bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 150: Establishment of diagnostic criteria for upper urinary tract urothelial carcinoma based on genome-wide DNA methylation analysis
Authors: Fujimoto Mao , Arai Eri , Tsumura Koji , Yotani Takuya , Yamada Yuriko , Takahashi Yoriko , Maeshima Akiko Miyagi , Fujimoto Hiroyuki , Yoshida Teruhiko , Kanai Yae 
Published: September 2020

Abstract
For diagnosis of upper urinary tract urothelial carcinoma (UTUC), retrograde ureteropyelography and ureteroscopy are invasive, and selective urine cytology has insufficient sensitivity and specificity. The aim of this study was to establish a less invasive and more accurate method for UTUC diagnosis based on genome-wide DNA methylation profiling. Single-CpG resolution genome-wide DNA methylation screening was performed using the Infinium assay, and DNA methylation quantification was verified using pyrosequencing. We analyzed 26 samples of normal control urothelial tissue (C), an initial cohort of 62 samples (31 samples of non-cancerous urothelium [N] from UTUC patients and 31 samples of the corresponding UTUCs), a validation cohort of 82 samples (41 N and 41 UTUC samples), and 14 samples of urinary bladder urothelial carcinoma (BUC). In the initial cohort, we identified 2,448 CpG sites showing significant differences in DNA methylation levels between both C and UTUC and N and UTUC, but not showing differences between C and N. Among these CpG sites, 10 were located within CpG islands or their shores and shelves included in genomic domains where DNA methylation levels are stably controlled, allowing discrimination of UTUC even from BUC. Receiver operating characteristic curve analysis for discrimination of UTUC from N in these 10 CpG and neighboring sites (37 diagnostic panels in total) yielded area under the curve values of 0.959-1.000, with a sensitivity and specificity of 86.6-100% and 93.5-100%, respectively. The reliability of the established criteria was successfully confirmed in the validation cohort. Application of our criteria to voided urine samples will ultimately allow non-invasive and reliable DNA methylation diagnosis of UTUC using an appropriate DNA methylation quantification system such as high-performance liquid chromatography.
Citation Format: Mao Fujimoto, Eri Arai, Koji Tsumura, Takuya Yotani, Yuriko Yamada, Yoriko Takahashi, Akiko Miyagi Maeshima, Hiroyuki Fujimoto, Teruhiko Yoshida, Yae Kanai. Establishment of diagnostic criteria for upper urinary tract urothelial carcinoma based on genome-wide DNA methylation analysis [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 150.
Abstract 1500: Understanding tumor cell community and its evolution by single cell analysis in liver cancer
Authors: Ma Lichun , Hernandez Maria O. , Zhao Yongmei , Mehta Monika , Tran Bao , Kelly Michael , Rae Zachary , Hernandez Jonathan M. , Davis Jeremy L. , Martin Sean P. , Kleiner David E. , Hewitt Stephen M. , Ylaya Kris , Wood Bradford J. , Greten Tim F. , Wang Xin Wei 
Published: September 2020

Abstract
Tumor cell biodiversity is a major contributing factor to therapeutic failures and lethal outcomes of solid malignancies. Primary liver cancer, comprising mainly hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), is the second most lethal malignancy worldwide. To understand the biodiversity of tumor cell community in liver cancer, we performed single-cell transcriptome profiling of primary HCC and iCCA from 19 patients, who were enrolled at the NIH Clinical Center for immune checkpoint inhibition clinical trials. We found malignant cells differed within and between tumors, indicating both intratumor and intertumor heterogeneity. We developed a method to measure intratumor heterogeneity. Strikingly, the degree of intratumor diversity was associated with patient outcome where tumors with high diversity was associated with poor prognosis while tumors with low diversity was linked to good prognosis. The link between intratumor diversity and patient prognosis was also observed in bulk genomic and transcriptomic profiles for hundreds of HCC as well as iCCA patients. We found a polarization of the diverse landscapes of tumor microenvironment (TME) from low diversity and high diversity tumors. By searching upstream regulators of TME, we found an increased VEGF expression in high diversity tumors linked to diversity-related polarization of stromal and immune cells. Additionally, tumor evolutionary trajectory was uncovered by single-cell transcriptomic profiles generated from tumor biopsies collected from patients at baseline and after treatment with immune checkpoint inhibitors. Our results offer insight into the diverse ecosystem of HCC and iCCA and determine an impact of tumor cell biodiversity on patient prognosis, which may further benefit the prediction of clinical response to immune therapy.
Citation Format: Lichun Ma, Maria O. Hernandez, Yongmei Zhao, Monika Mehta, Bao Tran, Michael Kelly, Zachary Rae, Jonathan M. Hernandez, Jeremy L. Davis, Sean P. Martin, David E. Kleiner, Stephen M. Hewitt, Kris Ylaya, Bradford J. Wood, Tim F. Greten, Xin Wei Wang. Understanding tumor cell community and its evolution by single cell analysis in liver 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 1500.
Abstract 1520: RAB31 triggers oxaliplatin resistance in colorectal cancer via epithelial-mesenchymal transition
Authors: Chen Chi-Long , Chang Yu-Chan , Hsiao Michael 
Published: September 2020

