tbuckley/cabot-search huggingface dataset:
Abstract 7355: Integration analysis of lncRNAs and R-loops in 3D genome organization and gene regulation in the cancer genome
Authors: Shengyuan Wang, Zhenjia Wang, Yuh-Hwa Wang, Hui Li, Peter Todd Stukenburg, Chongzhi Zang
Journal: Cancer Research (2024)

Abstract Existing evidence shows that some long non-coding RNAs (lncRNAs) can recruit chromatin regulators and form R-loops to mediate CCTCC-binding factor (CTCF) binding at topologically associated domain (TAD) boundaries to activate transcription of target genes. However, it remains unclear to what extent such lncRNA-dependent chromatin organization events occur genome-wide in normal and cancer cells. By curated public data of lncRNA, CTCF, RAD21 profiles and integrative analysis of multi-omics data using innovative computational approaches, we investigated global associations of lncRNAs and R-loops with activities of transcription factors and chromatin regulators in gene expression regulations across multiple human cell types. We developed a comprehensive computational pipeline for cross-cell-type analysis of lncRNA and protein-coding gene expression profiles and transcription factor binding profiles. We identified a total of 542 candidate genomic regions where lncRNAs play a pivotal role in regulating target genes by facilitating CTCF/cohesin binding. R-loops are enriched at CTCF/cohesin binding sites, suggesting their potential contribution to CTCF binding. Additionally, our findings underscore the significant cell-type specificity of CTCF binding patterns across the genome. This work adds knowledge to cancer genome organization and gene regulation, and builds foundations for further functional and mechanistic studies of lncRNAs and R-loops in the human genome. Citation Format: Shengyuan Wang, Zhenjia Wang, Yuh-Hwa Wang, Hui Li, Peter Todd Stukenburg, Chongzhi Zang. Integration analysis of lncRNAs and R-loops in 3D genome organization and gene regulation in the cancer genome [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 7355.
Abstract 2999: Evaluation of microRNA expression in metastatic and non-metastatic salivary gland mucoepidermoid carcinoma
Authors: Maria E. Trevizani, Katia K. Oliveira, Fabio A. Marchi, Daniela Bizinelli, Fernanda V. Mariano, Cibele P. Nagano, Felipe A. Costa, Clovis A. Pinto, Luiz P. Kowalski, Silvia V. Lourenço, Cláudia M. Coutinho-Camillo
Journal: Cancer Research (2024)

Abstract Salivary gland tumors are a heterogeneous group of lesions, being mucoepidermoid carcinoma (MEC) the malignant neoplasm with the highest incidence, occurring mainly in the parotid gland. Characterization of its histological grade (high, intermediate, and low) is important for determining patient prognosis. Metastasis is more common high-grade tumors and can occur at regional lymph nodes or distant sites. Although the mechanisms underlying the metastatic process are largely unknown, large-scale microRNA expression profiling studies of human cancers have demonstrated that dysregulation of miRNA is frequently associated with many cancer types. The aim of this study is to validate the use of microRNA expression for the discrimination of the metastatic potential of MEC samples. Using Real Time RT-PCR (qPCR) we have analyzed the expression of 384 miRNAs and controls in 4 non-metastatic MECs, 3 MECs with lymph node metastasis, 3 MECs with distant metastasis, and 2 non-neoplastic human salivary gland samples. Comparing the expression among these groups we identified 45 differentially expressed miRNAs that may be related with the metastatic potential of these tumors. To validate the microRNA expression associated with the metastatic potential, we selected 7 out of the 45 differentially expressed microRNAs and 7 MEC samples from the different groups of samples. Considering the 7 microRNAs evaluated, we validated that the expression of miR-191 was increased in non-neoplastic samples when compared to MECs with lymph node metastasis and the expression of miR-494 was increased in non-neoplastic samples when compared to MECs with distant metastasis, suggesting that loss of these microRNAs might be involved in the development of metastasis in mucoepidermoid carcinoma. The determination of a miRNA expression profile could provide a better understanding of the molecular basis of MEC and facilitate the determination of diagnosis and prognosis of patients. Citation Format: Maria E. Trevizani, Katia K. Oliveira, Fabio A. Marchi, Daniela Bizinelli, Fernanda V. Mariano, Cibele P. Nagano, Felipe A. Costa, Clovis A. Pinto, Luiz P. Kowalski, Silvia V. Lourenço, Cláudia M. Coutinho-Camillo. Evaluation of microRNA expression in metastatic and non-metastatic salivary gland mucoepidermoid carcinoma [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 2999.
