Background. Ductal carcinoma in situ (DCIS) is a non-invasive disease of the breast. This study assessed the impact of the CDK4/6 inhibitor palbociclib on halting cell cycle progression in DCIS between diagnostic biopsy and surgical resection of the lesion. Methods. A dual-arm study was conducted involving 17 participants with DCIS who were given either 100 mg of palbociclib PO daily for twelve days or no treatment before surgery. FFPE tissues from the diagnostic biopsy and from surgical specimens were analyzed to assess changes due to treatment. Results. Palbociclib treatment significantly reduced Ki67 staining in surgical tissues. RNA-seq analysis comparing the diagnostic biopsy and surgical specimens showed significant downregulation of cellular proliferation pathways after treatment. A cellular deconvolution analysis demonstrated a non-significant trend of a treatment-induced decrease in the abundance of mature luminal epithelial cells. Conclusions. Short-term palbociclib monotherapy before surgical resection was safe and well tolerated in participants. Tissue analysis showed a significant reduction in proliferation markers and the downregulation of cell cycle progression genes within DCIS. These results support further investigation of palbociclib in patients with DCIS. Trial registration. ClinicalTrials.gov NCT03535506.

The role of glucocorticoid receptor (GR) signaling in triple-negative breast cancer (TNBC) progression remains poorly defined. Here, we describe a GR-dependent mechanism driving TNBC invasion, mediated by the presence of a subpopulation of cancer cells that express an N-terminal truncated splice isoform of the nuclear receptor coactivator AIB1. Invasion was driven through direct contact of this subpopulation with neighboring cancer cells, and suppressed by GR antagonists or depletion of GR. Crosstalk between the AIB1 isoform-expressing cells and full-length AIB1-expressing cells triggered enhanced GR activation, GR signaling, and distinct patterns of AIB1 genomic engagement. Notably, GR signaling selectively activated pathways driven by Myc in the AIB1 isoform-expressing population, and the reduction of Myc reduced invasion. These findings identify the emergence of an AIB1 isoform-expressing subpopulation as a key mechanism driving progression in TNBC and suggest sensitivity to GR-targeted therapies.

Melanoma stands as the most dangerous type of skin cancer and 5th most commonly diagnosed cancer among new cases in the United States. Even with recent advancements in immune checkpoint inhibitors (ICIs), up to ∼70% of all recipients will not experience any significant benefit in progression free or overall survival. The ability to anticipate and understand resistance to ICIs has been exceptionally difficult due to shortcomings in the preclinical models used to study melanoma’s heterogeneous pathology. A potential barrier to therapeutic efficacy is cellular senescence that exists in the melanoma tumor microenvironment (TME). Cellular senescence is induced when various pressures push a cell to exit the cell cycle, enter growth arrest, and adopt a completely new molecular, secretory, and functional phenotype to facilitate the necessary repairs. In the acute setting, reversible cellular senescence can recruit immune cells that facilitate the necessary tissue repair and prevent tumor growth. However chronic exposure to pro-inflammatory factors secreted by senescent cells such as cytokines and proteases can be overwhelmingly negative through the promotion of tumorigenesis and therapeutic resistance. The intersection of these pro-tumorigenic mechanisms in melanoma has underscored the importance of using a comprehensive in vivo model system that incorporates stromal senescence into an immunocompetent murine model and relevant human mutational burdens that recapitulates patient profiles. To address this, our lab uses the Yale University Melanoma Model (YUMM) cell line that is syngeneic to INK-ATTAC mice that contain a cassette that regulates stromal senescence. This allows for the exploration of the immune response that patients experience after receiving ICI treatment in concert with senescent stromal cell burdens in the tumor microenvironment (TME). Mice bearing single cell clone YUMM tumors are treated with combination immune checkpoint inhibitors (aPD-1+aCTLA-4) to generate both responder and non-responder phenotypes. When senescent cells are cleared from the TME, the non-responder clone tumor is re-sensitized to immune checkpoint inhibition and significantly reduces the tumor size. Immunohistochemical analyses of the local TME shows a significant recovery of immune infiltration upon stromal senescent cell clearance in the non-responder clone, where CD8 and CD4 T cells are allowed to infiltrate exclusively with AP+ICI treatment. Systemic shifts in mice bearing non-responding, ICI treated tumors reveal significant correlations of conventional dendritic cell type 1 and 2 ratios in concert with increased senescent cell burden in the spleen that are recovered with stromal senescent cell clearance. Overall, this data reveals a local and systemic shift in immune cell populations of responder and non-responder phenotypes that may be shifted to improve tumor sensitivity to immune checkpoint inhibition via senolytic intervention. Giselle C. Burton Sojo, Marcel O. Schmidt, Dori Rosenstrauch, Anton Wellstein. Local and systemic impact of stromal senescence on melanoma response to immune checkpoint inhibition [abstract]. In: Proceedings of the AACR Immuno-Oncology Conference (AACR IO): Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2026 Feb 18-21; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2026;14(2 Suppl):Abstract nr C016.

