tbuckley/cabot-search huggingface dataset:
Abstract 4154: Cancer cells exhibit novel metabolic vulnerabilities when exposed to low lipid environments
Authors: Diya L. Ramesh, Keene L. Abbott, Raphael Ferreira, Matthew G. Vander Heiden
Journal: Cancer Research (2025)

Abstract Cancer cell metabolism is significantly influenced by microenvironmental factors such as nutrient availability, which can vary across different tissues and introduce exploitable therapeutic vulnerabilities. Notably, lipid availability is particularly low in the brain compared to other tissues. To identify metabolic vulnerabilities of cells in lipid-poor environments, we performed a CRISPR/Cas9 screen of metabolic synthesis genes in human cancer cells cultured in lipid-rich versus lipid-poor media. Through this screen, we observed a novel metabolic dependency in the cells when grown in lipid-depleted conditions. We verified this differential dependency by knockout (KO) of this target gene, which resulted in slower cell proliferation in lipid-depleted media. Additionally, wild-type cells displayed heightened sensitivity to inhibitors of other proteins in the pathway in lipid-depleted conditions, thereby phenocopying the KO. Polar metabolomics analyses by LC-MS revealed depletion of several nucleotide species in the KO cells cultured in lipid-depleted conditions, and supplementation with purine nucleotides rescued the proliferation of KO cells cultured in lipid-depleted media. We hypothesized that this nucleotide depletion could in turn result in nucleotide imbalance and DNA damage, and Western Blot analyses confirmed elevated DNA damage levels in the KO cells in lipid-depleted media. Our model is that in low-lipid environments, the KO redirects metabolic resources toward lipid synthesis, causing nucleotide imbalance, DNA damage, and cell death. Overall, our findings indicate that cancer cells exhibit novel metabolic vulnerabilities when exposed to lipid-depleted environments, which could be leveraged for treating tumors growing in lipid-poor organs such as the brain. Citation Format: Diya L. Ramesh, Keene L. Abbott, Raphael Ferreira, Matthew G. Vander Heiden. Cancer cells exhibit novel metabolic vulnerabilities when exposed to low lipid environments [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 4154.
Abstract 4035: Elucidating the DNA binding dynamics of EWSR1::FLI1 using biochemical methods
Authors: Jack Tokarsky, Blanche Chen, Michael G. Poirier, Emily Theisen
Journal: Cancer Research (2025)

Abstract Importance: This work signifies a breakthrough in our ability to study Ewing sarcoma by developing a protocol to purify functional WT EWSR1::FLI1. This development changes the level of detail to which we can study EWSR1::FLI1 and potentially other difficult to purify fusion oncoproteins. Objective: Ewing sarcoma is a pediatric bone and soft tissue sarcoma that arises in adolescents and young adults. The mutation that causes &amp;gt;85% of Ewing sarcoma cases is caused by the fusion oncoprotein, EWSR1::FLI1. Efforts to purify recombinantly expressed EWSR1::FLI1 have proven challenging for decades due to aggregation caused by the low complexity domain (LCD) of EWSR1. Our goal was to purify recombinantly expressed and functional EWSR1::FLI1 to quantitatively understand the nature of binding dynamics to various DNA sequences. Methods: We successfully expressed and purified EWSR1::FLI1 using a newly developed protocol. We performed electrophoretic mobility shift assays (EMSAs) to test binding of EWSR1::FLI1 on naked- and nucleosome-wrapped DNA. Binding constants were determined with DNA containing either a canonical high affinity (HA) ETS DNA binding sequence or a 2X GGAA microsatellite repeat. Results: Our laboratory has successfully developed a protocol to consistently achieve highly pure and functional EWSR1::FLI1. EWSR1::FLI1 has approximately 7-fold tighter binding to a 2X GGAA repeat, than to HA ETS sequence. For comparison, the minimal FLI DNA binding domain proteins (ETS85 and ETS102) bind to HA ETS sequences and GGAA microsatellites at similar affinities. These experiments suggest that the EWSR1 LCD alters the binding dynamics of the ETS DBD domain and that EWSR1::FLI1 preferentially binds to GGAA microsatellites. We tested the pioneer function of EWSR1::FLI1 by performing EMSAs with nucleosome-wrapped DNA. EWSR1::FLI1 bound to nucleosome-wrapped DNA containing GGAA repeats with only 3-fold less affinity than naked DNA. For comparison, when ETS85 and ETS102 bound nucleosome-wrapped DNA, this affinity was ∼30-fold less, showing potentially weak pioneering function of the FLI DBD. Conclusions&amp; Relevance to Pediatric Care: These studies allow us to understand the physical nature of fusion oncoproteins such as EWSR1::FLI1 and will be the foundation for therapeutics that could be used to treat Ewing sarcoma patients. Citation Format: Jack Tokarsky, Blanche Chen, Michael G. Poirier, Emily Theisen. Elucidating the DNA binding dynamics of EWSR1::FLI1 using biochemical methods [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 4035.
Abstract 3534: TPIPE, a pipeline for the identification and functional assessment of therapeutic cancer vaccine candidates
Authors: Christoph Schifflers, Martijn Vlaming, Emmanuelle Sidot, Jezabel Lefevre, Elise Pepermans, Ellen Boelen, Sofie Pattyn
Journal: Cancer Research (2025)

