bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2521: New predictive markers for dasatinib responsiveness in triple-negative breast cancer: A biomarker discovery study
Authors: Ortega-Álvarez Daniel , Tebar David , Casado Marta , Castillo Elena , Guardia Cristina , Olivares-Osuna David , Musulén Eva , Mereu Elisabetta , Luengo Ginés , Galán-Moya Eva M. , Rodilla Veronica 
Published: March 2024

Abstract
Triple negative breast cancer is the most heterogeneous and aggressive type of breast tumor type and is characterized by the lack of expression of clinical biomarkers (ER, PR, and HER2) and targeted therapies. In this regard, different clinical trials have failed, unable to stratify these patients to find an effective response to specific therapy. This study aimed to identify biomarkers exclusively expressed in the basal mammary compartment that can help us to subclassify the triple-negative breast cancer subtype. Based on computational analysis from single-cell RNA sequencing data, we have identified a list of basal identity-associated genes (BC-markers). Subsequent histological validation confirmed the expression pattern of these markers in a cohort of 50 samples, which has allowed us to stratify triple-negative breast cancer patients into BC-TNBC and luminal-like subtypes. Importantly, the expression of these markers correlated with poorer prognosis in TNBC patients. Functional analysis revealed that TAGLN played a significant role in cell proliferation and migration, potentially impacting tumor aggressiveness. Moreover, the expression of these BC-markers is associated with a mesenchymal phenotype which corresponds to the previously described Lehmannn’s mesenchymal-like signature. In this study, TAGLN appeared to influence dasatinib sensitivity, suggesting its potential as a predictive biomarker for dasatinib response in TNBC patients.
Citation Format: Daniel Ortega-Álvarez, David Tebar, Marta Casado, Elena Castillo, Cristina Guardia, David Olivares-Osuna, Eva Musulén, Elisabetta Mereu, Ginés Luengo, Eva M. Galán-Moya, Veronica Rodilla. New predictive markers for dasatinib responsiveness in triple-negative breast cancer: A biomarker discovery study [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 2521.
Abstract 2541: The landscape of circular extrachromosomal amplification in pediatric cancers
Authors: Sridhar Sunita , Chapman Owen S. , Wang Shanqing , Dutta Aditi , Mesirov Jill P. , Chavez Lukas 
Published: March 2024

Abstract
Circular extrachromosomal DNA (ecDNA, also known as double minutes, dm) has emerged as a driver of oncogenic copy number amplification, intratumoral heterogeneity, tumor evolution and therapy resistance. We recently screened the whole genomes of 481 medulloblatomas for ecDNA and concluded that medulloblastoma tumors harboring ecDNA are more than twice as likely to progress within 5 years of diagnosis. To evaluate the frequency and clincical impact of ecDNA across the spectrum of childhood cancers, we performed a retrospective analysis of 1671 tumors from 1482 patients across 47 pediatric tumor types from two large cloud pediatric cancer genomics resources, the Children’s Brain Tumor Network and St. Jude Cloud. ecDNA was detected in 15 pediatric tumor types, including ETMR (100%, n=4), osteosarcoma (47%, n=57), rhabdomyosarcoma (40%, n=35), neuroblastoma (30%, n=106), high-grade glioma (20%, n=157), and retinoblastoma (19%, n=32). Patients with tumors containing ecDNA had significantly poorer 5-year overall survival. In sequential samples from the same tumor at diagnosis and relapse, we observe evidence of ecDNA evolution including sequence instability and generation of new high-copy ecDNA amplification not detected at initial diagnosis. These results comprise the most detailed survey to date of the landscape of extrachromosomal amplifications across childhood cancers.
Citation Format: Sunita Sridhar, Owen S. Chapman, Shanqing Wang, Aditi Dutta, Jill P. Mesirov, Lukas Chavez. The landscape of circular extrachromosomal amplification in pediatric cancers [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 2541.
Abstract 2588: Bioengineering of site-specific antibody labeling from basic research to spatial omics platforms
Authors: Tao Kai , Rames Matthew J. , Dai MingChong , Sener Gulsu , Olson Samuel , Ranganathan Srivathsan , Ozdemir Sila , Oken Adam , Brasino Michael , Armstrong Randy , Chiu Yu-Jui , Eksi Ece , Branchaud Bruce , Esener Sadik 
Published: March 2024

