bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1390: Inhibition of the catalytic activity of hUNG2 sensitizes multiple cancer cell lines to 5-FdUrd killing
Authors: Christenson Eric S. , Cui Junru , Gizzi Anthony , Meshesha Mesfin , Stivers James T. 
Published: September 2020

Abstract
Previously reported shRNA knockdown studies have established that expression of the DNA repair enzyme human uracil DNA glycosylase (hUNG2) is protective against 5-flourodeoxyuridine (5FdUrd) cell killing in p53 mutated cancer cell lines, but not in cell lines with functional p53. Here we take a different approach to understanding the role of hUNG2 in 5FdUrd chemotherapy by selectively inhibiting the catalytic activity of hUNG2 using the small bacterial inhibitor protein UGI. UGI binds extremely tightly to the DNA binding and catalytic site of hUNG2, effectively mimicking the impact of a small molecule inhibitor and allowing us to explore the potential therapeutic vulnerabilities that loss of hUNG2 activity produces in p53 mutated and wild-type cancer cells. Accordingly, we used lentiviral transduction to introduce UGI, under control of a doxycycline-inducible promoter, into a large panel of cancer cell lines. In vitro hUNG2 activity measurements using cell extracts established that all lines had robust activity before induction of UGI and undetectable activity after induction. We find that some wild-type and mutant p53 cancer lines from different tissues show significant increases in drug sensitivity. For instance, the p53 wild-type MCF7 breast cancer line showed a 10,000-fold increase in sensitivity, while the p53 mutant HT29 colorectal cancer line showed a 50-fold increased sensitivity. Overall, the results do not support the proposal that p53 status itself determines whether a cancer cell will be sensitized to 5FdUrd in the presence of hUNG2 inhibition. Ongoing studies are focused on identifying the cellular factors that contribute to drug sensitivity under conditions of hUNG2 inhibition. Realizing the full therapeutic benefit of 5FdUrd requires identification of the cancer cell phenotypes that are sensitized upon hUNG2 inhibition.
Citation Format: Eric S. Christenson, Junru Cui, Anthony Gizzi, Mesfin Meshesha, James T. Stivers. Inhibition of the catalytic activity of hUNG2 sensitizes multiple cancer cell lines to 5-FdUrd killing [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 1390.
Abstract 1394: Gene expression profile in BCBL-1 cell line following activation of KSHV
Authors: Haines Samantha L. , Bishop Sabrina R. , Podlutskaya Viktorija , Podlutsky Andrej 
Published: September 2020

Abstract
Patients with HIV/AIDS are at a 3,400 times higher risk of developing Kaposi's sarcoma when compared to healthy populations. Our hypothesis is that the upregulation of viral associated proteins is causing an increase in DNA damage, allowing for the higher incidence rate of Kaposi's sarcoma in infected populations. The direct mechanisms leading to this increased risk is unknown, but the viral infection with Kaposi's sarcoma-associated herpesvirus (KSHV) is an apparent cause of this risk. The cell is under attack of endogenous threats including oxidative stress, causing DNA damage and leading to mutations, but the viral proteins may interfere with the repair mechanisms. In previous experiments we looked at DNA repair dynamics following X-ray exposure in the two different stages and determined there is an inefficiency in the DNA repair process in the cells during active production of viral particles. This project aimed to compare the transcriptomes of the BCBL-1 cell line during latent and acute phases of KSHV production. Our results are showing that genes involved in genome stability are differently expressed during the lytic stage. Comparison of these two transcriptomes allows for identification of which proteins are being upregulated during active viral production. This may be of importance for the HIV/AIDS cancer patients because it shows the mechanisms behind genome stability in KSHV-infected cells.
1) Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award Numbers UL1GM118991, TL4GM118992, or RL5GM118990. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
2) NASA EPSCoR, NNH15ZHA003C
Citation Format: Samantha L. Haines, Sabrina R. Bishop, Viktorija Podlutskaya, Andrej Podlutsky. Gene expression profile in BCBL-1 cell line following activation of KSHV [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 1394.
Abstract 142: Identification of symmetric methylation and hemimethylation patterns with optimal panel design, library preparation, and error correction
Authors: Huang Hsiao-Yun , Chakravarty Ushati Das , Lai Kevin , Barnes Timothy , Chen Tzu-Chun , Sheu Jessica , Lopez Ramses , Scott Karissa , Lewis Lynette , Potts Anastasia 
Published: September 2020

