tbuckley/cabot-search huggingface dataset:
Abstract 4072: Functional screen to optimize logic gate potency and selectivity
Authors: Sara Martire, Michele Mcelvain, Vasantika Suryawanshi, Mark Daris, Tanveer K. Gill, Timothy P. Riley, Alexander Kamb, Chawita Netirojjanakul
Journal: Cancer Research (2025)

Abstract Background: Logic-gated cell therapy systems are considerably more complicated than conventional therapeutics and, therefore, more challenging to optimize. One type of logic gate, the NOT gate, responds to two inputs: the presence of antigen A and absence of antigen B. Perhaps the best studied NOT gate is called Tmod which consists of an activator (eg, a chimeric antigen receptor [CAR]) that is co-expressed with an inhibitory receptor, or blocker (DiAndreth B, et al. Clin Immunol. 2022). However, the complexity of the system limits the amount of structure-activity information that can readily be obtained. If further modules (eg, potency boosters) are added to the system, the behavior of these synthetic circuits can be even more complex. Methods: A fluorescence-activated cell sorter (FACS)-based screening system was designed to rapidly select functional inhibitory receptors and inducible boosters from a pooled library of candidates. This screen incorporates an NFAT-responsive reporter cell line for iterative selection of reporter (+) and (-) cell populations by FACS after exposure to different stimuli. The selected populations were analyzed by sequencing to identify candidate blocker or booster sequences enriched during the process. Results: Proof-of-concept experiments using a library of blocker variants demonstrated enrichment of active blockers. Moreover, selected features were used to successfully predict the blocker behavior with 70-80% accuracy by machine-learning algorithm. In another set of experiments, a library of almost 30,000 variants of a signal 1 booster that activate signaling in the presence of a small molecule (rimiducid) was screened. Signal 1 boosters with specific domain structures were enriched and validated in subsequent experiments. Conclusions: The screening system described here identifies active blocker receptors and boosters from large libraries of variants. Its throughput is sufficient to generate large datasets and train machine learning models to better predict and optimize the function and control of logic-gated cell therapeutics. Citation Format: Sara Martire, Michele Mcelvain, Vasantika Suryawanshi, Mark Daris, Tanveer K. Gill, Timothy P. Riley, Alexander Kamb, Chawita Netirojjanakul. Functional screen to optimize logic gate potency and selectivity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4072.
Abstract 4067: Covaris truCOVER library prep kit: A streamlined PCR free WGS workflow for enhanced NGS library performance and data quality
Authors: Vanessa Process, Martina Werner, Madan Ambavaram, Thuy Dao, Heidi Giese, Sushant Khanal, Luca Beker, Sameer Vasantgadkar, Maura Berkeley, Zachary Herbert, Greg Endress, Eugenio Daviso, Ulrich Thomann
Journal: Cancer Research (2025)

Abstract Whole-genome sequencing (WGS) has become an indispensable tool in genomic research and clinical diagnostics, offering unprecedented insights into the underlying mechanisms of genetic diseases, cancer evolution, pharmacogenetics and pharmacology References: (1). Rosenquist et al., Clinical Utility of Whole-Genome Sequencing in Precision Oncology. Seminars in Cancer Biology, 84, 32-39 (2022).(2). Process et al., Optimization of Insert Sizes for Illumina’s WGS with Covaris AFA-Based Shearing and Bead-Based Size Selection. Covaris Application Note (2024). Citation Format: Vanessa Process, Martina Werner, Madan Ambavaram, Thuy Dao, Heidi Giese, Sushant Khanal, Luca Beker, Sameer Vasantgadkar, Maura Berkeley, Zachary Herbert, Greg Endress, Eugenio Daviso, Ulrich Thomann. Covaris truCOVER library prep kit: A streamlined PCR free WGS workflow for enhanced NGS library performance and data quality [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4067.
Abstract 4055: Estrogen receptor beta suppresses melanoma progression through modulation of melanocyte master regulator activity
Authors: Jocelyn Treneff, Amanda McCrary, Craig Burd
Journal: Cancer Research (2025)