Abstract
Over the last few years, spatial multi-omics platforms have emerged as a powerful tool for characterizing cancer biology in multiple dimensions. Notably, these systems typically rely on multiplex immunolabeling. Conventionally, multiplexing is accomplished through carefully selecting primary antibodies from different animal species, and in combination with their corresponding polyclonal secondary antibodies. However, given the practical complication related to the species availability of primary antibodies, the multiplexing labeling is still under constraint due to the necessity for matched secondary species labels and the availability. For decades, non-specific labeling of primary antibodies through amine- or thiol-reactive chemistries was widely performed. Evolving research and commercial products have sought to overcome this antibody-based multiplexing limitations by developing enzymatic reaction-directed chemical reaction or antibody targeting proteins that could contain affinity to the Fc or Fab regions of antibodies. However, these methods mentioned above have substantive limitations and side-effects on affinity, conjugation number, buffer incompatibilities, storage incompatibilities, insufficient conjugation, and uncontrolled stoichiometric labeling. Herein, we introduce an efficient, sustainable, reproducible site-specific antibody covalent labeling strategy through engineering anti-IgG secondary nanobodies. These infer the stability, high-affinity of species specific and easy-to-produce IgG binders with the permanence of controlled activation for proximity-driven intermolecular covalent conjugation, with a promise for efficient multiplexity. This labeling technology addresses antibody labeling challenges through currently available approaches, and would substantially enhance multiplexity in a wide variety of research and clinical settings.
Citation Format: Kai Tao, Matthew J. Rames, MingChong Dai, Gulsu Sener, Samuel Olson, Srivathsan Ranganathan, Sila Ozdemir, Adam Oken, Michael Brasino, Randy Armstrong, Yu-Jui Chiu, Ece Eksi, Bruce Branchaud, Sadik Esener. Bioengineering of site-specific antibody labeling from basic research to spatial omics platforms [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 2588.
Abstract 2590: Automating 6-plex chromogenic multiplexing with BOND RX
Authors: Talia Dean , Lindsay Stacey , Ketting Sarah , Williamson Rebecca , Cockfield Damian 
Published: March 2024

Abstract
Multiplex staining using a sequential approach provides a means of visualizing multiple targets in a single biopsy section, further evaluation paired with digital imaging provides a deeper analysis into the spatial relationship at a cellular level. Leica Biosystems enables researchers to complete proof of concept for sequential multiplex staining methods, on board the BOND RX system. Thus, paired with a compatible reagent workflow and a digital slide imaging offering (Aperio GT 450/Aperio AT2) enhances the possibilities for analysis. As with any assay there is a requirement for user optimization, in particular, marker/chromogen layer selection and the pertinent use of an elution step. Such elution step is specifically important within a sequential stain utilizing the same detection reagents on subsequent layers. The results from the multiple staining rounds show a successful 6-plex fully automated stain, possible without the removal and reapplication of the slide onto the BOND system between staining layers. The marker combinations chosen demonstrate compatibility of different host species (Rabbit & Mouse), cellular compartments and isotypes which are provided by Leica Biosystems as BOND Ready to Use reagents. Overall, chromogenic multiplexing provides a stained image which enables color separation, due to the assignment of each chromogen to a marker with an individual cell type and cellular compartment. Finally, the process outlined avoids the risk of signal quenching commonly associated with fluorescent offerings and negates the requirement for specialized equipment due to the enablement of brightfield primary analysis.
Citation Format: Dean Talia, Stacey Lindsay, Sarah Ketting, Rebecca Williamson, Damian Cockfield. Automating 6-plex chromogenic multiplexing with BOND RX [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 2590.
Abstract 2629: N6AMT1-mediated DNA 6mA modification in DNA repetitive elements LINE-1 dynamically regulates the IFN signal pathway in colorectal cancer
Authors: Yuan Ze , Liu Xiaoxia , Wang Xiaolin , Luo Yanxin , Yu Huichuan 
Published: March 2024

