tbuckley/cabot-search huggingface dataset:
Abstract 7662: Convolutional neural network algorithms and hematoxylin-and-eosin-stained images predict clinical outcomes in high-grade serous ovarian cancer patients with advanced age and stage
Authors: Chun Wai Ng, Kwong-kwok Wong, Berrett Lawson, Sammy Ferri-Borgogno, Samuel Mok
Journal: Cancer Research (2024)

Abstract Ovarian cancer is the deadliest among gynecologic cancers. It is partly due to the mild symptoms in early stages and relatively high diagnostic age (about 63-year-old median age). These factors contribute to the short chemotherapy response time and survival time with about 18- and 36-months median progression-free survival and overall survival duration, respectively. The advancements of convolutional neural network (CNN) machine learning algorithms provide opportunities for the development of cost- and time-effective models which is urgently needed for ovarian cancer patients, especially for those with elevated risk. A CNN model was trained with hematoxylin and eosin (H&amp;E) stained tumor whole slide images (WSIs) from ovarian cancer patients with advanced stages. 773 WSIs of 335 patients from TCGA-OV dataset were separated randomly for training and testing cohort. The model was then applied on testing cohort with advanced stage and age patients for H&amp;E survival score. The c-index of the predicted risk on overall survival (OS) and progression-free survival (PFS) were 0.66 and 0.63, respectively. The log-rank p-values of patients between low and high risk were 0.00137 and 0.00138, respectively. The model was then further evaluated with an external dataset. The c-index of the predicted risk were 0.64 and 0.72 for OS and PFS, respectively. And the log-rank test between patients with low and high risk achieved p-values 0.017 and 0.0047 for OS and PFS, respectively. In conclusion, a novel prognostic CNN model was developed for ovarian cancer patients with advanced age and stage for better disease management. Citation Format: Chun Wai Ng, Kwong-kwok Wong, Berrett Lawson, Sammy Ferri-Borgogno, Samuel Mok. Convolutional neural network algorithms and hematoxylin-and-eosin-stained images predict clinical outcomes in high-grade serous ovarian cancer patients with advanced age and stage [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 7662.
Abstract 210: Carcinogenic influence of e-cigarette aerosols on breast and lung cancer models
Authors: Rizwana Begum, Shilpa Thota, Naveen Chintala, Biplov Sapkota, Abhishek Pandit, Joseph Francis
Journal: Cancer Research (2024)

Abstract Background and Purpose: With the rising popularity of E-cigarettes among the youth, there is an urgent need to understand their long-term health implications, particularly the potential for carcinogenesis. Although tobacco smoking is established as a major cancer risk factor, the carcinogenic potential of E-cigarettes remains underexplored. Given that metastatic cancer accounts for most cancer-related deaths in the United States, elucidating the biological impacts of E-cigarette aerosols on cancer progression is critical for developing effective interventions. This study aims to address this critical gap by exploring the effects of E-cigarette aerosols on cellular models pertinent to breast and lung cancer. Methods: Mouse breast epithelial cells (HC11), triple-negative breast cancer cells (4T1), and human lung adenocarcinoma cells (Calu-3) were exposed to E-cigarette aerosol at the air-liquid interface for one hour, followed by a 24-hour recovery period. Results: Our study revealed that E-cigarette aerosols with mint flavor induce epithelial-to-mesenchymal transition (EMT) in both normal mammary epithelial and breast cancer cells. Furthermore, we also observed activation of the TGF pathway and an increased expression of stemness-related markers (OCT4, SOX2, NANOG, KLF4, and c-MYC) in 4T1 cells exposed to mint and menthol-flavored E-cigarette aerosols in both 2D and 3D cell culture environments. Microscopic examination at a 10X magnification level revealed that 4T1 and Calu-3 cells exposed to menthol-flavored E-cigarette aerosols exhibited signs of cellular disassociation and detachment whereas the control cells maintained discoidal aggregate morphology. Conclusion: The data presented here illuminate a potential link between E-cigarette use and carcinogenic processes, challenging the notion of E-cigarettes as a safe smoking alternative. This research is of paramount importance to cancer research as it unveils possible new avenues for tumor progression, emphasizing the necessity for a critical evaluation of E-cigarette products. Citation Format: Rizwana Begum, Shilpa Thota, Naveen Chintala, Biplov Sapkota, Abhishek Pandit, Joseph Francis. Carcinogenic influence of e-cigarette aerosols on breast and lung cancer models [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 210.
Abstract 5007: <i>Ex vivo</i> evaluation of mRNA lipid nanoparticle cancer vaccines
Authors: Tommy Lidström, Mara Blanco Arauzo, Nickolas Karlowatz, Mikael Johansson, Mattias Forsell, Jonas Nilsson
Journal: Cancer Research (2024)

