tbuckley/cabot-search huggingface dataset:
Abstract 3866: Azvudine: An emerging immunomodulator in the treatment of cancer and viral infections
Authors: Pan Li, Limin Jia, Zhaoyang Wang, Jinfa Du
Journal: Cancer Research (2024)

Abstract Azvudine (FNC) is a nucleoside analog that has secured approval from the CDE in China for the treatment of both AIDS and COVID-19. In these contexts, it has showed remarkable efficacy and safety when taken orally. Typically, nucleoside analog drugs function by integrating into DNA and impeding DNA synthesis, evident in drugs like 5-FU, Capecitabine, Ara-C, and Gemcitabine. Furthermore, FNC has been reported to exhibit robust anti-tumor properties, curbing cell proliferation, initiating G1 and S phase arrests, and advancing apoptosis across various human cancer cell lines. Grounded in this mode of action, we have ascertained that the anti-tumor effects of FNC intricately align with the expression of deoxycytidine kinase (dCK) both in vitro and in vivo. Remarkably, our studies delved into the effects and underlying mechanisms of FNC in enhancing the tumor microenvironment within solid tumors. Our findings, stemming from cell-based assays and in vivo animal experiments, elucidate the following: 1. FNC can trigger immunogenic cell death (ICD) in tumor cells. This is evidenced by the surface presentation and liberation of damage-associated molecular patterns (DAMPs) such as Calreticulin, HSP70, HSP90, Annexin A1, and HMGB1, which in turn stimulate both innate and adaptive immune responses. 2. FNC substantially reduces the population of monocytic-myeloid derived suppressor cells (M-MDSC) and Polymorphonuclear-myeloid derived suppressor cells (PMN-MDSC) in the tumor microenvironment. Concurrently, it boosts the infiltration and proliferation of CD8+T, CD4+T and NK cells. This instigates the transformation of the tumor microenvironment from a 'cold' state to a 'hot' one, enhancing the synergistic effects of PD-1 when used in tandem with FNC. This mechanism was substantiated through a high proportion of MDSCs observed in H22 and CT-26 syngeneic models, and contrastingly, a low proportion in MC38 and LL/2 in vivo syngeneic models. Notably, every animal subjected to combined FNC and PD-1 treatment in the H22 and CT-26 in vivo models witnessed complete tumor regression. Given these revelations, there's a compelling argument that FNC monotherapy possesses immense potential as an anti-tumor agent. The potent anticancer effects of FNC in vitro and in vivo warrants further investigation of its anticancer potential as immunomodulator. Citation Format: Pan Li, Limin Jia, Zhaoyang Wang, Jinfa Du. Azvudine: An emerging immunomodulator in the treatment of cancer and viral infections [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 3866.
Abstract 3135: BSI-730, a bispecific antibody targeting HER2 and PD-L1 for the development of a first-in-class bispecific ADC
Authors: Xiaoyao Hao, Hongyan Li, Xiaodong F. Liu, Jinyu Liu, Wenwen Dai, Ying Pan, Hui-Han Hu, Jun Li, Shukai Xia, Qun Lyu, Hugh M. Davis, Mingjiu Chen, Zeyu Peng
Journal: Cancer Research (2024)

