tbuckley/cabot-search huggingface dataset:
Abstract 1510: Immune regulators identified in undifferentiated pleomorphic sarcoma (UPS) subpopulations
Authors: Candace Lynn Haddox, Junjie Bao, Tomasa Barrientos, Benjamin A. Alman
Journal: Cancer Research (2020)

Abstract Introduction: UPS is a common subtype of soft tissue sarcoma with limited effective systemic therapies. We previously showed that a murine model of UPS has various subpopulations (SPs), characterized by distinct morphology, molecular changes, and oncogenic behaviors that likely contribute to the overall behavior of UPS. Here, we aimed to characterize interactions between UPS SPs to identify pathways important in UPS progression. Methods: We used a murine model of UPS that recapitulates the human disease. Cre recombinase drives oncogenic KRAS-G12D, P53 deletion, and expression of confetti fluorescent protein to allow for in vivo lineage tracing. Individual SPs were isolated via FACS and cultured in the presence of conditioned media (CM) from other individual SPs. Growth rate was assayed using the IncuCyte system (Essen BioScience), and cell proliferation was measured using the Click-iT EdU flow cytometry assay kit. Invasion and migration were assayed using a cell culture insert with or without Matrigel, with CM or non-CM in the lower chamber. Cells migrating/invading into the lower chamber were counted. We performed proteomics analysis on the CM from the SP that potentiated growth and invasion to define the secretome of this SP. The CCL2/CCL7/CCL8 inhibitor, bindarit, was added to CM and cell confluency was assessed as above. RNAseq data from The Cancer Genome Atlas (TCGA) were used to generate immune infiltration scores in human UPS samples. These scores were correlated with expression of lead candidates from our secretome analysis. Results: CM from one UPS SP (SP-1) increased the growth rate and invasion/migration of one other SP (SP-2). Proteomics analysis identified 233 secreted proteins in the CM from SP-1, including 37 with two-fold higher abundance compared to SP-2. Among these, several immunoregulatory proteins were identified, including serpine 1, CCL2, CCL7, CXCL1, and CX3CL1. Culture with bindarit abolished the effect of SP-1 CM on growth rate. Additionally, we found several semaphorins in the secretomes of SP-1 and SP-2, and emerging evidence suggests a key role for semaphorins in cancer progression and immune regulation. Semaphorin expression correlated with immune infiltration scores in human UPS samples. Conclusions: We identified a UPS SP that positively regulates oncogenic behaviors of other SPs through secreted factors. Additionally, several of these secreted proteins play key roles in immune regulation. Given promising activity of immunotherapy in UPS, these proteins warrant further investigation. Citation Format: Candace Lynn Haddox, Junjie Bao, Tomasa Barrientos, Benjamin A. Alman. Immune regulators identified in undifferentiated pleomorphic sarcoma (UPS) subpopulations [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1510.
Abstract 475: Preoperativechemoradiation increases levels of immune system modulators in tumor tissue in locally advanced rectal cancer
Authors: SungUk Bae, Shin Kim, Hye Won Lee, Sang Jun Byun, Jee Young Park, Hyeonji Min
Journal: Cancer Research (2020)

Abstract Purpose: Neoadjuvant chemoradiation therapy (CRT) is a widely and effectively used preoperative treatment strategy in locally advanced rectal cancers. However, little research has been done to characterize the molecular changes caused by neoadjuvant CRT in these cancer tissues. The purpose of this study was to investigate the effects of preoperative CRT on tumor gene expression in Korean patients with colorectal cancer (CRC). Materials and methods: We included 11 paired human rectal cancer tissues before and after irradiation between August 2016 and December 2017, and performed RNA sequencing analysis. Principal component analysis of CRC demonstrated strong similarity in respective groups of CRC tissues before and after CRT from CRC patients at the transcriptome level. Results: Volcano plot filtering identified 3325 differentially expressed genes (DEGs) in CRC tissues after CRT, compared to CRC tissues before CRT. Gene set enrichment analysis with DEGs revealed 45 signaling pathways associated with down-regulated target genes, significantly including the mismatch repair signaling pathway. CRT significantly increased tumor mutation burden (TMB) in CRC tissues. Notably, preoperative CRT increased immune signature scores including interferon-gamma, immune cytolytic score, and immune signature. Conclusion: Neoadjuvant CRT modulates immune-related characteristics of CRC, including increasing TMB and various immune signature scores, suggesting that neoadjuvant CRT has potential to improve responsiveness to immunotherapy. Citation Format: SungUk Bae, Shin Kim, Hye Won Lee, Sang Jun Byun, Jee Young Park, Hyeonji Min. Preoperativechemoradiation increases levels of immune system modulators in tumor tissue in locally advanced rectal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 475.
Abstract 6305: Monitoring the activities of ectonucleotidases CD39 and CD73 and their specific modulation by antibodies and small molecules using homogenous HTS formatted platform
Authors: Said A. Goueli, Kevin Hsiao, Hicham Zegzouti
Journal: Cancer Research (2020)

