bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 7401: High-level multiplexed virtual immunofluorescence staining using holotomography and deep learning
Authors: Park Juyeon , Shin Su-Jin , Kim Geon , Lee Kwang Suk , Heo Ji Eun , Park YongKeun 
Published: March 2024

Abstract
Multiplexed immunofluorescence (IF) staining plays a crucial role in cancer research, allowing simultaneous visualization of multiple biomarkers to elucidate complex cellular interactions within the tumor microenvironment. However, the conventional multiplexed IF approach has inherent limitations, characterized by labor-intensiveness and a constrained capacity for high-level multiplexing. These challenges hinder its scalability and comprehensive analysis of intricate molecular landscapes.To overcome the limitations of conventional multiplexed IF, we propose a novel approach that integrates holotomography (HT) and deep learning. HT is a label-free imaging technique that quantitatively measures the refractive index distribution of the specimen without any staining. To provide subcellular specificity to the label-free HT images, HT is integrated with virtual staining. Virtual staining is a deep learning-based framework that converts label-free images to the desired stained images, in this case, from HT images to multiplexed IF images. This synergistic combination of HT and deep learning may address the current limitations of multiplexed IF protocols.Our proposed methodology aims at high-level multiplexed virtual IF staining from label-free cancer tissue slides using HT and deep learning. This approach not only eliminates the need for chemical staining but also enhances the level of multiplexing through computational staining. Specifically, we acquire HT and fluorescence images of stained tissue slides for training. Utilizing this paired dataset, we then employ supervised learning to create a neural network that can map between label-free HT images and corresponding fluorescence images. Subsequently, the trained neural network is applied to label-free tissue slides, inferring fluorescence images without the need for chemical staining.We believe the proposed virtual staining framework will contribute to a more efficient and scalable paradigm for cancer research, facilitating a deeper understanding of tumor biology, and advancing the field of precision medicine.
Citation Format: Juyeon Park, Su-Jin Shin, Geon Kim, Kwang Suk Lee, Ji Eun Heo, YongKeun Park. High-level multiplexed virtual immunofluorescence staining using holotomography and deep learning [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 7401.
Abstract 7414: Claire: a search engine leveraging deep databases for reliable detection of peptides, with a special focus on proteogenomic applications
Authors: Hruska Miroslav , Dzubak Petr , Hajduch Marian 
Published: March 2024

Abstract
As the field of cancer diagnostics and treatment evolves, the significance of peptides characterized by post-translational modifications and amino acid substitutions is becoming increasingly prominent. These molecular alterations frequently offer critical insights into tumor biology, aiding the development of targeted therapies and methods for personalized medicine. However, despite ongoing advances in shotgun proteomics, the field still faces multiple challenges for the reliable detection of rare peptide forms, for instance, amino acid substitutions when the corresponding DNA or RNA sequencing is unavailable. As a response to these challenges, our group has developed Claire—a probabilistic search engine employing large peptide databases for detection. These databases, often on the terabyte scale, further incorporate the estimates of peptides' prior probabilities to improve detection accuracy and utilize several optimizations to allow fast interpretation of tandem mass spectra. Claire outperformed state-of-the-art software, such as MSFragger and TagGraph when evaluated on the protein-level detection of single nucleotide variants in the public NCI60 proteome dataset. Further, Claire's analysis of a range of NCI60 datasets revealed high protein-level mutational burdens in genomically unstable cancer cell lines and detected mislabeling and contamination across several omics datasets. In a clinical domain, Claire discerned the hypermutation status of colorectal cancer patients' tumors, identifying candidates suitable for immunotherapy. Protein-level variation in peripheral blood mononuclear cells also recognized individuals, monozygotic twins aside, revealing the pseudonymous nature of germline proteome datasets, and raising the need for their protection. From a computational perspective, Claire can be run as a standalone software in the Linux operating system, or its capabilities accessed remotely using an interface on our cloud computing infrastructure. Claire has thus shown remarkable potential in enhancing peptide detection, offers substantial advancements for both clinical and research applications, and allows direct incorporation of its capabilities into various computational workflows.
Citation Format: Miroslav Hruska, Petr Dzubak, Marian Hajduch. Claire: a search engine leveraging deep databases for reliable detection of peptides, with a special focus on proteogenomic applications [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 7414.
Abstract 744: Novel conditionally active biologic (CAB) tetravalent T-cell engagers targeting solid tumors
Authors: Cugnetti Ana Paula , Liu Haizhen , McNeeley Patricia , Xing Charles , Woodard Kathryn , Chang Hwai , Frey Gerhard , Boyle William J. , Short Jay M. 
Published: March 2024