Abstract Background: Antibody-drug conjugates (ADCs) have become a promising therapeutic option for patients with cancer. Bispecific ADCs targeting two tumor-associated antigens have potential differential anti-tumor advantages. HER2 and PD-L1 are co-expressed in some tumor cell types, such as breast cancer, gastric cancer, lung adenocarcinoma and urothelial carcinoma. A bispecific ADC targeting HER2 and PD-L1 should provide therapeutic benefit, particularly for patients with HER2 low cancer. Dual-target mediated cytotoxicity combined with PD-L1 mediated immunotherapy provides an innovative approach for cancer patients. Experimental procedures: An anti-PD-L1 monoclonal antibody was identified from A/J mice immunized with PD-L1-ECD-Fc and screened by the Biosion proprietary SynTracer® High Throughput Endocytosis Platform. A “knob-in-hole” bispecific antibody, BSI-730, targeting HER2 and PD-L1 was created with trastuzumab and the humanized anti-PD-L1 scFv. Target binding specificity, binding activity, and affinity of BSI-730 were evaluated by protein-based ELISA, cell-based FACS and Biacore-based SPR, and the ligand blocking activity of PD-L1 portion was measured by competitive ELISA and cell-based FACS. The internalization activities on various cancer cell lines with different expression levels of HER2 and PD-L1 were evaluated by using the SynTracer® Platform. Summary: BSI-730, a HER2/PD-L1 bispecific antibody, showed comparable binding affinity to HER2 as compared to trastuzumab, as well as comparable bioactivity to the parental anti-PD-L1 antibody regarding PD-L1 binding and PD-1/PD-L1 blocking. Based on a cell-based reporter assay, BSI-730 was able to reverse PD-L1 mediated T-cell suppression and exhibited comparable potency to the parental anti-PD-L1 antibody. The internalization of BSI-730 on HER2 low cancer cell lines was stronger than that of trastuzumab whereas the internalization of BSI-730 on HER2 high cancer cell lines was comparable to that of trastuzumab. Conclusion: BSI-730 is a novel bispecific antibody for the development of a first-in-class bispecific ADC with the potential advantage of increased potency that can be further investigated to treat HER2 and PD-L1 co-expression tumors, particularly HER2 low tumors. Citation Format: Xiaoyao Hao, Hongyan Li, Xiaodong F. Liu, Jinyu Liu, Wenwen Dai, Ying Pan, Hui-Han Hu, Jun Li, Shukai Xia, Qun Lyu, Hugh M. Davis, Mingjiu Chen, Zeyu Peng. BSI-730, a bispecific antibody targeting HER2 and PD-L1 for the development of a first-in-class bispecific ADC [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 3135.
Abstract 3859: HSP90 blockade activates antitumor immunity by suppressing tumor glycolytic flux in head and neck squamous cell carcinoma
Authors: Fanghui Chen, Chris Tang, Fan Yang, Asari Ekpenyong, Richard Qin, Nabil F. Saba, Yong Teng
Journal: Cancer Research (2024)

Abstract Accumulating evidence suggests that failure of antitumor immunity may be due to dysregulation of energy metabolism. Head and neck squamous cell carcinoma (HNSCC) exhibits increased activity of two key enzymes, pyruvate kinase M2 (PKM2) and platelet phosphofructokinase (PFKP), which are central to the glycolytic pathway responsible for the conversion of glucose to ATP energy. HSP90 is a molecular chaperone that plays a critical role in the folding, stabilization, and regulation of a wide range of client proteins involved in various cellular processes, including metabolism. However, whether HSP90 signaling contributes to tumor metabolism rewiring and antitumor immune response remains unknown. Using ganetespib as a drug model for HSP90 inhibition and combining results from clinical trials and animal treatment, our study demonstrated that HSP90 inhibition causes an obstruction of glycolytic flux in HNSCC cells by simultaneously suppressing both PKM2 and PFKP at the transcriptional and post-translational levels. In addition, ganetespib enhances T cell-driven antitumor immune responses by promoting CD8+ T cell infiltration into the tumor. Mechanistically, ganetespib downregulates IL8 signaling by inhibiting PKM2 and PFKP-mediated glycolysis in HNSCC cells, which in turn contributes to ganetespib-mediated T cell tumor infiltration. These findings provide a novel molecular basis for the use of effective HSP90 inhibitors to improve the outcome of HNSCC patients. Citation Format: Fanghui Chen, Chris Tang, Fan Yang, Asari Ekpenyong, Richard Qin, Nabil F. Saba, Yong Teng. HSP90 blockade activates antitumor immunity by suppressing tumor glycolytic flux in head and neck squamous cell 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 3859.
Abstract 5771: Utilizing a photoreactive chloroalkane capture tag for target deconvolution
Authors: Tetsuo Uyeda, Robin Hurst, Sergiy Levin, Mike Rosenblatt, Kris Zimmermann, Rachel F. Ohana
Journal: Cancer Research (2024)