Abstract The success of immune oncology for treating a wide variety of cancers ushered a new paradigm in cancer therapy. However, due to some limitations in some patients, it is imperative to identify other pathways that are exploited by cancer cells to circumvent immune surveillance, and possibly synergize immune checkpoint treatment in those cases. Recent recognition of significant increase in adenosine levels in the tumor microenvironment and that adenosine/adenosine receptors play a powerful role as immunosuppressant and attenuating several effector T cell functions have spurred interest in targeting ectonucleotidases that generate adenosine. The two main enzymes responsible for generating adenosine in the microenvironment are the ectonucleotidases CD39 and CD73, the former utilizes both ATP and ADP and producing AMP while the latter utilizes AMP and generates adenosine. Thus, these two enzymes combined are the major source for the bulk of adenosine produced in the microenvironment. They were shown to be validated targets in oncology leading to several clinical trials that include small molecules as well as antibodies, showing positive and encouraging results in the preclinical arena. To facilitate the development of novel drugs to target these enzymes, we have developed a platform that can be utilized to monitor the activities of both enzymes in vitro (biochemical) as well as in cells (cell based) assays. It is very sensitive, and the assays are homogenous and enabled us to monitor the activity of both purified enzymes and enzymes bound to the cellular membranes. Most significant is the ability to discern the selectivity of known small molecule inhibitors as well as selective monoclonal antibodies. Our recent expansion of testing of many small molecules and several antibodies have confirmed the utility of this approach for discovering novel therapeutics that might synergize other regiments such as chemotherapies, and in the design of targeting inhibitors. This should speed up screening for novel inhibitors leading to more effective cancer therapy Citation Format: Said A. Goueli, Kevin Hsiao, Hicham Zegzouti. Monitoring the activities of ectonucleotidases CD39 and CD73 and their specific modulation by antibodies and small molecules using homogenous HTS formatted platform [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6305.
Abstract LB-007: The emergence of tumor organoid engineering as a powerful tool for drug efficacy and mechanism of action profiling
Authors: Fei Wang, Rongyun Zhou, Xinlong Dong, Yuqing Ma, Jun Zhou, Xiaoxi Xu, Yujun Huang, Henry Li, Phillip S-Z Wang
Journal: Cancer Research (2020)