Objectives/Goals: Immune checkpoint inhibitors (IO) have dramatically improved survival outcomes in patients with metastatic melanoma. Still, many patients do not respond these treatments, and others may experience harmful adverse events (irAEs). Thus, there an unmet need for biomarkers for real-time monitoring and management of patients exposed to IO therapies. Methods/Study Population: Serial serum samples were collected from patients with BRAFV600-mutant metastatic melanoma treated with ipilimumab/nivolumab (IO, n = 14) or dabrafenib/trametinib (TT, n = 10). Methylated cell-free DNA (cfDNA) was isolated and sequenced using enzymatic methyl-seq. We develop a robust computational pipeline to identify the top 250 cell-type specific regions of differential methylation (DMRs) across 24 cell-types. Using these differentially methylated regions, a deconvolution tool was developed to determine the abundance of cell type-specific cfDNA in patient serum, and changes in abundance were tracked over treatment time-course to assess response treatment and identify signals of adverse events. Results/Anticipated Results: We demonstrated improved precision in DMR detection evidenced by a higher area under the receiver operator characteristic curve (AUROC) of 0.85 on average. Pathway and functional annotation analysis revealed melanocyte-specific methylation marker regions regulated genes related to melanocyte development and differentiation, including MITF, SOX9/10, and FOXD3. We show these regions are conserved through the transformation to malignant melanoma, indicating melanocyte cfDNA abundance can be used as a marker for tumor burden. We characterize the dynamics of melanocyte-derived cfDNA over the course of treatment in responders and nonresponders to both IO and TT. We observe that changes in concentrations of cfDNA from other cell types correlate with clinically observed irAE-mediated damage to normal tissue. Discussion/Significance of Impact: We demonstrated the utility of decoding the origins of cfDNA fragments obtained from serial liquid biopsy samples. Using cell-specific methylation marks, we identified a signature from the primary melanoma to assess response to treatment, while also obtaining a signal from other tissues throughout the body to monitor immune related adverse events.

Post-transplant complications reduce allograft and recipient survival. Current approaches for detecting allograft injury non-invasively are limited and do not differentiate between cellular mechanisms. Here, we monitor cellular damages after liver transplants from cell-free DNA (cfDNA) fragments released from dying cells into the circulation. We analyzed 130 blood samples collected from 44 patients at different time points after transplant. Sequence-based methylation of cfDNA fragments were mapped to an atlas of cell-type-specific DNA methylation patterns derived from 476 methylomes of purified cells. For liver cell types, DNA methylation patterns and multi-omic data integration show distinct enrichment in open chromatin and functionally important regulatory regions. We find that multi-tissue cellular damages post-transplant recover in patients without allograft injury during the first post-operative week. However, sustained elevation of hepatocyte and biliary epithelial cfDNA within the first month indicates early-onset allograft injury. Further, cfDNA composition differentiates amongst causes of allograft injury indicating the potential for non-invasive monitoring and intervention.

The Hippo pathway is dysregulated in many cancers, leading to pro-oncogenic effects. The transcription factor TEAD plays a critical role in early development, tissue homeostasis, and cell proliferation, and it binds to the downstream Hippo pathway co-activators YAP and TAZ. Numerous studies have examined the roles of YAP/TAZ and TEAD in cancer, with their activity frequently linked to poor clinical prognosis. This review discusses how targeting TEAD interactions with coregulators—most notably YAP and TAZ—represents a promising therapeutic strategy in oncology. Several pharmacological agents have been developed to disrupt the YAP/TAZ–TEAD complex, and many are currently being evaluated for clinical applicability across diverse cancer types. We review current knowledge on the structure and homology of TEAD, emphasizing the protein–protein interfaces that mediate binding to YAP/TAZ and other cofactors. Advances in understanding the YAP/TAZ–TEAD complex have informed the development of diverse strategies to inhibit downstream transcription of key oncogenic target genes. Finally, we highlight TEAD inhibitors currently in clinical trials, outlining their mechanisms of action, associated adverse effects, and potential impact on the future therapeutic landscape.