Abstract
The use of T-cell engagers (TCEs) has great therapeutic potential in oncology. This potential, however, is diminished due to severe toxicity (cytokine release effects, as well as on-target off-tumor toxicities). We leveraged BioAtla’s Conditionally Active Biologic (CAB) technology (1) to develop bispecific antibodies which have no or very little binding to CD3 and to the tumor target antigen (TAA) in healthy tissue (normal physiological conditions), yet have strong binding in diseased tissues (i.e. tumor microenvironment, TME) derived from glycolytic tumor metabolism, which supports tumor growth (Warburg effect). The conditional activity in the TME is achieved by optimizing the sequences of the binding domains and does not require masking and subsequent activation of the binding domain as used in pro-drugs. We have developed dual-CAB T-cell engagers targeting serval well-established tumor associated antigens. Data demonstrating superior potency with reduced off-target binding through in vitro and in vivo characterization of three new DualCAB TCEs, targeting PSMA, Trop2, and Tissue Factor (TF) will be presented.(1) Chang HW, Frey G, Liu H, Xing C, Steinman L, Boyle WJ and Short, JM Generating tumor-selective conditionally active biologic anti-CTLA4 antibodies via protein-associated chemical switches. Proc Natl Acad Sci U S A 2021;118.
Citation Format: Ana Paula Cugnetti, Haizhen Liu, Patricia McNeeley, Charles Xing, Kathryn Woodard, Hwai Chang, Gerhard Frey, William J. Boyle, Jay M. Short. Novel conditionally active biologic (CAB) tetravalent T-cell engagers targeting solid tumors [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 744.
Abstract 7466: Exploring tertiary lymphoid structures and immune cell interactions in gastric cancer prognosis
Authors: Zeng Zheng , Au-Yeung Yee Man , Huang Jiandong 
Published: March 2024

Abstract
Tertiary lymphoid structures (TLSs) are ectopic lymphoid aggregates found in chronically inflamed, infected, and tumor tissues. Prior research indicates that the presence of TLS and tumor-infiltrating lymphocytes (TILs) correlates with a more favorable prognosis in several cancers. Our study investigates the role of TLSs and TILs in gastric cancer, the 4th leading cause of cancer-related death worldwide. We analyzed tumor samples from 107 late-stage gastric cancer patients from mainland China, with a 5-year follow-up period. We performed H&E and multiplex immunofluorescence staining to assess the tumor area and infiltrating immune cells, and we evaluated potential relationships between TILs, clinicopathological features, and patient prognosis. Immunohistological analysis showed that CD4 T cells may have a more significant impact on patient prognosis than CD8 T cells. Notably, the presence of PDL1 and CD4 co-expressing cells was associated with better disease outcomes. We observed PDL1 expressing cells surrounding the tumor margin in a subset of cases, a distribution pattern that could lead to delayed recurrence or complete remission in gastric cancer. In the context of cancer-related TLS, we found that CD20 and CD86 co-expression in the center of the structures may indicate a higher maturation level. Additionally, the ratio and spatial distribution of CD86 and CD163 macrophages appear to play a crucial role in prognosis. We extracted the expression levels of markers from representative samples to examine the spatial relationships between cancer cells and each immune cell type. We then visualized these cellular interactions in the tumor microenvironment using topographic plots. This study broadens our understanding of tumor and immune cell interactions in gastric cancer, with the potential to inform future directions in immunotherapy treatments.
Citation Format: Zheng Zeng, Yee Man Au-Yeung, Jiandong Huang. Exploring tertiary lymphoid structures and immune cell interactions in gastric cancer prognosis [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 7466.
Abstract 7509: Evaluation ofHER-2 expression on circulating tumor cells as a real time biomarker in advanced breast cancer
Authors: Khandare Jayant , Aland Gourishankar , Andhari Saloni , Khutale Ganesh , Patil Prathamesh , Deshpande Tanvi , Garbhe Meghana , Jadhav Vikas , Vasudevan Aravindan , Jayant Sreeja 
Published: March 2024

