tbuckley/cabot-search huggingface dataset:
Abstract 4361: A systematic study of the impact of estrogens and selective estrogen receptor modulators on prostate cancer cell proliferation
Authors: Camille Lafront, Lucas Germain, Cindy Weidmann, Etienne Audet-Walsh
Journal: Cancer Research (2020)

Abstract The estrogen receptors ERα and ERβ are expressed in prostate cancer (PCa) cells and are believed to act as an oncogene and a tumor suppressor, respectively, and thus to be attractive therapeutic targets. Indeed, compounds modulating the activity of these receptors already exist and are currently used to treat ERα-positive breast tumors. However, there is a lot of discrepancies regarding the efficacy of anti-estrogen treatments for the management of PCa. Several factors explain these discrepancies, including unspecific antibodies against ERβ, lack of proper estrogenic positive controls, and usage of estrogens and anti-estrogens molecules at high dosages were off-target effects are observed. Our objective was to conduct a systematic study on the impact of estrogenic and anti-estrogenic ligands on PCa cell proliferation and survival. After optimization of our cellular assay using the human breast cancer cell line MCF7, we used five of the most commonly studied human PCa cell models, namely LNCaP, 22Rv1, LAPC4, DU145, and PC3 cells. These cells were treated with nine estrogenic/anti-estrogenic compounds, including five selective estrogen receptor modulators (SERMs), with and without co-treatment with androgens for androgen receptor (AR)-positive cells. In both AR-positive and AR-negative cells, we observed no significant modulation of proliferation following modulation of ERs activity. Using both RNA-seq and Western Blots, ERs expression was mostly undetectable in these models. Our study indicate that commonly used PCa models in vitro are not appropriate models to study the estrogen signaling pathway in PCa. Yet, expression data from PCa tissues indicate a significant expression of both receptors, and indicate that usage of new PCa models or of in vivo models are required to properly study drug repurposing of anti-estrogens and SERMs for PCa treatment. Citation Format: Camille Lafront, Lucas Germain, Cindy Weidmann, Etienne Audet-Walsh. A systematic study of the impact of estrogens and selective estrogen receptor modulators on prostate cancer cell proliferation [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 4361.
Abstract 3842: Histone methyltransferase G9a promotes migration, invasion of non-small cell lung cancer through enhancing FAK and NF-kB signal pathways
Authors: Ting Sun, Keqiang Zhang, Rajendra P. Pangeni, Wendong Li, Dan J. Raz
Journal: Cancer Research (2020)

Abstract Overexpression of euchromatic histone methyltransferase 2 (EHMT2 or G9a) is associated with carcinogenesis and poor prognosis in a number of cancer types. In this study, we investigated the effect of G9a on invasion of non-small cell lung cancer (NSCLC) cells and the mechanism underlying cancer cell invasion. Knockdown of G9a was shown to drastically suppress in vitro cellular proliferation, migration, and invasion of A549 and H1299 NSCLC cells, while overexpression of G9a significantly enhanced the proliferation and invasion of these NSCLC cells. Additionally, knockdown of G9a led to significant decrease in expression of focal adhesion kinase (FAK) gene and activation of FAK pathway. UNC0638, a selective inhibitor of G9a, significantly suppressed both the proliferation, migration and invasion of these NSCLC cells, and concurrently led to a dramatic drop of global demethylation of H3K9 (H3K9me2) and suppressed the activation of FAK pathway. In addition, Defactinib, a potent FAK inhibitor, partially abolished the enhanced invasion by overexpression of G9a in these NSCLC cells. Furthermore, G9a was proved to regulate nuclear NF-κB transcriptional activity in NSCLC cells, and NF-κB inhibitor partially abolished the activated FAK signaling pathway by overexpressed G9a, which indicates that G9a-enhanced invasion and activation of FAK pathway may be mediated by NF-κB transcriptional activity. Notably, immunohistochemistry analysis further revealed that activation of FAK pathway was associated with overexpressed G9a in about 150 cases of NSCLC tissues. Altogether, these data have strongly demonstrated that G9a may promote invasion of NSCLC cells by upregulating FAK protein and pathway via enhancing NF-κB transcriptional activity, indicating a therapeutic implication of targeting these two pathways in NSCLC with overexpressed G9a. Citation Format: Ting Sun, Keqiang Zhang, Rajendra P. Pangeni, Wendong Li, Dan J. Raz. Histone methyltransferase G9a promotes migration, invasion of non-small cell lung cancer through enhancing FAK and NF-kB signal pathways [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 3842.
Abstract 4034: High throughput synergy screening identifies therapeutic combinations for Merkel cell carcinoma
Authors: Khalid Garman, Tara Gelb, Daniel Urban, Matthew Hall, Isaac Brownell
Journal: Cancer Research (2020)