Abstract Lipid nanoparticle vaccines have recently been developed broadly against pathogens and recently, in precision medicine targeting mutations in different tumors. Evaluating vaccine candidates typically require animal models using orthotopic or allogenic transplantations to evaluate efficiency. Evaluating vaccine efficacy using ex vivo systems is faster and less technically demanding. Here we aim to develop individualized cancer vaccines based on neoantigen identified within established human organoids or directly from patient tissue. The selected neoantigens are enriched for epitopes identified on gene fusions. Identified gene fusions encoding predicted immunogenic proteins are inserted into a vaccine backbone and used to make mRNA lipid nanoparticle vaccines. The neoantigen candidates are then evaluated in a personalized ex vivo testbed. Within the ex vivo testbed personal tumor neoantigens are tested on the patients own isolated CD8+ T cells and monocytes. Monocytes are in vitro differentiated into monocyte derived dendritic cells (moDCs), which specialize in antigen cross presentation. The moDCs are inoculated with mRNA lipid nanoparticle vaccines or loaded with peptides. The moDCs are then co-cultured with syngeneic T cells. Vaccine candidates are evaluated based on CD8+ T cell activation and cytotoxicity in the co-culture ex vivo testbed. Our pipeline offers a fast and efficient means of evaluating individualized vaccine candidates. Effective vaccines developed through this process can be administered as a standalone therapy or in combination with checkpoint inhibitors, to generate a strong durable immune response against a variety of solid tumor types. Citation Format: Tommy Lidström, Mara Blanco Arauzo, Nickolas Karlowatz, Mikael Johansson, Mattias Forsell, Jonas Nilsson. Ex vivo evaluation of mRNA lipid nanoparticle cancer vaccines [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 5007.
Abstract 116: Generation of humanized PD-1/PD-L1/CD94/NKG2A mice for evaluating novel combination therapies
Authors: Fang He, Jiangfeng Yuan, Yawen Shan, Huwatibieke Bahetiyaer, Qingqing Xu, Jenna Frame, Qingcong Lin, Xiaofei Zhou, Chengzhang Shang
Journal: Cancer Research (2024)

Abstract NKG2A and its co-receptor, CD94, are expressed on the surface of NK cells, and function to send inhibitory signals to NK cells upon recognition of the HLA-E complex on adjacent cells. Blockade of the NKG2A/CD94 complex is a promising strategy for cancer immunotherapy, due to the potential to trigger NK-mediated tumor killing. Previously, we generated humanized NKG2A/CD94 mice for testing novel therapeutics targeting human NKG2A/CD94. To explore the potential that this complex could be targeted as part of a novel combination therapy, we crossed humanized NKG2A/CD94 mice with humanized PD-1/PD-L1 mice, which were previously engineered to express the extracellular regions of human PD-1/PD-L1. Flow cytometric data from splenocytes isolated from the quadruple humanized mice confirmed expression of human NKG2A and CD94 in NK cells and activated CD8 T cells, as well as PD-1/PD-L1 on the surface of T cells. To test the efficacy of antibodies targeting these checkpoints in vivo, B-hHLA-E plus/hPD-L1 MC38 colon cancer cells were subcutaneously implanted into the quadruple humanized mice and treated with antibodies targeting human NKG2A, human PD-L1, or both antibodies. Results indicate that the combination therapy significantly reduced tumor growth when compared to NKG2A single antibody treatment. Together, these data suggest that humanized PD-1/PD-L1/CD94/NKG2A mice are a validated model for further evaluation of novel combination therapies. Citation Format: Fang He, Jiangfeng Yuan, Yawen Shan, Huwatibieke Bahetiyaer, Qingqing Xu, Jenna Frame, Qingcong Lin, Xiaofei Zhou, Chengzhang Shang. Generation of humanized PD-1/PD-L1/CD94/NKG2A mice for evaluating novel combination therapies [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 116.
Abstract 6954: Glycine decarboxylase regulates renal carcinoma progression and DNA damage response via interferon stimulated gene factor 3-mediated pathway
Authors: Jin Young Kim, Byung Hoon Kim, Misun Choe, Thi Tuyet Mai Pham, Mikyung Kim, Ji Hae Seo, So Jin Shin
Journal: Cancer Research (2024)