Multiple sclerosis (MS) is a chronic inflammatory disease characterized by immune-mediated demyelination of the central nervous system, resulting in extensive neurological deficit and remyelination impairment. We have previously found that interleukin-four induced one (IL4I1) protein modulates CNS inflammation and enhances remyelination in mouse models of experimental demyelination. However, it remained unclear if IL4I1 regulates lymphocyte activity in MS. To assess the therapeutic potential of IL4I1 in MS, we investigated the impact of IL4I1 treatment on human lymphocytes from peripheral blood mononuclear cells (PBMCs) obtained from healthy individuals and MS patients. We found that IL4I1 increased the relative densities of Th2 and regulatory T-cells, while reducing Th17 cell density in healthy control (HC) samples. Furthermore, IL4I1-treated lymphocytes promoted CNS remyelination when grafted into demyelinated spinal cord lesions in mice. We found that baseline endogenous IL4I1 expression was reduced in people with MS. However, unlike HCs, IL4I1 treatment had no significant effect on IL17 or TOB1 expression in lymphocytes derived from MS patients. These results suggest that IL4I1 skews CD4+ T-cells to a regulatory state in healthy human lymphocytes, which may be essential for promoting remyelination. However, IL4I1 appears unable to exert its influence on lymphocytes in MS, indicating that impaired IL4I1-mediated activity may underlie MS pathology.

The Hippo pathway signaling mediated through YAP/TAZ, and the transcription factor TEAD is known to be involved in primary tumor progression. Here we report that novel TEAD inhibitors (iTEAD) cause a significant reduction in the outgrowth of lung metastases from triple negative breast cancer (TNBC) models mediated predominantly through changes in stromal immune signaling. TEAD inhibition did not affect the proliferation of TNBC cancer cells in vitro or the growth of the primary tumor in vivo . In normal mice that were treated with iTEAD in the absence of tumors, the lungs showed a decrease in pro-tumor inflammatory pathways. However, the IL12 signaling pathway was enhanced and its production from isolated lung tissue resident macrophages, but not bone marrow derived macrophages, was elevated. In syngeneic TNBC mouse models, inhibition of TEAD suppressed pro-tumor inflammation and the M2-like macrophage phenotype in lung tissues, and increased the infiltration of CD8+ T cells into the lung as well as Th1 CD4+ T cells, restoring an immune responsive microenvironment. iTEAD-treated T cells showed enhanced cytotoxicity and degranulation when co-cultured with cancer cells via increased IL-2 activity. Furthermore, TEAD inhibition or knockdown, enhanced T-cell macrophage crosstalk and anti-tumor activity in 3D tumorspheres which was reversed by IL12 neutralizing antibodies. Our data supports a multifaceted model of TEAD inhibition on the innate and adaptive immune cells as they respond to tumor cell signals and reveals an important stromal phenotype by which TEAD inhibitors could reverse immune suppression and eliminate seeded metastases in the lungs.