Abstract Introduction: Patient-derived models such as organoids are a powerful translational tool for preclinical research with several advantages over current conventional models: 1) they are derived from stem cells with self-organizing and renewal properties reflecting the 3D structure and morphology of original tissue; 2) they preserve the original genomic, physiological, and multicellular identity thereby representing patient diversity and heterogeneity in a dish; 3) they provide in vitro convenience for greater throughput for screening large numbers of compounds and/or patients; 4) they are amenable to genetic engineering. Methods: We have used Hubrecht Organoid Technology (HUB) protocols to systematically create a biobank of organoids derived from a well-annotated patient-derived xenograft (PDX) library (the world's largest commercially available PDX library with over 2,500 models, covering a variety of carcinomas, with extensive pathology, genomic, and treatment information), referred to as PDX-derived organoids or PDXOs. Results: We have currently developed more than 200 PDXOs covering many cancer types, including colorectal, gastric, liver, lung, bladder, breast, ovarian, pancreatic cancer, etc. Genomic analyses have demonstrated that PDXOs largely preserve the histo- and molecular pathology of the original PDX. In vitro maintenance of PDX models as organoids enables genetic manipulation to be performed, which is not possible for in vivo PDX models, thereby creating new models to facilitate drug development. We have employed both lentivirus-based and CRISPR/Cas9-based approaches to modify various tumor organoid models with luciferase, tumor associated antigens (TAA), and some EGFR mutants unavailable in current preclinical model panels. These engineered organoid models, alongside corresponding in vivo matched models, have been incorporated into a new drug efficacy platform. Preliminary results show that these engineered organoid models greatly expand the capacity and application of our current organoid bank. Conclusions: In summary, engineered cancer organoids are a great tool to enrich and diversify current tumor organoid biobanks, particularly for unavailable and clinically relevant models to be used for drug testing, as well as for studies on mechanisms of action and drug resistance. Citation Format: Fei Wang, Rongyun Zhou, Xinlong Dong, Yuqing Ma, Jun Zhou, Xiaoxi Xu, Yujun Huang, Henry Li, Phillip S-Z Wang. The emergence of tumor organoid engineering as a powerful tool for drug efficacy and mechanism of action profiling [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-007.
Abstract 2234: Development of caninized monoclonal antibodies against PD1
Authors: Mikolaj Kocikowski, Katarzyna Dziubek, Borek Vojtesek, David Argyle, Ted Hupp, Maciej Parys
Journal: Cancer Research (2020)

Abstract Immune blockade of inhibitory immune checkpoint (IC) mediated by Programmed cell death protein 1 (PD1) significantly increases survival of patients with advanced melanoma and other cancers. Dogs constitute a unique model for studying cancer types relevant to humans. Canine malignancies occur spontaneously and share many pathogenic pathways as well as therapy responses with their human counterparts. Dogs have a fully functional immune system, share the owners' lifestyle, environmental exposures, and their genome is more similar to the human one than the murine one is. Canine cancer research may be a superior alternative to mouse studies in the context of immunotherapy development. Unfortunately, IC-blocking antibodies are not available for companion animals. Monoclonal antibody against canine ICs has been previously developed by our group using mouse hybridoma technology. While functional, it couldn't be used clinically due to immunogenicity. To create a viable therapeutic, the antibody sequence was caninized. The murine constant regions of heavy and light chains were substituted with corresponding canine sequences. Following that, the variable regions' structural frameworks were replaced with canine sequences generated based on a canine library of antibody sequences.Additionally, we developed an antibody against the PDL1 protein using a previously established canine antibody phage library. The PD1 and PDL1 antibodies are being characterized by ELISA and cell-based blocking assays, T-cell activation assays and growth assessment of the impact on spheroid growth in patient-derived cultures.The characterized antibodies will widen the availability of canine IC blockers and pave the path for further research in comparative oncology. Citation Format: Mikolaj Kocikowski, Katarzyna Dziubek, Borek Vojtesek, David Argyle, Ted Hupp, Maciej Parys. Development of caninized monoclonal antibodies against PD1 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2234.
Abstract 2983: A synthetic derivative of 1,2,3-triazole-pyrimidine hybrid reverses multidrug resistance mediated by MRP7
Authors: Jing-Quan Wang, Zi-Ning Lei, Qiu-Xu Teng, Bo Wang, Li-Ying Ma, Hong-Min Liu, Zhe-Sheng Chen
Journal: Cancer Research (2020)