Abstract Glycine decarboxylase (GLDC) is a mitochondrial enzyme of glycine cleavage system which catalyzes glycine to donate for one-carbon metabolism. It is implicated as a tumor suppressor in hepatocellular carcinoma but as an oncogene in lung cancer. Although GLDC expression in the kidney is second highest next to the liver, the role of GLDC in the kidney remains unclear. Thus, this study was designed to determine the role of GLDC in renal carcinoma. We found markedly increased expressions of GLDC in patients with renal cell carcinoma (RCC) classified as poor-risk group based on the Memorial Sloan Kettering Cancer Center prognostic model. In vitro studies revealed that cellular proliferation, colony formation was decreased in GLDC-deficient renal carcinoma cells. Additionally in vivo xenograft studies with GLDC-deficient and -overexpressing cells also revealed that tumor sizes were noticeably decreased in GLDC-deficient cell-injected mice while those were increased in GLDC-overexpressing cell-injected mice. Mechanistically, we found GLDC regulates renal carcinoma progression via interferon (IFN) stimulated gene factor 3 (ISGF3)-mediated pathway. Expressions of IRF9 and STAT2 were increased in GLDC-deficient cells while those were decreased in GLDC-overexpressing cells. Upon inducing expression of ISGF3 subunits, GLDC deletion elevated DNA damage, mitotic catastrophe, mitochondrial deficiency induced by chemotherapy. Finally, GLDC knockdown diminished pyrimidine synthesis to impair renal cancer progression. In summary, our finding reveals that GLDC regulates renal carcinoma progression and DNA damage response via ISFG3-medated pathway and lays a scientific foundation that could support a therapeutic strategy that targets GLDC for the treatment of renal carcinoma. Citation Format: Jin Young Kim, Byung Hoon Kim, Misun Choe, Thi Tuyet Mai Pham, Mikyung Kim, Ji Hae Seo, So Jin Shin. Glycine decarboxylase regulates renal carcinoma progression and DNA damage response via interferon stimulated gene factor 3-mediated pathway [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 6954.
Abstract 494: Fluorescent carbon dots: A novel bioimaging tool to reveal the mechanism of action of anticancer drugs in cells
Authors: Adryanne Clermont-Paquette
Journal: Cancer Research (2024)

Abstract The mechanism of action of many cancer drugs at the subcellular level remains unknown. Yet, this knowledge could be critical in driving structure-activity-relationship studies to improve their efficacy and selectivity. To gain a deeper understanding of the mechanisms governing the action of anticancer drugs within cells, we are developing an innovative methodology to visualize drug interactions. Carbon dots (CDs) are carbon-based nanoparticles, distinguished not only by their remarkable optical properties but also by their minimal cytotoxicity, rendering them highly suitable for bioimaging applications. We recently found that amine-passivated CDs with a negative surface charge and amphiphilic properties were enriched in the cytosol of cultured human cells. These CDs emit fluorescence in the blue spectra with high quantum yields and are not cytotoxic. Importantly, their surface is decorated with amine functional groups that can be used for coupling to polyethylene glycol to create a linker that can be covalently attached to drugs of interest. First, we are covalently linking amine-passivated CDs to Doxorubicin (Dox), a well-known anti-cancer drug that intercalates DNA and also has fluorescence properties that differ from the CDs. This will permit us to monitor and validate the conjugation of Dox to CDs, their cellular uptake and localization. The next step will be to use this approach to reveal the cellular mechanism of action of novel anticancer drugs. Specifically, our group has rationally designed thienoisoquinoline compounds with selectivity and high efficacy for triple negative breast cancer cells. In vitro they disrupt microtubule polymerization in the nanomolar range. However, in cells they cause mitotic arrest and spindle phenotypes that are distinct from colchicine, another microtubule-targeting drug. Our approach will reveal if these compounds target the centrosomes and/or microtubules and if this varies with cell types. This innovative approach could yield profound insights into the intracellular mechanisms of anticancer drugs to facilitate structure-activity-relationship studies, to improve their efficacy and selectivity for drug development. Citation Format: Adryanne Clermont-Paquette. Fluorescent carbon dots: A novel bioimaging tool to reveal the mechanism of action of anticancer drugs in 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 494.
Abstract 2619: A novel EGFR × HER3-targeting bispecific antibody drug-conjugate, BCG019, demonstrates robust anti-tumor efficacy in preclinical evaluation
Authors: Zhuolin Li, Chengzhang Shang, Gao An, Chaoshe Guo, W. Frank An, Yi Yang
Journal: Cancer Research (2024)

