tbuckley/cabot-search huggingface dataset:
Abstract 7025: Advancing methylation analysis: TAPS v1.0: A fast, scalable, and non-destructive sequencing method
Authors: Josh Haimes, Craig Marshall, Travis Sanders, Sam Vogel, Martin Ranik, Eduard Casas, Doug Wendel, Leo Karamanof, Bjarne Faurholme, Abre de Beer, Lee French, Ross Wadsworth, Kristina Giordia, Eric van der Walt, Brian Kudlow
Journal: Cancer Research (2024)

Abstract In the pursuit of advancing multi-cancer early detection, the exploration of cell-free DNA (cfDNA) through methylation profiling has emerged as a promising avenue. However, the realization of its full potential is impeded by limitations inherent in conventional methodologies, notably the 'gold standard' bisulfite conversion methods. These approaches pose challenges such as DNA destruction and the generation of low-complexity sequences resulting from the conversion of unmethylated cytosines to thymine. TET Assisted Pyridine-Borane Sequencing (TAPS) holds the potential as a non-destructive, rapid, and scalable alternative for base-level methylation analysis. In this context, we introduce TET Assisted Pyridine-Borane Sequencing version 1.0 (TAPS v1.0), showcasing advancements to the technology originally introduced by Schuster-Böckler, Song, and their collaborators. TAPS v1.0 transforms 5mC into dihydrouracil (DHU) through a series of oxidation and reduction reactions. Ultimately, DHU is recognized as dU during PCR resulting in C-to-T conversions at 5mC sites, leaving unmethylated cytosines, the majority of cytosines, unchanged. The nondestructive nature of 5mC conversion yields significantly higher library yield and complexity compared to BS-seq. By leveraging Watchmaker's proprietary polymerase evolution platform, a DNA polymerase tolerant to DHU was selected for library amplification post DHU conversion, enabling unimpeded detection of 5mC, particularly in densely packed CpG repeats. Coupled with an optimized End Repair and A-tailing chemistry preceding TAPS v1.0, clinically relevant cfDNA samples of low quality and/or quantity can be analyzed in methylation detection pipelines. To evaluate the performance of TAPS v1.0, human genomic DNA with control spike-ins featuring varying methylation statuses were employed. TAPS v1.0 exhibited significantly higher final library yield and greater complexity compared to BS-seq. Similar outcomes were observed in clinically relevant cfDNA samples. Citation Format: Josh Haimes, Craig Marshall, Travis Sanders, Sam Vogel, Martin Ranik, Eduard Casas, Doug Wendel, Leo Karamanof, Bjarne Faurholme, Abre de Beer, Lee French, Ross Wadsworth, Kristina Giordia, Eric van der Walt, Brian Kudlow. Advancing methylation analysis: TAPS v1.0: A fast, scalable, and non-destructive sequencing method [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 7025.
Abstract 4247: Miniaturizing patient-derived organoid screening assays for predictive drug testing
Authors: Yasmine Abouleila, Roel Verkerk, Mayke Doorn, Timo Voskuilen, Gakuro Harada, Masahiko Watanabe, Lidwien Smabers, Hideaki Kyan, Takahiko Kumagai, Yuichi Hikichi, Rene Overmeer, Jeanine Roodhart, Kiyotaka Matsuno, Carla Verissimo, Sylvia Boj
Journal: Cancer Research (2024)