Abstract Therapeutic vaccination is a promising strategy for personalized cancer therapy. Using this approach, anadaptive T cell mediated immune response can be mounted against peptides presented by cancer cells, allowing for a systemic cancer cell eradication and immune memory formation.A key challenge for this approach is the identification of target peptides that are ubiquitously presented bycancer cells and capable of eliciting a cytotoxic T cell response. In this context, IQVIA Laboratories, In Vitro Immunology (formerly known as ImmunXperts) developed a pipeline for the Target Peptide Identification and the (functional) Peptide Evaluation (TPIPE) using in vitro generated peptide-specific T cells. This approach can be customized to be applicable to various therapeutic vaccine platforms. In brief, in silico prediction tools are used for the identification and pre-selection of candidate peptides.Peptide presentation is assessed by immunopeptidomics/MHC-associated peptide proteomics (MAPPs) in collaboration with ImmuneSpec. Upon identification of relevant targets, peptide-specific T cells aregenerated in vitro by co-culturing T cells with peptide-loaded/transfected dendritic cells. Peptide-reactivityis monitored over time by assessing the ability of the antigen-specific T cells binding to multimers via flowcytometry and in peptide re-stimulation FluoroSpot assays. The cytotoxic functionality of in vitro enriched peptide-specific T cells is subsequently evaluated in live-cell imaging, flow cytometry or colorimetry-based killing assays. Taken together, the TPIPE pipeline provides a customizable approach of the identification and functionalevaluation of therapeutic vaccines. TPIPE relies on high-quality pre-screened PBMCs, as provided by IQVIA Laboratories, In Vitro Immunology’s own biobank, covering a wide range of 4-digit HLA-typed healthy donor preparations. Citation Format: Christoph Schifflers, Martijn Vlaming, Emmanuelle Sidot, Jezabel Lefevre, Elise Pepermans, Ellen Boelen, Sofie Pattyn. TPIPE, a pipeline for the identification and functional assessment of therapeutic cancer vaccine candidates [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 3534.
Abstract 3860: Metastasis score: A powerful tool to determine the metastatic potential and the appropriate adjuvant therapy of melanoma
Authors: Kangjie Shen, Chuanyuan Wei, Jianying Gu
Journal: Cancer Research (2025)

