Abstract Epigenetic regulation is essential for mammary gland development, yet the specific chromatin remodelers that govern mammary epithelial cell fate remain poorly defined. Mutations in SWI/SNF chromatin remodeling complex subunits occur in more than 20% of human cancers, with ARID1A being the most frequently altered. In breast cancer, ARID1A loss of function mutations are enriched in metastatic estrogen receptor-positive (ER+) disease and associated with endocrine therapy resistance. To define the developmental role of Arid1a in vivo, we generated mice with mammary epithelium specific Arid1a deletion. These animals displayed disrupted ductal branching and aberrant terminal end bud formation. Mammary organoids derived from Arid1a deficient tissue further revealed abnormal cystic morphology and impaired differentiation. To dissect the molecular consequences of Arid1a loss, we performed single cell multiomic profiling that combine single nucleus RNA and chromatin accessibility sequencing from the same cells, together with H3K27ac and BRG1 CUT&RUN-seq. Arid1a loss caused a collapse of normal mammary epithelial lineage architecture, with single cell analyses showing failure to maintain basal, luminal progenitor, and alveolar identities. Instead, Arid1a deficient cells were restricted to an undifferentiated luminal hormonal like state characterized by reduced estrogen receptor signaling competence. Chromatin profiling revealed profound remodeling, including decreased accessibility and impaired SWI/SNF targeting at lineage defining transcription factors (TF) such as Foxa1, Gata3, and Sox9. A CRISPR/Cas9 pooled loss of function screen identified Foxa1 and Meis1 as essential regulators whose deletion recapitulated the Arid1a null phenotype, positioning them as downstream effectors required for mammary cell fate specification. Notably, Meis1 emerged as a previously unrecognized regulator of luminal hormonal identity. Our work provides a framework for understanding how Arid1a rewires the chromatin landscape and transcriptional network in normal mammary development. By identifying lineage specific TF motifs and critical regulators like Meis1, we identify new opportunities for targeted therapeutic intervention. Citation Format: Erik Ladewig, Amaia Arruabarrena-Aristorena, Estelle Deby, Srushti Kittane, Fresia Pareja, Ryan Blawski, Yangzhenyu Gao, Laura Baldino, Vito Rebecca, Emiliano Cocco, Hongkai Ji, Pau Castel, Christina Leslie, Wouter Karthaus, Eneda Toska. Arid1a directs lineage specification in mammary epithelial cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3219.

Abstract Acral melanoma is an aggressive melanoma subtype with a predilection for metastasis and poor clinical outcomes, yet no FDA-approved therapies are tailored specifically for this population. Progress has been hindered by limited clinico-genomic data and a lack of orthotopic preclinical models. Here, we integrate genomic profiling and longitudinal clinical annotations from 29 patients with metastatic acral melanoma—alongside a comparison cohort of 455 patients with cutaneous melanoma—revealing an enhanced metastatic capacity in acral disease. We further show that the plantar skin microenvironment fosters a human acral melanoma, pro-metastatic cell state through elevated matrix stiffness, and identify a matrix stiffness-induced FAK-SRC-YAP vulnerability as a therapeutically actionable axis to combat distant metastasis. This work establishes the first series of orthotopic models of metastatic acral melanoma and uncovers tractable drivers of distant organ metastasis, offering new avenues for tailored therapeutic strategies. Citation Format: Marie Elena Portuallo, Tyler Aprati, Limin An, Steffanus Pranoto Hallis, Kuai Yu, MiKaela N. Field, Sheri L. Holmen, David Liu, Vito Rebecca. A site-specific microenvironmental program in plantar skin confers heightened metastatic capacity to acral melanomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 6144.

Rare melanoma subtypes, including acral, mucosal, and uveal melanomas, exhibit limited responses to immune checkpoint inhibitors (ICIs), yet the molecular mechanisms of immune resistance remain poorly defined. Here, we performed transcriptomic profiling of patient-derived xenografts (PDXs) and publicly available tumor datasets to systematically compare intratumoral gene expression across cutaneous and rare melanoma subtypes. We identified a convergent downregulation of innate immune pathogen sensing (IIPS) and type I interferon signaling pathways in rare melanomas compared to cutaneous, with lower expression also observed in anti-PD-1 non-responder tumors. CIBERSORT deconvolution of immune populations revealed that lower IIPS gene-expressing tumors exhibited reduced CD8⁺ T cell and memory CD4⁺ T cell infiltration, and enrichment of M2 macrophages, consistent with a more immunosuppressive tumor microenvironment. In vitro screening of epigenetic and immunomodulatory compounds revealed that the DNA hypomethylating agent decitabine robustly induced IIPS and adaptive immune gene expression in rare melanoma cell lines. In vivo treatment of mucosal and uveal melanoma xenograft models with decitabine resulted in durable upregulation of IIPS and antigen presentation genes, and whole transcriptome analysis confirmed that IIPS gene re-expression was the dominant transcriptional consequence of decitabine treatment. These findings highlight silencing of IIPS genes as a recurrent immune evasion mechanism in rare melanomas and nominate decitabine as a potential immunomodulatory strategy for enhancing immune responsiveness.