Abstract
Introduction: Breast cancer accounts for 12.5% of all new annual cancer cases worldwide. Cases classified as HER2-positive tend to proliferate, metastasize, and often lead to relapse. HER-2 is the most valid tumor marker, used as a diagnostics and prognostic biomarker in metastatic breast cancer (MBC). Thus, analysis of expression of HER-2 on CTCs can offer a real time dynamic biomarker for treatment options between endocrine therapy versus chemotherapy in advanced breast cancer. Functional assays on CTCs with HER-2 biomarker offer evolving biomarkers especially when the tissue is not accessible and inadequate.
Methods: Retrospectively, 179 breast cancer patients' blood was analyzed for the presence of CTCs using the OncoDiscover® platform approved by Drug Controller General of India (CDSCO). Consisting of immunomagnetic multi-components mediated by anti EpCAM antibodies. The isolated cells were immunostained consisting of a nuclear dye DAPI, CK-18, CD45 and HER-2 antibodies. CTCs were identified by the presence of HER-2 + ve, CK 18 + ve, DAPI + ve and CD 45 -ve staining. Validation of HER-2 expression on the CTCs was analyzed based on the linear intensity gradients of the fluorescence signals. CTCs were termed as HER-2 -ve based on weak or no detectable fluorescence signal and termed +ve based on high fluorescence signal.
Results: Among the cohort of 179 patient samples, 63.68 % samples showed the presence of CTC (CTC ranged from 1-7). 47.84% of these CTCs showed the expression of HER-2 signal. The mean value for fluorescence intensity for expression of HER-2 in CTCs was found to be 3.23. The observed mean fluorescence intensity for HER-2 expression further emphasizes the robustness of CTCs as a viable source for molecular characterization.
Conclusion: Integration of HER-2 analysis on CTCs into the clinical assessment of metastatic breast cancer, may offer a non-invasive, real-time strategy for profiling and possibly paving the way for more precise and tailored therapeutic interventions.
Citation Format: Jayant Khandare, Gourishankar Aland, Saloni Andhari, Ganesh Khutale, Prathamesh Patil, Tanvi Deshpande, Meghana Garbhe, Vikas Jadhav, Aravindan Vasudevan, Sreeja Jayant. Evaluation ofHER-2 expression on circulating tumor cells as a real time biomarker in advanced breast 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 7509.
Abstract 7524: Targeting siglec-7/9 glyco-immune checkpoints in prostate cancer for enhanced immune responses and tumor suppression
Authors: Wen Ru , Marti G Edward , Stark Jessica , Marques Fernando Jose Garcia , Riley Nick , Bermudez Abel , Zhao Hongjuan , Bertozzi Carolyn , Pitteri Sharon , Brooks James 
Published: March 2024