Abstract 5015: Genomic profiling of colorectal cancer - insights from liquid biopsy comparisons between U.S. and China cohorts
Authors: Haoran Tang, Cancan Jia, Feng Xie, Yue Zhang, Xiaoxi Dong, Yong Huang, Shidong Jia
Journal: Cancer Research (2024)

Abstract Background: Molecular characteristics play a pivotal role in cancer diagnosis, treatment selection, and disease monitoring across various tumor types. While previous research has elucidated the molecular classification of colorectal cancer using tissue NGS, limited investigation has explored the molecular profile of colorectal cancer through liquid biopsy, especially across diverse human races. This study presents a comprehensive genomic profiling analysis of colorectal cancer patients, using a globally harmonized liquid biopsy assay to compare patient cohorts from both the U.S. and China. Methods: The prospective study is part of Predicine’s Phoenix Program, a global molecular biomarker screening initiative across multiple solid tumors. At present, the study has enrolled 57 patients in the U.S. and 62 patients in China, all presenting with advanced colorectal cancer. A 10ml blood sample was collected from each patient and tested using PredicineCARE, an NGS-based liquid biopsy assay, to profile somatic mutations, copy number variations, and gene fusions among these patients. Results: The assay, validated in both the U.S. and China using the same reference materials, achieved a LOD of 0.25% mutation allele frequency, with a positive predictive value exceeding 99%. Subsequently, the assay was applied to profile molecular aberrations in colorectal patients in both the U.S. and China. Among U.S. patients, the most commonly altered genes were APC (60%), KRAS (56%), TP53 (54%), MYC (25%), PIK3CA (16%), and EGFR (14%). In Chinese patients, the predominant altered genes were TP53 (48%), APC (42%), KRAS (32%), GNAS (21%), EGFR (16%), and PIK3CA (11%). The prevalence of GNAS variations was significantly higher in China than in the U.S. (p &amp;lt; 0.05), while the prevalence of APC (p &amp;lt; 0.05), KRAS (p &amp;lt; 0.01), and MYC (p &amp;lt; 0.001) variations was significantly higher in the U.S. than in China. Conclusions: This study reveals the extensive mutational landscape in advanced colorectal cancer patients through liquid biopsy. Distinct prevalence patterns in certain genes between the U.S. and China cohorts offer novel biomarkers for clinical diagnosis and provide insights for targeted therapy mechanism studies. Citation Format: Haoran Tang, Cancan Jia, Feng Xie, Yue Zhang, Xiaoxi Dong, Yong Huang, Shidong Jia. Genomic profiling of colorectal cancer - insights from liquid biopsy comparisons between U.S. and China cohorts [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 5015.