Abstract Female sex is associated with lower overall melanoma incidence and mortality, with estrogen signaling thought to protect against disease progression. Genomic estrogen signaling is mediated by estrogen receptors alpha (ERα) and beta (ERβ), which function as ligand-activated transcription factors. Notably, ERβ expression shows an inverse correlation with tumor thickness in the skin and is often lost in advanced melanomas, suggesting that ERβ activity may repress melanoma development. Here, we demonstrate that germline ERβ knockout leads to reduced melanoma-free survival in a murine model of NRASQ61R spontaneous melanomas. While this implicates ERβ as a tumor suppressor, little is understood about the molecular activities of ERβ in melanomas and in melanocytes prior to transformation. To elucidate the genomic actions of the receptor, we performed ChIP-Seq in immortalized human melanocytes. We found that ERβ binding regions significantly overlap with those of MITF, a transcription factor that acts as a master regulator of melanocyte development. Changes in melanoma cellular phenotypes, such as increased proliferation, dedifferentiation, or invasiveness, are thought to be driven by differences in MITF activity. Therefore, we hypothesize that ERβ modulates MITF transcriptional activity in a way that suppresses melanoma progression. Using a reporter construct with activity driven by the tyrosinase (TYR) promoter, we showed that ERβ activation coincided with altered MITF regulation of reporter activity. As we have characterized overlapping ERβ and MITF recruitment in the TYR promoter, this result supports the hypothesis that ERβ co-binding can influence MITF transcriptional programs. Additionally, transcriptome analysis revealed that estrogen-responsive genes in melanocytes are enriched for migration and differentiation, biological processes that are directed by MITF and dysregulated in melanomas. Taken together, these findings indicate that ERβ functions as a tumor suppressor in melanoma by reprogramming MITF activity, identifying a new avenue through which melanoma may be better understood at the molecular level. Citation Format: Jocelyn Treneff, Amanda McCrary, Craig Burd. Estrogen receptor beta suppresses melanoma progression through modulation of melanocyte master regulator activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4055.
Abstract 4066: High throughput single-cell TCR sequencing method identifies cancer-specific TCR clonotypes
Authors: Efthymia Papalexi, Crina Curca, Bryan Hariadi, Alexa Suyama, Simone Marrujo, Gary Geiss, Charles Roco, Alexander Rosenberg
Journal: Cancer Research (2025)

Abstract Cancer cells produce tumor-specific antigens and neoantigens that can be recognized by T cells and induce their clearance. Single cell profiling of T cell receptors (TCRs) and gene expression enables the identification and characterization of tumor infiltrating T cells that have antigen recognition and killing capabilities. Existing microfluidic-based single cell sequencing methods have limited cell and sample throughput making it hard to perform longitudinal studies to capture changes in TCR repertoire dynamics during tumor progression and therapeutic interventions. Understanding these dynamics will be key in designing the next generation of immunotherapies. To overcome these limitations, we developed a combinatorial barcoding approach to simultaneously characterize the TCRs alongside the full transcriptomes of up to 1 million fixed T cells from up to 96 unique samples in a single experiment. To demonstrate this approach, we profiled 1 million human T cells stimulated with a variety of antigens including the tumor antigens MART-1, NY-ESO-1, HER2/Neu, MAGE-A10, WT-1 and Tyrosinase. Using our technology, we recovered paired TCR alpha and beta clonotype information in 82% of all T cells. We estimated the clonotype diversity and found that the tumor antigen-stimulated samples had lower diversity than the controls. Specifically, when looking at the top three most expanded clonotypes for each sample we show that they account for 8-99% of all detected clonotypes. Next, we searched publicly available databases and showed our method not only detects previously annotated disease-specific CDR3 sequences but also uncovers previously unknown ones. Finally, we ran multiple sequence alignments and identified CDR3 sequence motifs unique to each antigen-stimulated population. In summary, we present a highly flexible and scalable method to single cell TCR profiling to allow researchers to profile up to 1 million T cells and up to 96 samples in a single experiment. We envision our approach to be invaluable in investigating T cell functional responses during infection, cancer, autoimmunity, or therapeutic interventions and pave the way for the development of new immune-based therapies. Citation Format: Efthymia Papalexi, Crina Curca, Bryan Hariadi, Alexa Suyama, Simone Marrujo, Gary Geiss, Charles Roco, Alexander Rosenberg. High throughput single-cell TCR sequencing method identifies cancer-specific TCR clonotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4066.
Abstract 1705: MUC1-C is a target for antibody-drug conjugate treatment of MRTX1133-resistant KRAS G12D mutant pancreatic ductal adenocarcinomas
Authors: Hiroki Ozawa, Keisuke Shigeta, Shinkichi Takamori, Atrayee Bhattacharya, Donald Kufe
Journal: Cancer Research (2025)