Abstract EGFR and HER3 are receptor tyrosine kinases that are highly expressed in multiple epithelial tumors. EGFR point mutations and small insertions within the kinase domain are common in lung cancer. HER3 is overexpressed in patients who are resistant to EGFR-TKI therapy, and is one of the common resistance mechanisms of EGFR and HER2-targeted therapy. We hypothesize that simultaneous targeting of EGFR and HER3 with a bispecific ADC will have the potential to overcome the resistance caused by HER3 after EGFR-targeted therapy and obtain better efficacy than the combination of EGFR monotherapy and HER3 monotherapy. We first generated fully human bispecific antibodies (bsAbs) targeting EGFR and HER3 using RenLite® mice, which contain the full human heavy chain variable domain with a common human kappa light chain to facilitate bispecific antibody assembly. The anti-EGFR × HER3 bsAb demonstrated reactivity to human and cynomolgus monkey antigens and binding to multiple cancer cell lines, including NSCLC, gastric, pancreatic, colorectal, and breast cancer cell lines. The anti-EGFR × HER3 bsAb also showed high internalization activity in cell lines expressing EGFR and HER3. The anti-EGFR × HER3 bsAb was then conjugated with vc-MMAE (valine-citrulline-monomethyl auristatin E) for proof-of-concept studies, as well as BLD1102, Biocytogen’s novel, proprietary linker/payload system composed of a DNA Topo I inhibitor payload (BCPT02) and highly hydrophilic protease-cleavable linker, to generate EGFR- and HER3-targeting bispecific ADC candidates BCG019. In vivo efficacy of the bsADC candidates were evaluated in cell-derived NSCLC and gastric cancer xenografts and in patient-derived gastric and colorectal xenograft models. Both bsADCs showed superior anti-tumor activity when compared to benchmark ADCs. Collectively, these results suggest that our novel anti-EGFR × HER3 bsADC has therapeutic potential for EGFR and HER3 co-expressing tumors. Citation Format: Zhuolin Li, Chengzhang Shang, Gao An, Chaoshe Guo, W. Frank An, Yi Yang. A novel EGFR × HER3-targeting bispecific antibody drug-conjugate, BCG019, demonstrates robust anti-tumor efficacy in preclinical evaluation [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 2619.
Abstract 433: BCAT1 promotes HCC metabolic reprogramming and survival through HIF-1α stabilization
Authors: Misty Shuo Zhang, Kenneth Kin-Leung Kwan, Weixing Li, Adonia E. Papathanassiu, Irene Oi-Lin Ng, Carmen Chak-Lui Wong
Journal: Cancer Research (2024)