Abstract
Colorectal tumorigenesis during Epithelial-Mesenchymal transition (EMT) is associated with cancer metastasis and drug resistance. The small G-proteins family has been implicated in the regulation of cell cytoskeleton, cell movement, and vesicle transport. Small G-proteins family is divided into five main families. The Rab protein family is a member of the Ras superfamily of small G-proteins. We analyzed all probes of the Rab family members from microarray datasets and RNA-sequencing. We further calculated the EMT scores by using an algorithm. Our results showed that the RAB31 expression levels of the three probes are positively correlated with EMT score (Pearson rho=0.72, 0.71 and 0.68, respectively). Compared with other family members, RAB31 had most significantly value in colorectal cancer cell lines. We established several two-way model with cDNA and shRNAs of RAB31, respectively. Furthermore, we observed that the expression of epithelial type marker CDH1 was inhibited, and mesenchymal type markers SNAI1 and SNAI2 were upregulated in RAB31 overexpression models. Moreover, we found that the protein level of RAB31 was correlated with several clinicopathological parameters (N status, M status) and disease-free survival in tissue arrays through immunohistochemistry staining. According to The Cancer Genome Atlas Program (TCGA) and online meta-database, high RNA level of RAB31 was consistent in colorectal cancer (HR=1.38, n=466 and HR=1.29, n=482) and correlated with poor prognosis of patients. In addition, we identified that RAB31 may associated with IC50 of oxaliplatin and EGFR trafficking. We concluded that RAB31 regulates the sensitivity of oxaliplatin, an additional chemotherapy strategy and an independent prognostic factor for colorectal cancer.
Citation Format: Chi-Long Chen, Yu-Chan Chang, Michael Hsiao. RAB31 triggers oxaliplatin resistance in colorectal cancer via epithelial-mesenchymal transition [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 1520.
Abstract 153: Epigenetic loss of NSUN5 in glioma drives a global protein synthesis depletion along with the emergence of a stress adaptive translational program
Authors: Barahona Vanessa Ortiz , Janin Maxime , Esteller Manel 
Published: September 2020