Background Pancreatic ductal adenocarcinoma (PDAC) is mostly refractory to immunotherapy due to immunosuppression in the tumor microenvironment and cancer cell-intrinsic T cell tolerance mechanisms. PDAC is described as a “cold” tumor type with poor infiltration by T cells and factors leading to intratumoral T cell suppression have thus received less attention. Here, we identify a cancer cell-intrinsic mechanism that contributes to a T cell-resistant phenotype and describes potential combinatorial therapy.Methods We used an unbiased screening approach of T cell resistant and sensitive murine KPC (KrasLSL-G12D/+; Trp53fl/fl; Ptf1aCre/+) PDAC cells in a three-dimensional co-culture platform with syngeneic antigen-educated T cells to identify potential cell-intrinsic drivers of T cell suppression in PDAC. Comparative transcriptomic analysis was performed to reveal promising candidates that mediate resistance to T cells. We investigated their contribution by shRNA-mediated knockdown and pharmacological inhibition in murine in vitro and in vivo studies, as well as in patient-derived organoids (PDOs). A combination of transcriptomic analyses, cytometric and immunohistochemistry techniques allowed us to validate the underlying T cell response phenotypes of PDAC cells. The action of TGM2 via interaction with tubulin and the impact of microtubule dynamics and vesicle trafficking were evaluated by protein analyses and live-cell imaging. Correlation analyses via TCGA data complemented the functional studies.Results We identified transglutaminase 2 (TGM2) as a mediator of T cell suppression in PDAC. We report that high levels of TGM2 expression in patients’ tumors correlate with immunosuppressive signatures and poor overall survival. We found that TGM2 regulates vesicle trafficking by modulating microtubule network density and dynamics in pancreatic cancer cells, thus facilitating the secretion of immunosuppressive cytokines, which impair effector T cell functionality. In TGM2-expressing PDOs, pharmacological TGM2 inhibition or treatment with nocodazole increased T cell-mediated apoptosis. Also, pretreatment of TGM2high PDOs with sublethal doses of the spindle poisons paclitaxel or vincristine increased CD8+T cell activation and sensitized PDOs toward T cell-mediated cytotoxicity.Conclusions These findings indicate that targeting microtubular function therapeutically may enhance antitumor T cell responses by impacting activity of immunosuppressive cytokines in the PDAC microenvironment.

Physiologic aging and insults from the environment lead to DNA damage. In response, cells in any organ will undergo senescence-induced growth arrest to prevent damaged cells from further propagation. This review focuses on senescence pharmacology. First, we describe senescence induction mechanisms and a unique feature of senescent cells, the SASP (senescence-associated secretory phenotype). Signaling pathways that control and respond to the SASP provide the framework for a better understanding of senescence pharmacology. We describe how several commonly used drugs can induce cellular senescence and how that impacts their efficacy and produces unexpected effects. Thereafter, we discuss the potential and challenges of senolytic drugs that eliminate senescent cells, and we describe targeting of components of the SASP as well as pathways that control expression of genes contributing to the SASP. Lastly, we discuss studies that have exemplified the significant impact of senescence-targeted therapy in various disease states.

Poor treatment responses of pancreatic ductal adenocarcinoma (PDAC) are in large part due to tumor heterogeneity and an immunosuppressive desmoplastic tumor stroma that impacts interactions with cells in the tumor microenvironment (TME). Thus, there is a pressing need for models to probe the contributions of cellular and noncellular crosstalk. Organoids are promising model systems with the potential to generate a plethora of data including phenotypic, transcriptomic and genomic characterization but still require improvements in culture conditions mimicking the TME. Here, we describe an INTERaction with Organoid-in-MatriX ("InterOMaX") model system, that presents a 3D co-culture-based platform for investigating matrix-dependent cellular crosstalk. We describe its potential to uncover new molecular mechanisms of T cell responses to murine KPC (LSL-KrasG12D/+27/Trp53tm1Tyj/J/p48Cre/+) PDAC cells as well as PDAC patient-derived organoids (PDOs). For this, a customizable matrix and homogenously sized organoid-in-matrix positioning of cancer cells were designed based on a standardized agarose microwell chip array system and established for co-culture with T cells and inclusion of stromal cells. We describe the detection and orthogonal analysis of murine and human PDAC cell populations with distinct sensitivity to T cell killing that is corroborated in vivo. By enabling both identification and validation of gene candidates for T cell resistance, this platform sets the stage for better mechanistic understanding of cancer cell-intrinsic resistance phenotypes in PDAC.