Metastasis is the onerous challenge in the prognosis of melanoma patients. Accurately predicting the metastatic potential of non-metastatic melanoma (NMM) and determining effective postoperative adjuvant therapy for inhibiting metastasis remain uncertain. In this study, we conducted comprehensive analyses of melanoma metastases using bulk and single-cell RNA sequencing data, enabling the construction of a metastasis score (MET score) through multiple machine-learning algorithms. The reliability and robustness of the MET score were validated by various in vitro and in vivo assays. Our findings revealed a distinct molecular landscape in metastatic melanoma summarized by the enrichment of metastasis-related pathways, complex cell-cell communication, and heightened infiltration of pro-angiogenic tumor-associated macrophages compared to NMM. Importantly, patients of the high MET score group exhibited poorer prognoses and immunosuppressive microenvironment, featuring increased infiltration of regulatory T cells and decreased infiltration of CD8+ T cells, compared to the low MET score patient group. Expression of PD-1 was markedly higher in patients of low MET scores. Anti-PD-1 (aPD-1) therapy profoundly affected antitumor immunity activation and metastasis inhibition in these patients. In summary, our study demonstrates the effectiveness of the MET score in predicting melanoma metastatic potential. For patients with low MET scores, aPD-1 monotherapy may be a potential treatment strategy to inhibit metastasis. Patients with high MET scores may benefit from combination therapies. Citation Format: Kangjie Shen, Chuanyuan Wei, Jianying Gu. Metastasis score: A powerful tool to determine the metastatic potential and the appropriate adjuvant therapy of melanoma [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 3860.
Abstract 6151: The investigation of a new combinatorial immunotherapy strategy to treat platinum-resistant penile cancer
Authors: Yaoyin Li, Jad Chahoud, Xin Lu
Journal: Cancer Research (2025)

Abstract Penile cancer is a rare malignancy, with penile squamous cell carcinoma (PSCC) accounting for 95% of cases. Human papillomavirus (HPV) infection plays a key role in the carcinogenesis of HPV-positive PSCC. In addition to surgical treatment, multimodal therapies combining neoadjuvant cisplatin-based chemotherapy regimen is required for advanced and metastatic PSCC. However, disease-specific survival analysis showed disappointing results after systemic treatments. To identify an alternative treatment with more favorable outcomes, we investigated the effectiveness of a new combinatorial immunotherapy strategy for refractory PSCC. Here, we identify a therapeutic role of combining poly (ADP-ribose) polymerase inhibitors (PARPi) with anti-PD1 antibody treatment in the SAP (PB-Cre4+ Smad4L/L ApcL/L PtenL/L) model of PSCC, which was the first genetically engineered mouse (GEM) model of penile cancer in our previous report (Nat Commun. 2020; PMID 32358507). Mechanistically, PARPi-induced PARP1 trapping and dsDNA micronuclei activated cGAS-STING signaling pathway in both murine derived SA (PB-Cre4+Smad4L/LApcL/L) and SAP (PB-Cre4+ Smad4L/L ApcL/L PtenL/L) cell lines. HPV overexpression greatly downregulated the expression of type I interferons (IFNα and IFNβ) and pro-inflammatory chemokines (CCL5, CXCL9, CXL10 and CXCL11), while increasing the proliferation and motility of human PSCC cell lines. Furthermore, Niraparib, an FDA approved PARP inhibitor, reversed the effect of HPV overexpression on tumor growth by upregulating the expression of IFN-α/β and PD-L1 in vivo. Overall, this study revealed that the combination therapy of Niraparib and anti-PD1 inhibits the progression of PSCC via reprogramming tumor microenvironment, offering promising strategy for the treatment of refractory PSCC. Citation Format: Yaoyin Li, Jad Chahoud, Xin Lu. The investigation of a new combinatorial immunotherapy strategy to treat platinum-resistant penile 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 6151.
Abstract 5373: ALDOA reprograms stemness and mitochondrial function in lung cancer by facilitating lactylation of m6A regulators
Authors: Han-Hsi Kuo, You-Yu Lin, Zhao-Jing He, Yu-Chan Chang
Journal: Cancer Research (2025)