Abstract Identifying the physiologically relevant targets of bioactive compounds is often the rate limiting step toward understanding their mechanism of action. To this end, we developed a streamlined chemical proteomic strategy that utilizes a novel photoreactive cleavable chloroalkane tag, which can be attached to bioactive compounds to isolate their respective cellular targets for identification by mass spectrometry. The tag does not significantly affect compounds potency and membrane permeability, allowing for binding interactions to be established within intact cells under appropriate physiological conditions. UV-induced covalent photo-crosslinking “freezes” the cellular interactions and prevents their dissociation upon cell lysis. Effective enrichment of the cellular targets is achieved through their selective covalent capture onto HaloTag coated particles and subsequent selective release by tag cleavage. Putative targets identified by mass spectrometry can be readily verified using resonance energy transfer. By exchanging the chloroalkane tag for a fluorophore, direct binding to the targets can be revealed through proximity of the fluorophore to a small NanoLuc luciferase genetically fused to the putative target. This approach was used to identify physiologically relevant targets for bioactive compounds including those with low affinity and/or low abundance as well as insoluble targets with multiple trans membrane domains. Citation Format: Tetsuo Uyeda, Robin Hurst, Sergiy Levin, Mike Rosenblatt, Kris Zimmermann, Rachel F. Ohana. Utilizing a photoreactive chloroalkane capture tag for target deconvolution [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 5771.
Abstract 1548: Olfactomedin 4 deficiency promote de novo progression of prostate cancer in TRAMP mouse model
Authors: Hongzhen Li, Wenli Liu, Jianqiong Zhu, Kyung Chin, Griffin P. Rodgers
Journal: Cancer Research (2024)

Abstract Prostate cancer is the most diagnosed solid tumor and the second leading cause of cancer-related death in American men. Olfactomedin (OLFM4) plays tumor suppressor roles and is associated with the initiation, growth, and clinical outcome of human prostate cancer. Olfm4-null mouse sporadically developed prostate epithelial neoplasia through up-regulated hedgehog signaling pathways. In this study, we have generated Olfm4+/+/GFP/TRAMP and Olfm4−/−/TRAMP mouse models to investigate Olfm4 gene biological functions underlying prostate cancer de novo progression. We have observed that Olfm4−/−/TRAMP mice developed more advanced prostate cancer at 47.6% (20/42) compared to Olfm4+/+/TRAMP at 11.9 % (5/42) and had poor survival compared to Olfm4+/+/TRAMP mice (P&amp;lt;0.01). Histopathological and immunofluorescent staining revealed that tumor tissues containing more heterogeneous cells such as Ar+/Ck8+ epithelial or Syn+ neuroendocrinal cells or Vim+/Ck8+ epithelium mesenchymal transition cells in the primary tumors obtained from Olfm4−/−/TRAMP mouse. We found more tumor angiogenesis and metastases into lymph nodes, liver, lung, kidney, and soft tissues in Olfm4−/−/TRAMP mice. The accumulations of the dendritic cell population in primary tumor and lung metastasis tumors were detected. The primary tumor was sensitive to androgen deprivation therapy by using castration with both Olfm4+/+/GFP/TRAMP and Olfm4−/−/TRAMP mice. However, castration-resisted EMT tumor cells or expressing neuroendocrine marker cells regrew after castration 7-8 months in both Olfm4+/+/GFP/TRAMP and Olfm4−/−/TRAMP mice. Furthermore, we tested JQ1, a BET bromodomain inhibitor, as an epigenetic targeted therapy reagent and found that JQ1 significantly inhibited tumor cell growth of Olfm4−/−/TRAMP mouse tumor in the organoids culture. Taken together, we have provided novel evidence that Olfm4 plays a tumor-suppressing role during prostate cancer de novo progression. Citation Format: Hongzhen Li, Wenli Liu, Jianqiong Zhu, Kyung Chin, Griffin P. Rodgers. Olfactomedin 4 deficiency promote de novo progression of prostate cancer in TRAMP mouse model [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 1548.
Abstract 5784: Structure-based drug design against caPCNA for selective cancer chemotherapy development
Authors: Jennifer Jossart, Pouya Haratipour, Long Gu, Carone M. li, Robert Lingeman, Yilun Liu, Robert J. Hickey, Linda H. Malkas, Jeff J. Perry
Journal: Cancer Research (2024)