Abstract Colorectal cancer (CRC) ranks as the third leading cause of both cancer incidence and cancer-related mortality. A significant portion of CRC patients diagnosed with de novo metastatic disease face limited benefits from conventional treatment options, often accompanied by substantial side effects. This underscores the pressing need for more effective preclinical models to predict patient responses in clinical settings. Patient-derived organoids (PDOs or HUB Organoids®) represent a pivotal breakthrough in preclinical modeling. These organoids are directly derived from patient tissue, faithfully mirroring the patient's disease. While HUB Organoid Technology is currently applicable for preclinical drug screening, it is essential to expedite the transition from patient diagnosis to the delivery of PDO-based results to directly benefit patients. In a collaborative effort with Yamaha Motor, we have optimized the Yamaha CELL HANDLERTM for the automated transfer of organoids, offering enhanced precision and efficiency in handling a significantly reduced number of organoids per screening plate, compared to conventional methods. Moreover, we have developed an image-based readout system that enables precise quantification of organoid numbers, ensuring high assay quality. Utilizing this developed automated platform, we conducted a proof-of-concept investigation into PDO responses to chemotherapy in comparison to corresponding patient responses. The correlation between PDO and patient responses demonstrated a strong connection, highlighting the potential of the developed automated platform for predictive drug testing. In summary, this work signifies the development of an automated workflow that synergizes patient-representative HUB Organoids® with cutting-edge robotics from Yamaha Motor. The described workflow reduces the number of organoids needed per screening well, streamlining patient response prediction, potentially leading to faster diagnoses, and ultimately optimizing patient outcomes. Citation Format: Yasmine Abouleila, Roel Verkerk, Mayke Doorn, Timo Voskuilen, Gakuro Harada, Masahiko Watanabe, Lidwien Smabers, Hideaki Kyan, Takahiko Kumagai, Yuichi Hikichi, Rene Overmeer, Jeanine Roodhart, Kiyotaka Matsuno, Carla Verissimo, Sylvia Boj. Miniaturizing patient-derived organoid screening assays for predictive drug testing [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 4247.
Abstract 1672: PKC-ι and 14-3-3 are crucial regulators of c-Raf and the Erk pathway in human medulloblastoma
Authors: Luke Lajmi, Wishrawana S. Ratnayake, Joseph Palathinkal, Sloan Breedy, Aaron Todman, Mildred Acevedo-Duncan
Journal: Cancer Research (2024)

Abstract Medulloblastoma is the second most common childhood cancer, behind leukemia, and the most common pediatric brain tumor, comprising 20% of all childhood brain cancers. Current treatment options are limited to radiation therapy, surgical resection, and chemotherapy, which are extremely invasive. This underscores the need for more targeted and effective therapeutic treatments to improve patient outcomes. The following study will focus on exploring the PKC-ι specific inhibitor 5-amino-1-((1R,2S,3S,4R)-2,3-dihydroxy-4-methylcyclopentyl)-1H-imidazole-4-carboxamide (ICA-1S) and its effects on medulloblastoma cell lines Daoy and ONS-76. Our in-vitro treatments showed that PKC-ι functions an oncogenic protein that is necessary for Daoy and ONS-76 cell proliferation and that ICA-1S was found to be cytostatic to both Daoy and ONS-76 cells. The inhibition of PKC-ι in both cell lines resulted in a decreased phosphorylation of PKC-ι as well as downregulation of 14-3-3 and crucial components of the c-Raf/Erk pathway including total and phosphorylated levels of c-Raf, Mek1/2, and Erk1/2. This comes as a result of ICA-1S blocking the association of PKC-ι with 14-3-3 while PKC-ι and c-Raf were not found to directly associate with each other, indicating indirect modulation of c-Raf by PKC-ι. Additionally, PKC-ι inhibition decreased its association with Stat3. Expression levels of Stat1, Stat3, c-Fos, and c-Myc transcription factors were significantly downregulated, which is likely the result of reduced transcriptional activation due to upstream inhibition of PKC-ι and Erk signaling. Treatment with ICA-1S was also shown to substantially decrease cellular invasion of Daoy and ONS-76 cells and induce apoptosis. Taken together, these data suggest that PKC-ι likely plays a critical role in the regulation of the c-Raf/Erk pathway, which controls the proliferation and invasion of human medulloblastoma. Citation Format: Luke Lajmi, Wishrawana S. Ratnayake, Joseph Palathinkal, Sloan Breedy, Aaron Todman, Mildred Acevedo-Duncan. PKC-ι and 14-3-3 are crucial regulators of c-Raf and the Erk pathway in human medulloblastoma [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 1672.
Abstract 6833: Microenvironment-specific transcriptomic changes in osteosarcoma metastasis
Authors: Shimara Gunawardana-Zeigler, Dan Peng, Patrick Cahan, David Loeb
Journal: Cancer Research (2024)