Overview of IGFBP2 expression in patient data bases, additional pAKT staining, and oil red O zoom out.

Translocation renal cell carcinoma (tRCC) presents a significant clinical challenge due to its aggressiveness and limited treatment options. It is primarily driven by fusion oncoproteins (FOs), yet their role in oncogenesis is not fully understood. Here, we investigate TFE3 fusions in tRCC, focusing on NONO::TFE3 and SFPQ::TFE3. We demonstrate that TFE3 FOs form liquid-like condensates with increased transcriptional activity, localizing to TFE3 target genes and promoting cell proliferation and migration. The coiled-coil domains (CCDs) of NONO and SFPQ are essential for condensate formation, prolonging TFE3 FOs' chromatin binding time and enhancing transcription. Compared with wild-type TFE3, TFE3 FOs bind to new chromatin regions, alter chromatin accessibility, and form new enhancers and super-enhancers at pro-growth gene loci. Disruption of condensate formation via CCD modification abolishes these genome-wide changes. Altogether, our integrated analyses underscore the critical functions of TFE3 FO condensates in driving tumor cell growth, providing key insights for future therapeutic strategies.

Supp Fig 3 shows the zoom -out of Figure 4, to show a larger field of view for staining of mCherry cells

Supplemental Figure 2 shows melanoma cells treated with Albumax, as well as an additional cell line showing the contribution of IGFBP2 to invasion

ABSTRACT Chimeric antigen receptor (CAR) T cells express antigen-specific synthetic receptors, which upon binding to cancer cells, elicit T cell anti-tumor responses. CAR T cell therapy has enjoyed success in the clinic for hematological cancer indications, giving rise to decade-long remissions in some cases. However, CAR T therapy for patients with solid tumors has not seen similar success. Solid tumors constitute 90% of adult human cancers, representing an enormous unmet clinical need. Current approaches do not solve the central problem of limited ability of therapeutic cells to migrate through the stromal matrix. We discover that T cells at low and high density display low- and high-migration phenotypes, respectively. The highly migratory phenotype is mediated by a paracrine pathway from a group of self-produced cytokines that include IL5, TNFα, IFNγ, and IL8. We exploit this finding to “lock-in” a highly migratory phenotype by developing and expressing receptors, which we call velocity receptors (VRs). VRs target these cytokines and signal through these cytokines’ cognate receptors to increase T cell motility and infiltrate lung, ovarian, and pancreatic tumors in large numbers and at doses for which control CAR T cells remain confined to the tumor periphery. In contrast to CAR therapy alone, VR-CAR T cells significantly attenuate tumor growth and extend overall survival. This work suggests that approaches to the design of immune cell receptors that focus on migration signaling will help current and future CAR cellular therapies to infiltrate deep into solid tumors.

Patients with metastatic acral lentiginous melanoma (ALM) suffer worse outcomes relative to patients with other forms of cutaneous melanoma (CM), and do not benefit as well to approved melanoma therapies. Identification of cyclin-dependent kinase 4 and 6 (CDK4/6) pathway gene alterations in >60% of ALMs has led to clinical trials of the CDK4/6 inhibitor (CDK4i/6i) palbociclib for ALM; however, median progression free survival with CDK4i/6i treatment was only 2.2 months, suggesting existence of resistance mechanisms. Therapy resistance in ALM remains poorly understood; here we report hyperactivation of MAPK signaling and elevated cyclin D1 expression serve as a mechanism of intrinsic early/adaptive CDK4i/6i resistance. ALM cells that have acquired CDK4i/6i resistance following chronic treatment exposure also exhibit hyperactivation of the MAPK pathway. MEK and/or ERK inhibition increases CDK4i/6i efficacy against therapy naïve and CDK4i/6i-resistant AM cells in xenograft and patient-derived xenograft (PDX) models and promotes a defective DNA repair, cell cycle arrested and apoptotic program. Notably, gene alterations poorly correlate with protein expression of cell cycle proteins in ALM or efficacy of CDK4i/6i, urging additional strategies when stratifying patients for CDK4i/6i trial inclusion. Concurrent targeting of the MAPK pathway and CDK4/6 represents a new approach for patients with metastatic ALM to improve outcomes.