Abstract
DNA methylation patterns are epigenetic modifications with direct implications in gene expression and chromatin structure regulation. Altered DNA methylation has been reported in various human cancers. The methylation profile of cell-free DNA (cfDNA) from plasma can be exploited to detect and diagnose tissue pathologies and is therefore of great diagnostic interest. Due to limitations of existing NGS library preparations, we present a new workflow, that integrates Unique Molecular Identifier (UMI) based error correction and optimizes library preparation and target enrichment. This workflow incorporates an engineered mutant ligase and proprietary methylated adapters that together prevent chimeras, suppress dimer-formation, and maximize conversion. Our library preparation provides &gt;80% unique mapping efficiency and high conversion efficiency which creates superior sensitivity and specificity for detecting epigenetic signatures from a wide range of inputs (1-250 ng) and samples, including genomic DNA, FFPE DNA and cfDNA.
This workflow is suitable for both genome-wide and targeted methylation sequencing. We implemented the target methyl-seq workflow to distinguish between fully methylation and hemimethylation on only one strand of the DNA by ligating in-line UMIs prior to target enrichment, followed by bisulfite conversion and PCR. Using a custom panel for targeted methylation sequencing, we detected &gt;60% of CpG methylation in normal human samples and &gt;95% of CpG methylation in in vitro methylated HCT116 samples. Employing ultra-deep sequencing to an average target depth of 10,000X followed by double-stranded consensus building analysis enables accurate low frequency methylation and hemimethylation detection. The studies presented here offer tools to advance epigenetics research.
Citation Format: Hsiao-Yun Huang, Ushati Das Chakravarty, Kevin Lai, Timothy Barnes, Tzu-Chun Chen, Jessica Sheu, Ramses Lopez, Karissa Scott, Lynette Lewis, Anastasia Potts. Identification of symmetric methylation and hemimethylation patterns with optimal panel design, library preparation, and error correction [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 142.
Abstract 1455: NANOG binds polycomb repressive complex 2 to reprogram metabolism to promote slow cycling phenotype in experimental mouse and clinical carcinoma
Authors: Yeh Da-Wei , Hernandez Juan Carlos , Machida Keigo 
Published: September 2020

Abstract
Pluripotency transcription factor NANOG represses mitochondrial oxidative phosphorylation (OXPHOS) genes, but activates fatty acid oxidation (FAO) to support self-renewal and drug resistance of tumor-initiating stem-like cells (TICs). Hepatoceullular carcinomas (HCCs: 39%) associated with HCV and alcohol have mutations in ARID1A, a component of the chromatin remodeling complex SWI/SNF. We hypothesized that NANOG binds polycomb repressive complex 2 (PRC2) to reprogram metabolism to promote slow cycling phenotype. Here, the Genome-scale CRISPR Knock-Out (GeCKO) screening with ARID1A mutation identified PRC2 complex genes (EZH2, SUZ12 and EED) in patient-derived TICs. NANOG together with the PRC2 complex inhibits OXPHOS to generate TICs with label-retaining ability and therapy resistance. NANOG binds PRC2 complex. ARID1A gene loss promotes sorafenib-resistance phenotype and self-renewal through PRC2 complex genes. ARID1A mutation promoted HCC development in humanized FRG mice with HCCs. The studies established a novel therapy to overcome the chemoresistance of TICs for HCC treatment.
Citation Format: Da-Wei Yeh, Juan Carlos Hernandez, Keigo Machida. NANOG binds polycomb repressive complex 2 to reprogram metabolism to promote slow cycling phenotype in experimental mouse and clinical 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 1455.
Abstract 1457: Akt phosphorylation of mitochondrial Lonp1 protease enables oxidative metabolism and advanced tumor traits
Authors: ghosh Jagadish C. , Seo Jae Ho , Agarwal Ekta , Wang Yuan , Kossenkov Andrew V. , Tang Hsin-Yao , Speicher David W. , Altieri Dario C. 
Published: September 2020