Abstract
One of the known hallmarks of cancer is an aberrant RNA transcriptome, and yet, it cannot always be fully due to genetic or epigenetic alterations at the transcriptional start sites of the genes. Indeed, recent evidences point out to new malignant alterations at the RNA level itself. RNA molecules have been found to show more than 100 differently chemically modified nucleotides, and such post-transcriptional modifications play a role in controlling RNA homeostasis, being all grouped under the term ‘epitranscriptome'. In our study, we reported that human glioma cells undergo DNA methylation-associated epigenetic silencing of NSUN5, a candidate 5-methylcytosine RNA methyltransferase. As NSUN5 activity has not been formally described in human cells yet, we studied its potential targets in the human transcriptome, demonstrating its role in the methylation of the cytosine 3782 in the 28S ribosomal RNA (rRNA). Logically, we found that NSUN5 loss generates an unmethylated status at the C3782 position of 28S rRNA, and this depletion drives an overall depletion of protein synthesis under stress conditions, analyzed by O-propargyl-puromycin (OP-Puro) and [3H] leucine incorporation into nascent proteins. However, together with the depletion of global protein synthesis, we observed the emergence of an adaptive translational program for survival under conditions of cellular stress, assessed by combining three NGS-experiments: RNA-seq, Ribo-seq and SILAC. Moreover, as one of the genes increasing its expression upon NSUN5 silencing is the stress-related enzyme NQO1, we found out that NSUN5-depleted gliomas are sensitive to bioactivatable substrates of the NQO1 enzyme. Most importantly, we observed that NSUN5 epigenetic inactivation is a hallmark of glioma patients with long-term survival, conferring it value as a predictor of better patient outcome for this otherwise devastating disease.
Citation Format: Vanessa Ortiz Barahona, Maxime Janin, Manel Esteller. Epigenetic loss of NSUN5 in glioma drives a global protein synthesis depletion along with the emergence of a stress adaptive translational program [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 153.
Abstract 1534: Vimentin prevents a miR-dependent negative regulation of tissue factor mRNA during epithelial-mesenchymal transitions and facilitates early metastasis
Authors: Vanwynsberghe Aline , Francart Marie-Emilie , Gilles Christine 
Published: September 2020

Abstract
Epithelial-Mesenchymal Transitions (EMTs) are high-profile in the field of circulating tumor cells (CTCs). EMT-shifted CTCs are considered to encompass pre-metastatic subpopulations though underlying molecular mechanisms remain elusive. Our previous work identified Tissue Factor (TF) as an EMT-induced gene providing tumor cells with coagulant properties and supporting metastatic colonization by CTCs. We here report that vimentin, the type III intermediate filament considered a canonical EMT marker, contributes to TF regulation and positively supports coagulant properties and early metastasis. Different evidence further pointed to a new post-transcriptional regulatory mechanism of TF mRNA by vimentin: (i) vimentin silencing accelerated TF mRNA decay after actinomycin-D treatment, reflecting TF mRNA stabilization, (ii) RNA immunoprecipitation revealed enriched levels of TF mRNA in vimentin immunoprecipitate, (iii) TF 3'-UTR-luciferase reporter vector assays implicated the 3'-UTR of TF mRNA in vimentin-dependent TF regulation, and (iv) using different TF 3'UTR luciferase reporter vectors mutated for potential miR binding sites and specific Target Site Blockers identified a key miR binding site in vimentin-dependent TF mRNA regulation. All together, these data support a novel mechanism by which vimentin interferes with a miR-dependent negative regulation of TF mRNA, thereby promoting coagulant activity and early metastasis of vimentin-expressing CTCs.
Citation Format: Aline Vanwynsberghe, Marie-Emilie Francart, Christine Gilles. Vimentin prevents a miR-dependent negative regulation of tissue factor mRNA during epithelial-mesenchymal transitions and facilitates early metastasis [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 1534.
Abstract 1536: MiRNA expression profile of exosomes derived from breast cancer cells following induction of the epithelial-to-mesenchymal transition
Authors: Showalter Christian A. , Huang Yinan , Burdick Monica M. 
Published: September 2020