Abstract Multidrug resistance protein 7 (MRP7) is an important member of ABC transporter superfamily and has been revealed to transport a wide range of chemotherapeutic agents including taxanes, epothilone B, vinca alkaloids, daunorubicin and etoposide. In our previous study, a 1,2,3-triazole-pyrimidine hybrid 25 was synthesized and found significantly reversing multidrug resistance (MDR) mediated by ABCB1. In this study, we evaluated the efficacy of compound 25 in reversing MDR mediated by MRP7 in vitro. The results showed that 25 significantly sensitized cells overexpressing MRP7 to anticancer drugs that are MRP7 substrates at 3 μ;;M. Mechanism study showed that 25 reversed MRP7-mediated MDR by increasing the intracellular accumulation of anticancer drugs and decreasing drug efflux, without altering protein expression level or intracellular localization. Ligand-protein interactions were also modeled by docking with homology MRP7 model. Since limited researches on synthetic MRP7 modulators have been published, our findings provide a valuable prototype for structures which have the potential to be used in combination with conventional anticancer drugs to overcome MDR-mediated by MRP7. Citation Format: Jing-Quan Wang, Zi-Ning Lei, Qiu-Xu Teng, Bo Wang, Li-Ying Ma, Hong-Min Liu, Zhe-Sheng Chen. A synthetic derivative of 1,2,3-triazole-pyrimidine hybrid reverses multidrug resistance mediated by MRP7 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2983.
Abstract 368: Defining the invasive gene signature using patient derived pancreatic cancer organoids
Authors: Yea Ji Jeong, Michael G. Lerner, Yuchen Ge, Hildur Knutsdottir, Bernat Navarro-Serer, Peter E. Chianchiano, Andrew J. Ewald, Joel S. Bader, Laura D. Wood
Journal: Cancer Research (2020)

Abstract Pancreatic cancer mortality is rising due to late detection and established metastasis. Despite the recent advances in cancer research, metastasis research has been hampered by the lack of models that recapitulate this complex process. Traditional cell culture and animal models provided insights on cancer cell migration and dissemination. But local invasion, which precedes all the events in the metastatic cascade, remains poorly understood. Patient-derived organoids (PDO) present an innovative platform in which the earliest step of metastasis can be observed and manipulated ex vivo. We developed a pancreatic cancer organoid model using surgically resected tumors from The Johns Hopkins Hospital. We previously reported that there are two invasive patterns in pancreatic cancer PDOs - Mesenchymal and Collective invasion, with one dominating pattern in every PDO culture. Here, we describe the gene expression signature associated with local invasion in pancreatic cancer by comparing the whole transcriptome of matched invasive and non-invasive organoids from the same tumor. For this study, PDOs were cultured for 7 days ex vivo and we manually collected 50 invasive and non-invasive organoids from each culture for RNA-seq analysis. To date, the invasive and non-invasive organoids from 6 PDO lines have been analyzed. The list of differentially expressed genes between invasive and non-invasive organoids includes 1,106 genes with FDR 0.001, with DACT1, DKK3 and KIF26B being most differentially expressed. Pathway analysis identifies that the invasive phenotype is associated with extracellular matrix receptor interaction, focal adhesion and PI3K-Akt signaling pathways. In conclusion, our findings revealed a distinct gene expression signature between invasive and non-invasive cells in PDOs. Interestingly, we did not find significant up or down-regulation in the classical EMT markers in our results, which suggests possible pancreatic cancer-specific metastasis programs exist. We believe our results can inform new diagnostic and prognostic tools and help identify anti-metastasis targets in pancreatic cancer. Citation Format: Yea Ji Jeong, Michael G. Lerner, Yuchen Ge, Hildur Knutsdottir, Bernat Navarro-Serer, Peter E. Chianchiano, Andrew J. Ewald, Joel S. Bader, Laura D. Wood. Defining the invasive gene signature using patient derived pancreatic cancer organoids [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 368.
Abstract 276: Mir-139 regulates autophagy in prostate cancer cells through Beclin-1 and mTOR signaling proteins
Authors: Tania C. Benatar, Robert Nam, Christopher Sherman, Yutaka Amemiya, Arun Seth
Journal: Cancer Research (2020)