Abstract Proliferating cell nuclear antigen (PCNA) is critical to DNA replication and repair processes, and it is also a proliferation biomarker in a variety of human tumors. A unique cancer-associated isoform of the protein, caPCNA, has been previously identified, allowing for rational-based drug discovery studies to develop leads with the potential for selective therapeutic targeting of cancer cells. Several strategies have been employed to develop agents targeting caPCNA, including peptide and small molecule-based inhibitors, but the success in developing therapeutically tractable compounds has been limited so far. Here, we present the crystal structures and corresponding biochemical characterizations of our novel small molecule-based caPCNA inhibitors, which bind into the PIP-box binding pocket of PCNA. One of our lead compounds is now an investigational new drug that we observed selectively kills cancer cells, and it appears to induce replication stress, apoptosis and increase cancer cell sensitivity to genotoxic agents, while these effects are not observed in non-malignant cell controls. This caPCNA inhibitor is orally administrable, metabolic stable and it suppresses tumor growth as a monotherapy or as a combination treatment, and it has entered clinical trials in the United States. PCNA plays a critical role in temporarily dislodging RNA polymerase II from transcription replication conflict sites, to enable the replication fork to proceed. Thus, structure-based drug discovery approaches to target transcription replication conflict resolution machinery, such as PCNA protein, may open a novel therapeutic avenue for exploiting this cancer-selective vulnerability. Citation Format: Jennifer Jossart, Pouya Haratipour, Long Gu, Carone M. li, Robert Lingeman, Yilun Liu, Robert J. Hickey, Linda H. Malkas, Jeff J. Perry. Structure-based drug design against caPCNA for selective cancer chemotherapy development [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 5784.
Abstract 7078: Targeting eIF6 to modulate ribosomal subunit association dynamics in cancers
Authors: Kavya Meena Harish, Poonam Roshan, Aparna Biswas, Stella Anagnos, Riley Luebbers, Sofia Origanti
Journal: Cancer Research (2024)

Abstract Deregulation of ribosomal subunit levels and accessibility are hallmarks of cancer. Eukaryotic translation initiation factor 6 (eIF6) is a key regulator of ribosomal subunit association that is over expressed in many cancers including lung, colon, ovarian and breast cancers, and deregulation of eIF6 is correlated with a poor cancer prognosis. Association of eIF6 with 60S is critical for 60S assembly. However, eIF6 must be released from 60S prior to translation to permit inter subunit interactions between 60S and 40S and to facilitate the formation of translationally proficient 80S monosome. Release of eIF6 is deregulated in the ribosomopathy- Shwachman Diamond Syndrome that is predisposed to leukemias. Also, loss of eIF6 markedly delays tumorigenesis without affecting normal growth, which presents eIF6 as a viable therapeutic target. A potential therapeutic strategy is to target the eIF6 and 60S ribosomal interaction interface. Through biophysical analyses we had identified residues that are critical for the interaction between eIF6 and 60S ribosomal subunit. We show that targeting these key residues in the eIF6-60S interaction interface markedly delays colonic cancer growth and inhibits protein synthesis. Furthermore, we show that the levels of other eIFs and the release factors: SBDS, and EFL1-GTPase are unaltered in the mutant cells suggesting that the translational inhibition is primarily attributed to the deregulation of eIF6. Interestingly, targeting eIF6 leads to an upregulation of p53 independent of the DNA damage response, suggesting that ribosomal stress contributes to the stabilization of p53. Previously, it was shown that translation of Cdc42 was upregulated by eIF6 to promote invasiveness. However, Cdc42 levels were unaltered in the mutant cells. Future studies will determine the mRNA substrates that are translationally deregulated in the mutants. We will also determine the effect of disrupting eIF6 function in inhibiting tumor growth and progression in vivo. Category: MCB, Subcategory: MCB07-Gene regulation sub classification: Translational Control Citation Format: Kavya Meena Harish, Poonam Roshan, Aparna Biswas, Stella Anagnos, Riley Luebbers, Sofia Origanti. Targeting eIF6 to modulate ribosomal subunit association dynamics in cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7078.
Abstract 7423: BATCH-FLEX: Feature-level equalization of x-batch in heterogeneous cancer data
Authors: Joshua Davis, Alyssa Obermayer, Thac Duong, Rebecca Hesterberg, Xuefeng Wang, Mingxiang Teng, G. Daniel Grass, Timothy Shaw
Journal: Cancer Research (2024)