Abstract Merkel cell carcinoma (MCC) is a rare and aggressive neuroendocrine skin cancer. MCC is virus-positive (VP-MCC) in the majority of cases wherein Merkel cell polyomavirus is integrated into the host genome. The remainder of cases are virus-negative (VN-MCC) and are associated with mutations induced by ultraviolet light. Primary MCC is effectively treated by surgical resection and radiotherapy, but for metastatic MCC, outcomes for conventional chemotherapy are poor. Immune checkpoint inhibitors are more likely to produce durable responses in metastatic MCC, but they are not effective in all cases and are not a viable option for patients with immunosuppression. To address the need for better therapeutic options, we utilized high-throughput small molecule screening to assess the efficacy of ~4,000 drugs in reducing VP-MCC and VN-MCC viability. Among the compounds we screened, navitoclax was identified as an effective agent against VP-MCC cell lines, compared to VN-MCC or control cells. However, navitoclax clinical application is limited by dose-dependent thrombocytopenia. One strategy to reduce thrombocytopenia risk is to combine a lower dose of navitoclax with another MCC-effective agent. To identify effective drug combinations, we performed a synergy screen with 1912 pairings of navitoclax with each of the clinically relevant compounds in the NCATS Mechanism Interrogation PlatE (MIPE). We were able to identify synergy between navitoclax and multiple drug classes. High priority drug combinations are now being evaluated for toxicity and efficacy in pre-clinical xenograft models of MCC. Our study has identified novel therapeutic combinations for the treatment of VP-MCC. By focusing on drugs already in clinical use, validated combinations will be quickly available to patients for whom immunotherapy is not available or effective. Citation Format: Khalid Garman, Tara Gelb, Daniel Urban, Matthew Hall, Isaac Brownell. High throughput synergy screening identifies therapeutic combinations for Merkel cell carcinoma [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 4034.
Abstract 3223: The Cancer Genomics Cloud enables complex and multi-omic data science in the cloud
Authors: Manisha Ray, Jack DiGiovanna, Jelena Radenkovic, Marko Tosic, Nikola Mirkovic, Boris Majic, Vladan Andjus, Brandi Davis-Dusenbery
Journal: Cancer Research (2020)