Abstract Background: The MUCIN 1 (MUC1) gene evolved in mammals to protect barrier tissues from biotic and abiotic insults. MUC1 encodes a transmembrane MUC1-C subunit that is activated in response to the loss of homeostasis and promotes proliferative, inflammatory, and remodeling responses necessary for wound repair. However, in contrast to its protective function, prolonged activation of MUC1-C by chronic inflammation drives cancer progression. In cancer cells, MUC1-C forms complexes with receptor tyrosine kinases (RTKs), such as EGFR, at the cell membrane, contributing to downstream RTK→RAS signaling pathways. Previous research identified MUC1-C addiction in KRAS G12D mutant pancreatic ductal adenocarcinoma (PDAC) cells, against which there are limited therapeutic options. Treatment of KRAS G12D mutant PDACs has been advanced by development of the MRTX1133 inhibitor; however, resistance to this agent invariably occurs by unclear mechanisms. Results: We report that treatment of PDAC KRAS G12D cells with the MRTX1133 inhibitor is associated with marked induction of cell surface MUC1-C expression. Our results demonstrate that MRTX1133 activates an inflammatory MUC1-C/NF-κB p65 auto-inductive pathway. We further demonstrate that MRTX1133-induced MUC1-C/NF-κB signaling (i) regulates the gasdermin E (GASDME) pore-forming protein that paradoxically protects PDAC cells from pyroptosis, (ii) drives ZEB1 and the epithelial-mesenchymal transition (EMT), and (iii) is necessary for MRTX1133 resistance. These results indicate that MUC1-C is a target for the treatment of MRTX1133 resistant PDAC tumors. There are presently no effective antibody-drug conjugates (ADCs) for PDAC treatment. In extending our results, we show that an anti-MUC1-C ADC is highly effective against MRTX1133-resistant PDAC KRAS G12D cells and that targeting MUC1-C with the ADC is synergistic with MRTX1133 in vitro. We also demonstrate that the anti-MUC1-C ADC inhibits growth of PDAC MRTX1133 resistant tumor xenografts and PDX models. Conclusions: These findings indicate that MUC1-C confers resistance of PDAC KRAS G12D mutant cells to MRTX1133 and identify MUC1-C as a target for ADC treatment of patients refractory to MRTX1133 treatment. Citation Format: Hiroki Ozawa, Keisuke Shigeta, Shinkichi Takamori, Atrayee Bhattacharya, Donald Kufe. MUC1-C is a target for antibody-drug conjugate treatment of MRTX1133-resistant KRAS G12D mutant pancreatic ductal adenocarcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1705.
Abstract 2915: WRN depletion sensitizes the ARID1A-mutated cancers by inducing a distinct DNA damage response
Authors: Jiwon Kim, Sung-Yup Cho
Journal: Cancer Research (2025)

Abstract SWI/SNF complex, which remodels chromatin structure to regulated transcription, is frequently mutated in various cancer types. ARID1A, a critical subunit of the SWI/SNF complex, is mutated in approximately 20% of colorectal cancers. Several synthetic lethal targets have been identified to address ARID1A-mutated cancers in various studies; ARID1B, EZH2, ATR, and AURKA-CDC25C. Notably, around 15% of ARID1A mutations are associated with microsatellite instability (MSI). In this study, we propose that WRN, already established as a synthetic lethal target of MSI cancers, is a promising therapeutic target in ARID1A-mutated cancers. In ARID1A-mutated cancer cells, WRN depletion reduced proliferation and increased apoptosis, underscoring its potential as a selective vulnerability. Interestingly, we observed distinct DNA damage response pathways triggered by WRN depletion depending on the presence of ARID1A mutations. In ARID1A wild type cells, WRN knockdown predominantly activated Chk1, whereas in ARID1A-mutated cells, Chk2 activation was more prominent. Further investigation revealed that ATR and Chk1 expression were downregulated in ARID1A-mutated cells. These findings suggest that Chk1 defects drive Chk2 activation in ARID1A-mutated cancers, presenting a distinct therapeutic opportunity to exploit this differential DNA damage response mechanism in ARID1A-mutated cancers. Citation Format: Jiwon Kim, Sung-Yup Cho. WRN depletion sensitizes the ARID1A-mutated cancers by inducing a distinct DNA damage response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2915.
Abstract 3227: Components of interleukin-4 signaling are enriched in melanoma patients who respond to anti-PD-1 or anti-CTLA-4 therapy
Authors: Szonja Anna Kovacs, Janos Tibor Fekete, Balazs Gyorffy
Journal: Cancer Research (2025)