Abstract Osteosarcoma (OS) is the most common primary malignancy of bone in children and adolescents. While conventional chemotherapy has improved 5-year survival rates for localized disease to 70%, metastatic disease remains at 20-30%. Failure of modern treatment options to improve survival reflects the failure of agents that appear promising in preclinical models to demonstrate clinical efficacy in human patients. We hypothesize that this is because most preclinical testing is performed on tumors implanted subcutaneously in immune deficient mice. Our previous work has shown that tumors implanted subcutaneously do not metastasize, whereas genetically identical tumors implanted orthotopically (in the tibia) metastasize to lungs and bones. Thus, to better understand non-genetic drivers of metastasis, we implanted patient-derived xenografts (PDXs) either orthotopically or subcutaneously into NSG mice. Once tumors reached 1.5cm, tumors were extracted along with distant metastases and analyzed by single-cell RNA sequencing. Transcriptomic analysis reveals 1) that fragments of the same tumor implanted subcutaneously have a vastly different transcriptome than fragments implanted orthotopically, 2) the transcriptome of distant metastases is dramatically different from the transcriptome of the primary tumor, and 3) the gene expression profile of metastases is different in different metastatic sites. In all 3 of these circumstances, these differences reflect differences in differentiation status, signaling pathway activation, and immune cell infiltrate. Thus, we conclude that the environment in which a tumor grows significantly alters its gene expression and phenotype. Our study highlights the need for careful consideration of the tumor microenvironment when designing pre-clinical studies to ensure accurate representation of human osteosarcoma and may help to explain the dismal record of translating novel agents from preclinical studies into standard therapy. Citation Format: Shimara Gunawardana-Zeigler, Dan Peng, Patrick Cahan, David Loeb. Microenvironment-specific transcriptomic changes in osteosarcoma 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 6833.
Abstract 361: Targeting the suppressor of ferroptosis to improve the treament effeciency of glioblastoma
Authors: Jing Wang
Journal: Cancer Research (2024)

Abstract Glioma is the most frequent tumor in central nervous system (CNS), which makes up about 30% of CNS tumors. The current standard strategy for glioma treatment is surgery plus adjuvant chemotherapy and concurrent radiotherapy. Even though, the prognosis of glioma is still poor. It’s encouraging that temozolomide (TMZ) prolongs the overall survival of glioma patients, but the following TMZ resistance is really frustrating. It’s urgent to figure out efficient ways to improve the long term prognosis of patients, such as antagonizing the TMZ resistance. Ferroptosis was a newly discovered type of regulated cell death characterized by iron-dependent aberrant lipid peroxidation and membrane damage in the last decade. Ferroptosis-associated iron transport proteins modulate the process precisely through controlling the iron content. ZIP14, also known as SLC39A14, is an eight-transmembrane protein which could transport divalent metal ion like Mn2+, Zn2+ and Fe2+. Our preliminary data showed that the expression level of ZIP14 was higher in tumor tissues than paired normal tissue, which was corelated with poor prognosis of glioma. Knock down ZIP14 could induce cell death, and which could be rescued by inhibitors for ferroptosis but not for apoptosis or necrosis. Knock down ZIP14 decreased the ferroptosis inhibition by Ferroptosis suppress protein 1 (FSP1) which through reduction of lipid peroxidation, and sensitized cells to TMZ. Furthermore, we found that ZIP14 formed a complex with Ubiquinone. And it was known that FSP1 is critical in the switch of ubiquinone to ubiquinol. Therefore, we propose that ZIP14 suppress lipid peroxidation through blockage of the transition of ubiquinone to ubiquinol. While ZIP14 was knocked down, the complex with Ubiquinone wad damaged, and could not further change to Ubiquinol, so the suppression to lipid peroxidation was released, and then, ferroptosis was upregulated. In this study, we are going to figure out the molecular mechanism about how ZIP14 suppress ferroptosis and find out efficient small molecule inhibitors to activate ferroptosis by abolishing ZIP14 and improve the prognosis of glioma patients. Citation Format: Jing Wang. Targeting the suppressor of ferroptosis to improve the treament effeciency of glioblastoma [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 361.
Abstract 5355: A novel subset of Treg-like MDSCs expressing LAG-3 found in advanced gastric cancer
Authors: Takumi Iwasawa, Suguru Yamauchi, Tetsu Fukunaga, Hajime Orita, Tomoaki Ito, Kato Kazunori
Journal: Cancer Research (2024)