Abstract The Cancer Genomics Cloud (CGC), powered by Seven Bridges, is an NCI-funded platform to make the analysis of cancer data faster, easier, and more accessible. As datasets grow larger, more diverse, and more complex, they have become increasingly challenging for many cancer researchers. The CGC provides a centralized resource for analysis by co-localizing three components within the same cloud platform: 1) large cancer datasets like The Cancer Genome Atlas (TCGA); 2) tools and workflows for analyzing public and private data; and 3) the computational capabilities to do large-scale analyses. In addition to the simplicity of data access; the CGC also contains &amp;gt;400 of best-practice workflows, the flexibility to bring private tools and notebooks, and the ability to complete interactive analyses, all with the speed of cloud computing. The number of available datasets and tools are rapidly increasing, connecting researchers to datasets from a wide range of sources and data types, such as proteomics and imaging. The platform has been continuously expanded to include new applications and features since its launch in 2016. Here we describe how new features have been implemented to broaden the data and workflows accessible to cancer researchers. First, we have integrated with several new nodes within the Cancer Research Data Commons to enable access and analysis on proteomics, canine, and other cancer datasets, which alongside with the genomics data on the CGC, enables true multi-omic analysis. Second, we have expanded our infrastructure to enable computation on both Google and Amazon cloud environments, allowing for analysis of data held in either environment. We have also added support for RStudio within the CGC, along with Python and Julia notebooks. Researchers can complete their entire workflow on the platform, from data discovery through visualizations, while streamlining collaboration and speeding the time from hypothesis to conclusion. Altogether, these added features enable a network of Findable, Accessible, Interoperable, and Reusable (FAIR) datasets towards making cancer data analysis faster, easier, and more accessible for all. Citation Format: Manisha Ray, Jack DiGiovanna, Jelena Radenkovic, Marko Tosic, Nikola Mirkovic, Boris Majic, Vladan Andjus, Brandi Davis-Dusenbery. The Cancer Genomics Cloud enables complex and multi-omic data science in the cloud [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 3223.
Abstract 500: Discovering epigenetic regulators of cells states in triple negative breast cancers
Authors: Joseph Patrick Burnett, Garrett Johnson, Nathan Truchan, Michael Brooks, Max S. Wicha, Duxin Sun
Journal: Cancer Research (2020)

Abstract The implementation of targeted therapies have been instrumental in achieving clinical responses for ER, PR, and HER2 receptor expressing breast cancers. However, triple negative breast cancers in themselves do not respond to such therapies and are highly heterogeneous diseases with significantly worse progression and survival. Our preliminary data and literature have also shown that in TNBC different cancer cell subpopulations are present in any given tumor, each with its own unique chemo-response and resistance. To discover novel targets regulating cancer cell states in TNBCs, we have created a reporter cell line using CRISPR/Cas9 mediated knock-in of fluorescent reporter proteins after the endogenous loci of major cell type markers in SUM149. Using this reporter line allows for the direct visualization of ALDH1A3+/- and CD24+/- cells, facilities tracking of distinct cell state transitions in a given cell, and allows for lineage tracing following cell divisions. These reporter cells were subjected to HTS-FACS analysis after exposure to a siRNA library of known epigenetic regulators. Following secondary screening, three siRNA targets are able to uniquely inhibit distinct subpopulations of cells within the cell line DCAF1 (ALDH-/CD24- cells), MLL2 (ALDH-/CD24+ cells), and TRIM24 (ALDH+ cells). In combination, these siRNA's proportionally eliminated all cell types. Due to the inherent heterogeneity of TNBCs we then sought to determine if efficacy was consistent or unique across different cell lines with varying percentages of CD44, CD24, and Aldefluor+ cell populations. Most notably, in MDA-MB-468 which contains similar cell population percentages to SUM149 each siRNA was capable of reducing cell proliferation. Similarly, TRIM24 was also capable of reducing cellular proliferation in BT20, MLL2 in MDA-MB-231, and DCAF1 in HCC1937. Knockdown of TRIM24 consistently reduced Aldefluor+ cells in MDA-MB-468 and BT20 cells. Finally, coupled with sc-Omics technologies we utilized this efficacy data identify a subset of TNBC patients likely to respond to therapies which will target these genes in the future. Citation Format: Joseph Patrick Burnett, Garrett Johnson, Nathan Truchan, Michael Brooks, Max S. Wicha, Duxin Sun. Discovering epigenetic regulators of cells states in triple negative breast cancers [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 500.
Abstract 6059: Targeting the anthracycline metabolizing enzyme AKR1C3 in adipocytes to improve cytotoxicity
Authors: Vladislava Paharkova, Etan Orgel, Michael Neely, Stan. Louie, Steven Mittelman
Journal: Cancer Research (2020)