Abstract Lactic acid-derived lactylation has recently emerged as a novel post-translational modification (PTM). This modification has been shown to regulate the N6-methyladenosine (m6A) modification mechanism, thereby influencing RNA function. In lung cancer progression, dysfunctional aldolase (ALDOA) forms a positive feedback loop with HIF-1α, promoting lactate accumulation in the tumor and its microenvironment. We observe increased lactate production, hypoxia, acidification of the tumor microenvironment and increased lactylation levels of m6A regulators. In particular, METTL16, a key m6A transcription factor, was found to be modified by lactate. We also developed a methylated m6A RNA immunoprecipitation (MeRIP) platform and identified ATPIF1, an inhibitor of mitochondrial F0F1-ATP synthase, as a direct target of lactylation. In our overexpression model, ATPIF1 was degraded following m6A modification, which activated ATP biosynthesis. In a METTL16 knockout model, ATPIF1 expression was restored, leading to impaired ATP production and mitochondrial membrane potential. In addition, cancer spheroid formation and associated markers were reduced. Our in vivo model mirrored these findings, showing lactate-induced acidification and up-regulation of molecules involved in cancer stemness and mitochondrial function within the tumor region. Using multiplex staining, we detected reduced ATPIF1 expression alongside ALDOA overexpression, increased mitochondrial membrane potential and increased expression of OXPHOS-related molecules. In conclusion, we propose that ALDOA accelerates glycolysis in lung cancer progression and increases the global lactylation status of m6A regulators. These findings highlight lactylation as a critical aspect of metabolic reprogramming in cancer. Citation Format: Han-Hsi Kuo, You-Yu Lin, Zhao-Jing He, Yu-Chan Chang. ALDOA reprograms stemness and mitochondrial function in lung cancer by facilitating lactylation of mA regulators [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 5373.
Abstract 4215: Targeting TNBC with a novel vorinostat conjugate that selectively inhibits and degrades HDAC3 and HDAC6
Authors: Ping Gong, Min Huang, Haoling Wang, Xin Li, Linxiang Zhao, Samuel Waxman, Yongkui Jing
Journal: Cancer Research (2025)

Abstract Triple-negative breast cancer (TNBC) once metastatic is often a fatal disease with few molecular targets. HDAC3 is highly expressed in TNBC and regulates metastatic and cell death genes. The clinically approved pan-HDAC inhibitors exhibit limited efficacy with side effects in clinical trials. We have reported that the semisynthetic 18β-glycyrrhetinic acid analogues (10a-10e) bearing the 1-en-2-cyano-3-oxo substitution degrade HDAC3/6 proteins without direct enzymatic inhibition. We constructed AH3 to produce both HDAC 3/6 degradation and enzyme activity inhibition by 10a conjugation with the HDAC inhibitor vorinostat. AH3 has increased selectivity to HDAC3 and HDAC6 inhibition as compared to vorinostat. TNBC (MDA-MB-321, MDA-MB-468 and BT-459 cells) are more growth inhibited by AH3 (GI50:0.6-1 μM) comparing to vorinostat (GI50:1.9-2.9 μM) and exhibits selectivity for TNBC compared to normal mammary epithelial cells. Modification of the hydroxamic acid of AH3 with a methyl group (AH3-OCH3) loses HDAC inhibition and cell growth inhibition, confirming that HDAC3 and HDAC6 are the targets of AH3. AH3 inhibits colony formation, cellular invasion and migration in TNBC cells. AH3, but not AH3-OCH, induces apoptosis with downregulation of c-FLIP and upregulation of NOXA, associated with upregulation of acetyl-H3 and acetyl-tubulin as well as down-regulation of HDAC3 and HDAC6 proteins. AH3 has better tumor growth inhibition ability than verinostat in MDA-MB-231 xenograft model. AH3 is novel since both degrades and acts as an HDAC3/HDAC6 selective inhibitor with enhanced selectivity and antitumor ability against TNBC. Citation Format: Ping Gong, Min Huang, Haoling Wang, Xin Li, Linxiang Zhao, Samuel Waxman, Yongkui Jing. Targeting TNBC with a novel vorinostat conjugate that selectively inhibits and degrades HDAC3 and HDAC6 [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 4215.
Abstract 4337: SYS6051, a next-generation tissue factor-targeted antibody-drug conjugates for the treatment of TF-expressing malignancies
Authors: Xiaojuan Wu, Mingyue Shen, Mo Dan, Xiwu Hui, Bing Yao, Yanling Li, Wei Yang, Hanqian Xu, Can Yuan, Yufei Sun, Bin Kang, Yang Zhang, Linlin Xiao
Journal: Cancer Research (2025)