Abstract
Background: DNA N6-methyldeoxyadenosine (6mA) modification is the most prevalent DNA modification in prokaryotes, like bacteria, which participates in the host defense system. However, the presence and function of DNA 6mA in eukaryotes remains elusive. Many studies have reported that DNA 6mA modification is distributed across the genome and regulates transcription and the activity of transposable elements, in which the DNA 6mA methyltransferases and demethylases are involved, including the methyltransferase N6AMT1. LINE-1 is a genome-wide DNA repetitive element that acts as a diagnostic and prognostic biomarker for colorectal cancer. Therefore, we aimed to map the DNA 6mA in LINE-1 and investigate its role in the colorectal cancer (CRC) development.
Methods: The restriction-enzyme-digestion assay followed by quantitative PCR (6mA-RE-qPCR) was used to evaluate the LINE-1 DNA 6mA levels in the tumor and normal tissues. The DNA Nanopore sequencing was utilized to determine DNA 6mA and 5mC modifications. After the knockdown of N6AMT1, the dynamic changes of LINE-1 DNA 6mA methylation and RNA transcription under various stresses were determined by 6mA-RE-qPCR and qPCR, and the subsequent RNA-seq was performed to explore the downstream regulated pathways.
Results: The DNA 6mA methylation in LINE-1 is highly variant in the tumor and normal tissues, and it was significantly less prevalent in tumor tissues. The genomic distribution of LINE-1 DNA 6mA is significantly different from that of LINE-1 5mC. The LINE-1 DNA 6mA methylation and RNA transcription levels were dynamically changed in response to various stimuli, including 5-FU and H2O2. Knockdown of N6AMT1 downregulated LINE-1 DNA 6mA methylation and RNA transcription, promoted the proliferation, migration and invasion of CRC cells in vitro, and suppressed the IFN-gamma pathway. The co-culture assay showed N6AMT1 facilitated chemotaxis of macrophages and cytotoxicity of T cells via the IFN-gamma signal pathway.
Conclusions: The heterogeneity of DNA 6mA methylation in LINE-1 and its dynamic change in response to stimuli indicate a biological role of LINE-1 6mA methylation in the primary and adaptive tumor heterogeneities, which provides a novel insight into cancer development. The N6AMT1-mediated DNA 6mA modification in LINE-1 regulates CRC development through the IFN-gamma pathway.
Keywords: N6AMT1, LINE-1, DNA 6mA methylation, colorectal cancer
Citation Format: Ze Yuan, Xiaoxia Liu, Xiaolin Wang, Yanxin Luo, Huichuan Yu. N6AMT1-mediated DNA 6mA modification in DNA repetitive elements LINE-1 dynamically regulates the IFN signal pathway in colorectal cancer [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 2629.
Abstract 2638: Sensitizing immunotherapy-refractory prostate cancer to immune checkpoint blockade therapy with optimized ketogenic diet regimens
Authors: Murphy Sean , Rahmy Sharif , Gan Dailin , Li Jun , Lu Xuemin , Lu Xin 
Published: March 2024