Abstract The development and progression of cancers are frequently promoted by immunosuppressive cells, such as Treg and myeloid-derived suppressor cells (MDSCs) mediated by various immune checkpoint molecules. Therefore, MDSCs are potential diagnostic and therapeutic targets in cancer. However, the definitive cell surface markers for defining MDSC and the subset that correlates with cancer progression are not clear. In our previous studies, there was no difference in the amount of total granulocyte MDSCs (G-MDSCs) between early and advanced gastric cancer. We inferred that there is a novel subset of G-MDSCs involved in cancer progression rather than the previous marker-based classification. The purpose of this study is to analyze MDSCs in gastric cancer patients at different stages of progression and to identify subsets of G-MDSCs that are involved in cancer progression. As a result, we identified a subset of novel G-MDSCs that correlate with cancer progression by expressing LAG-3. LAG-3 is a molecule that is expressed in Tregs and causes strong immunosuppression, suggesting that it is involved in the immunosuppressive potential of MDSCs. Citation Format: Takumi Iwasawa, Suguru Yamauchi, Tetsu Fukunaga, Hajime Orita, Tomoaki Ito, Kato Kazunori. A novel subset of Treg-like MDSCs expressing LAG-3 found in advanced gastric 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 5355.
Abstract 4583: Development of selective HDAC6 inhibitors to improve cancer immunotherapy
Authors: Nithya Gajendran, Manasa Suresh, David Quiceno, Xintang Li, Marie Durr, Karen Tan, Satish Kumar Reddy Noonepalle, Alejandro Villagra
Journal: Cancer Research (2024)

Abstract Histone Deacetylases (HDACs) are enzymes that modify histones and non-histone proteins. Our group has previously demonstrated that HDAC6 inhibitors (HDAC6is) modulate multiple immune pathways, including those that suppress the antitumoral M2 phenotype, leading to improved antitumor immunity. Despite the potential of HDAC6is, current inhibitors have poor selectivity and off-target effects and only work at micromolar concentrations. In this work, we designed a screening pipeline of HDAC6i, considering selectivity, potency, capacity to prevent the protumoral phenotype of macrophages, and low cytotoxicity on macrophages and other immune cells. This approach has not been tested before, as the standard screening method for antitumoral HDACis has focused on its cytotoxic effect on cancer cells. We initially designed in silico 980 compound derivatives from previously reported HDAC6i, such as SS208, Nexturastat A, and Suprastat. Twenty-four compounds with a high capacity to bind HDAC6 and chemical stability were screened by their ability to inhibit HDAC6 in cell-free conditions. Sixteen compounds demonstrated high potency and were further evaluated in murine macrophages by their cytotoxic effect using CellTox. The capacity to impede tubulin deacetylation was assessed by western blot and deacetylase activity by HDAC-Glo. The top six candidates were then evaluated by their selectivity compared to other HDAC members and by their effect on repressing the expression of protumoral M2 macrophages Arginase 1 and Fizz1, and activation of antitumoral markers TNFa and iNOS by western blot and qRT-PCR. The best three candidates were then evaluated at nanomolar concentrations to explore their immunomodulatory potential of M1 against M2 by performing antigen presentation (SIINFEKL presentation) and phagocytic capacity using microscopy. Two of these compounds, SM-06-09 and SM-05-947, will be further tested in syngeneic murine melanoma models for their ability in tumor regression and antitumor immunity. This study has yielded important insights into developing new and improved HDAC6is with minimal cytotoxicity, and we believe our work will help advance cancer research and ultimately lead to better patient outcomes. Citation Format: Nithya Gajendran, Manasa Suresh, David Quiceno, Xintang Li, Marie Durr, Karen Tan, Satish Kumar Reddy Noonepalle, Alejandro Villagra. Development of selective HDAC6 inhibitors to improve cancer immunotherapy [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 4583.
Abstract 1826: New inhibitors of oncology targets discovered using the affinity-mediated selection of DNA-encoded chemical libraries followed by machine-learning
Authors: Anthony D. Keefe, Mohamed AbouZleikha, AJ Baghaie, Matthew A. Clark, Marie-Aude Guie, John P. Guilinger, Ryan Walsh, Ying Zhang
Journal: Cancer Research (2024)

