tbuckley/cabot-search huggingface dataset:
Abstract 7243: Mapping the isoaspartylation site(s) in the N-terminal region of ELAVL4 by using deletion constructs and testing against SCLC patient sera
Authors: Shiori Fukutome, Diego A. Velarde, Davin Pan, Chunli Yan, Pamela R. Duarte, Provati Devi, Ite A. Offringa
Journal: Cancer Research (2025)

Abstract Small cell lung cancer (SCLC) is the most aggressive type of lung cancer. Standard of care consists of a platin-based therapy with etoposide, combined with immune checkpoint inhibition. While 2/3 of patients respond, the cancer usually recurs, and patients have a 5-year survival rate of only 8%. New therapies are urgently needed. About 15% of SCLC patients spontaneously develop a low-titer immune response against Embryonic Lethal, Abnormal Vision Drosophila-like 4 (ELAVL4). This protein is expressed throughout the nervous system but in the lung is unique to pulmonary neuroendocrine cells (the main cells of origin of SCLC) and is present on the surface of SCLC cells. Patients with low titer anti-ELAVL4 antibodies show improved response to chemotherapy and significantly improved survival. Our previous work indicates that the anti-ELAVL4 immune response is triggered by isoaspartylation of the unstructured N-terminal ELAVL4 region; asparagine or aspartic residues spontaneously form a succinimide intermediate, followed by hydrolysis resulting in an isoaspartyl link. This creates an antigenic kink in the protein, an appears to favor dimerization/aggregation. The unstructured N-terminal region of ELAVL4 contains 6 asparagine residues and 2 aspartic acid residues. Here we aim to understand which asparagine/aspartic acid residues in the N-terminal region undergo isoaspartylation and contribute to the anti-ELAVL4 immune response. To this end, we have constructed four deletion clones with different regions of the ELAVL4 N-terminal region carrying one or two possible sites of isoaspartylation (residues 1-13, 8-18, 16-29, and 28-38). Recombinant proteins generated from these constructs will be incubated under isoaspartyl-inducing conditions (neutral pH, 37ºC) and will use Western Blot and ELISA assays todetermine reactivity of SCLC patient sera as well as sera from mice immunized with Elavl4 (1-117). Understanding the sites of isoaspartylation in ELAVL4 will help identify the optimal target for the development of anti-isoaspartylated ELAVL4 monoclonal antibodies, which may provide a novel, targeted immunotherapy for SCLC patients. Supported by the Robert E. and May R. Wright Foundation Transformative Cancer Research Grant, USC’s Undergraduate Research Associates Program, and the Norris Comprehensive Cancer Center core grant, award number P30CA014089 from the NIH/NCI. Citation Format: Shiori Fukutome, Diego A. Velarde, Davin Pan, Chunli Yan, Pamela R. Duarte, Provati Devi, Ite A. Offringa. Mapping the isoaspartylation site(s) in the N-terminal region of ELAVL4 by using deletion constructs and testing against SCLC patient sera [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 7243.