Abstract Background: Decoding the origins of cell-free DNA (cfDNA) released from dying cells in a liquid biopsy sample offers the potential to provide insight into the dynamic, organism-wide changes reflective of health and disease, making cfDNA an ideal target for serial, minimally invasive monitoring of disease-related changes. To this end, cell-type specific DNA methylation patterns offer a promising target to facilitate tissue of origin analysis, yet limited methods exist to identify differentially methylated regions that distinguish cell-types. Methods: We develop a robust differentially methylated marker region identification pipeline, DiMMER, that leverages cfDNA fragment level information of neighboring, co-regulated CpG sites on methylome-wide sequencing reads. Compared to prior methods that utilize simple heuristics in one-vs-all average methylation rate comparisons, we implement an individual pairwise statistical test procedure across all cell-types or groups under consideration. We assess the cell-specific nature of identified differentially methylated marker regions by generating in-silico mixtures from known cell-type of origin at each region, and calculating the area under the receiver operating characteristic curve (AUROC). We utilize our differentially methylated marker finding pipeline to identify melanocyte specific methylation marker regions and assess their functional role through annotations. We show these cell-specific regions are conserved in melanoma cell-lines and are distinct from the aberrant changes in a cancer context. Results: We identified the most cell-type specific differentially methylated marker regions across 24 distinct cell-type groups using our pipeline. Compared to a simpler one-vs-all heuristic, we demonstrate improved cell-type specificity evidenced by a higher AUROC on average. Using our pipeline we identified melanocyte-specific marker regions, which were commonly found in intronic and promoter regions of genes related to melanocyte development and differentiation. When comparing methylation patterns between melanocytes and melanoma cell-lines, we demonstrate melanocyte specific methylation marks are conserved through the transformation to malignant melanoma. Conclusion: As methylome-wide sequencing methods continue to rapidly develop and more cell-specific methylation data is generated, there is unmet need for more statistically robust differentially methylated marker finding tools. Here we present one such tool, DiMMER, and demonstrate the potential utility of identifying such regions to be used to assess organ-specific load as a measure of residual disease, as opposed to traditional circulating tumor DNA quanitification. Citation Format: Arthur P McDeed, Sidharth S Jain, Megan E McNamara, Amber Alley, Anton Wellstein, Jaeil Ahn. DiMMER: A robust computational pipeline for differential methylation marker evaluation in R of cell-free DNA fragments [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B063.

Cellular senescence accumulates with age and has been shown to impact numerous physiological and pathological processes, including immune function. The role of cellular senescence in cancer is multifaceted, but the impact on immune checkpoint inhibitor response and toxicity has not been fully evaluated. In this review, we evaluate the impact of cellular senescence in various biological compartments, including the tumor, the tumor microenvironment, and the immune system on immune checkpoint inhibitor efficacy and toxicity. We provide an overview of the impact of cellular senescence in normal and pathological contexts and examine recent studies that have connected aging and cellular senescence to immune checkpoint inhibitor treatment in both the pre-clinical and clinical contexts. Overall, senescence plays a multi-faceted, context-specific role, and has been shown to modulate immune-related adverse event incidence as well as immune checkpoint inhibitor response.

Tumor tissue collections are used to uncover pathways associated with disease outcomes that can also serve as targets for cancer treatment, ideally by comparing the molecular properties of cancer tissues to matching normal tissues. The quality of such collections determines the value of the data and information generated from their analyses including expression and modifications of nucleic acids and proteins. These biomolecules are dysregulated upon ischemia and decompose once the living cells start to decay into inanimate matter. Therefore, ischemia time before final tissue preservation is the most important determinant of the quality of a tissue collection. Here we show the impact of ischemia time on tumor and matching adjacent normal tissue samples for mRNAs in 1664, proteins in 1818, and phosphosites in 1800 cases (tumor and matching normal samples) of four solid tumor types (CRC, HCC, LUAD, and LUSC NSCLC subtypes). In CRC, ischemia times exceeding 15 min impacted 12.5% (mRNA), 25% (protein), and 50% (phosphosites) of differentially expressed molecules in tumor versus normal tissues. This hypoxia- and decay-induced dysregulation increased with longer ischemia times and was observed across tumor types. Interestingly, the proteomics analysis revealed that specimen ischemia time above 15 min is mostly associated with a dysregulation of proteins in the immune-response pathway and less so with metabolic processes. We conclude that ischemia time is a crucial quality parameter for tissue collections used for target discovery and validation in cancer research.