Abstract Purpose: Develop a shiny application to help integrate cancer datasets and guide researchers in selecting an appropriate method of correction for their technical artifacts. Description: Integrative analysis of heterogeneous expression data remains challenging due to variations in platform, RNA quality, sample processing, and other unknown technical effects. As the field performs omics profiling of samples from cancer patients and murine models, there is the need for harmonizing, identifying, and correcting these technical effects to ensure robust analysis on the treatment and conditional effects of the underlying genetics or biological events. However, selecting and implementing different approaches for removing unwanted batch effects can be a time-consuming and tedious process, especially for more biologically focused investigators. In this project, we present Shiny BATCH-FLEX, a Shiny app to rapidly visualize batch correction by established batch correction methods such as ComBat, Mean Centering, ComBatSeq, and Limma RemoveBatchEffect. With BATCH-FLEX, users can visualize the contribution of variance of a factor before and after correction using principal component analysis, relative log expression plots, heatmaps, and explanatory variables. Users can also save all plots and matrices as a single ZIP file for further downstream analysis. Results: As a proof of concept, we assessed BATCH-FLEX using simulated data generated from a linear model framework introduced by Gagnon-Bartsch and Speed, which assumes that gene expression measurements can be distilled to a combination of the biological signal, systemic nose, and random noise. BATCH-FLEX was able to successfully identify and remove the introduced effect using each of the batch correction methods listed above. Next, we evaluated BATCH-FLEX using a comprehensive collection of bladder cancer data consisting of microarray data from 13 studies spanning 1452 samples. Following the cleaning of study-dependent noise, BATCH-FLEX was successful in revealing the heterogeneity among bladder cancer based on known sample type annotations. Conclusion: We have developed BATCH-FLEX, a tool for oncologic researchers to rapidly assess, select, and implement commonly used batch correction methods. This tool is available at https://github.com/shawlab-moffitt/BATCH-FLEX. Our integrative web portal of a Bladder Cancer Resource for Translational Science (BEACON) will also be shared at the meeting. Citation Format: Joshua Davis, Alyssa Obermayer, Thac Duong, Rebecca Hesterberg, Xuefeng Wang, Mingxiang Teng, G. Daniel Grass, Timothy Shaw. BATCH-FLEX: Feature-level equalization of x-batch in heterogeneous cancer data [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 7423.
Abstract 1466: Tobacco carcinogen impacts redox pathway to facilitate pancreatic ductal adenocarcinoma (PDAC) initiation and progression
Authors: Xiaoxue Lin, McKenna Stamp, Alexandra Fowler, Chelsea Bottomley, Shira Okhovat, Kristina Peck, Dannielle Engle
Journal: Cancer Research (2024)

Abstract The 5-year survival rate for pancreatic ductal adenocarcinoma (PDAC) is only 10%. PDAC is projected to soon become the second leading cause of cancer death. Tobacco is one of the main risk factors for PDAC. Incidence of PDAC increases 2-fold among tobacco users, and 20-35% of PDAC cases are attributed to smoking. However, the specific pathways activated by tobacco carcinogens remain elusive.This research project addresses the impact of carcinogens in pancreatic cancer etiology. We hypothesize that carcinogens in tobacco increase reactive oxygen species (ROS), which elevates the Nrf2 redox pathway to facilitate PDAC initiation and progression. Specifically, we focus on two major subclasses of carcinogens: the heavy metal cadmium (Cd) and the polycyclic aromatic hydrocarbon (PAH) benzo(a)pyrene (BaP). Using mouse pancreatic ductal organoid cultures, we found that acute carcinogen exposure increases Nrf2 activity, which is sustained after "intermediate" exposure (5 passages). Intriguingly, chronic exposure (10 passages) downregulates Nrf2 activity, which has been shown to be associated with acquired metastatic potential. Furthermore, we found an upregulation in NFkB and EGFR signaling after intermediate exposure, which are involved in microenvironment remodeling and increased proliferative potential. Overall, we demonstrate that acute carcinogen exposure elevates ROS levels and activates the Nrf2 pathway, whereas prolonged exposure upregulates NFkB and EGFR pathways. Furthermore, we have established a novel carcinogenesis model using 3D organoid culture to recapitulate each step in pancreatic tumorigenesis. Collectively, this project contributes to our understanding of tobacco-related PDAC pathogenesis. Citation Format: Xiaoxue Lin, McKenna Stamp, Alexandra Fowler, Chelsea Bottomley, Shira Okhovat, Kristina Peck, Dannielle Engle. Tobacco carcinogen impacts redox pathway to facilitate pancreatic ductal adenocarcinoma (PDAC) initiation and progression [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 1466.