tbuckley/cabot-search huggingface dataset:
Abstract 3900: Integrating single-molecule localization microscopy and computational pipelines to elucidate ecDNA dynamics
Authors: Mesut Unal, Jessica Alsing, Gabrielle S. Dewson, Guy Nir, Kadir C. Akdemir
Journal: Cancer Research (2025)

Abstract Extrachromosomal DNA (ecDNA) is prevalent across various cancer types, notably Glioblastoma Multiforme (GBM), where it facilitates the rapid acquisition of high oncogene copy numbers by cancer cells. These ecDNAs exhibit self-replication and are randomly distributed to daughter cells during mitosis, resulting in uneven segregation. This leads to variations in oncogene copy numbers among subclones, contributing to significant intratumoral heterogeneity. Traditional sequence-based analyses are insufficient for addressing spatial heterogeneity. To overcome this limitation, we propose utilizing sequential OligoSTORM imaging combined with single-molecule localization microscopy (SMLM), an innovative hybridization technique, and a computational pipeline. Our hybridization method significantly enhances imaging speed: whereas imaging approximately 40 loci with typical sequential OligoSTORM requires 11 days to obtain data from about 20 cells, this method enables imaging of 104 loci within the same time frame. Additionally, we developed a computational pipeline to complement this technique. Together, these tools enable 3D imaging of chromosomes with a high resolution of 20 kb. Our hybridization approach allows imaging at both 100-kb and 20-kb resolution steps, organized hierarchically in a Matryoshka-like structure. Our pipeline incorporates advanced computational algorithms, including iterative closest point (ICP) and space-partitioning data structures, to precisely align each 20-kb sub-step to its corresponding 100-kb step. Using this methodology, we target the EGFR gene locus with high resolution. To validate our approach, we are applying it to a non-cancerous microglial cell line (HMC3) as a control and a patient-derived glioblastoma stem-like cell (GSC) line as our GBM model. The GSC line, rich in ecDNA content with an average of 18 ecDNAs per cell, demonstrates pronounced tumor heterogeneity, including significant EGFR amplifications among subclones. Through this methodology, we can elucidate the structural organization of ecDNAs containing oncogenes and their regulatory elements with fine precision. Furthermore, our approach seamlessly integrates these structural insights with matched single-cell genomic data. This combined strategy offers a comprehensive understanding of ecDNA dynamics in cancer, shedding light on tumor heterogeneity at both spatial and genomic levels and paving the way for novel insights into oncogene-driven cancer biology. Citation Format: Mesut Unal, Jessica Alsing, Gabrielle S. Dewson, Guy Nir, Kadir C. Akdemir. Integrating single-molecule localization microscopy and computational pipelines to elucidate ecDNA dynamics [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 3900.
Abstract 5407: Identifying synthetic lethality targets in DDX41-mutated MDS/AML
Authors: Sohaumn Mondal, Shizuo Yang, Vincent Maranda, Frederick Vizeacoumar, Franco Vizeacoumar, Yuliang Wu
Journal: Cancer Research (2025)

DDX41 (DEAD-box helicase 41) is a member of the DEAD-box helicase family, critical for RNA metabolism and genome stability. Mutations in DDX41 are strongly associated with myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), particularly in patients carrying inherited mutations or somatic alterations. Among these, the R525H missense mutation in DDX41 is found in over 70% of affected individuals, impairing helicase activity and contributing to disease pathology. Directly targeting mutant DDX41 (e.g., R525H) with inhibitors remains challenging due to the structural similarity of mutant and wild-type (WT) proteins, as well as the conserved helicase domains shared by the 37 DEAD-box helicases in humans. To overcome these challenges, we are leveraging synthetic lethality (SL) as an innovative therapeutic strategy. Bioinformatic analyses identified potential SL partners of DDX41, including WRN and DDX23. Functional validation experiments revealed that inhibiting WRN helicase selectively impairs the growth of DDX41-deficient cells. In DDX41-knockout HeLa cells, treatment with WRN inhibitors NSC 617145 and HRO761 significantly reduced cell growth compared to WT controls. Similarly, in DDX41-knockdown U2OS cells, WRN inhibitors markedly inhibited cell proliferation compared to WT cells. Future studies aim to elucidate the molecular mechanisms underlying SL interactions between DDX41 and its partners, providing insights into the therapeutic potential of targeting these vulnerabilities. This work offers a promising avenue for developing novel treatments for MDS/AML patients harboring DDX41 mutations, ultimately improving clinical outcomes. Citation Format: Sohaumn Mondal, Shizuo Yang, Vincent Maranda, Frederick Vizeacoumar, Franco Vizeacoumar, Yuliang Wu. Identifying synthetic lethality targets in DDX41-mutated MDS/AML [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 5407.