Abstract Background: Immune checkpoint inhibitors represent an advanced class of immunotherapy drugs used to treat various cancers, including melanoma, particularly in advanced stages. These therapies work by targeting immune checkpoints — proteins such as PD-1, PD-L1, and CTLA-4 — that act as brakes on the immune system. Prognostic biomarkers are essential for predicting disease outcomes, thereby enabling improved patient management. Methods: We obtained transcriptomic and clinical data from melanoma patients treated with immune checkpoint inhibitors through the NCBI Gene Expression Omnibus and CRI iAtlas. After reviewing 246 datasets, we excluded those involving cell lines, unrelated diseases, or treatments. The expression data were quantile-normalized, and statistical analyses were conducted using the R environment. Survival data were excluded for patients without an event if follow-up ended before 12 months. Cox regression was applied to overall survival (OS) data. Results: Altogether, 423 melanoma samples had sufficient data for survival analysis. Elevated expression of IL4R (interleukin-4 receptor, HR=0.33, FDR=2%, log-rank P=5.7E-04), JAK1 (Janus kinase 1, HR=0.3, FDR=1%, log-rank P=2.8E-04), GFI1 (growth factor independence 1, HR=0.35, FDR=5%, log-rank P=2.2E-03), and PTPN6 (protein tyrosine phosphatase non-receptor type 6, also known as SHP-1, HR=0.31, FDR=5%, log-rank P=1.9E-03) correlated with improved OS after anti-PD-1 therapy. Similar findings were observed after anti-CTLA-4 therapy for IL4R (HR=0.13, FDR=1%, log-rank P=3.2E-04), JAK1 (HR=0.14, FDR=1%, log-rank P=9.3E-04), and PTPN6 (HR=0.09, FDR=1%, log-rank P=2E-04). Signals mediated by interleukin-4 and interleukin-13 through these genes promote improved immune responses, cell survival, and differentiation. Finally, the Kaplan-Meier Plotter (www.kmplot.com) web platform was updated with our newly compiled immunotherapy cohort. Conclusions: In melanoma patients, elevated expression of IL4R, JAK1, GFI1, and PTPN6 following anti-PD-1 and anti-CTLA-4 immunotherapies may enhance immune cell recognition, increase treatment efficacy, and extend survival. Our analytical platform supports a deeper understanding of patient responses and facilitates biomarker validation in a large cohort of melanoma patients. Citation Format: Szonja Anna Kovacs, Janos Tibor Fekete, Balazs Gyorffy. Components of interleukin-4 signaling are enriched in melanoma patients who respond to anti-PD-1 or anti-CTLA-4 therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3227.
Abstract 1499: Combination HIF-2alpha inhibition with cholesterol biosynthesis inhibition decreases colorectal carcinoma growth
Authors: Prarthana Dalal, Boyan Hu, Rashi Singhal, Yatrik Shah
Journal: Cancer Research (2025)