Abstract
Breast cancer-derived exosomes are small extracellular vesicles that play a crucial role in the metastatic progression of breast cancer due to their ability to transport a variety of biologically active molecules (e.g., miRNAs) to local and distant sites in the body. The molecular cargo transported by breast cancer-derived exosomes alters the transcriptome of recipient cells at these sites to stimulate pro-metastatic events, including the epithelial-to-mesenchymal transition (EMT). Importantly, the molecular cargo loaded into exosomes can vary depending on cell state. However, it is unclear whether the expression of miRNAs in breast cancer-derived exosomes is altered following inducement of the EMT. Regulation of exosomal miRNAs following the EMT may enhance the ability of circulating tumor cells to target specific tissue sites or improve formation and maintenance of metastatic tumors compared to miRNAs packaged into exosomes secreted from cancer cells without induction of the EMT. To address this knowledge gap, we hypothesized that the EMT alters expression of miRNAs in exosomes derived from EMT-induced MDA-MB-468 breast cancer cells. To induce the EMT, MDA-MB-468 cells were treated with exogenous epidermal growth factor. MDA-MB-468 cells treated with epidermal growth factor exhibited greater mRNA expression of the mesenchymal marker Vimentin compared to non-treated MDA-MB-468 cells by qRT-PCR. Subsequently, exosomes were isolated from the conditioned cell culture medium of MDA-MB-468 cells, with and without induction of the EMT, using ExoQuick exosome isolation reagent. Molecular size analysis of isolated exosomes revealed that they were similar in size to the typical size range reported for exosomes (40 - 150nm). Moreover, a common exosomal marker protein, CD9, was enriched in the MDA-MB-468-derived exosome fractions compared to whole cell lysates by Western blot. Furthermore, next generation sequencing and bioinformatic analysis were performed to determine the miRNA expression profiles of these exosomes. Results from this study reveal expression of miRNAs in breast cancer cell-derived exosomes before and after activation of the EMT and may indicate how exosomes secreted from advanced stage breast cancer enhance metastatic tumor progression.
Citation Format: Christian A. Showalter, Yinan Huang, Monica M. Burdick. MiRNA expression profile of exosomes derived from breast cancer cells following induction of the epithelial-to-mesenchymal transition [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 1536.
Abstract 1539: NDRG1 promotes epithelial-mesenchymal transition in lung cancer cells by upregulation of SLUG expression
Authors: Liu En-Chu , Liu Hui-Chia , Chen Jeremy J. M. , Tsai Meng-Feng 
Published: September 2020

Abstract
N-myc down-regulated gene 1 (NDRG1) is a member of the NDRG family which belongs to α/β hydrolase superfamily, but without presenting a hydrolytic catalytic site. NDRG1 gene has been proposed that involved in cellular stress response pathways, including the heavy metal response, hypoxia response, DNA damage response, cellular differentiation, and proliferation. An oncogenic and tumor-promoting role of NDRG1 has been suggested in lung cancer and various malignant cancers. However, the biological functions and downstream molecular mechanisms of NDRG1 gene in lung cancer are still unclear. In this study, we detected the expression of NDRG1 in various lung adenocarcinoma cell lines using quantitative RT-PCR and Western blotting methods. The constitutive NDRG1-expression, and NDRG1-knockdown stable transfectants were established. Over-expression of NDRG1 in lung cancer cells exhibited markedly promoting in the proliferation and anchorage independent growth, whereas reduced of NDRG1 was found to suppress lung cancer cell progression. We also indicated that NDRG1 play an important role in the epithelial-mesenchymal transition (EMT) features, including a morphological change, increased migratory and invasive ability, reduction the epithelial marker expression and up-regulated EMT regulators. In addition, microarray assays were performed to further explore the potential molecular mechanisms of NDRG1 in lung cancer. The candidate NDRG1-regulated genes, including IL11, SOX7, TCF4, IGF2, SLUG and SLIT2, were verified by quantitative RT- PCR. Finally, we demonstrated that NDRG1 induces EMT and invasion process in lung cancer cell through up-regulation SLUG expression. These results will provide information and help us to understand the roles of NDRG1 in lung cancer cells.
Citation Format: En-Chu Liu, Hui-Chia Liu, Jeremy J. M. Chen, Meng-Feng Tsai. NDRG1 promotes epithelial-mesenchymal transition in lung cancer cells by upregulation of SLUG expression [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 1539.
Abstract 1547: LOXL1 is a novel responsible gene for peritoneal dissemination potentially via promoting EMT and motility in gastric cancer
Authors: Hu Qingjiang , Masuda Takaaki , Zaitsu Yoko , Tsuda Yasuo , Hisamatsu Yuichi , Nakashima Yuichiro , Ando Koji , Kimura Yasue , Oki Eiji , Mori Masaki , Mimori Koshi 
Published: September 2020