Abstract Breast cancer is the most common type of cancer in females and recurrence increases over time, unlike many other cancers. Treatment for recurrent cancer is often the same as the primary with no additional biopsies taken. Current research suggests that subtype switching and tumor character changes frequently occur between primary and recurrent breast cancers. Therefore, it may be beneficial to patients to switch treatment based on these changes. Since physical biopsies are cumbersome and not always feasible, liquid biopsies open a way to monitor tumor changes less invasively and more comprehensively. It has been previously established that cell free DNA (cfDNA) shed into the bloodstream from dying cells can reflect cell type of origin via methylation pattern and rate of death via concentration of cfDNA. In this pilot study, we seek to look at the cfDNA of fifteen late stage pre-/ post-surgical breast cancer patients who also received radiation treatment. We will perform cfDNA extraction on the serum of these patients and both whole genome bisulfite sequencing (WGBS), which chemically converts unmethylated cytosine to uracil/thymine in the DNA and is the current gold-standard of methylation sequencing, and a newer method, enzymatic methylation sequencing (EM-seq), which enzymatically converts (TET2/APOBEC) unmethylated cytosine to uracil/thymine and potentially preserves more of the cfDNA. To validate any signatures found in the cfDNA of the breast cancer patients, we have begun the genomic DNA (gDNA) extraction and WGBS/ EM-seq protocols on a variety of breast cancer cell lines including: MCF10A, MCFDCIS, MCF7, T47D, BT474 MDA MB453, MDA MB436 and MDA MB231 (including in-lab brain, bone, and lung metastatic clones). Bioanalyzer traces are produced from the extracted cfDNA/gDNA and also for the final sequencing libraries. The success of the methylation conversion is evaluated after sequencing data is returned and conversion rates of the cytosine to uracil/thymine are compared to unmethylated DNA control (lambda) and methylated DNA control (pUC19). Once this sequencing data is obtained, we use an in-lab deconvolution algorithm to detect cell types of origin and intend to make the algorithm more robust for cancer cell types as well. We have currently produced breast cancer cell line methylation sequencing libraries and are in the process of producing the libraries for the patient samples. Our current data suggests that there are changes in the cfDNA general fragmentation patterns and cfDNA concentrations between pre-/post- surgery samples. Once our sequencing data is obtained for the patient samples, we will run our deconvolution algorithm. The potential of characterizing breast cancer subtype and progression signatures in cfDNA of late stage pre-/ post-surgical breast cancer patients can have significant impact on patient treatment options. Identifying these breast cancer signatures less invasively and, therefore, more frequently may allow for early and more targeted intervention to improve breast cancer patient outcomes. Citation Format: Amber Alley, Megan McNamara, Sidharth Jain, Anton Wellstein. Investigating distinct methylation signatures characteristic of breast cancer subtypes in residual disease via cell free DNA methylation [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B005.

OBJECTIVES/GOALS: Decoding the origins of cell-free DNA (cfDNA) released from dying cells in a liquid biopsy sample (e.g. blood) offers the potential to provide insight into the dynamic, organism-wide changes reflective of health and disease. Thus, making cfDNA an ideal target for serial, minimally invasive monitoring of disease-related changes. METHODS/STUDY POPULATION: We develop a probabilistic method that leverages the co-regulation of neighboring CpG sites on individual methylome-wide sequencing (WGBS) reads to more flexibly model cell-specific methylation compared to prior methods that focus on the methylation rate of a single CpG site. We then extend our cross-sectional model to account for sequential sampling within the same subject. The increased sampling frequency is critical to identifying the evolutionary dynamics of disease progression influencing treatment response and resistance, and disease recurrence. We utilize Bayesian inference techniques to model patient-specific longitudinal profiles of cell-type turnover in simulated serial samples. RESULTS/ANTICIPATED RESULTS: We found our model more effective at capturing a range of methylation patterns on cfDNA fragments with lower Root Mean Square Error across simulations compared to a single CpG model. We apply our model to detect significant (p < 0.05, Friedman’s test) increases in cellular contributions from lung and cardiac tissue in breast cancer patients (n=15) undergoing radiation therapy compared to baseline. We also identify signals of radiation induced toxicity to the liver in right-sided breast cancer patients (n=8) receiving radiation treatment compared to left-sided breast cancer patients (n=7). Finally, we show our extended model results in more efficient estimates of simulated cell-type turnover profiles compared to analyzing serial samples cross-sectionally, ignoring the longitudinal nature of the data. DISCUSSION/SIGNIFICANCE: Here we address an unmet need in developing novel statistical methodologies to decode the origins of methylated cfDNA obtained from liquid biopsy samples. We demonstrate the far-ranging clinical utility of serial liquid biopsy sampling to complement and advance the standards of clinical care in oncology and other pathologies.