Abstract
Prostate cancer is one of the leading causes of death in men worldwide. Despite significant advancements in the fight against cancer, immune checkpoint inhibitors have limited effectiveness in treating prostate cancer. Evidence shows that disrupting the interactions between Siglec-7/9 and sialic acids can enhance immune responses and effectively inhibit tumor growth in several cancers. However, the understanding of Siglec-7/9-sialic acid interactions in prostate cancer remains limited. Here, we found that tumor-infiltrating immune cells derived from prostate cancer patients exhibited high levels of Siglec-7 and Siglec-9. TCGA data analysis suggests that high levels of Siglec-7/9 are correlated to worse patient survival. Elevated levels of Siglec-7/9 ligands were found in prostate tumor tissues compared to adjacent normal tissues. Prostate cancer cell lines exhibited significant expression levels of Siglec-7 and Siglec-9 ligands, and cell surface sialic acids. Proteomic analysis suggests that increased sialylation was observed in tumor tissues in comparison to adjacent normal tissues. Disrupting interactions between Siglec-7/9 and sialoglycans enhanced T cell-mediated cytotoxicity against prostate cancer cells. Treatment with anti-Siglec-7/9 antibodies effectively suppressed the growth of PC3 and 22Rv1 tumors in a humanized mouse model. Immunohistochemistry analysis of tumor tissues showed that PC3 and 22Rv1 tumors treated with anti-Siglec-7/9 exhibited reduced proliferation, decreased vascularization, increased apoptosis, and enhanced immune cell infiltration. The CRISPR screen and mass spectrometry analysis suggested CD59 as a potential ligand for Siglec-9. Knockout of CD59 in prostate cancer cells decreased their binding activity of Siglec-9-Fc chimera proteins and promoted T cell-mediated killing ability. These findings provide valuable insights into the potential therapeutic strategy of targeting Siglec-7/9 and their ligands for prostate cancer treatment.
Citation Format: Ru Wen, G Edward Marti, Jessica Stark, Fernando Jose Garcia Marques, Nick Riley, Abel Bermudez, Hongjuan Zhao, Carolyn Bertozzi, Sharon Pitteri, James Brooks. Targeting siglec-7/9 glyco-immune checkpoints in prostate cancer for enhanced immune responses and tumor suppression [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 7524.
Abstract 7648: COL6A1 expression as a potential prognostic biomarker for risk stratification of T1HG bladder cancer: Unveiling the aggressive nature of a distinct non-muscle invasive subtype
Authors: Piao Xuan-Mei , Byun Young Joon , Zheng Chuang-Ming , Kim Seon-Kyu , Park Seong-Hwan , Min Kyungchan , Park Hansoo , Moon Sungmin , Kim Kyeong , Kang Ho Won , Kim Won Tae , Yun Seok Joong 
Published: March 2024

Abstract
Introduction and Objectives: T1 high grade (T1HG) bladder cancer (BC) is a type of non-muscle invasive BC (NMIBC) that is recognized as an aggressive subtype with a heightened propensity for progression. Current risk stratification methods for NMIBC rely on clinicopathological indicators; however, these approaches do not adequately capture the aggressive nature of T1HG BC. Thus, new, more accurate biomarkers for T1HG risk stratification are needed. Here, we enrolled three different patient cohorts and investigated expression of COL6A1, a key component of the extracellular matrix, at different stages and grades of BC, with a specific focus on T1HG BC. Materials and Methods: Samples from 298 BC patients were subjected to RNA sequencing and real-time PCR. Results: We found that T1HG BC and muscle invasive BC (MIBC) exhibited comparable expression of COL6A1, which was significantly higher than that by other NMIBC subtypes. In particular, T1HG patients who later progressed to MIBC had considerably higher expression of COL6A1 than Ta, T1 low-grade patients, and patients that did not progress, highlighting the aggressive nature and higher risk of progression associated with T1HG BC. Moreover, Cox and Kaplan-Meier survival analyses revealed a significant association between elevated expression of COL6A1 and poor progression-free survival of T1HG BC patients (multivariate Cox hazard ratio, 16.812; 95% confidence interval, 3.283-86.095; P=0.001 and P=0.0002 [log-rank test]). Conclusion: These findings suggest that COL6A1 may be a promising biomarker for risk stratification of T1HG BC, offering valuable insight into disease prognosis and guidance of personalized treatment decisions.
Citation Format: Xuan-Mei Piao, Young Joon Byun, Chuang-Ming Zheng, Seon-Kyu Kim, Seong-Hwan Park, Kyungchan Min, Hansoo Park, Sungmin Moon, Kyeong Kim, Ho Won Kang, Won Tae Kim, Seok Joong Yun. COL6A1 expression as a potential prognostic biomarker for risk stratification of T1HG bladder cancer: Unveiling the aggressive nature of a distinct non-muscle invasive subtype [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 7648.
Abstract 7651: Evaluating epigenetic markers for naive, memory and overall B cells for disease diagnosis and prognosis in patients with B-CLL
Authors: Schildknecht Konstantin , Bourquain Kati , Werner Jeannette , Schulze Janika , Walter Steffi , Raschke Eva , Phippard Deborah , Bisconte Angelina , Seliger Barbara , Wickenhauser Claudia , Olek Sven 
Published: March 2024