Abstract 4568: Biochemical mitigation of technical artifacts improves performance of a ctDNA methyl sequencing assay
Authors: James Yu, Peter George, Jason Close, Andy Eang, Neil Peterman, Yu Sun, Nafisa Bulsara, Eileen Dimalanta, Alexander Robertson, Yexun Wang, Nicole Lambert
Journal: Cancer Research (2025)

In addition to accumulating mutations that may drive tumor growth, cancer cells also show broad changes in DNA methylation patterns genomewide. For example, a colorectal cancer sample may have fewer than 10 driver mutations, fewer than 100 passenger mutations, but may have nearly 800 differentially methylated regions. In contrast to the traditional method of using sequencing to find these scarce mutations in the genome, probing for these relatively abundant aberrantly methylated regions in the genome can be a powerful alternative approach for the detection of cancer. However, assessing DNA methylation via methyl sequencing is complicated by artifacts introduced during the traditional NGS library prep process. In vivo, CpG sites in mammals are typically methylated on both strands of the double stranded DNA; however, we observe that the majority of read fragments display some level of hemimethylation (only one strand displays methyl modifications), and roughly 10% of all reads are hemimethylated across the read. Furthermore, we observe that the fraction of methylated bases gradually decreases over the course of a sequencing read; the methylation state of DNA should not be expected to be impacted by the cycle number of a sequencing run. These artifacts are collectively known as M-bias and can be mitigated computationally, but these methods are an incomplete solution and may sacrifice valuable base coverage. We have devised a strategy to correct M-bias biochemically, using a custom formulated end repair mix. We show that this novel library prep workflow reduces M-bias by ∼50% in diverse ctDNA assays. This reduction in M-bias results in more accurate methylation status calls and reduces the number of reads needed to confidently cover a CpG region of interest. Finally, we show that biochemical M-bias mitigation methods lower healthy hypomethylation background signal by ∼10x. These changes increase robustness of hypomethylation biomarker quantitation and utility in ctDNA detection assays. Citation Format: James Yu, Peter George, Jason Close, Andy Eang, Neil Peterman, Yu Sun, Nafisa Bulsara, Eileen Dimalanta, Alexander Robertson, Yexun Wang, Nicole Lambert. Biochemical mitigation of technical artifacts improves performance of a ctDNA methyl sequencing assay [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 4568.
Abstract 5883: Estimation of blood volume collected on plasma-separating dried blood spots using gravimetric and imaging analysis
Authors: Elise C. Dietmann, Michelle D. Stephens, Olivia Krebs, Everlyne N. Nkadori, Pallavi Tiwari, Stephanie M. McGregor, Muhammed Murtaza
Journal: Cancer Research (2025)

Abstract Background: Analysis of plasma-separating dried blood spots (psDBS) holds promise for circulating tumor DNA (ctDNA) measurement, enabling at-home sample collection, room temperature storage, and easy shipment. However, unlike collection in a blood tube, it is not feasible to directly measure blood volume collected from a fingerstick using psDBS. Here, we evaluate whether analysis of psDBS mass, color, and area can infer blood volume and enable downstream measurement of DNA concentration. Methods: Whole blood from patients with head and neck, breast, gynecologic, genitourinary, and gastrointestinal malignancies was collected on psDBS devices by the University of Wisconsin-Madison Carbone Cancer Center BioBank. In addition, whole blood from healthy individuals was commercially obtained and between five and nine psDBS were prepared with volumes ranging from 50 to 250 μL. All samples underwent analysis for mass, area, and color. psDBS were imaged using a flatbed scanner. Total area of erythrocytes and mean grey value of center erythrocytes were measured using image segmentation. Using mass of the psDBS membrane, erythrocyte area, erythrocyte mean grey value, and sex as predictors, a linear regression model was developed to predict whole blood volume. Mean absolute percent error (MAPE) was used to assess model accuracy. Results: One hundred ninety psDBS samples from 30 healthy individuals and 100 psDBS from 100 patients with cancer were analyzed. Using 132 samples from 20 healthy individuals (training set), a linear regression model was fit to the data, showing a very strong correlation between actual and predicted blood volume (MAPE = 7.6, Pearson r = 0.97). The model was then tested using 58 samples from 10 different healthy individuals (independent validation set), as well as psDBS from patients with cancer, and predicted blood volume collected on psDBS with high accuracy (MAPE = 6.8 and 9.3, respectively). Conclusion: Our results suggest estimating blood volume from psDBS is feasible using gravimetric and imaging analysis. By establishing a linear regression model that incorporates weight, area, and color, we can infer blood volume collected on psDBS samples for healthy individuals and patients with cancer. Ongoing work will incorporate this approach to enable measurement of plasma DNA concentration in blood spots. Citation Format: Elise C. Dietmann, Michelle D. Stephens, Olivia Krebs, Everlyne N. Nkadori, Pallavi Tiwari, Stephanie M. McGregor, Muhammed Murtaza. Estimation of blood volume collected on plasma-separating dried blood spots using gravimetric and imaging analysis [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 5883.