Abstract
Introduction: The control of protein homeostasis, or proteostasis is essential for cellular adaptation to disparate environmental cues and relies on protein (re)folding or proteolytic removal of aggregated or misfolded proteins. Defective proteostasis can irreversibly impair organelle functions and activate cell death through an unfolded protein response. Tumor mitochondria have heightened protein folding quality control, but the regulators of this process and how they impact cancer traits are not completely understood. In this study, we investigated the mechanisms of stress-regulated LonP1 (ATP-dependent protease) in tumor mitochondria and their implications for advanced cancer traits.
Experimental procedures: We monitored kinase activity in immunoprecipitation, protein expression by immunoblotting, mitochondrial ROS quantification in live cells, mitochondrial electron transport chain (ETC) activity, mitochondria time-lapse video microscopy, protein folding, proteomics analysis, mitochondrial bioenergetics, mitochondrial trafficking and tumor cell motility, and tumor growth and metastasis. A xenograft prostate cancer model was used to study antitumor activity in vivo.
Results: We showed that the ATP-directed mitochondrial protease, LonP1 is upregulated by stress conditions, including hypoxia, in tumor, but not normal cells. In mitochondria, LonP1 is phosphorylated by Akt on Ser173 and Ser181, enhancing its protease activity. Interference with this pathway induces accumulation of misfolded subunits of electron transport chain complex II and complex V, resulting in impaired oxidative bioenergetics and heightened ROS production. Functionally, this suppresses mitochondrial trafficking to the cortical cytoskeleton, shuts off tumor cell migration and invasion, and inhibits primary and metastatic tumor growth, in vivo.
Conclusion: These data identify LonP1 as a key effector of mitochondrial reprogramming in cancer and potential therapeutic target.
Citation Format: Jagadish C. ghosh, Jae Ho Seo, Ekta Agarwal, Yuan Wang, Andrew V. Kossenkov, Hsin-Yao Tang, David W. Speicher, Dario C. Altieri. Akt phosphorylation of mitochondrial Lonp1 protease enables oxidative metabolism and advanced tumor traits [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 1457.
Abstract 1475: Blockade of IL17-GCSF-Bv8 inflammation axis ameliorate resistant to anti-angiogenic therapy for colon cancer
Authors: Itatani Yoshiro , Yamamoto Takamasa , Ferrara Napoleone 
Published: September 2020

Abstract
Anti-angiogenic therapy in combination with chemotherapy is one of the standard strategies for metastatic/unresectable colon cancers. Therefore, resistance to anti-angiogenic therapy causes a critical problem for the treatment of colon cancer patients. While some resistant mechanisms of anti-angiogenic therapy were proposed, it is not yet completely unveiled. The aim of this study was to investigate the resistant mechanism against anti-angiogenic therapy using spontaneous colon cancer mouse models. We established a mouse model of anti-VEGF resistant colon cancer. Genetically-engineered Apc/Smad4 knockout mice developed several intestinal tumors that are sensitive to anti-VEGF neutralizing antibody. When Apc/Smad4 mice were treated with dextran sulfate sodium (DSS) (DSS-Apc/Smad4 mice), they developed colon tumors that were resistant to anti-VEGF antibody. Sera from DSS-Apc/Smad4 mice showed significant upregulation of granulocyte-colony stimulating factor (GCSF) compared to water-drinking Apc/Smad4 mice. Colon tumors from DSS-Apc/Smad4 mice also showed GCSF upregulation. It also showed upregulation of IL17, one of inflammatory cytokines upstream of GCSF, and Bv8, one of angiogenic factors downstream of GCSF, suggesting that IL17-GCSF-Bv8 inflammation axis contributes to obtaining anti-VEGF resistant. Immunostaining of the tumors from DSS-Apc/Smad4 mice revealed significant accumulation of neutrophils in the tumors. Neutrophils from tumor-bearing mice showed upregulation of Bv8 expression when stimulated with GCSF. Immunostaining confirmed that neutrophils in the tumors were positive for Bv8. When DSS-Apc/Smad4 mice were treated with either anti-IL17, anti-GCSF, or anti-BV8 neutralizing antibody in combination with anti-VEGF antibody, colonic tumor formation was significantly suppressed. We also performed ELISA analysis using human serum samples from subcohort of AVF2107 trial in which metastatic colon cancer patients were treated with chemotherapy (IFL with or without bevacizumab). Higher Bv8 serum levels by ELISA were significantly correlated with poor overall survival in human colon cancer patients. Collectively, inflammatory neutrophils in the tumor microenvironment of colon cancer provide anti-VEGF resistant through IL17-GCSF-Bv8 axis, and blockade of this pathway ameliorate resistance to anti-angiogenic therapy of colon cancer mouse models.
Citation Format: Yoshiro Itatani, Takamasa Yamamoto, Napoleone Ferrara. Blockade of IL17-GCSF-Bv8 inflammation axis ameliorate resistant to anti-angiogenic therapy for colon 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 1475.
Abstract 1495: A transcriptional lineage tracing approach to unravel crucial gene expression patterns in breast cancer progression
Authors: Roda Niccolò , Hillje Roman , Gambino Valentina , Cheloni Stefano , Falvo Paolo , Tirelli Andrea , Bertolini Francesco , Pelicci Pier Giuseppe 
Published: September 2020