Abstract
The purpose of this study is to investigate strategies for enhancing immune checkpoint blockade (ICB) therapy in prostate cancer (PCa).
To achieve this, we established a series of ICB-resistant PCa cell lines derived from a previously sensitive cell line, which originated from a murine model of metastatic PCa. Notably, we observed a reduction in major histocompatibility complex (MHC) class I protein levels in the resistant sublines.
Our study demonstrated synergistic efficacy through the combination of anti-PD1 and anti-CTLA4 antibodies with histone deacetylase inhibitor (HDACi) vorinostat, a cyclic ketogenic diet (CKD), or β-hydroxybutyrate (BHB) supplementation. Importantly, these interventions significantly delayed PCa tumor progression. Furthermore, our analysis revealed that the effects of these interventions were contingent on both BHB and adaptive immunity. In-depth single-cell transcriptomic and proteomic profiling unveiled mechanisms involving cancer-cell-intrinsic changes (upregulated MHC class I molecules) and extrinsic factors, including CD8+ T cell chemoattraction, M1/M2 macrophage rebalancing, monocyte differentiation toward antigen-presenting cells, and reduced neutrophil presence.
In conclusion, our findings provide valuable insights into the potential clinical utility of combining HDACi and optimized ketogenic diet regimens to enhance ICB therapy for PCa.
Citation Format: Sean Murphy, Sharif Rahmy, Dailin Gan, Jun Li, Xuemin Lu, Xin Lu. Sensitizing immunotherapy-refractory prostate cancer to immune checkpoint blockade therapy with optimized ketogenic diet regimens [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 2638.
Abstract 2655: Unexpected role of the NuRD component, Chd4, in Foxp3+ Treg cells and its relevance to tumor immunotherapy
Authors: Hancock Wayne W. , Wang Liqing , Minisini Martina , di Giorgio Eros , Babic Ivan , Nurmemmedov Elmar 
Published: March 2024

Abstract
We are investigating basic questions like why do Foxp3+ T-regulatory (Treg) cells have at least 3 nuclear complexes involving Hdac1 and Hdac2 (CoREST, Sin3, NuRD), and how can the inhibitory effects of Foxp3+ Tregs on host anti-tumor immune responses be targeted therapeutically? Here, we report on the immune functions of chromodomain-helicase-DNA-binding protein 4 (Chd4), a key enzyme of the nucleosome remodeling and deacetylase complex (NuRD) complex. TCGA analysis showed increased Chd4 expression and Foxp3+ Tregs within lung tumors, leading us to assess the effects of conditional gene deletion within Foxp3+ murine Tregs. Chd4 knockout led to systemic autoimmunity and death of mice within 3 weeks of life and RNAseq studies showed Chd4 loss led to derepression of ~1400 genes and repression of &gt;700 further genes resulting in a Treg signature markedly different from conditional deletion of Hdac1, Hdac2 or Mbd2 in Treg cells. Chd4 is an intrinsically disordered therapeutic target without a defined structure outside its physiological cell environment. To date, no specific inhibitors targeting Chd4 have been developed. We have identified Ch41, a novel and potent inhibitor of Chd4, using a novel cellular target engagement platform. Transcriptomic and mass-spec investigations showed that Ch41 impaired thymic Treg function and iTreg development, led to decreased CNS2 demethylation within the Foxp3 locus, and significantly impaired growth of lung tumors and hepatocellular carcinomas in immunocompetent but not in immunodeficient C57BL/6 mice (p&lt;0.01). Following Chd4 inhibitor therapy, intratumoral conventional T cells had increased activation and cytokine production (IL-2, IFN-g) compared to intratumoral T cells in control tumor-bearing mice but, perhaps unexpectedly, treated mice did not show histologic or biochemical evidence of autoimmunity. We conclude that while tumor associated Tregs have unique properties that include their increased suppressive activity compared to non-tumor associated Treg cells, they are also more susceptible than the latter and conventional T cells to newly developed therapeutic interventions, including targeting of the Chd4 chromodomain of the NuRD complex.
Citation Format: Wayne W. Hancock, Liqing Wang, Martina Minisini, Eros di Giorgio, Ivan Babic, Elmar Nurmemmedov. Unexpected role of the NuRD component, Chd4, in Foxp3+ Treg cells and its relevance to tumor immunotherapy [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 2655.
Abstract 2671: Sustained inhibition of CSF1R signaling effectively augments antitumor immune responses through inhibiting tumor-associated macrophages
Authors: Sato Takahiko , Sugiyama Daisuke , Kojima Yasuhiro , Hattori Satomi , Sone Kazuki , Ishikawa Tomohiro , Ishikawa Yuichi , Kato Takuma , Kiyoi Hitoshi , Nishikawa Hiroyoshi 
Published: March 2024