Abstract 4591: Development and validation of a molecular classifier of meningiomas
Authors: Alex Landry, Justin Wang, Jeff Liu, Vikas Patil, Chloe Gui, Andrew Ajisebutu, Yosef Ellenbogen, Qingxia Wei, Olivia Singh, Julio Sosa, Sheila Mansouri, Aaron Cohen-Gadol, Ghazaleh Tabatabai, Marcos Tatagiba, Felix Behling, Jill Banholtz-Sloan, Andrew Sloan, Lola Chambless, Serge Makarenko, Stephen Yip, Alireza Mansouri, Derek Tsang, Kenneth Aldape, Andrew Gao, Farshad Nassiri, Gelareh Zadeh
Journal: Cancer Research (2025)

Abstract Background: Meningiomas exhibit considerable clinical and biological heterogeneity. We previously identified four distinct molecular groups (immunogenic, NF2-wildtype, hypermetabolic, proliferative) that address much of this heterogeneity. Despite the utility of these groups, the stochasticity of clustering methods and the use of multi-omics data for discovery limits the potential for classifying prospective cases. We sought to address this with a dedicated classifier. Methods: Using an international cohort of 1698 meningiomas, we constructed and rigorously validated a machine learning-based molecular classifier using only DNA methylation data as input. Original and newly-predicted molecular groups were compared using DNA methylation, RNA sequencing, copy number profiles, whole exome sequencing, and clinical outcomes. Results: We show that group-specific outcomes in the validation cohort are nearly identical to those originally described, with median PFS of 7.4 (4.9-Inf) years in hypermetabolic tumors and 2.5 (2.3-5.3) years in proliferative tumors (not reached in the other groups). Tumors classified as NF2-wildtype had no NF2 mutations, and 51.4% had canonical mutations previously described in this group. RNA pathway analysis revealed upregulation of immune-related pathways in the immunogenic group, metabolic pathways in the hypermetabolic group and cell-cycle programs in the proliferative group. Bulk deconvolution similarly revealed enrichment of macrophages in immunogenic tumors and neoplastic cells in hypermetabolic and proliferative tumors with similar proportions to those originally described. Conclusions: Our DNA methylation-based classifier, which is publicly available for immediate clinical use, recapitulates the biology and outcomes of the original molecular groups as assessed using multiple metrics/platforms that were not used in its training. Citation Format: Alex Landry, Justin Wang, Jeff Liu, Vikas Patil, Chloe Gui, Andrew Ajisebutu, Yosef Ellenbogen, Qingxia Wei, Olivia Singh, Julio Sosa, Sheila Mansouri, Aaron Cohen-Gadol, Ghazaleh Tabatabai, Marcos Tatagiba, Felix Behling, Jill Banholtz-Sloan, Andrew Sloan, Lola Chambless, Serge Makarenko, Stephen Yip, Alireza Mansouri, Derek Tsang, Kenneth Aldape, Andrew Gao, Farshad Nassiri, Gelareh Zadeh. Development and validation of a molecular classifier of meningiomas [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 4591.
