bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 6081: DNA integrity and preanalytical handling of endocervical samples for use in liquid biopsy-based diagnostics and monitoring of gynecological cancer
Authors: Lauesgaard Jacob Malchau , Carlsson Therese , Linder Anna , Schumacher Sara , Sundfeldt Karin 
Published: March 2024

Abstract
Background: Liquid biopsies from the gynecological tract can be useful for analysis of cell free DNA (cfDNA) (1, 2, 3). Sampling procedure and optimal preanalytical handling are poorly investigated. In this study, we aimed to evaluate how the profile and integrity of DNA, sampled from the female genital tract, were affected by preanalytical handling.
Methods: Biobanked/archival (stored at -80℃ after 48h at room temperature (RT)) and freshly obtained clinical samples were analyzed together with standardized in vitro samples. Archival and in vitro samples were preserved in methanol-based solution, imitating clinical handling of endocervical samples which are initially stored at RT for 48h before further handling. The fragmentation profile of archival and in vitro samples was analyzed. Time series of in vitro samples at RT and 4℃, with extraction at 6-hour intervals from 0 to 96h, were performed. The fresh clinical samples were collected from the endocervix in methanol-based solution and from the vagina in a solution designed to preserve DNA and placed at 4℃ resp RT. Extraction was performed within 4h and at 48h.
Results: Accumulation of short DNA fragments were observed in the archival samples and in the in vitro samples, indicating that fragmentation was initiated prior to 48h. Time series showed that the quantity of short DNA fragments gradually increased with time at both RT and 4℃ but at a slower rate in 4℃. At RT the percentage of fragments between 100-350bp increased 12-fold (0.39% vs 4.75%, p=0.002). The freshly obtained endocervical samples showed a similar significant increase in short fragments in samples stored at RT compared with samples stored at 4℃ (p= 0.02 for 100-230bp; p= 0.007 for 230-350bp; p= 0.03 for 100-2500bp) at 4h-48h.
Conclusion: Pre-analytical handling of endocervical samples can be optimized. Lowering temperature from RT to 4℃ immediately haltered DNA fragmentation.
Citation Format: Jacob Malchau Lauesgaard, Therese Carlsson, Anna Linder, Sara Schumacher, Karin Sundfeldt. DNA integrity and preanalytical handling of endocervical samples for use in liquid biopsy-based diagnostics and monitoring of gynecological 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 6081.
Abstract 61: A novel immunotherapy for metastatic prostate cancer: A monoclonal antibody that can bind both STEAP1 and STEAP2
Authors: Sheng Minzhi , Thillainadesan Gobi , Sparkes Amanda , Su Boyang , Matus Esther , Wright Jessica , Liu Stanley , Gariepy Jean , Leong Hon S. 
Published: March 2024

Abstract
Prostate cancer (PCa) is the second most prevalent cancer among males, and the 5-year survival rate for patients with metastatic PCa (mPCa) is ~30%. Although significant progress has been made in improving survival in mPCa patients, many of these patients experience relapse or systemic toxicities. Protein expression of prostate-specific membrane antigen (PSMA), a common PCa antigen often targeted in PCa therapy, is unfortunately lost in the later stages of mPCa. In contrast, six transmembrane epithelial antigen of the prostate 1 and 2 (STEAP1 and STEAP2) are both overexpressed in most PCa compared to normal and vital organs and has emerged as a next-generation target in mPCa.
We hypothesize that an antibody that binds to both STEAP1 and STEAP2 via their second extracellular domain (60% homology) could be useful therapeutically. Using an immunogen of this second extracellular domain, we raised several antibody clones that appear to have an affinity towards both STEAP1 and STEAP2 (STEAP1/2). The specificity and affinity of these antibody clones were successfully determined by immunofluorescence, flow cytometry and ELISA. Immunofluorescence results in PCa cell lines and those that overexpress STEAP1 and STEAP2 demonstrate the potential specificity of one clone for human STEAP1 and STEAP2. In addition, ELISA data revealed that the binding affinity of this clone to STEAP1 and STEAP2 is in the low nanomolar and low micromolar range, respectively. This monoclonal STEAP1/2 antibody has been sequenced and will become the basis for future development of immunotherapies thus expanding the therapeutic armamentarium for mPCa.
Citation Format: Minzhi Sheng, Gobi Thillainadesan, Amanda Sparkes, Boyang Su, Esther Matus, Jessica Wright, Stanley Liu, Jean Gariepy, Hon S. Leong. A novel immunotherapy for metastatic prostate cancer: A monoclonal antibody that can bind both STEAP1 and STEAP2 [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 61.
Abstract 6191: Simultaneous prediction of tumor microenvironment biomarkers from pathology slides using multi-task deep regression
Authors: Nahhas Omar S. El , Ligero Marta , Kather Jakob N. 
Published: March 2024