Abstract
Tumor-associated macrophages (TAMs) are one of the key immunosuppressive components in the tumor microenvironment (TME) and contribute to tumor development, progression, and resistance to cancer immunotherapy. Several reagents targeting TAMs have been tested in preclinical and clinical studies, but they have had limited success. Here, we show that a novel reagent, FF-10101, exhibits a sustained inhibitory effect against colony stimulating factor 1 receptor by forming a covalent bond and reduces immunosuppressive TAMs in the TME, which leads to strong antitumor immunity. In preclinical animal models, FF-10101 treatment significantly reduced immunosuppressive TAMs and increased antitumor TAMs in the TME. In addition, tumor antigen-specific CD8+ T cells were increased; consequently, tumor growth was significantly inhibited. Moreover, combination treatment with an anti-PD-1 antibody and FF-10101 exhibited a far stronger antitumor effect than either treatment alone. In human cancer specimens, FF-10101 treatment reduced PD-L1 expression on TAMs, as observed in animal models. Thus, FF-10101 acts as an immunomodulatory agent that can reduce immunosuppressive TAMs and augment tumor antigen-specific T cell responses, thereby generating an immunostimulatory TME. We propose that FF-10101 is a potential candidate for successful combination cancer immunotherapy with immune checkpoint inhibitors, such as PD-1/PD-L1 blockade.
Citation Format: Takahiko Sato, Daisuke Sugiyama, Yasuhiro Kojima, Satomi Hattori, Kazuki Sone, Tomohiro Ishikawa, Yuichi Ishikawa, Takuma Kato, Hitoshi Kiyoi, Hiroyoshi Nishikawa. Sustained inhibition of CSF1R signaling effectively augments antitumor immune responses through inhibiting tumor-associated macrophages [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 2671.
Abstract 2732: NB203: A Novel therapeutic bispecific antibody targeting CEACAM1/VEGF for tumor immunity and angiogenesis modulation in the tumor microenvironment
Authors: Dong Jinyu , Wang Binbin , Wang Dong , Ni Jie , Bu Tingting , Wang Haojie , Nayak Bishnu , Wang Baiyang , Dong Xin , Zhang Yu 
Published: March 2024

Abstract
The carcinoembryonic antigen cell adhesion molecule 1 (CEACAM1) is detected on leukocytes, epithelia and endothelia, and involved in cell adhesion through homophilic or heterophilic binding. In various gastrointestinal cancers, NSCLC (non-small cell lung cancer), and melanoma, CEACAM1 is highly expressed on tumor cells and tumor stroma, with its levels increasing as the disease progresses. Notably, CEACAM1 has been found to dampen T and NK cell functions while promoting tumor angiogenesis and metastasis. In this study, we present NB203, a novel CEACAM1/VEGF bispecific antibody developed using Neologics CEACAM-plus, a bifunctional molecule engineering platform designed to target and modulate the tumor microenvironment (TME). NB203 effectively accumulated in the TME and hindered the homophilic or heterophilic interactions of CEACAM1. It demonstrated a significant enhancement in T cell activities and NK cell-mediated killing of CEACAM1-expressing tumor cells, and the inhibition of tumor cell migration and polyploidy through macrophages. More importantly, NB203 was specifically designed to impede tumor angiogenesis. It exhibited an increased binding capacity to both CEACAM1 and VEGF in pro-angiogenic TME, and undermined intratumoral vessel maturation by blocking VEGF and negatively regulating myeloid cell-dependent tumor angiogenesis. In summary, our preclinical data indicate that NB203 exhibits effective anti-tumor activity by mediating NK and cytotoxic T cell activities, improving the immune-suppressive TME, and suppressing tumor angiogenesis. The use of NB203 holds promise in overcoming resistance to anti-VEGF therapy and substantially improving the safety of therapeutic targeting of angiogenesis in cancer treatment.
Citation Format: Jinyu Dong, Binbin Wang, Dong Wang, Jie Ni, Tingting Bu, Haojie Wang, Bishnu Nayak, Baiyang Wang, Xin Dong, Yu Zhang. NB203: A Novel therapeutic bispecific antibody targeting CEACAM1/VEGF for tumor immunity and angiogenesis modulation in the tumor microenvironment [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 2732.