Abstract Hepatocellular carcinoma (HCC) is a highly lethal primary liver malignancy characterized by hypoxia, a common feature of solid tumors, particularly in HCC. Hypoxia-inducible factors (HIFs) play a pivotal role in mediating various cellular processes, such as metabolic adaptation, to support the survival of hypoxic cells. The cytosolic form of branched-chain amino transferase (BCAT1) is responsible for the reversible transamination reaction between branched-chain keto-amino acids (BCKAs) and branched-chain amino acids (BCAAs), facilitating the interconversion between α-ketoglutarate (α-KG) and glutamate. Interestingly, we found that in the context of HCC, BCAT1 consumes α-KG, thereby favoring the stabilization of HIF-1α through suppressing the α-KG-dependent prolyl hydroxylase (PHD). Knockdown (KD) or knockout (KO) of BCAT or BCAT inhibitor (ERG245) suppressed HIF-1 stability, as well as HIF-1 dependent transcriptomic and metabolic changes. Mass spectrometry (MS)-based isotopic carbon tracing showed that KD/KO or ERG 245 suppressed hypoxia/HIF-1-induced glycolytic flux. Interestingly, ERG245 effectively inhibited the proliferative output of hypoxic HCC cells and suppressed HCC growth. ERG245 also profoundly inhibited HCC growth in vitro and in vivo together with Sorafenib, a tyrosine kinase inhibitor (TKI) used in HCC by increasing the apoptotic cell death. Furthermore, we confirmed that the expressions of BCAT1 and the HIF-1α-targeted metabolic genes are positively correlated in human HCCs. Our findings unequivocally demonstrate that BCAT1 confers a growth advantage to HCC cells by stabilizing HIF-1α and orchestrating HIF-1α-mediated metabolic reprogramming. Consequently, targeting BCAT1 emerges as a promising therapeutic strategy for HCC patients. Funding Support: This work was supported by the Centre for Oncology and Immunology under the Health@InnoHK initiative funded by the Innovation and Technology Commission, The Government of Hong Kong SAR, China and National Natural Science Foundation of China (NSFC) (82173123, C.C.-L.W.) Citation Format: Misty Shuo Zhang, Kenneth Kin-Leung Kwan, Weixing Li, Adonia E. Papathanassiu, Irene Oi-Lin Ng, Carmen Chak-Lui Wong. BCAT1 promotes HCC metabolic reprogramming and survival through HIF-1α stabilization [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 433.
Abstract 427: A molecular signature for the G6PC3/SLC37A2/SLC37A4 interactors in glioblastoma disease progression and in the acquisition of a brain cancer stem cell phenotype
Authors: Sima Torabidastgerdooei, Borhane Annabi
Journal: Cancer Research (2024)

Abstract Background: Glycogen plays an important role in glucose homeostasis and contributes to key functions related to brain cancer cell survival in glioblastoma multiforme (GBM) disease progression. Such adaptive molecular mechanism is dependent on the glycogenolytic pathway and intracellular glucose-6-phosphate (G6P) sensing by brain cancer cells residing within those highly hypoxic tumors. The involvement of components of the glucose-6-phosphatase (G6Pase) system remains however elusive. Objective: We questioned the gene expression levels of components of the G6Pase system in GBM tissues and their functional impact in the control of the invasive and brain cancer stem cells (CSC) phenotypes. Methods: In silico analysis of transcript levels in GBM tumor tissues was done by GEPIA. Total RNA was extracted and gene expression of G6PC1-3 as well as of SLC37A1-4 members analyzed by qPCR in four human brain cancer cell lines and from clinically annotated brain tumor cDNA arrays. Transient siRNA-mediated gene silencing was used to assess the impact of TGF-β-induced epithelial-to-mesenchymal transition (EMT) and cell chemotaxis. Three-dimensional (3D) neurosphere cultures were generated to recapitulate the brain CSC phenotype. Results: Higher expression in G6PC3, SLC37A2, and SLC37A4 was found in GBM tumor tissues in comparison to low-grade glioma and healthy tissue. The expression of these genes was also found elevated in established human U87, U251, U118, and U138 GBM cell models compared to human HepG2 hepatoma cells. SLC37A4/G6PC3, but not SLC37A2, levels were induced in 3D CD133/SOX2-positive U87 neurospheres when compared to 2D monolayers. Silencing of SLC37A4/G6PC3 altered TGF-β-induced EMT biomarker SNAIL and cell chemotaxis. Conclusion: Two members of the G6Pase system, G6PC3 and SLC37A4, associate with GBM disease progression and regulate the metabolic reprogramming of an invasive and CSC phenotype. Such molecular signature may support their role in cancer cell survival and chemoresistance and become future therapeutic targets. Citation Format: Sima Torabidastgerdooei, Borhane Annabi. A molecular signature for the G6PC3/SLC37A2/SLC37A4 interactors in glioblastoma disease progression and in the acquisition of a brain cancer stem cell phenotype [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 427.