Abstract
Breast cancer represents a major clinical hurdle, with intra-tumor heterogeneity and metastatic outcome accounting both for poor prognosis and therapeutic failure. Traditionally, its poly-clonal structure has been investigated through the genetic barcoding of cells followed by the tracing of the offspring. However, this analysis does not allow a solid investigation of the transcriptional profile associated to clones throughout tumor progression. In this work, we exploited a recently published library of expressed barcodes to perform both clonal and trancriptional tracing in breast cancer by single-cell RNA sequencing. To this aim, human breast cancer cell line MDA-MB-231 was transduced with the above mentioned library and orthotopically transplanted in immune-deficient mice. To analyze our data we generated a pipeline aimed at identifying the barcodes at single-cell level and subsequently sequenced more than 20000 cells.Our clonal distribution analysis strongly suggested that clones within the same tumor possess different proliferative potential. Additionally, we found that breast tumors show transcriptional intra-clonal heterogeneity, since cells within the same clone display multiple transcriptional patterns. Notably, clones similar in terms of proliferative potential show profound differences in the transcriptomic profile and in the upregulated pathways. All these results represent a launching pad for further experiments aimed at identifying the transcriptional determinants involved in the spreading of breast cancer clones and in the metastatic progression.
Citation Format: Niccolò Roda, Roman Hillje, Valentina Gambino, Stefano Cheloni, Paolo Falvo, Andrea Tirelli, Francesco Bertolini, Pier Giuseppe Pelicci. A transcriptional lineage tracing approach to unravel crucial gene expression patterns in breast cancer progression [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 1495.
Abstract 152: SOX2-mediated 5hmC dysregulation in GBM stem cells
Authors: Lopez-Bertoni Hernando M. 
Published: September 2020