Abstract Introduction: We have reported that mouse and human adipocytes take up and metabolize the anthracycline, daunorubicin (DNR), reducing its concentration in the adipocyte microenvironments. This may contribute to anthracycline resistance for cancers, which reside in adipocyte rich environments such as omentum and bone marrow. Adipocytes express several carbonyl- and aldo-keto reductases (CBRs and AKRs) which metabolize and inactivate anthracyclines, and it is unclear which of these might be important targets to improve treatment outcome. Experimental Procedures: We knocked out AKR1C3 in the human preadipocyte cell line Chub S7 using CRISPR/Cas9 gene editing technology. We chose AKR1C3 first as it is one of the overexpressed enzymes in adipocytes with the highest anthracycline-metabolizing activity. We delivered ribonucleoprotein complexes of CRISPR-Cas9 enzyme plus guide RNAs by nucleofection. Then we established single-cell derived clones and tested for successful KO by Western blot. Finally, we quantified adipocyte lysate AKR activity using a colorimetric assay based on NADPH-dependent reduction of phenanthrenequinone. Data Summary: We chose three Chub S7 preadipocyte clones that demonstrated successful AKR1C3 knockout based on almost undetectable protein expression by western blot. AKR activity was significantly reduced in all three clones; control preadipocytes had 44±4.7, while clones had activity of 28±7.3, 33±3.4, and 35±5.7 pmol/min/µg (p&amp;lt;0.05 for all comparisons, n=3 for each assay). Conclusions: These findings demonstrate that AKR1C3 knockout can be successfully done in human preadipocytes using a CRISPR-Cas9 system. Knockout of AKR1C3 significantly reduces overall aldoketoreductase activity in preadipocyte cells. This implies that a substantial portion of preadipocyte AKR activity is dependent on the isoenzyme, AKR1C3. Future testing is needed to determine whether AKR1C3 KO will reduce the clearance of anthracyclines from the cancer microenvironment, and may represent a treatment target to enhance anthracycline cytotoxicity. Citation Format: Vladislava Paharkova, Etan Orgel, Michael Neely, Stan. Louie, Steven Mittelman. Targeting the anthracycline metabolizing enzyme AKR1C3 in adipocytes to improve cytotoxicity [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 6059.
Abstract 5173: Identification of new targets in SMAD4-deficient cancers by whole genome CRISPR screening
Authors: Christophe Marcireau, Hélène Erasimus, Vanessa Kolnik, Frederic Lacroix, Stéphane D'agostino, Olivier Lemaitre, Alexandre Rohaut, Isabelle Sanchez, Sukhvinder Sidhu, Gilbert Thill, Michel Didier, Laurent Debussche
Journal: Cancer Research (2020)

Abstract The TGF-β signaling mediator SMAD4 is frequently mutated or deleted in colorectal cancer (CRC) and pancreatic cancers (PC) and is associated with poorer prognosis. This makes SMAD4 loss interesting to harness for synthetic lethality-based therapy. In this study, we first restored SMAD4 in SMAD4-deficient cell lines (HT29 and SW620) and showed that SMAD4 restoration reestablished the TGF-β-induced growth inhibition in vitro and in vivo, thereby confirming the tumor suppressive role of SMAD4 in these cell lines. In order to identify genetic vulnerabilities of SMAD4-deficient cells, we conducted pooled genome-wide loss-of-function CRISPR/Cas9 screens across four non-isogenic cell lines harboring altered (HT29 and SW620) or wild-type (DLD1 and MIAPACA2) SMAD4. We identified candidate genes, including the Krüppel-like factor 5 (KLF5), which has already been suggested as a potentially interesting target for drug therapy in SMAD4-deficient cancers. Novel candidates that might be interesting synthetic lethal targets in SMAD4-negative cancers will be presented. Citation Format: Christophe Marcireau, Hélène Erasimus, Vanessa Kolnik, Frederic Lacroix, Stéphane D'agostino, Olivier Lemaitre, Alexandre Rohaut, Isabelle Sanchez, Sukhvinder Sidhu, Gilbert Thill, Michel Didier, Laurent Debussche. Identification of new targets in SMAD4-deficient cancers by whole genome CRISPR screening [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 5173.
Abstract 5725: Epigenetic and transcriptional profiling reveal endosomal protein sorting as a glioblastoma cancer stem cell dependency
Authors: Ryan C. Gimple, Guoxin Zhang, Jeremy N. Rich
Journal: Cancer Research (2020)