Abstract 2617: BCG022, a novel HER3 × MET bispecific antibody-drug conjugate (bsADC), demonstrates promising anti-tumor efficacy
Authors: Zhuolin Li, Chengzhang Shang, Zhenyan Han, Gao An, Chaoshe Guo, W. Frank An, Yi Yang
Journal: Cancer Research (2024)

Abstract HER3 and MET expression act as bypass resistance mechanisms, conferring resistance to multiple therapeutic agents, such as EGFR TKI treatment. HER3 and MET are also co-expressed at high prevalence in multiple tumor types, including gastric, colorectal, breast, and non-small-cell lung cancer (NSCLC). In addition, HER3 and MET are frequently overexpressed in liver metastases from patients with colorectal cancer, indicating that targeting both targets may provide clinical benefit. We previously reported generation of a fully human bispecific antibody (bsAb) targeting HER3 and MET using RenLite® mice, which contain the full human heavy chain variable domain with a common human kappa light chain to facilitate bispecific antibody assembly. This bsAb demonstrated reactivity to human and cynomolgus monkey antigens and binding to multiple cancer cell lines, including NSCLC, gastric, colorectal, and hepatocellular cancer cell lines. The bsAb also showed enhanced internalization activity compared to parental monovalent antibodies in the NUGC-4 cell line expressing HER3 and MET. Here, we evaluated the efficacy of the bsAb when conjugated to two distinct payloads: vcMMAE and BLD1102, Biocytogen’s novel, proprietary linker/payload system composed of a DNA Topo I inhibitor payload (BCPT02) and a highly hydrophilic protease-cleavable linker. The in vivo efficacy of BCG022-vcMMAE and BCG022-BLD1102 was evaluated in cell-derived NSCLC and gastric cancer xenografts, and in patient-derived gastric and pancreatic xenograft models. Both demonstrated strong anti-tumor activity, with efficacy greater than or comparable to benchmark ADCs. Taken together, these promising preclinical results suggest that the BCG022 bsADC could be a novel treatment for HER3 and MET co-expressing tumors. Citation Format: Zhuolin Li, Chengzhang Shang, Zhenyan Han, Gao An, Chaoshe Guo, W. Frank An, Yi Yang. BCG022, a novel HER3 × MET bispecific antibody-drug conjugate (bsADC), demonstrates promising anti-tumor efficacy [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 2617.
Abstract 7295: A novel XNA technology-based assay to detect JAK2 V617F mutation by real-time PCR
Authors: Shuo Shen, Robert Brown, Daniel Kim, Larry Pastor, Andrew Y. Fu, Pushpinder Kaur, Alisha Babu, Wei Liu, Aiguo Zhang, Hiromi Tanaka, Michael Y. Sha
Journal: Cancer Research (2024)

Abstract The Janus kinase 2 (JAK2) gene is located on chromosome 9p24.1 and encodes a non-receptor tyrosine kinase that plays a central role in cytokine and growth factor signaling. The JAK2 protein is especially important for controlling the production of blood cells from hematopoietic stem cells. In fact, the JAK2 mutation at amino acid 617 (Valine 617 to Phenylalanine, V617F) is the most frequently detected mutation in myeloproliferative neoplasms (MPN), including essential thrombocythemia (ET), polycythemia vera (PV), and primary myelofibrosis (PMF). This dominant gain-of-function V617F mutation results in constitutive tyrosine phosphorylation activity, leading to uncontrolled blood cell production, including increased numbers of erythrocytes, neutrophils, and platelets. To detect the JAK2 V617F mutation in DNA from patient blood samples, we developed a unique real-time PCR assay using our proprietary XNA technology that enables the assay to selectively amplify the mutant sequence by using a synthetic DNA analog XNA (Xenonucleic Acid). The JAK2 V617F mutation detection assay is designed to detect a valine-to-phenylalanine mutation at amino acid 617 (V617F). PCR primers, TaqMan probes, and XNA were designed for the JAK2 V617F mutation, along with primers and probes for an internal control gene in the duplex setting. The analytical performance of the assay was verified and validated using a variety of control samples. The results revealed that the XNA completely suppressed the amplification of wildtype sequence while only the V617F mutant sequence was amplified. The JAK2 V617F mutation detection assay is highly reproducible with intra- and inter-assay coefficients of variation of less than 10%. Results for the assay’s analytical sensitivity indicated that V617F could be detected with about 0.25% mutant allele frequency in 10 ng DNA input. In addition, no significant cross-amplification between V617F and V617I was observed. Thus, the JAK2 V617F mutation detection assay is specific for the V617F mutation. The JAK2 V617F mutation detection assay, using XNA-based technology, provides high sensitivity and specificity to detect the JAK2 V617F mutation. Thus, this assay would be a useful tool for clinical decision-making in determining the presence of the JAK2 V617F mutation in DNA from patient blood samples. Citation Format: Shuo Shen, Robert Brown, Daniel Kim, Larry Pastor, Andrew Y. Fu, Pushpinder Kaur, Alisha Babu, Wei Liu, Aiguo Zhang, Hiromi Tanaka, Michael Y. Sha. A novel XNA technology-based assay to detect JAK2 V617F mutation by real-time PCR [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 7295.