Abstract ID 87546Poster Board 444Overall, metastasis is a major cause of mortality in cancer patients. Triple-negative breast cancer (TNBC) has the worst prognosis out of all breast cancer subtypes with the highest metastasis rate. In TNBC, almost 50% of patients will have distant metastases. The current standard of care has not progressed from the use of broadly cytotoxic agents such as anthracyclines, taxanes, and platinum agents which are limited by their adverse effects and emerging drug resistance in cancerous tissue. This indicates a significant need for further investigation of understudied drivers of metastatic TNBC to determine new and more selective therapeutic targets. Our lab has shown that metastatic progression and invasion in vitro and in vivo is associated with increased activation of the transcription factor TEAD (TEA family domain member) which is the final nuclear coactivator of the Hippo signaling pathway. The TEAD (1-4) family bind to and are coactivated by YAP/TAZ which are known oncogenes in TNBC. TEADs also bind to the SRC family of transcriptional coactivators that have oncogenic effects in TNBC. Using TEAD inhibitors (TEADi) that prevent TEAD palmitoylation and reduce binding to YAP/TAZ, there is a significant reduction in the invasive capability of TNBC cell lines in 3D sphere models in vitro and reduced lung metastasis in vivo. Furthermore, concurrent TEADi treatment increased sensitivity to doxorubicin treatment in the 4T1 TNBC cell line in vitro. In a pilot experiment in naïve non-tumor bearing mice treated with TEADi, we detected changes in immune cell abundance within the lungs using a transcriptomic analysis, most notably an increase in the alveolar macrophage population. From these observations, I developed the hypothesis that inhibition of TEAD-dependent target genes reduces the primary tumor invasive capability and metastasis through direct effects on tumor epithelium. Furthermore, this is coupled with the anti-metastatic effects of TEADi directly on the tumor niche microenvironment. I further propose that these pleiotropic effects of TEADi will sensitize TNBC to potential combinations with current standard of care (SOC) therapies.Funded by Pharmacological Sciences Training Grant (NIH NIGMS T32 GM142520)

Abstract Background: The DREAMseq trial (EA6134, NCT02224781) was a national multi-center randomized phase III trial coordinated by ECOG-ACRIN that found that immune checkpoint inhibitor (IO) treatment achieves improved survival outcomes compared to targeted therapy (TT) in patients with BRAF V600-mutant metastatic melanoma. Still, approximately 40% of patients do not respond to IO, and existing biomarkers fail to distinguish this subset of patients who do not benefit from IO therapy. Additionally, as many as 80% of patients may experience immune- related adverse events (irAEs), which range from mild dermatological symptoms to life- threatening myocarditis. Here, we explore the use of the methylation status of cell-free DNA (cfDNA) in serially collected blood samples to measure response and toxicity in the context of IO- and TT-treated metastatic melanoma. Methods: Serial serum samples were collected from patients with BRAF V600-mutant metastatic melanoma treated with ipilimumab/nivolumab (IO) or dabrafenib/trametinib (TT). Circulating cfDNA was isolated from serially collected serum samples, enriched for regions of interest by hybridization capture and sequenced using enzymatic methyl-seq. Cell-type deconvolution was performed to determine the abundance of cell type- specific methylation patterns of cfDNA molecules in patient serum at different time points of treatment. The BRAF V600 mutation abundance in total cfDNA was also assessed. Results: We identified melanocyte lineage-specific DNA methylation regions and demonstrate that the methylation status of these regions remains conserved in malignant melanoma. We characterized the changes in abundance of the melanocyte-lineage cfDNA over the course of treatment and show that these changes distinguish responders from non-responders to either IO or TT. Furthermore, we track the abundance of cell type-specific DNA from normal tissues to identify markers indicative of adverse effects or disease progression. Conclusions: We established melanocyte-lineage methylation markers and evaluated the use of cell-type specific DNA methylation to monitor treatment effects of immune checkpoint or BRAF/MEK inhibitors in metastatic melanoma using serially collected blood samples. Citation Format: Sidharth S Jain, A. Patrick IV McDeed, Megan E McNamara, Amber R Alley, Dori S Rosenstrauch, Harry Sun, Natalie Thompson, John M Kirkwood, Geoffrey T Gibney, Michael B Atkins, Anton Wellstein. Monitoring treatment response and toxicity in BRAF V600-mutant metastatic melanoma with circulating cell-free DNA [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B047.