Abstract X-Chem’s DNA-Encoded Chemical Library platform generates a large amount of binding data for each target it is screened against. Here, we report the application of machine learning to these large datasets with case studies that include the identification of novel inhibitors of two oncology targets. One, ERα, is an estrogen-activated receptor that controls transcription and stimulates breast cell proliferation including in breast cancer. The second, DCAF1, is the substrate-recognition component of an E3 ligase complex that is associated with the proliferation of colon cancer cells. Over 100 billion DNA-Encoded compounds were synthesized and screened for their affinity to each target. The selection output data was then featurized and used to train multiple machine-learned models. Models with demonstrated predictive power were then used to score virtual catalogue compounds which were subsequently acquired and tested. A range of successful data-science strategies will be described including those that lead to double-digit nM inhibitors of each of DCAF1 and ERα. Citation Format: Anthony D. Keefe, Mohamed AbouZleikha, AJ Baghaie, Matthew A. Clark, Marie-Aude Guie, John P. Guilinger, Ryan Walsh, Ying Zhang. New inhibitors of oncology targets discovered using the affinity-mediated selection of DNA-encoded chemical libraries followed by machine-learning [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1826.
Abstract 4226: Human-derived hydrogels for 3D models of bone and osteosarcoma organoids and adipose tissue interactions
Authors: Cecilia G. Sanchez, Arman Raz, Haley Lassiter, Trivia Frazier
Journal: Cancer Research (2024)

Abstract The goal of the study was to determine the metabolic and morphological changes, via high Content Imaging, in 3D models of osteosarcoma cancer cells using human derived hydrogels with different protein composition, Obagel and Obagel ECM. Furthermore, we evaluated the relevance of the adipose tissue microenvironment in Adipose Derived Stem Cells (ADSC) linage and Tumoroids development. Methods: Adipose derived Stem cells were cultured in a modified 3D human and fat and bone linage differentiation as studied via histology and Immunofluorescence. Osteosarcoma spheroids were cultured in Obatala Sciences’ human-derived hydrogels ObaGel and ObaGelECM and control media. Organoid structure and phenotypic changes were analyzed via live cell imaging on the Incucyte S3 and Nikon high content imaging device. Then, adipocyte- cancer cell crosstalk was evaluated using pooled adipocytes co-cultured with KHOS spheroids. Adipose derived Stem cells were cultured in a modified 3D human derived hydrogel dictates that promotes the differentiation potential toward fat and adipose tissue simultaneously in microenvironments within the organoid. Furthermore, the results demonstrated that ObaGel and ObaGel-ECM 3D cultures can support the growth and proliferation of KHOS tumor spheres during an extended culture period. Metabolic changes and phenotypic changes associated to ObaGel and ObaGel-ECM differentially facilitated tumoroids growth and migratory behavior. Conclusions: Human derived hydrogels are developed to support 3D culture of Bone and Osteosarcoma cells to recapitulate the phenotypic changes associated with their metastatic potential. The use of human derived 3D culture systems can accelerate the understanding of the role of the microenvironment in bone development and the pathogenesis and progression of Cancers like Osteosarcoma as well as screening for drug development. Citation Format: Cecilia G. Sanchez, Arman Raz, Haley Lassiter, Trivia Frazier. Human-derived hydrogels for 3D models of bone and osteosarcoma organoids and adipose tissue interactions [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 4226.