Abstract
Understanding the Tumor Microenvironment (TME) is crucial for tailoring personalized cancer treatments and improving patient outcomes. Using deep learning, we can predict properties of the TME from standard Hematoxylin and Eosin (H&E) stained slides, including specific gene expression signatures. While past models were limited to single signature predictions, we explore the potential of multi-task deep learning to identify multiple biomarkers at once, allowing more complex relationships and interactions to be modeled simultaneously. Our study focuses on the prediction of expression patterns of tumor, stromal, and immune cells in breast cancer (BC).
We developed a multi-task transformer-based deep regression model, trained in a weakly-supervised setting, to predict biomarkers in the TME from routine H&E-stained pathology slides of a BC cohort (n=876). The performance was evaluated using Pearson’s correlation coefficient (r) and spatial heatmaps generated via gradient-weighted class activation mapping.
Our model achieved a significant correlation coefficient above 0.40 (p&lt;0.0001) for all predicted TME biomarkers in the holdout test set (n=176). This includes the biomarkers lymphocyte infiltrating signature score (r=0.46, p&lt;0.0001), tumor infiltrating lymphocyte regional fraction (r=0.48, p&lt;0.0001), leukocyte fraction (r=0.43, p&lt;0.0001), stromal fraction (r=0.42, p&lt;0.0001), and tumor cell proliferation (r=0.47, p&lt;0.0001). Notably, the model's heatmaps highlighted the pertinent cells and histological characteristics for its predictions.
These data show that our deep learning model accurately predicts multiple TME biomarkers concurrently from routine pathology slides. This approach offers a promising avenue for cost-effective and efficient biomarker quantification in the TME, with potential applicability across various cancer types.
Citation Format: Omar S. El Nahhas, Marta Ligero, Jakob N. Kather. Simultaneous prediction of tumor microenvironment biomarkers from pathology slides using multi-task deep regression [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 6191.
Abstract 6201: Early-onset CRC, vitamin A deficiency, and stem cell origin of cancer
Authors: Boman Bruce M. , Hunsu Victoria O. , Facey Caroline O. 
Published: March 2024

Abstract
The recent surge in early-onset CRC (EOCRC) has been attributed to a Westernized lifestyle, but the underlying molecular mechanism is largely unknown. In our cancer genetics clinic, we provide care for 10-20 young (&lt;50 age) CRC patients per year. But, only a fraction (~15%) of these young CRC patients are found to have CRC-predisposing germline mutations which doesn’t provide a hereditary factor that can explain EOCRC. Other genetic studies have found that the spectrum of somatic alterations was largely comparable between EOCRC and adult-onset CRC, particularly common are mutations occurring in APC and other members of the WNT pathway. Since a genetic etiology has not turned-up, we are exploring possible lifestyle factors. We hypothesize that vitamin A (retinol) deficiency is a likely etiologic factor because vitamin A is an essential nutrient that is not made by the human body. Thus, young individuals might be prone to any cancer-initiating effects of a vitamin A deficient diet. Indeed, many population-based studies (including ones on well-nourished populations) have reported a high prevalence of vitamin A deficiency in pre-school-aged children. Since APC mutation commonly occurs in early-onset CRCs, we conjecture that vitamin A (retinol) metabolism and APC mutation-induced activation of WNT signaling may be co-factors in promoting EOCRC. Accordingly, we have been investigating whether there is a functional connection between WNT and vitamin A/retinoic acid (RA) signaling, and if APC mutation generates an imbalance in a WNT:RA-linked mechanism that contributes to CRC development by impeding retinoid-induced colonic stem cell (SC) differentiation. We previously reported that RA signaling mainly occurs in aldehyde dehydrogenase-positive (ALDH+) SCs and that APC mutation leads to overpopulation of ALDH+ SCs and incomplete differentiation during CRC development. Thus, our findings suggest that APC mutation attenuates RA signaling in ALDH+ SCs, which might explain how vitamin A deficiency contributes to EOCRC development.
Citation Format: Bruce M. Boman, Victoria O. Hunsu, Caroline O. Facey. Early-onset CRC, vitamin A deficiency, and stem cell origin of 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 6201.
Abstract 6207: Exploring colorectal cancer with ARIA: Biomedical insights
Authors: Nikolic Nevena , Kleinstein Sarah , Radenkovic Jelena , Kovacevic Milan 
Published: March 2024

