be done outside of the National Cancer Institute (NCI) clinical trials network. Clinical studies for rare cancers need many institutions to participate and, due to their low incidence, are unlikely to be as profitable to the pharmaceutical industry as compared to advancements in treatment for more common cancers. Anaplastic thyroid cancers and oncocytic (formerly known as Hürthle cell) thyroid cancers are two prime examples of rare tumors with minimal prior research being done. Eric Sherman, MD, led and completed the first randomized studies conducted through the NCI clinical trials network that were focused on these cancers (RTOG-0912, A091302) as well as accrued the highest number of patients to both studies. Further support will help in these endeavors as Dr. Sherman focuses on developing future studies in rare cancers of the head and neck as well as supporting the success of both these and other studies of rare head and neck cancers both in the cooperative group setting (through both the Alliance in Clinical Trials for Oncology and NRG Oncology groups) and the Cancer Therapy Evaluation Program (CTEP; as part of the CTEP Anaplastic Thyroid Cancer Task Force and the NCI Head and Neck Rare Tumor Task Force). As part of his role at Memorial Sloan Kettering Cancer Center (MSK) as the Scientific Director of the Head and Neck Oncology Service and Co-Chair of the MSK Research Council, he will play a significant role in bringing NCI-supported studies to the institution and helping with their success.

NIH Research Projects · FY 2025 · 2025-09

Project Summary Efferocytosis, the phagocytic uptake of apoptotic cells (ACs), is a critical homeostatic mechanism that regulates all metazoan tissues. These ACs, produced daily during tissue turnover, are cleared by professional phagocytes (typically tissue-resident macrophages) in a sequence that first involves the sensing of an AC, followed by the engulfment and digestion of that AC. Digestion of ACs is potentially hazardous, as the AC contains dangerous biomass that a phagocyte must handle in order to maintain cellular and tissue homeostasis. For example, in atherosclerosis, aberrant macrophage lipid digestion causes “foamy cell” build-up which prevents subsequent efferocytosis, causing plaque formation and inflammatory necrosis. In lung granulomatous and lysosomal storage diseases, macrophages feature undigested ACs. Critically, these diseases often implicate lysosome-associated proteins that are often uniquely expressed in tissue-resident macrophages. As a result, our lab has proposed that the failure to appropriately digest ACs (FAD) during efferocytosis is a main driver of pathogenesis. However, the cellular mechanisms behind FAD have not been fully characterized. To understand how FAD impacts lung homeostasis, we will target lysosome-associated proteins in alveolar macrophages implicated in pulmonary diseases (Aim 1). We will utilize our novel, highly resolved ex vivo efferocytosis assay that better-represents physiological tissue turnover to identify candidate genes that disrupt AC digestion. We will then investigate putative AC digestion genes using a medium throughput assay that allows us to rapidly generate and study the functional and physiological consequences of gene deletions in alveolar macrophages in vivo. In parallel, we will use novel fluorescence reporters to visualize organelle dynamics during efferocytosis in order to understand how FAD impacts cellular homeostasis (Aim 2). As AC- derived biomass must be shuttled through solute transport carriers to organelles such as the ER and mitochondria, we hypothesize that FAD impacts cellular homeostasis by impairing metabolite transport between organelles. As part of this aim, we will visualize contact site formation and duration between the phagolysosome (site of AC digestion) and the ER/mitochondria. To test our hypothesis, we will quantify these contact sites during healthy efferocytosis and in macrophages with digestion deficiency to assess whether FAD disrupts cellular organelle homeostasis. Collectively, these studies will probe FAD in both cellular and tissue (lung) settings. These studies will demonstrate a direct link between lysosome-associated proteins and FAD in promoting lung pathogenesis. Additionally, this work will explore the mechanisms of cellular dysfunction during aberrant AC digestion in macrophages and provide novel visualizations of subcellular organelle dynamics during real-time efferocytosis. The completion of these studies will provide tools to dissect FAD during efferocytosis and highlight the importance of AC digestion in maintaining tissue, especially lung, homeostasis.

NIH Research Projects · FY 2025 · 2025-09

Project Summary/Abstract Urothelial carcinoma (UC) involves the urothelial cells that line the bladder, kidney and ureters and is a major cause of morbidity and mortality in the US, especially in men. Bladder UC can be clinically separated into nonmuscle invasive (NMIBC) and muscle invasive (MIBC). MIBC accounts for the vast majority of metastasis and mortality, having only a ~50% cure rate. Patients with treated NMIBC are at risk of recurrence or progression to MIBC at prior or de novo sites. Over half of urothelial cancer, regardless of site of origin, harbor loss of function mutations in the histone demethylase KDM6A (UTX) and in two highly homologous histone methyltransferases KMT2C (MLL3) and KMT2D (MLL4). These proteins form the MLL3/4-COMPASS (COMplex of Proteins ASsociated with Set1)-like complex that regulate enhancer function, partly through methylation of histones at enhancers. Enhancers are regions of DNA that regulate lineage specific transcriptional programs. Recent studies have shown that patients with two urothelial carcinomas in far away sites (ureter and bladder) harbor the same COMPASS-like mutation. Further sequencing of histologically benign urothelium identify frequent mutations in the complex at expand over time. Our hypothesis is that these mutations under “field-cancerization” of the urothelium. Our lab has generated a genetically engineered mouse model with deletion of Kmt2c, Kmt2d, or the combination in the urothelium. The urothelium of these mice exhibit no histologic abnormalities. However, transcriptome analysis shows the urothelium exhibit increased stemness and functional studies show they exhibit increased organoid forming abilities. When crossed into the Pten conditional deletion mouse, there was robust cooperativity in tumorigenesis. The overall objective of this proposal is to utilize our recently generated mouse models of urothelial this COMPASS-like complex loss to mechanistically understand its role in tumor urothelial suppression. Specifically, in Aim 1, we seek to determine the stemness, clonal dynamics, oncogene and carcinogen susceptibility of urothelium harboring mutations in this COMPASS-like complex, using lineage tracing, organoid culture, and single-cell RNA-sequencing. In Aim 2, we seek to determine the functional interplay between MLL3/4-COMPASS dysfunction and oncogene activation. In Aim 3, we will seek to define how loss of Kmt2c and Kmt2d in urothelial cells affect enhancer and promoter function. Active enhancers are genomic regions of open chromatin with transcription factor binding, divergent transcription of enhancer RNA, and looping to promoters. We will study each step by global mapping of histone marks, chromatin accessibility, mRNA transcription of associated gene and looping to promoters using state-of the art epigenetics techniques.