Abstract
Primary brain tumors are among the most devastating forms of cancer and glioblastoma (GBM) represents the most aggressive and lethal form of the disease. We now know that GBM contain small subsets of cells that display tumor-propagating stem-like phenotypes (i.e. glioma stem cells or GSCs) that act as critical determinants of GBM resistance to current treatments and tumor recurrence for which there is no proven therapy. Altered patterns of DNA methylation are widely reported in human GBM. However, substantial knowledge gaps remain in our understanding of the molecular mechanisms responsible for this epigenetic dysregulation, its downstream consequences and role in the GBM tumor propagating phenotype. Understanding and ultimately targeting the epigenetic mechanisms that induce and maintain these tumor-propagating cell subsets is critical to improving GBM therapy and patient outcomes.
DNA methylation generally occurs in cytosine-guanine (CpG) sequences and is established by DNMTs, which catalyze the conversion of cytosine to 5-methylcytosine (5mC). DNA methylation is a reversible process and is partially mediated by the ten-eleven translocation (TET) family of enzymes which function as deoxygenases to catalyze the conversion of 5mC to 5-hydroxymethylcytosine (5hmC). Multiple studies found negative correlations between 5hmC levels and glioma grade and loss of 5hmC correlates with poor prognosis of GBM patients. TET enzymes and regulation of 5mC and 5hmC have the capacity to function on a global scale to regulate tumor suppressing mechanisms.
We have found that SOX2 represses the TET2 demethylase and decreases 5hmC, the enzymatic product catalyzed by TET proteins, in GSCs. TET2 repression using 2 independent shRNA hairpins efficiently decreases 5hmc levels and significantly enhances self-renewal capacity and tumor growth capacity of low-passage GSC isolates. We also show that SOX2 induces expression of miR-10b-5p, a known onco-miR predicted to target TET2, and inhibiting this miRNA rescued the reduction in 5hmC expression observed in GSCs, thus identifying miR-10b-5p as a critical mediator of SOX2-induced onco-methylation, GSC induction and glioma malignancy. Our results identify a novel targetable pathway by which SOX2 regulates the epigenetic landscape of GBM-propagating cells. This novel mechanism combined with our recent reports that SOX2 regulates DNMTs and the HMGA1 chromatin remodeling protein identified a multi-dimensional epigenetic mechanism by which oncogenic signals control GBM cell stemness and tumor propagation.
Citation Format: Hernando M. Lopez-Bertoni. SOX2-mediated 5hmC dysregulation in GBM stem 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 152.
Abstract 1545: IGF2BP2 over-expression induces epithelial mesenchymal transition & promotes tumor progression in ESCC cells
Authors: Li Pei , HU Xuan-Yu , Liu Xing-Ge , Sha Bei-Bei , DU Ying , CHEN Ping 
Published: September 2020

Abstract
Esophageal cancer (EC) is a common form of malignant tumor with high morbidity & mortality worldwide. IGF2BP2/ IMP2 (insulin-like growth factor 2 mRNA binding protein 2) belongs to a large family of RBPs (RNA binding proteins) that coordinates the export, trafficking, precise localization and translation of RNA in cells. Analysis of TCGA data (results from GEPIA, http://gepia.cancer-pku.cn/) showed that IGF2BP2 over-expressed in ESCA and many other types of human cancers. However, whether and how IGF2BP2 affects EC progression is still unclear. In this study, the expression of IGF2BP2 in esophageal squamous cancer cell lines and normal esophageal epithelial cells(Het) were investigated to explore the relationship between IGF2BP2 and epithelial-mesenchymal transition(EMT)in the ESCC. Methods: IGF2BP2 was knocked down in the Kyse150 cells by siRNA while upregulated by infection lentivirus with IGF2BP2 cDNA in the Eca109 cells. Then Western blotting was used to detect the protein expression of IGF2BP2, p38, P-p38, ERK and EMT markers in these cells. Results: In this study, the results showed that the expression of the epithelial marker, E-cadherin protein increased and the mesenchymal markers, N-cadherin, Snail, and Slug protein decreased after IGF2BP2 knockdown in Kyse150 cells. Meanwhile, the EMT features were promoted in the Eca109 cell after IGF2BP2 upregulation, shown as a reduction in epithelial marker E-cadherin with an increase in mesenchymal markers: N-cadherin, Snail, and Slug. Results from Western blotting showed that IGF2BP2 protein expression was independent of p38 and ERK protein levels. Conclusion: These data indicated that IGF2BP2 could promote the process of EMT in ESCC cells and might serve as a new therapeutic target for the treatment of esophageal cancer. Keywords: IGF2BP2; esophageal cancer; EMT
Citation Format: Pei Li, Xuan-Yu HU, Xing-Ge Liu, Bei-Bei Sha, Ying DU, Ping CHEN. IGF2BP2 over-expression induces epithelial mesenchymal transition & promotes tumor progression in ESCC 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 1545.