Abstract 3294: Subtype-specific genetic drivers of immune evasion in breast cancer
Authors: Otilia Menyhart, Balazs Gyorffy
Journal: Cancer Research (2025)

Abstract Introduction: Immune evasion is a hallmark of cancer and a significant driver of therapeutic resistance. While immunotherapy has shown promise in highly immunogenic cancers, its efficacy in breast cancer (BC) remains limited, particularly in less immunogenic subtypes. We aimed to investigate the prognostic relevance of two immune-related gene signatures—106 genes associated with evasion of immune destruction (EID) and 182 genes linked to evasion of killing by cytotoxic T lymphocytes (ECTL)—across distinct BC subtypes. Methods: Transcriptomic and clinical data from three integrated datasets (GEO, n=1, 965; TCGA, n=1, 069; and GSE96058, n=2, 976) were analyzed. Expression of immune evasion-related genes was stratified by BC subtype using PAM50 classification. Survival analysis was conducted using Kaplan-Meier curves and Cox regression models, stratifying gene expression into high- and low-expression groups. A False Discovery Rate (FDR) correction was applied to ensure statistical robustness. Subtype-specific survival associations were further evaluated with individual gene-level analyses. Results: High mean expression of the ECTL signature was significantly associated with improved overall survival (OS) in triple-negative BC (TNBC) patients (HR = 0.25, 95% CI = 0.16-0.4, p = 8.6e−10, FDR &amp;lt; 1%). Similar trends were observed in HER2-enriched BC but were less pronounced after FDR correction. For the 106 EID genes, high mean expression correlated with favorable OS in TNBC (HR = 0.3, 95% CI = 0.18-0.49, p = 3.4e−7). Gene-level analysis identified essential immune evasion genes, including CXCL10, CXCL9, CXCR4, and JAK3, as robust predictors of survival in TNBC, validated across independent datasets. The new, combined four-gene signature showed significant predictive power for response to immune checkpoint inhibitors (ICI), with an AUC of 0.722 (p = 1.3e−7). Conclusions: Immune evasion-related gene signatures exhibit subtype-specific prognostic value, particularly in TNBC and HER2-enriched BC. A signature based on genes within these signatures represent potential biomarkers for predicting survival outcomes and guiding immunotherapy. Citation Format: Otilia Menyhart, Balazs Gyorffy. Subtype-specific genetic drivers of immune evasion in breast cancer [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 3294.