Abstract 77: Real-time multiparametric assessment of immune cell-mediated cytotoxicity
Authors: Grace Yang, Yan Lu, Tian Wang, Peifang Ye, Xiaoyu Zhang
Journal: Cancer Research (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.
Abstract 507: HLS-22001 induces G2/M cell cycle arrest and apoptotic cell death via tubulin depolymerization in colon cancer
Authors: Chi-hyun Ahn, Gyu-beom Jang, Chunhwa Kim, Junho Lee, Taewon Kim, Youngeun Yang, Eunji Cho, Minchae Kim, Yun-tai Kim, Yong-Hae Han, Heebum Kang
Journal: Cancer Research (2024)

Abstract Colorectal cancer (CRC) is one of the main malignant tumors and among the leading cause of death in cancer patients worldwide considering that recurrence and chemotherapeutic drug resistance are highly common in the advanced stage of CRC. Mutations in KRAS and BRAF occur frequently in colorectal cancers, and abnormal cell cycles caused by these mutations affect tumor progression and metastasis. Accordingly, inhibition of cell cycle has been a potential target for colorectal cancers and therefore, we have developed a new lead compound, HLS-22001. Our studies confirmed that HLS-22001 inhibited the proliferation of several cancer cells and significantly induced G2/M arrest and apoptosis of colon cancer cells and chemotherapy resistant colon cancer cells. The docking model studies showed that HLS-22001 was expected to bind to the colchicine binding site of beta-tubulin, and in fact, as a tubulin inhibitor, it had the effect of inhibiting tubulin dimerization and polymerization in the microtubule dynamics. Consistently, in xenograft mouse model, oral administration of HLS-22001 significantly suppressed tumor weight and volume without acute toxicity in mice. Collectively, these results suggest further development of HLS-22001 as a novel and promising oral drug for colorectal cancer. Citation Format: Chi-hyun Ahn, Gyu-beom Jang, Chunhwa Kim, Junho Lee, Taewon Kim, Youngeun Yang, Eunji Cho, Minchae Kim, Yun-tai Kim, Yong-Hae Han, Heebum Kang. HLS-22001 induces G2/M cell cycle arrest and apoptotic cell death via tubulin depolymerization in colon 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 507.