Abstract 4569: MiRNA signatures in liquid biopsy for early detection of non-small cell lung cancer
Authors: Alessandro Pascon Filho, Giovana M. Stanfoca Casagrande, Rodrigo Sampaio Chiarantano, Fabiana de Lima Vazquez, Rui Manuel Reis M. Reis, Leticia Ferro Leal
Journal: Cancer Research (2025)

Background: Liquid biopsy-based biomarkers present a promising approach for non-invasive risk assessment and early detection of lung cancer. Aim: To identify a miRNA signature in sputum and plasma samples as a non-invasive biomarker for early detection of non-small cell lung cancer (NSCLC). Methods: A case-control study was conducted within the Barretos Cancer Hospital Screening Program, utilizing a low-dose CT mobile unit. Sputum and plasma samples were collected from high-risk controls (NLST and/or PLCO criteria; n=61) and NSCLC patients (n=62), matched for age, sex, and smoking history. MiRNA expression was analyzed using the nCounter HumanV3 miRNA panel (Nanostring™). Counts were normalized by the top stable miRNAs, followed by differential expression analysis (p&amp;lt;0.05). MiRNA selection was conducted using Boruta and LASSO. Dataset was partitioned into training and validation sets (85/15 split). Machine learning models (ML) were conducted (Azure) and performance was assessed using AUC (Table 1). Results: In plasma, 68 miRNAs were identified as differentially expressed, and 8 miRNAs were retained following filtering. Among the all-tested models (Table 1), the best ML (Voting Ensemble) for the 8-miRNA plasma signature showed a high accuracy in both training (80.3%, AUC = 0.931) and validation set (73.3%, AUC = 0.892). In sputum, 46 miRNAs were identified as differentially expressed, and 7 miRNAs were retained. The best ML (SVD,Logistic Regression) for the 7-miRNA sputum signature showed a high accuracy in both training (81.42%, AUC = 0.943) and validation set (78.57%, AUC = 0.916). The two defined signatures exhibited no overlap in miRNAs between fluids. Conclusion: This study identified two distinct miRNA fluid-specific signatures in sputum and plasma as potential non-invasive biomarkers for the early detection of lung cancer, underscoring their potential to advance precision-based screening and improve clinical decision-making in lung nodules management. Citation Format: Alessandro Pascon Filho, Giovana M. Stanfoca Casagrande, Rodrigo Sampaio Chiarantano, Fabiana de Lima Vazquez, Rui Manuel Reis M. Reis, Leticia Ferro Leal. MiRNA signatures in liquid biopsy for early detection of non-small cell lung 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 4569.
Abstract 3486: Click-to-release for controlled immune cell activation: tumor-targeted unmasking of an IL-12 prodrug <i>in vivo</i>
Authors: Martijn H. den Brok, Kim E. de Roode, Luc M. Zijlmans, Laurens H. Kleijn, Marleen H. van Stevendaal, Ron M. Versteegen, Lieke W. Wouters, Raffaella Rossin, Marc S. Robillard
Journal: Cancer Research (2025)

Abstract Immunotherapy utilizing immune stimulating cytokines such as IL-12 holds great promise for the treatment of cancer. However, clinical use of IL-12 is hampered by severe toxicity following systemic administration resulting in a narrow therapeutic window. Tagworks is pioneering the use of in vivo click chemistry (Click-to-Release platform) to enable effective on-tumor activation of prodrugs, with the aim to increase the therapeutic index and application scope of potent anticancer drugs. We here present a novel treatment strategy in which IL-12 is inactivated by lysine conjugation to trans-cyclooctene(TCO)-linked PEG masks that can be released through the Click-to-Release reaction between the TCO linker and a tetrazine molecule (the trigger), restoring the native cytokine. Selective activation in the tumor microenvironment is achieved by pre-targeting the trigger to the tumor by i.v. injection of a tetrazine-protein conjugate, triggering local activation of the masked IL-12 when it is given in a subsequent i.v. injection. Evaluation of several Click-to-Release designs in vitro resulted in the selection of an IL-12-TCO-PEG construct with 9 conjugated lysines, exhibiting superior masking (&amp;gt;100 fold attenuated) combined with instantaneous and complete re-activation upon reaction with tetrazine. Next, we developed a tumor-targeted tetrazine based on a diabody against TAG72, a pan-carcinoma marker in the tumor microenvironment, modified with 4 tetrazine moieties. The diabody-tetrazine showed good tumor uptake in mice bearing colorectal (LS174T) xenografts combined with rapid blood clearance (&amp;lt; 0.5 %ID/g 24h p.i.). Also IL-12-TCO-PEG showed nearly complete clearance in 24 hours (&amp;lt; 0.5 %ID/g 24h p.i.). Administration of diabody-tetrazine to tumor-bearing mice followed by IL-12-TCO-PEG 24 hours later afforded selective IL12 unmasking in tumors and not in blood, demonstrating the feasibility of locally activating systemically administered immune stimulating cytokines with the versatile Click-to-Release platform. Citation Format: Martijn H. den Brok, Kim E. de Roode, Luc M. Zijlmans, Laurens H. Kleijn, Marleen H. van Stevendaal, Ron M. Versteegen, Lieke W. Wouters, Raffaella Rossin, Marc S. Robillard. Click-to-release for controlled immune cell activation: tumor-targeted unmasking of an IL-12 prodrug in vivo [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 3486.