Abstract 3902: Evolution of esophageal adenocarcinoma from precursor lesion stem cells
Authors: Wa Xian, Frank McKeon, Jaffer Ajani, Caycel Desales, Ashley Hoffman, Amber Su, Crystal Nguyen, Rick Russell, William Bachovchin
Journal: Cancer Research (2025)

Abstract Metastatic cancers arise from a decades-long succession of increasingly virulent precursor lesions, each of which represents prospective targets for therapeutic intervention. This evolutionary process has been particularly vivid in esophageal adenocarcinoma (EAC), as this cancer and associated precursor lesions, including Barrett's esophagus (BE), low-grade dysplasia (LGD), and high-grade dysplasia (HGD), co-exist in an accessible, two-dimensional pattern in esophageal mucosa. Given the durability of these precursor lesions, it is likely that they, like EAC, rely on stem cells for their regenerative growth. To assess the role of stem cells in the evolution of EAC, we applied technology that selectively clones stem cells from the gastrointestinal tract to patient-matched endoscopic biopsies from each of the precursor lesions implicated in EAC. Histologically validated, endoscopic biopsy series including EAC, HGD, LGD, BE, and normal esophageal mucosa were obtained from patients presenting with early (T1) EAC. Rare (1:1, 000) cells from each of these lesions proved clonogenic and were assessed by in vitro differentiation, tumorigenicity in mice, and by molecular genetics. Each of the lesions in the evolution of EAC possess a discrete set of clonogenic cells marked by immaturity, enormous proliferative potential, and lesion-specific differentiation fate. DNA sequencing of these clones reveal intralesional heterogeneity and clonal resolution of the mutation progression within a given patient from BE, LGD, HGD, and EAC. High-throughput chemical screens against BE stem cells reveal drug combinations that are similarly effective against stem cells of LDG, HGD, and EAC. Citation Format: Wa Xian, Frank McKeon, Jaffer Ajani, Caycel Desales, Ashley Hoffman, Amber Su, Crystal Nguyen, Rick Russell, William Bachovchin. Evolution of esophageal adenocarcinoma from precursor lesion stem cells [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 3902.
Abstract 3339: Evaluation of GATA6 and KRT17 immunostaining for subtype classification in pancreatic ductal adenocarcinoma
Authors: Ruomeng Fang, Joan Miguel Romero, Yifan Wang, Alicia Gomez Mendez, Adeline Cuggia, George Zogopoulos
Journal: Cancer Research (2025)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy with poor survival outcomes. Transcriptomic profiling has identified distinct PDAC subtypes associated with survival, highlighting their clinical relevance. However, reliance on RNA sequencing for subtype classification is not feasible in routine clinical practice, underscoring the need for surrogate biomarkers that are both effective and practical for predicting patient outcomes. This study evaluated GATA6 and KRT17 as multiplex immunohistochemistry (IHC) biomarkers to develop a prognostic model for PDAC subtype classification. Using a tissue microarray (TMA) comprising 130 patient-derived xenografts (PDXs), we quantified cell IHC positivity and stratified samples into subtypes based on GATA6 and KRT17 expression. Whole-slide staining of representative patient tumors validated the consistency of subtype classifications between PDXs and corresponding patient tumors. Patient TMAs (224 cores from 82 tumors) were subsequently analyzed to refine the classification system, incorporating GATA6 and KRT17 positive cell percentages, staining intensity (H-scores), and clinical variables into a comprehensive prognostic model. Initial classification based on PDX models demonstrated non-significant distinct survival trends (p=0.14), likely due to sample size limitations. However, a refined model applied to patient TMAs that incorporated additional parameters effectively stratified patients into prognostic groups with significantly different overall survival (p=0.042). These findings highlight the utility of GATA6 and KRT17 as surrogate classifiers for PDAC subtype classification and prognostication, offering a practical alternative to transcriptomic sequencing in HR-proficient PDAC. Citation Format: Ruomeng Fang, Joan Miguel Romero, Yifan Wang, Alicia Gomez Mendez, Adeline Cuggia, George Zogopoulos. Evaluation of GATA6 and KRT17 immunostaining for subtype classification in pancreatic ductal adenocarcinoma [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 3339.