Abstract Glioblastoma is a highly lethal primary intrinsic brain tumor for which current standard-of-care therapies are merely palliative. Functionally defined glioblastoma stem cells (GSCs) contribute to this poor prognosis by driving therapeutic resistance, maintenance of cellular heterogeneity, and disease recurrence. A deeper appreciation for the specific features that distinguish normal from neoplastic stem cells may inform selective therapeutic targeting. To further understand the molecular processes essential for maintaining cancer stem cell populations, we interrogated the active enhancer landscapes and transcriptional output of GSCs and normal neural stem cells (NSCs) through H3K27ac ChIP-seq and RNA-seq respectively. GSC-specific targets that held prognostic significance in patient datasets and which were essential in whole genome CRISPR screening data implicated endosomal protein sorting as a key feature in GSC biology. Targeting endosomal sorting impaired GSC viability and proliferation and contributed to apoptosis, while NSCs displayed a reduced cell proliferation deficit. Impaired endosomal protein sorting led to a reduction in the mRNA and protein levels of the stem and neuro-developmental transcription factors SOX2 and OLIG2 and reduced self-renewal capacity of GSCs, suggesting a role in the maintenance of stemness. Mechanistically, regulation of endosomal sorting may impact localization and stability of receptor tyrosine kinases and WNT signaling elements to control GSC maintenance. High expression of this endosomal sorting factor is associated with poor glioblastoma patient prognosis, suggesting its clinical importance. Thus, targeting the endosomal sorting pathway may represent a novel therapeutic approach for glioblastoma treatment. Citation Format: Ryan C. Gimple, Guoxin Zhang, Jeremy N. Rich. Epigenetic and transcriptional profiling reveal endosomal protein sorting as a glioblastoma cancer stem cell dependency [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 5725.
Abstract 4491: Characterizing long non-coding RNA expression of tumor-infiltrating lymphocytes across solid cancers
Authors: Wikum Dinalankara, Eddie-Luidy Imada, Christopher M. Jackson, Thomas R. Nirschl, Michael Lim, Charles G. Drake, Luigi Marchionni
Journal: Cancer Research (2020)

Abstract Usually recognized as transcripts of length more than 200 bp and devoid of open reading frames, long non-coding RNAs (lncRNAs) span a vast range of the human genome. Once thought to be of relatively little biological importance, they have been shown to be involved in many biological processes and diseases, highlighting their important regulatory function, which is now gradually starting to be understood. For instance, the recent discovery of immune gene priming lncRNAs (IPLs) – a subset of lncRNAs that facilitate epigenetic priming of immune gene promoters – has demonstrated the hitherto unappreciated role of lncRNAs in orchestrating inflammatory and immune responses. In this study we generated and analyzed bulk RNA sequencing data from a collection of purified cell populations obtained from patients with prostate cancer, glioblastoma, bladder cancer, and renal cell carcinoma. Each cohort was comprised of tumor infiltrating lymphocytes (TILs) and paired circulating lymphocytes, derived from matched peripheral blood samples, obtained by fluorescence-activated cell sorting (FACS). The high depth of coverage in our data allowed the examination of expression patterns of CD4 and CD8 cell types at a level not possible with single cell sequencing, across relevant tumor phenotypes including T-cell exhaustion. To this end, we used the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) annotation, quantifying expression levels for over 100,000 coding and non-coding genes, encompassing enhancers and promoters recently characterized by the FANTOM consortium and examined their behavior with respect to immune function. We compared the behavior of coding genes and various categories of lncRNAs against each other, and identified important candidate lncRNAs for further functional study. Overall, our comprehensive study of TILs gene expression provides novel insights into lncRNA-directed networks controlling immune response mechanisms in cancer. Citation Format: Wikum Dinalankara, Eddie-Luidy Imada, Christopher M. Jackson, Thomas R. Nirschl, Michael Lim, Charles G. Drake, Luigi Marchionni. Characterizing long non-coding RNA expression of tumor-infiltrating lymphocytes across solid cancers [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 4491.