Abstract Background: Prostate cancer represents the second leading cause of cancer death in men and develops as a result of the accumulation of genetic and epigenetic alterations. We previously identified a panel of five miRNAs associated with biochemical recurrence and metastasis following prostatectomy from prostate cancer patients using NGS-based whole miRNome sequencing and qPCR-based validation analysis. We have shown that expression of miR-139, one of the downregulated miRNAs from this panel, was associated with improved prognosis in patients with localized prostate cancer. Furthermore, miR-139 overexpression inhibited prostate cancer cell growth through signaling pathways mediated in part through downregulation of AXL and IGF1R. Here, we further investigated the molecular mechanisms by which miR-139 could inhibit prostate cancer cell growth. Methods: We examined miR-139 transfected PC3, DU145 and LNCaP cells by morphology as well as by cell-based assays, confocal microscopy and immunoblotting. Results and Discussion: We found that treatment of prostate cancer cells with miR-139 resulted in phenotypic changes characteristic of autophagic cells. Conversion of the microtubule-associated protein light chain 3 (LC3-I to LC3-II) was used to monitor autophagy. We observed that the treatment of PC3 and LNCaP cells with miR-139 increased the conversion of LC3-I to LC3-II protein that was specifically inhibited by addition of miR-139 antagomir. The upregulation of LC3 II was further confirmed by confocal microscopy of PC3 cells treated with miR-139. Mammalian target of rapamycin (mTOR) and Beclin1 are two important autophagy-related molecules playing significant roles in different stages. mTOR negatively regulates autophagy machinery. Treatment of cells with miR-139 inhibited both activation and expression of mTOR. We also observed increased levels of phospho-Beclin 1 in PC3 cells treated with mir-139. Beclin 1 is a scaffold protein that assembles components for promoting or inhibiting autophagy and its phosphorylation controls autophagy. The cargo adaptor protein, p62/SQSTM1, interacts with autophagic substrates, delivering them to the autophagosome for degradation, and is degraded during autophagy. We found that during early treatment of cells with miR-139, p62 expression is inhibited, while at later stages, p62 expression accumulates, suggesting that autophagic flux may be blocked. These results suggest that miR-139 is regulating autophagy in prostate cancer cells at least in part through the mTOR and Beclin-1 proteins. Citation Format: Tania C. Benatar, Robert Nam, Christopher Sherman, Yutaka Amemiya, Arun Seth. Mir-139 regulates autophagy in prostate cancer cells through Beclin-1 and mTOR signaling proteins [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 276.
Abstract 5041: Inhibition of RUNX-CBFβ binding reduces RSPO3 expression and EMT features in breast cancer cells
Authors: Carla M. Felcher, Johanna M. Tocci, Martin E. Garcia Sola, John H. Bushweller, Lucio H. Castilla, Edith C. Kordon
Journal: Cancer Research (2020)

Abstract We have recently identified R-spondin3 (RSPO3) as a novel key modulator of breast cancer development that may become a potential target for treatment of the basal subtype, which lacks efficient therapeutic options to date. RSPO3 is expressed in the basal stem cell-enriched compartment of mouse mammary glands whereas it is absent in the mature luminal cells. RSPO3 knockdown in mouse mammary tumor cells reduces canonical Wnt signaling pathway, epithelial-to-mesenchymal transition (EMT)-like features, migration capacity, and tumor formation in vivo. To evaluate the relevance of RSPO3 in human breast cancer, we analyzed samples from 75 patients with ductal infiltrating breast carcinomas, where we found a high prevalence of positive immunoreactivity for RSPO3 (70%). Expression data of The Cancer Genome Atlas Network from 1985 human breast carcinoma samples showed that RSPO3 is primarily expressed in Claudin-low breast cancer subtype, which is characterized for having stem cells features. In culture assays revealed that knockdown of RSPO3 expression reduced SOX2 expression and impaired mammary tumor cell ability to form mammospheres. Previous reports suggested the potential involvement of RUNX1-CBFβ on RSPO3 transcription in mammary tumor cells. Therefore, we evaluated if pharmacologic inhibition of RUNX1 activity would reduce RSPO3 expression and activity in the cancer stem cell compartment. Treatment of breast cancer cells with AI-10-104, a small molecule that inhibits CBFβ-RUNX interaction, reduced RSPO3 mRNA and protein levels, and reduced the migration ability of MDA-MB231 breast cancer cells, ability that was recovered upon treatment with recombinant RSPO3. In addition, AI-10-104 inhibited the expression of canonical Wnt pathway targets, EMT and stem-cell markers. Therefore, our results demonstrate that inhibition of RUNX-CBFβ transcriptional activity leads to a down-regulation of RSPO3 expression, constituting a new molecular target for therapeutic modulation in breast cancer treatment. Citation Format: Carla M. Felcher, Johanna M. Tocci, Martin E. Garcia Sola, John H. Bushweller, Lucio H. Castilla, Edith C. Kordon. Inhibition of RUNX-CBFβ binding reduces RSPO3 expression and EMT features in breast cancer cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5041.