Abstract
Chronic lymphocytic leukemia (CLL) is a hematological cancer classified as low-malignancy non-Hodgkin lymphoma that accounts for approximately a quarter of all leukemias. Since only some patients will develop aggressive cancer and require treatment, accurate disease prognosis is crucial. A wide range of parameters with prognostic value have been described, including age, clinical stage, mutational status, protein markers, and flow cytometry levels of CD19+CD38+ B cells above 20%. Here, we investigated epigenetic markers for B cell types including a marker for overall B cells, naïve B cells, memory B cells and IgM positive B cells in a cohort of more than 40 patients with B-CLL. When comparing to a cohort of more than 100 healthy donors, the epigenetic B cell marker identified all patients with 100% sensitivity and specificity. In addition, the epigenetic B cell markers for naïve and memory B cells identified with high sensitivity and excellent specificity a subgroup of B-CLL patients with CD19+CD38+ B cell levels above 20% which is associated with an unfavorable prognosis. The results suggest that the epigenetic analysis of B cells in capillary blood may be a promising tool for B-CLL diagnosis and disease prognosis.
Citation Format: Konstantin Schildknecht, Kati Bourquain, Jeannette Werner, Janika Schulze, Steffi Walter, Eva Raschke, Deborah Phippard, Angelina Bisconte, Barbara Seliger, Claudia Wickenhauser, Sven Olek. Evaluating epigenetic markers for naive, memory and overall B cells for disease diagnosis and prognosis in patients with B-CLL [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 7651.
Abstract 77: Real-time multiparametric assessment of immune cell-mediated cytotoxicity
Authors: Yang Grace , Lu Yan , Wang Tian , Ye Peifang , Zhang Xiaoyu 
Published: March 2024

Abstract
A hallmark of effective immunotherapy is the reliance on the cytotoxic effects of immune cells, such as T-cells and natural killer (NK) cells, on tumor lesions. Cell cluster formation is an important sign of activation, and proliferation, as well as an indication of the killing capability of immune cells. Understanding and modulating the mechanisms underlying the activation, proliferation, and clustering of immune cells is essential for the development of innovative approaches to promote immune cell-induced cytotoxicity and address tumor progression. Here, we report a novel kinetic immuno-oncology assay using the Agilent xCELLigence RTCA eSight, which can simultaneously and quantitatively assess effector/immune cell clustering and proliferation through brightfield live cell time-lapse imaging and immune cell-mediated cytotoxicity of target/cancer cells through real-time monitoring cancer cell viability over a chronic treatment. In this study, we validated the assay using 2 cell models, including CD19 CAR T-cells against Raji cells and NK-92 cells against A549 cells, in a 96-well plate format. The activation, clustering, and proliferation of CD19 CAR T-cells and NK-92 at different Effector: Target (E: T) ratios, as well as the sequential killing of the target cancer cells, were plotted using imaging and cellular-impedance-based readouts throughout the entire assay, respectively. Our results showed 1) the clustering and proliferation of the effector cells could be accurately assessed by brightfield without the facilitation of fluorescent label using the image analysis module of the system; 2) the killing efficacy of the effector cells quantified by the impedance readout highly correlated to their clustering and proliferation assessed by the live-cell imaging; 3) cellular impedance provided a sensitive readout CAR-T killing of immobilized Raji cell count, independent of fluorescent labeling; 4) the kinetics of cluster formation/proliferation and killing efficacy of CD19 CAR T-cells were different from NK cells. The capability of multiparametric assessment of immune cell-medicated cytotoxicity from both effector and target cell perspectives of the assay provides a simple and real-time workflow to understand the correlation and interaction between effector and target cells, which could be an addition of immense value to the development of innovative immunotherapies.
Citation Format: Grace Yang, Yan Lu, Tian Wang, Peifang Ye, Xiaoyu Zhang. Real-time multiparametric assessment of immune cell-mediated cytotoxicity [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 77.