Metastatic melanoma is among the most enigmatic advanced cancers to clinically manage despite immense progress in the way of available therapeutic options and historic decreases in the melanoma mortality rate. Most patients with metastatic melanoma treated with modern targeted therapies (for example, BRAFV600E/K inhibitors) and/or immune checkpoint blockade (for example, anti-programmed death 1 therapy) will progress, owing to profound tumor cell plasticity fueled by genetic and nongenetic mechanisms and dichotomous host microenvironmental influences. Here we discuss the determinants of tumor heterogeneity, mechanisms of therapy resistance and effective therapy regimens that hold curative promise. Rebecca and colleagues discuss the complex biology of metastatic melanoma, as well as determinants of resistance to therapy and existing and promising therapy strategies.

Aged patients with melanoma (>65 years old) have more aggressive disease relative to young patients (<55 years old) for reasons that are not completely understood. Analysis of the young and aged secretome from human dermal fibroblasts identified >5-fold levels of IGF-binding protein 2 (IGFBP2) in the aged fibroblast secretome. IGFBP2 functionally triggers upregulation of the PI3K-dependent fatty acid biosynthesis program in melanoma cells. Melanoma cells co-cultured with aged dermal fibroblasts have higher levels of lipids relative to those co-cultured with young dermal fibroblasts, which can be lowered by silencing IGFBP2 expression in fibroblasts prior to treating with conditioned media. Conversely, ectopically treating melanoma cells with recombinant IGFBP2 in the presence of conditioned media from young fibroblasts or overexpressing IGFBP2 in melanoma cells promoted lipid synthesis and accumulation in melanoma cells. Treatment of young mice with rIGFBP2 increases tumor growth. Neutralizing IGFBP2 in vitro reduces migration and invasion in melanoma cells, and in vivo studies demonstrate that neutralizing IGFBP2 in syngeneic aged mice reduces tumor growth and metastasis. Our results suggest that aged dermal fibroblasts increase melanoma cell aggressiveness through increased secretion of IGFBP2, stressing the importance of considering age when designing studies and treatment. Significance: The aged microenvironment drives metastasis in melanoma cells. This study reports that IGFBP2 secretion by aged fibroblasts induces lipid accumulation in melanoma cells, driving an increase in tumor invasiveness. Neutralizing IGFBP2 decreases melanoma tumor growth and metastasis.

Abstract Metastatic burden and organ failure are the root causes of mortality in patients with advanced melanoma; however, little is known of the metabolic drivers that enable organ colonization and the formation of overt metastases. Recent studies have drawn attention to the importance of metabolism in the survival and colonization of cancer cells. In melanoma, there have been studies focusing on the invasive capabilities of cells; however, not much is known regarding metabolic plasticity in melanoma migratory, invasive and ultimately metastatic capabilities.We have previously shown changes in the lipid landscape of the aged microenvironment promotes melanoma resistance to targeted therapy. Here, we find a distinct metabolite landscape in the aged microenvironment elevates melanoma metastatic capacity. We utilized a panel of well characterized melanoma models and tested their invasiveness and motility under different metabolite levels modeled after the aged microenvironment. Transcriptomic and proteomic analysis identifies distinct signatures that explain the migratory and invasive differences in cells cultured in varying metabolic environments. We hypothesize that different nutrient availabilities melanoma cells are exposed to during the metastatic phase affect the migratory and invasive capacity of the cell. We tested this by performing 3D migration assays, organoids and transwell assays of cells grown in media with varying nutrient levels. Further analysis is currently underway to better understand the mechanisms in which these metabolic differences facilitate cell migration, invasion and eventually colonization. This work has important implications for our understanding of the metabolic determinants of melanoma migration and metastatic colonization, and we hypothesize restraining tumor metabolic plasticity is vital to prevent and treat metastases in melanoma. Citation Format: Gretchen Marie Alicea, Payal Patel, Meihan Wei, Vito Rebecca, Denis Wirtz. The unique metabolite landscape of the aged microenvironment dictates melanoma migratory and invasive capacity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5541.

Activating mutations in PIK3CA are frequently found in estrogen-receptor-positive (ER+) breast cancer, and the combination of the phosphatidylinositol 3-kinase (PI3K) inhibitor alpelisib with anti-ER inhibitors is approved for therapy. We have previously demonstrated that the PI3K pathway regulates ER activity through phosphorylation of the chromatin modifier KMT2D. Here, we discovered a methylation site on KMT2D, at K1330 directly adjacent to S1331, catalyzed by the lysine methyltransferase SMYD2. SMYD2 loss attenuates alpelisib-induced KMT2D chromatin binding and alpelisib-mediated changes in gene expression, including ER-dependent transcription. Knockdown or pharmacological inhibition of SMYD2 sensitizes breast cancer cells, patient-derived organoids, and tumors to PI3K/AKT inhibition and endocrine therapy in part through KMT2D K1330 methylation. Together, our findings uncover a regulatory crosstalk between post-translational modifications that fine-tunes KMT2D function at the chromatin. This provides a rationale for the use of SMYD2 inhibitors in combination with PI3Kα/AKT inhibitors in the treatment of ER+/PIK3CA mutant breast cancer.