Abstract 4248: Statin-derived small-molecule inhibitors of metastasis (SIM) for high-risk epithelial cancers
Authors: Moe Ishihara, Junhui Hu, Glen Brodie, Elizabeth Bowen, Shannon Shams, Diana Vaca, Jimin Kim, Stuart Conway, Robert Damoiseaux, Lily Wu
Journal: Cancer Research (2025)

Abstract Background: Metastasis is the deadliest cancer stage, and there is no universal treatment. Different tumors have distinct tissue-specific signatures, but as cancer progresses, they follow a common evolutionary trajectory toward invasiveness and metastasis. Targeting this shared vulnerability in metastatic tumors holds significant translational potential. Recent insights from kidney cancer reveal a novel metastatic mechanism, leading to the discovery of small-molecule drugs, SIMs, that selectively inhibit metastasis across cancers. By understanding SIMs, we aimed to create safer, more effective treatments, potentially saving over 500, 000 lives annually in the U.S. Methods &amp; Results: 1) New concept: Metastasis requires cooperation between VHL+ and VHL- cells, with VHL- cells driving growth and migration in VHL+ cells. 2) SIM candidates: In high-throughput screening of 2, 530 FDA-approved drugs, small-molecule compounds selectively inhibiting VHL cells were identified, with fluvastatin being the most potent ("SIM-1"). Subsequent SAR studies identified SIM-2, four times more potent than fluvastatin (IC50 &amp;lt; 0.1uM). 3) Older statins (fluvastatin, simvastatin) were more cytotoxic than newer statins (e.g., atorvastatin and rosuvastatin) despite a lower affinity for their known target, HMG-CoA reductase (HMGCR). Thus, SIMs target a pathway distinct from cholesterol-lowering or HMGCR.4) Transcriptomics and proteomics analyses suggest that older statins may target a non-HMGCR molecule in their anti-metastatic activities, possibly explaining mixed clinical trial results regarding statin use as antineoplastics.5) SIMs are effective in treating various cancers, including kidney, breast (TNBC), and prostate (NEPC). Conclusions: Critical steps to advancing SIM development toward clinical translation are (i) target identification and (ii) target and therapeutic validation. While our focus is on metastatic renal cell carcinoma (mRCC) to identify SIM's drug target, strategic findings from this project will be directly relevant to other high-risk urological cancers. By investigating this further, we could develop a novel pan-cancer anti-metastatic drug. Citation Format: Moe Ishihara, Junhui Hu, Glen Brodie, Elizabeth Bowen, Shannon Shams, Diana Vaca, Jimin Kim, Stuart Conway, Robert Damoiseaux, Lily Wu. Statin-derived small-molecule inhibitors of metastasis (SIM) for high-risk epithelial cancers [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 4248.
Abstract 5395: CDK12 regulates cellular metabolism to promote therapy resistance in glioblastoma
Authors: Jeong-Yeon Mun, Chang Shu, Qiuqiang Gao, Hasan O. Akman, Mike-Andrew Westhoff, Georg Karpel-Massler, Markus D. Siegelin
Journal: Cancer Research (2025)

Abstract Glioblastoma IDH-wildtype, the most common primary brain cancer in adults, has an exceedingly poor prognosis of only one to two years despite standard treatment involving surgery, temozolomide, and radiation. We evaluated patient-derived xenograft GBM cultures to determine their sensitivity to disrupting the function of CDK12, which was achieved through genetic manipulation, shRNA, or the novel inhibitor SR-4835. GBM metabolism was assessed using extracellular flux analysis and LC/MS-based carbon tracing. The in vivo efficacy was evaluated in orthotopic GBM mouse models. Comprehensive screening approaches identified CDK12 as essential for GBM growth. Consistently, inhibiting CDK12 function led to reduced growth in GBM PDX lines in vitro, but not in human astrocytes. Notably, SR-4835 inhibited GBM growth at low nanomolar concentrations and synergistically enhanced the potency of temozolomide. In vivo, SR-4835 activated cell death machinery related to intrinsic apoptosis. Metabolic analyses demonstrated that the loss of CDK12 function substantially impaired cellular respiration, coupled with the suppression of key metabolic transcriptional regulators, PGC1A and PPARD. This resulted in energy depletion and apoptotic cell death, partially mediated by the pro-apoptotic protein Noxa. The inactivation of CDK12 significantly extended the overall survival time without any harmful side effects in orthotopic mouse models of GBM. In some subjects, it also led to the complete elimination of brain tumors. When used together with temozolomide, blocking CDK12 eradicated brain tumors in all animals studied, indicating that CDK12 is a highly promising treatment target for GBM and providing a solid foundation for future clinical trials involving patients with this devastating disease. Citation Format: Jeong-Yeon Mun, Chang Shu, Qiuqiang Gao, Hasan O. Akman, Mike-Andrew Westhoff, Georg Karpel-Massler, Markus D. Siegelin. CDK12 regulates cellular metabolism to promote therapy resistance in glioblastoma [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 5395.