Abstract
Gaining the promised benefits from the population-scale datasets, both clinical and genomic, is often hindered by the inability to easily access, explore and manipulate such complex data - a difficulty that ARIA was designed to overcome.
In the field of biomedicine, organizations harness extensive datasets, gaining profound insights into patients and participants, thereby unleashing possibilities for accelerating research, especially in the realms of drug development and precision medicine. To facilitate navigation through the intricate landscape of biomedical data, Velsera has innovated ARIA to catalyse efficient and insightful analysis, with a keen emphasis on user-friendliness to ensure accessibility across a diverse professional audience. To demonstrate the practical application of ARIA, we explore genomic and clinical datasets to identify key differences in colorectal cancer progression. CRC, the third most common cancer globally, has unique characteristics in origination and progression from benign to pathogenic. Here we investigate differences between patients with polyps that do and do not progress to CRC, including key environmental factors such as smoking history, inactive lifestyle and obesity in conjunction with their known clinical and genetic risk factors. This exploration into the abilities of ARIA demonstrate the ability to analyse complex datasets combining both clinical and genomics data at a large scale.
For the purpose of this demonstration, a Synthea Dataset, encompassing synthetic clinical and genomic data for 122,011 patients across various age groups, was utilized. This dataset was generated by Velsera specifically for testing ARIA functionalities.
In conclusion, ARIA empowers efficient analysis of complex biomedical datasets, providing a comprehensive understanding of disease mechanisms and facilitating valuable insights.
Citation Format: Nevena Nikolic, Sarah Kleinstein, Jelena Radenkovic, Milan Kovacevic. Exploring colorectal cancer with ARIA: Biomedical insights [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 6207.
Abstract 6317: Developing a fully human heavy chain only Claudin-18.2-specific CAR-T cell therapy
Authors: Noon Jason , Lu Yao , Kaushik Itishree , Ay Oyku , Luk Adam , Delaney Bradley , DeMeritt David , Bao Musheng 
Published: March 2024

Abstract
Camelid VHH/nanobodies have been widely applied as the antigen binding domain of CAR-T cell therapies due to a smaller size and simpler structure compared to the traditionally used single chain variable fragment (scFv). Additionally, camelid VHH/nanobodies provide greater flexibility for dual-targeting CAR-T cell therapies. However, camelid VHH/nanobodies require laborious and costly humanization and still have a significant risk of inducing anti-drug antibodies when administered to patients. Transgenic mice exclusively harboring the most stable human VH genes (HCAb Harbour Mice®) provide one of the best solutions to get fully human heavy chain only antibodies (HCAbs). To efficiently identify lead HCAb VHs for Claudin-18.2-targeting CAR-T cells, we developed an innovative direct CAR-function based HCAb library screening platform. From Claudin-18.2-immunized HCAb Harbour Mice®, we constructed a total VH library in a CAR lentiviral vector that we developed in-house. After producing the lentiviral particle library, we transduced a Jurkat-NFAT-GFP reporter cell line and stimulated with Claudin-18.2 overexpression cell line. Subsequently, GFP positive reporter cells, representing Claudin-18.2-specific CARs, were isolated through FACS sorting, expanded, and further stimulated with Claudin-18.2-positive NUGC-4 tumor cells. Then, Next Generation Sequencing and abundance ranking was performed on VHs recovered from sorted CAR-reporter cells. Lead VH candidates were cloned into the CAR-P2A-RFP lentiviral vector, and many of these VH clones exhibited superior Claudin-18.2-specific functionality compared to a clinically-validated reference scFv in both reporter and primary CAR-T cells. Many lead VH clones also exhibited excellent developability as soluble HCAbs. These data suggest that this innovative method of combining our fully human HCAb and CAR-based library screening platform will provide new avenues for CAR-T cell therapies.
Citation Format: Jason Noon, Yao Lu, Itishree Kaushik, Oyku Ay, Adam Luk, Bradley Delaney, David DeMeritt, Musheng Bao. Developing a fully human heavy chain only Claudin-18.2-specific CAR-T cell therapy [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 6317.
Abstract 6360: A novel CAR-NK cell therapy to target lung adenocarcinoma cells
Authors: Zolov Sergey , Chuikov Sergei , Katkam Shiva Krishna , Shield Delaney , Keshamouni Venkateshwar G. 
Published: March 2024