Abstract Hypoxic stress in solid tumors promotes cancer cell growth and survival and confers therapeutic resistance. Hypoxia inducible factors (HIFs) are transcription factors that help cells adapt to hypoxic stress. HIFs are often overexpressed in tumors and are associated with worse clinical outcomes. HIF inhibition is a novel therapeutic strategy and belzutifan is a first-in-class HIF-2α inhibitor. Belzutifan has recently been approved for metastatic renal cell carcinoma treatment. However, despite studies showing that HIF-2α is a critical regulator of colorectal carcinoma, belzutifan is not effective in pre-clinical studies of colorectal carcinoma (CRC) growth. HIF-2α inhibition with a small molecule inhibitor, belzutifan, does not affect proliferation of CRC cells (HCT116, SW480) under normoxic or hypoxic conditions. The primary objective of this study was to identify metabolic vulnerabilities in CRC caused by HIF-2α inhibition that can be synergistically targeted to increase cancer cell death. We first performed an unbiased CRISPR screen and identified the cholesterol biosynthesis pathway as a potential target. Inhibiting the cholesterol biosynthesis pathway with HMG-CoA reductase inhibitors, statins, potentiates cell death and reduces in vitro proliferation of HCT116 and SW480 cells when combined with HIF-2α genetic knockdown or HIF-2α inhibition. This effect is dose-dependent in nature and is preserved across the statins class as tested with pitavastatin, simvastatin, and atorvastatin. Planned future studies include in vivo experimentation with autochthonous mouse models of CRC to assess how combination treatment with statin and HIF-2α inhibition affects tumor progression. Ultimately, statins are a widely used, safe, and affordable treatment for atherosclerosis and our data shows that combining statins with belzutifan may be a synergistic therapeutic strategy for CRC. Citation Format: Prarthana Dalal, Boyan Hu, Rashi Singhal, Yatrik Shah. Combination HIF-2alpha inhibition with cholesterol biosynthesis inhibition decreases colorectal carcinoma growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1499.
Abstract 3232: Developing PRMT5 inhibition-based Immuno-oncology combination therapies in MTAP-loss tumors
Authors: Si Chen
Journal: Cancer Research (2025)

Abstract Hyperactivated protein arginine methyltransferases (PRMTs) are implicated in human cancers. Inhibiting tumor-intrinsic PRMT5 has been shown to enhance antitumor immune responses, suggesting the potential of combining PRMT5 inhibitors (PRMT5i) with immunotherapy. However, global PRMT5 inhibition can impair immune cells functions. This study aims to identify strategies for tumor-specific PRMT5 inhibition and PRMT5i-based immuno-oncology (IO) combinations, especially for methylthioadenosine phosphorylase (MTAP)-loss cancers. Isogeneic tumor lines with and without MTAP loss were generated using CRISPR/Cas9 knockout. MTAP inactivation was confirmed by methylthioadenosine (MTA) accumulation and reduced symmetric dimethylarginine levels in MTAP-KO cell lines. Two PRMT5 inhibitors, GSK3326595 (substrate-competitive) and MRTX1719 (MTA-cooperative), were evaluated on tumor and immune cells. As shown in the Table 1, GSK3326595 suppressed PRMT5 activity and cell proliferation in both tumors and immune cells, regardless of MTAP status. Conversely, MRTX1719 selectively inhibited PRMT5 in MTAP-loss tumors, while treated T cells retained cytokine production and cytotoxicity. Transcriptomic and proteomic analyses revealed that MRTX1719 reduced PI3K pathway activation, a well-characterized immune resistant mechanism. In MTAP-loss syngeneic murine models, MRTX1719 combined with anti-PD-1 slowed tumor growth and extended survival (e.g., MC38/gp100 MTAP-KO tumor day 21: Ctrl 95.82±8.87 mm2, PRMT5i 99.99±6.34 mm2, anti-PD-1 94.47±6.76 mm2, combination 72.81±4.14 mm2; B16 MTAP-KO tumor day 18: Ctrl 108.24±9.13 mm2, PRMT5i 106.45±22.54 mm2, anti-PD-1 92.72±28.07 mm2, combination 47.97±22.23 mm2). The combination also increased CD8+ T cell proliferation in MTAP-KO tumor tissues. Collectively, our results provide a strong rationale for the clinical development of MRTX1719-based IO combinations in MTAP-loss tumors. Citation Format: Si Chen. Developing PRMT5 inhibition-based Immuno-oncology combination therapies in MTAP-loss tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3232.
State-Level Policies and Antibiotic Use for Pediatric Conjunctivitis
Authors: Isdin Oke, Alexandra T. Geanacopoulos, S.V. Subramanian, Ann Chen Wu, Naomi S. Bardach, Daniel J. Shapiro
Journal: JAMA Pediatrics (2025)

This cross-sectional study examines the patterns of topical antibiotics dispensation to commercially insured school-aged children with acute infectious conjunctivitis.