Prurigo nodularis (PN) is an intensely pruritic, chronic inflammatory skin disease that disproportionately affects black patients. However, the pathogenesis of PN is poorly understood. We performed single-cell transcriptomic profiling, ligand receptor analysis and cell trajectory analysis of 28,695 lesional and non-lesional PN skin cells to uncover disease-identifying cell compositions and genetic characteristics. We uncovered a dysregulated role for fibroblasts (FBs) and myofibroblasts as a key pathogenic element in PN, which were significantly increased in PN lesional skin. We defined seven unique subclusters of FBs in PN skin and observed a shift of PN lesional FBs towards a cancer-associated fibroblast (CAF)-like phenotype, with WNT5A+ CAFs increased in the skin of PN patients and similarly so in squamous cell carcinoma (SCC). A multicenter PN cohort study subsequently revealed an increased risk of SCC as well as additional CAF-associated malignancies in PN patients, including breast and colorectal cancers. Systemic fibroproliferative diseases were also upregulated in PN patients, including renal sclerosis and idiopathic pulmonary fibrosis. Ligand receptor analyses demonstrated increased FB1-derived WNT5A and periostin interactions with neuronal receptors MCAM and ITGAV, suggesting a fibroblast-neuronal axis in PN. Type I IFN responses in immune cells and increased angiogenesis/permeability in endothelial cells were also observed. As compared to atopic dermatitis (AD) and psoriasis (PSO) patients, increased mesenchymal dysregulation is unique to PN with an intermediate Th2/Th17 phenotype between atopic dermatitis and psoriasis. These findings identify a pathogenic role for CAFs in PN, including a novel targetable WNT5A+ fibroblast subpopulation and CAF-associated malignancies in PN patients.

The loss of intercellular adhesion molecule E-cadherin is a hallmark of the epithelial-mesenchymal transition (EMT), during which tumor cells transition into an invasive phenotype. Accordingly, E-cadherin has long been considered a tumor suppressor gene; however, E-cadherin expression is paradoxically correlated with breast cancer survival rates. Using novel multi-compartment organoids and multiple in vivo models, we show that E-cadherin promotes a hyper-proliferative phenotype in breast cancer cells via interaction with the transmembrane receptor EGFR. The E-cad and EGFR interaction results in activation of the MEK/ERK signaling pathway, leading to a significant increase in proliferation via activation of transcription factors, including c-Fos. Pharmacological inhibition of MEK activity in E-cadherin positive breast cancer significantly decreases both tumor growth and macro-metastasis in vivo. This work provides evidence for a novel role of E-cadherin in breast tumor progression and identifies a new target to treat hyper-proliferative E-cadherin-positive breast tumors, thus providing the foundation to utilize E-cadherin as a biomarker for specific therapeutic success.

Supplementary Tables 1-2, Figures 1-12 from PTEN Loss Confers BRAF Inhibitor Resistance to Melanoma Cells through the Suppression of BIM Expression

Preclinical activity of MFF targeting

Young BODIPY-C12 fibroblasts with GFP-Tagged melanoma cells showing lipid uptake

AbstractPurpose: BRAF and MEK inhibitors (BRAFi and MEKi) are actively used for the treatment of metastatic melanoma in patients with BRAFV600E mutation in their tumors. However, the development of resistance to BRAFi and MEKi remains a difficult clinical challenge with limited therapeutic options available to these patients. In this study, we investigated the mechanism and potential therapeutic utility of combination BRAFi and adoptive T-cell therapy (ACT) in melanoma resistant to BRAFi. Experimental Design: Investigations were performed in vitro and in vivo with various human melanoma cell lines sensitive and resistant to BRAFi as well as patient-derived xenografts (PDX) derived from patients. In addition, samples were evaluated from patients on a clinical trial of BRAFi in combination with ACT. Results: Herein we report that in human melanoma cell lines, senstitive and resistant to BRAFi and in PDX from patients who progressed on BRAFi and MEKi therapy, BRAFi caused transient upregulation of mannose-6-phosphate receptor (M6PR). This sensitized tumor cells to CTLs via uptake of granzyme B, a main component of the cytotoxic activity of CTLs. Treatment of mice bearing resistant tumors with BRAFi enhanced the antitumor effect of patients' TILs. A pilot clinical trial of 16 patients with metastatic melanoma who were treated with the BRAFi vemurafenib followed by therapy with TILs demonstrated a significant increase of M6PR expression on tumors during vemurafenib treatment. Conclusions: BRAF-targeted therapy sensitized resistant melanoma cells to CTLs, which opens new therapeutic opportunities for the treatment of patients with BRAF-resistant disease. See related commentary by Goff and Rosenberg, p. 2682