Abstract
Background. In gastric cancer (GC), peritoneal dissemination (PD) occurs frequently and is incurable. We have identified 25 PD-associated genes in GC by in silico analysis in previous research. In this study, we focused on Lysyl oxidase-like 1 (LOXL1), one of the 25 PD-associated genes, because LOXL1 is a member of the lysyl oxidase (LOX) gene family and may have the ability to promote EMT in GC.
Materials and Methods. We assessed LOXL1 expression using a public GC dataset (GSE15459) and a highly-disseminated peritoneal GC cell line (RT-qPCR). Next, we performed gene expression analysis, including gene set enrichment analysis (GSEA) with two public GC datasets (GSE15459 and TCGA). Moreover, we performed a series of in vitro experiments using GC cells. Finally, we evaluated the clinicopathological significance of LOXL1 expression using RT-qPCR and immunohistochemistry staining in the Kyushu cohort. We also performed survival analyses of LOXL1 expression in the Kyushu cohort, GSE15459, and TCGA datasets.
Results. The expression of LOXL1 was higher in GC patients with PD compared with GC patients without PD in the GSE15459 dataset. LOXL1 was also overexpressed in highly-disseminated peritoneal GC cells relative to its control cells. Moreover, LOXL1 expression positively correlated with the EMT gene set in GSEA. Additionally, LOXL1 overexpression reduced CDH1 expression, increased VIM expression, CDH2 expression, SNAI2 expression, and PLS3 expression, and promoted migration capacity in GC cells. Finally, high LOXL1 expression was associated with poorly-differentiated, lymph node metastasis, and PD in the Kyushu cohort, and was a poor prognostic factor in three GC datasets.
Conclusions. LOXL1 was a novel responsible gene for PD in GC, possibly through the activation of EMT and cell motility.
Citation Format: Qingjiang Hu, Takaaki Masuda, Yoko Zaitsu, Yasuo Tsuda, Yuichi Hisamatsu, Yuichiro Nakashima, Koji Ando, Yasue Kimura, Eiji Oki, Masaki Mori, Koshi Mimori. LOXL1 is a novel responsible gene for peritoneal dissemination potentially via promoting EMT and motility in gastric 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 1547.
Abstract 157: Pervasive promoter hypermethylation of silenced TERT alleles in human cancers
Authors: Graham Mindy K. , Esopi David , Brosnan-Cashman Jacqueline A. , Gupta Anuj , De Marzo Angelo , Nelson William G. , Heaphy Christopher M. , Meeker Alan K. , Wheelan Sarah J. , Yegnasubramanian Srinivasan 
Published: September 2020

Abstract
In cancers, the epigenetic regulation of telomerase expression is not fully characterized, with multiple conflicting reports. In particular, the role of DNA methylation of cytosine residues in the control of TERT expression remains unclear. Here, we have carried out the most comprehensive characterization of TERT promoter methylation using ultra-deep bisulfite sequencing spanning more than 310 CpGs within and surrounding the core TERT promoter in 96 different cell lines, including primary, immortalized, and cancer cell types, as well as in control and reference samples. In general, we observed that immortalized and cancer cell lines were hypermethylated in a region upstream of the recurrent G228A and G250A TERT promoter mutations, while non-malignant primary cells were comparatively hypomethylated in this region. Notably, in cancers, the hypermethylated alleles were associated with repressed expression while remaining unmethylated alleles were enriched with the open chromatin marks, H3K4me3 and H3K27ac. Furthermore, the hypomethylated alleles of the TERT promoter were responsible for the observed TERT expression in cancer. This association of hypomethylated alleles with active expression and hypermethylated alleles with repressed expression is particularly evident in cancers harboring TERT promoter mutations, and cancers displaying allele-specific expression. Reporter assays confirmed that DNA methylation of the TERT promoter greatly suppressed reporter expression in heterologous TERT promoter-reporter constructs. Overall, our findings suggest that hypermethylation of the TERT promoter alleles signals transcriptional repression of those alleles, leading to the attenuation of TERT activation in cancer cells.
Citation Format: Mindy K. Graham, David Esopi, Jacqueline A. Brosnan-Cashman, Anuj Gupta, Angelo De Marzo, William G. Nelson, Christopher M. Heaphy, Alan K. Meeker, Sarah J. Wheelan, Srinivasan Yegnasubramanian. Pervasive promoter hypermethylation of silenced TERT alleles in human 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 157.