Abstract Tissue factor (TF) is an integral membrane protein, normally separated from the blood by the vascular endothelium, which plays a key role in the initiation of blood coagulation. However, TF is aberrantly expressed in solid tumors and its expression associated with poor prognosis. The first TF targeting antibody-drug conjugate (ADC) , a microtubule inhibitor based ADC(MTI-ADC), is approved for the treatment of cervical cancer. It had several prespecified adverse effects (AEs) including bleeding risks, ocular toxicity and perpheral neuropathy, the last two of which were known MMAE related AEs. In order to mitigate the safety concerns, we developed a novel ADC, SYS6051. It was composed of a humanized TF-targeting IgG1 antibody site-specifically conjugated to a topoisomerase I inhibitor (Exatecan) at a drug-to-antibody ratio (DAR) of 6 via a protease-cleavable linker. In addition, SYS6051 had improved resistance towards retro-Michael elimination reactions, resulting in improved stability compared to cysteine thiol-maleimide conjugated ADCs. The naked SYS6051-mAb did not interfere with the interaction among TF, Factor FVII and Factor X, and had no impact on coagulation cascade. SYS6051-mAb could quickly enter cells through endocytosis 3 hours after treatment, faster than the antibody of the MTI-ADC. Treatment with SYS6051 resulted in significant tumor growth inhibition in a panel of TF-positive cell line derived xenografts (CDXs), including pancreatic and cervical cancer xenografts. Furthermore, SYS6051 was well tolerated in a toxicity study in cynomolgus monkey at dosages ≤30 mg/kg. A stable PK profile of SYS6051 was also observed in NHP. Neither coagulation disorder nor skin rash was observed, superior to the historical toxicity data in NHP of the MTI-ADC. Taken together, SYS6051 has a wide therapeutic window because of promising efficacy, higher tolerability, stable PK profile, and could potentially provide benefits for the patients carrying TF positive malignancies. Citation Format: Xiaojuan Wu, Mingyue Shen, Mo Dan, Xiwu Hui, Bing Yao, Yanling Li, Wei Yang, Hanqian Xu, Can Yuan, Yufei Sun, Bin Kang, Yang Zhang, Linlin Xiao. SYS6051, a next-generation tissue factor-targeted antibody-drug conjugates for the treatment of TF-expressing malignancies [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 4337.
Abstract 3884: Uneven inheritance and functional heterogeneity derived from extrachromosomal DNA enable rapid adaptation of cancer cells
Authors: Shu Zhang, Aditi Gnanasekar, Ellis J. Curtis, Jun Tang, Vishnu Shankar, Ivy Tsz-Lo Wong, Xiaowei Yan, Rui Li, Lu Yang, Howard Y. Chang, Paul S. Mischel
Journal: Cancer Research (2025)

Abstract The amplification of oncogenes on extrachromosomal DNA (ecDNA) is common in cancer and associated with poor outcomes. Uneven inheritance of ecDNA during cell division leads to intratumoral ecDNA copy number heterogeneity. However, the relationship between shifts in ecDNA copy number and the rapid environmental adaptation of cancer cells remains unclear. In this study, we utilized imaging and single-cell multi-omics analyses to demonstrate that the transcript and protein expression of ecDNA oncogenes, along with functional heterogeneity, correlate with ecDNA copy number heterogeneity. Using fluorescence-activated cell sorting (FACS) and live-cell imaging, we found that cells with “middle” ecDNA copy numbers display the highest growth rates compared to cells with the lowest or highest copy number statuses, indicating greatest fitness is achieved by the balance of promoting cell proliferation while minimizing heightened replication stress arising from increasing copy numbers of ecDNA oncogenes. Through simulations based on random segregation and optimal copy number models, we found that ecDNA-bearing cells can rapidly adjust their copy numbers to achieve optimal growth in new environments. Notably, compared to chromosomally amplified cells, those with ecDNA exhibited superior growth following xenograft injection and treatment with single drugs targeting replication stress or oncogenes, aligning with our simulation findings. Our results reveal that functional heterogeneity resulting from uneven ecDNA inheritance enhances cancer cells' adaptability to tumor microenvironments and rapid acquisition of drug resistance, warranting that the development of combinatorial therapies that synergistically target a wide range of copy numbers is critical for effectively treating ecDNA-containing cancers. Citation Format: Shu Zhang, Aditi Gnanasekar, Ellis J. Curtis, Jun Tang, Vishnu Shankar, Ivy Tsz-Lo Wong, Xiaowei Yan, Rui Li, Lu Yang, Howard Y. Chang, Paul S. Mischel. Uneven inheritance and functional heterogeneity derived from extrachromosomal DNA enable rapid adaptation of cancer 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 3884.