Abstract 4279: FAK inhibitor APG-2449 induces immunogenic cell death and enhances anti-tumor immunity in cervical cancer through the PERK-eIF2α pathway
Authors: Lin Zhang, Mingyue Zhang, Weihan Kang, Jing Xiao, Maple Tse, Yong Du, Dajun Yang
Journal: Cancer Research (2025)

The focal adhesion kinase (FAK) inhibitor APG-2449, a multi-target tyrosine kinase inhibitor that also targets ALK and ROS1, has demonstrated significant potential for inducing anti-tumor immunity. In this study, we explored the effects of APG-2449 on cervical cancer, emphasizing its capacity to induce immunogenic cell death (ICD) and stimulate immune responses via the PERK-eIF2α pathway. Our findings indicate that APG-2449 enhances ATP release and calreticulin (CRT) exposure on the surface of tumor cells, which are key indicators of ICD. Moreover, treatment with APG-2449 led to a notable increase in dendritic cell (DC) maturation and promoted their differentiation into classical dendritic cells (cDCs), which are essential for antigen presentation and the subsequent activation of T-cells.In vitro co-culture models, APG-2449 effectively boosted the activation of DCs and increased the frequency of tumor-specific CD8+ T cells. These observations underscore that APG-2449 elicits a robust immunogenic response, suggesting that inhibition of FAK/ALK/ROS1 could be a promising therapeutic approach for enhancing anti-tumor immunity in cervical cancer.These results highlight the potential of APG-2449 as an innovative therapeutic agent capable of modifying the tumor microenvironment to foster an effective anti-tumor immune response via the FAK/PERK-eIF2α axis. Future studies are needed to determine the clinical efficacy of APG-2449, particularly in combination with other immunotherapies. Citation Format: Lin Zhang, Mingyue Zhang, Weihan Kang, Jing Xiao, Maple Tse, Yong Du, Dajun Yang. FAK inhibitor APG-2449 induces immunogenic cell death and enhances anti-tumor immunity in cervical cancer through the PERK-eIF2α pathway [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 4279.
Abstract 5674: StarBrightTM Dyes for flow cytometry, western blotting, microscopy and Genesis System with CelSelect Slides
Authors: Michael Blundell, Leon Huang, Sharon Sanderson
Journal: Cancer Research (2025)

Abstract There are many antibody-based applications in the researcher’s toolbox that rely on both high-quality antibodies and bright stable fluorescent dyes. Antibodies are usually validated for specific applications and may only work on fresh samples and not work if a sample is fixed. The same application specificity can also be observed with fluorescent dyes. Some dyes are easily bleached, may not be stable after fixation and have spectral profiles that make it impossible to multiplex in some applications. To be able to use multiple applications, researchers may need to purchase three or four versions of an antibody or use sub-optimal choices to keep costs manageable. Here we present data on StarBright Dyes, a range of 33 fluorescent dyes, in a multitude of antibody-based applications. They are bright, have low cross laser excitation, can be fixed in PFA and alcohol-based buffers and work in all protocols without specific buffers, especially when multiplexing. StarBright Dyes have been developed to give researchers high quality data whilst providing flexibility and choice regardless of the application. They work in flow cytometry, allowing very high plex panels to be developed with manageable spillover and spreading, require no special buffer and even allow storage of premixed panels. In western blot their brightness, short exposure time and low background makes them ideal for detection of a single target, or in multiplexing. Their brightness allows easy identification and enumeration in cell enrichment systems such as the Genesis SystemTM. Finally in microscopy, both wide field and confocal, their photostability, range of emission, and brightness, not only gives more choice, but as they can be used as primaries without the need for secondary amplification can speed up staining protocols and allow panel expansion without species cross reactivity. Here we demonstrate how you can reduce the number of fluorophores and antibodies required for each application and simplify your protocols by including StarBright Dye conjugated antibodies in your experiments. Citation Format: Michael Blundell, Leon Huang, Sharon Sanderson. StarBrightTM Dyes for flow cytometry, western blotting, microscopy and Genesis System with CelSelect Slides [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 5674.