Abstract
Cell Adhesion Molecule (CADM1) is a Bonafede tumor suppressor with 40% of NSCLC tumors lose CADM1 expression either by loss of heterozygosity or promoter hypermethylation. The tumor suppressive ability of CADM1 is attributed to its cell adhesion function. However, we previously demonstrated that CADM1 also mediates its tumor suppression through regulation of NK-mediated immunosurveillance. In tumors that do not lose CADM1, it is expressed on cell surface and up regulated during TGF-β-induced EMT making it a biomarker for potential therapeutic targeting. Here we report the design and development of T and NK specific CAR that would specifically target lung cancer cells in CADM1 dependent manner. Anti-CADM1 single chain variable fragment (CADM1-scFv) was fused to NK or T cell specific transmembrane and co-stimulatory domains. The resulting CAR constructs were cloned into a retroviral vector, from which viral stocks were generated to transduce human and mouse cells. Next, we introduced anti-CADM1-CAR-NK construct into NK92 cell line and tested it in a cytotoxicity assay using A549-GFP-ffluc cell line as a target. We observed a significant increase in the killing of target cells with anti-CADM1-CAR-NK cells compared with non-transduced NK92 cells. This effect was significantly reduced when A549- GFP-ffluc-CADM1 KO cells were used as target. Next, we generated anti-CADM1-CAR-T cells by transducing human CD3+ T-cells purified from human PBMCs. Similar to anti -CADM1-CAR-NK, anti-CADM1-CAR-T cells showed increased T-cell specific cytotoxicity in a CADM1-dependent manner. Next, we evaluated the efficacy of anti-CADM1-CAR-T cells through adoptive transfer into NSG mice xenografted with human lung adenocarcinoma cells into mouse lungs. The administration of anti-CADM1-CAR-T cells markedly reduced tumor size and enhanced the survival rate of the mice. Importantly this effect was dependent on CADM1 expression, as mice xenografted with human CADM1 KO cells showed neither tumor size reduction nor increased survival. Finally, using IHC staining, we demonstrated that anti-CADM1-CAR-T cells directly target xenografted tumors in the mouse lungs. In conclusion, our findings indicate that CAR-NK and CAR-T cells targeting CADM1-expressing lung tumors have a significant therapeutic potential for the treatment of NSCLC.
Citation Format: Sergey Zolov, Sergei Chuikov, Shiva Krishna Katkam, Delaney Shield, Venkateshwar G. Keshamouni. A novel CAR-NK cell therapy to target lung adenocarcinoma cells [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 6360.
Abstract 6404: GRB2 stabilizes RAD51 at reversed replication forks restricting genomic instability and associated innate immune response
Authors: Ahmed Zamal , Ye Zu , Xu Shengfeng , Shi Yin , Cheng Xueqian , Zhang Yuan , Roy Sunetra , Namjoshi Sarita , Longo Michael A. , Link Todd , Schlacher Katharina , Peng Guang , Yu Dihua , Wang Bin , Tainer John 
Published: March 2024