Abstract 7241: Tumor-derived APi1 inhibits antigen cross-presentation in dendritic cells and impairs anti-tumor immunity in breast cancer
Authors: Erwei Song, Di Huang, Ruxin Wang
Journal: Cancer Research (2025)

Abstract Tumor mutational burden (TMB), usually representing high immunogenicity, could not always predict treatment response of immune checkpoint blockade (ICB). Here, we showed that defective antigen cross-presentation in type 1 conventional dendritic cells (cDC1) was responsible for lacking tumor-specific cytotoxic T lymphocytes (CTLs) in triple-negative breast cancer (TNBC) patients. Mechanistically, we found a tumor-derived protein, termed antigen presentation inhibitor 1 (APi1) , was shuttled via extracellular vesicles (EVs) into the endosomes of intratumor DCs, inhibited antigen cross-presentation by locking antigen binding to HSP90 and precluding their translocation from endosomes to cytoplasm. APi1 knockdown in tumor cells or inhibiting APi1/HSP90 interaction in DCs efficiently promoted antigen translocation and enhanced their cross-presentation, which improved ICB therapeutic responses. Clinically, high tumor APi1 expression was associated with low infiltration of antigen-specific CTLs and poor ICB efficacy in TNBC patients. Therefore, tumor EV-shuttled APi1 locks antigen/chaperone interaction and impairs antigen cross-presentation in DCs. Moreover, targeting APi1 is promising to enhance anti-tumor immunity and reverse ICB resistance. Citation Format: Erwei Song, Di Huang, Ruxin Wang. Tumor-derived APi1 inhibits antigen cross-presentation in dendritic cells and impairs anti-tumor immunity 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 7241.
Abstract 1632: EGFR-TKIs facilitate cuproptosis via regulating SLC31A1 in cancer cells
Authors: Xiyi Wei, Weiyu Kong, Zijie Yu, Chao Qin, Bing Yao, Zhou Yang
Journal: Cancer Research (2025)

Abstract Cuproptosis, a novel cellular demise pathway linked to copper homeostasis and copper ionophores, offers promising therapeutic avenues across diverse human ailments. However, the effectiveness of copper ionophores in cancer treatment is not that satisfactory. Tyrosine kinase inhibitors (TKIs) have revolutionized the approach to combating various types of cancer by regulating different cell death manners. In this research, we identified EGFR-TKIs and MEK-TKIs significantly sensitized cuproptosis. Our investigation delineates that the EGFR/MEK signaling cascade phosphorylates JUND, augmenting its transcriptional prowess as a key repressor of SLC31A1. Interestingly, EGFR-TKIs enhance the interaction between EGFR and SLC31A1, impeding UBE3C-mediated degradation, thereby stabilizing SLC31A1 levels. Moreover, copper binding to the extracellular domain of EGFR promotes its dimerization and downstream phosphorylation, orchestrating a protective mechanism under copper-induced stress, whereas EGFR-TKIs interrupt EGFR-SLC31A1 cascade to sensitize cuproptosis. Overall, our findings shed light on the dual roles of EGFR-TKIs and MEK-TKIs in sensitizing cuproptosis within cancer contexts through intricate transcriptional and post-transcriptional regulation of SLC31A1. The prospective combination of EGFR/MEK-TKIs with copper emerges as a promising strategy for cuproptosis-targeted therapies across multiple malignancies with or without EGFR mutation, underscoring the innovative contributions of our study. Citation Format: Xiyi Wei, Weiyu Kong, Zijie Yu, Chao Qin, Bing Yao, Zhou Yang. EGFR-TKIs facilitate cuproptosis via regulating SLC31A1 in 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 1632.