Abstract 3012: Characterizing the functional significance of "variant of uncertain significance" of the tumour suppressor <i>CDH1</i>
Authors: Jasmine Wen, Ajay Singh, David Nguyen, Kaitlynn Meier-Ross, Ben Martin, Vedanta Khan, Kiran Dhami, Jesse Chao
Journal: Cancer Research (2024)

Abstract We aim to develop a new approach to systematically characterize the functional significance of “variant of uncertain significance (VUS),” focusing on the tumor suppressor gene CDH1. Genetic testing is a powerful clinical tool for identifying individuals at risk of developing inherited or familial cancers. If a potential cancer-causing genetic variant (mutation) is found, clinicians can begin managing the patient’s risk early by initiating surveillance or prophylactic treatment. For an aggressive form of inherited stomach cancer called hereditary diffuse gastric cancer (HDGC), the most commonly mutated gene is CDH1, which encodes the tumor suppressor E-Cadherin. However, due to insufficient clinical evidence, over 50% of all publicly reported CDH1 variants either have conflicting interpretations or cannot be classified, thus are not actionable. Consequently, almost 1 in 2 patients who undergo genetic testing for HDGC will not have a definitive test result and cannot benefit from early screening, causing strain on the healthcare system and psychological burden for the patients. To overcome this challenge, we developed a single-cell screening system to accurately classify CDH1 variants using a combination of functional assays, machine learning, and deep learning. Our hypothesis, now supported by preliminary data, is that pathogenic variants will disrupt normal E-Cadherin’s ability to control its signaling partner beta-catenin. Thus, loss-of-function (LoF) CDH1 variants would cause protein mislocalization and altered signaling which lead to abnormal proliferation, an early indicator for carcinogenesis. We express CDH1 variants in human cell lines and use multiplexed high-content imaging to visualize E-Cadherin and beta-catenin. Next, our deep learning pipeline extracts single-cell phenotypic profiles, and our classifier then classifies variants as functional or LoF. Initial analysis of prioritized variants show that our pipeline can accurately separate clinically pathogenic and benign variants based on their functional status as predicted by our pipeline. The outcomes of this project will contribute to a systematic approach to reclassify VUS. Citation Format: Jasmine Wen, Ajay Singh, David Nguyen, Kaitlynn Meier-Ross, Ben Martin, Vedanta Khan, Kiran Dhami, Jesse Chao. Characterizing the functional significance of "variant of uncertain significance" of the tumour suppressor CDH1 [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 3012.
Abstract 2779: The significance of TIMP-1 and hypoxia in cancer stemness: A synergistic role in chemoresistance
Authors: Ilamathi Thirusenthilarasan, Wei Xiao, Mumtaz V. Rojiani
Journal: Cancer Research (2024)

Abstract Chemotherapeutic resistance in non-small-cell lung cancer (NSCLC) poses a formidable clinical challenge. Numerous studies have highlighted the critical role of tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) in tumorigenesis and, increasingly, in the development of chemoresistance. We have studied multiple aspects of the MMP-independent, tumor-promoting function of TIMP1 in human NSCLC. Our recent studies have found a pivotal role for TIMP1 in chemoresistance. In order to gain an enhanced comprehension of the mechanisms underpinning TIMP-1-mediated chemoresistance, we have sought to determine the contribution of CSCs and hypoxia. TIMP-1 plays a role in propagating stemness, although relatively unexplored in the context of CSCs within NSCLC. A second crucial factor in the development of chemoresistance in NSCLC is the interplay between intratumoral hypoxia and CSCs. As the tumor grows, metabolic demand for oxygen increases and hypoxic regions are seen in areas furthest from the blood vessels. We have shown TIMP1 levels to increase under experimentally-induced hypoxia. In the present study, we cultured NSCLC cell lines and their TIMP1 KD clones in an assay with serum-free media and found a significant decrease in spheroid size in TIMP1 KD clones. Postulating a reduction in CSC population in KD clones, we determined the NSCLC CSC markers CD133 and ALDH’s expression in the NT and KD TIMP1 clones. Flow cytometry results showed that CD133pos and ALDHhigh populations were significantly decreased in TIMP1 KD clones relative to NT clones. Moreover, KD clone of TIMP1 showed a decrease in the levels of CSC-specific Transcription factors Oct 4A and Nanog. Taken together, our findings confirm that reduction in TIMP1 expression negatively impacts CSC populations. Furthermore, we determined the mRNA levels of CD44, another CSC marker also expressed in lung cancer is upregulated under hypoxia (1% O2) in both the NT and KD clones of TIMP1. Thus, we postulate that TIMP1 enhances chemoresistance by promoting CSC propagation within a hypoxic tumor microenvironment. Citation Format: Ilamathi Thirusenthilarasan, Wei Xiao, Mumtaz V. Rojiani. The significance of TIMP-1 and hypoxia in cancer stemness: A synergistic role in chemoresistance [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 2779.