Abstract
Growth factor receptor-bound protein 2 (GRB2) is a cytoplasmic adapter for tyrosine kinase signaling and a nuclear adaptor for homology-directed-DNA repair. Here we find nuclear GRB2 protects DNA at stalled replication forks from MRE11-mediated degradation in the BRCA2 replication fork protection axis. Mechanistically, GRB2 binds and inhibits RAD51 ATPase activity to stabilize RAD51 on stalled replication forks. In GRB2-depleted cells, PARP inhibitor (PARPi) treatment releases DNA fragments from stalled forks into the cytoplasm that activate the cGAS-STING pathway to trigger pro-inflammatory cytokine production. Moreover in a syngeneic mouse metastatic ovarian cancer model, GRB2 depletion in the context of PARPi treatment reduced tumor burden and enabled high survival consistent with immune suppression of cancer growth. Collective findings unveil GRB2 function and mechanism for fork protection in the BRCA2-RAD51-MRE11 axis and suggest GRB2 as a potential therapeutic target and an enabling predictive biomarker for patient selection for PARPi and immunotherapy combination.
Citation Format: Zamal Ahmed, Zu Ye, Shengfeng Xu, Yin Shi, Xueqian Cheng, Yuan Zhang, Sunetra Roy, Sarita Namjoshi, Michael A. Longo, Todd Link, Katharina Schlacher, Guang Peng, Dihua Yu, Bin Wang, John Tainer. GRB2 stabilizes RAD51 at reversed replication forks restricting genomic instability and associated innate immune response [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 6404.
Abstract 6458: Clinical significance of cancer genome profiling tests for gastrointestinal cancer patients with liver metastasis
Authors: Sakuma Takashi , Yashiro Masakazu , Fukui Yasuhiro , Maruo Koji , Tsujio Gen , Yamamoto Yurie , Kasashima Hiroaki , Maeda Kiyoshi 
Published: March 2024

Abstract
Introduction: Distant metastasis is one of critical prognostic factors for patients with gastrointestinal cancer. Especially, liver metastasis shows high effects on prognosis of patients with gastrointestinal cancer. In Japan, cancer genome profiling (CGP) testing have been available for patients who have no selective standard treatment options since 2019. Based on the genetic mutations by CGP test, therapeutic drugs with evidence have been discussed at expert panels. CGP data has been accumulated in around 60,000 cases. It is necessary to evaluate the clinical significance of CGP tests for gastrointestinal cancer patients with liver metastasis to receive high benefits of CGP testing through C-CAT. Aims: We aimed to analyze the clinical significance CGP tests for gastrointestinal cancer patients with liver metastasis. Materials and methods: A total of 3,738 patients of gastrointestinal cancer with liver metastases including 215 cases of esophageal cancer, 347 cases of gastric cancer, and 3,176 cases of colorectal cancer, was enrolled in this study. Three types of CGP tests, including NCC Oncopanel, FoundationOne CDx, and FoundationOne Liquid, were performed, and the CGP data was collected to Center for Cancer Genomics and Advanced Therapeutics in Japan (C-CAT) database. Adequate treatment for each patient was discussed at the expert panel meeting according to the results from the CGP tests. Results: A total of 2,882 cases (77.1%) in 3,176 cases have been revealed druggable. However, only 216 cases (13.3%) were medicated by anti-cancer treatments. In the 216 treated cases, disease control case, complete response (CR), partial response (PR), or stable disease (SD) was only 52 cases. In 52 cases, six cases (4 of SD cases and 2 of PR cases) was administered encorafenib-based chemotherapies based on BRAF gene mutation. Five genes, ZNF217, SRC, ARFRP1, BARD1, FGF10, were significantly more frequently expressed on liver metastasis cases, in compared to other metastasis cases in gastrointestinal cancer. Conclusion: Around 13% of gastrointestinal cancer patients with liver metastasis might have a druggable benefit by CGP testing. BRAF mutation might be promising target for patients with liver metastasis. ZNF217, SRC, ARFRP1, BARD1, FGF10 might be associated with metastatic process to liver in gastrointestinal cancer.
Citation Format: Takashi Sakuma, Masakazu Yashiro, Yasuhiro Fukui, Koji Maruo, Gen Tsujio, Yurie Yamamoto, Hiroaki Kasashima, Kiyoshi Maeda. Clinical significance of cancer genome profiling tests for gastrointestinal cancer patients with liver metastasis [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 6458.