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https://www.readbyqxmd.com/read/28926105/loss-of-runx1-is-associated-with-aggressive-lung-adenocarcinomas
#1
Jon Ramsey, Kelly Butnor, Zhihua Peng, Tim Leclair, Jos van der Velden, Gary Stein, Jane Lian, C Matthew Kinsey
The mammalian runt-related factor 1 (RUNX1) is a master transcription factor that regulates lineage specification of hematopoietic stem cells. RUNX1 translocations result in the development of myeloid leukemias. Recently, RUNX1 has been implicated as a tumor suppressor in other cancers. We postulated RUNX1 expression may be associated with lung adenocarcinoma etiology and/or progression. We evaluated the association of RUNX1 mRNA expression with overall survival data from The Cancer Genome Atlas (TCGA), a publically available database...
September 19, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28923030/the-eef1a2-gene-expression-as-risk-predictor-in-localized-prostate-cancer
#2
Thomas Stefan Worst, Frank Waldbillig, Abdallah Abdelhadi, Cleo-Aron Weis, Maria Gottschalt, Annette Steidler, Jost von Hardenberg, Maurice Stephan Michel, Philipp Erben
BACKGROUND: Besides clinical stage and Gleason score, risk-stratification of prostate cancer in the pretherapeutic setting mainly relies on the serum PSA level. Yet, this is associated with many uncertainties. With regard to therapy decision-making, additional markers are needed to allow an exact risk prediction. Eukaryotic translation elongation factor 1 alpha 2 (EEF1A2) was previously suggested as driver of tumor progression and potential biomarker. In the present study its functional and prognostic relevance in prostate cancer was investigated...
September 18, 2017: BMC Urology
https://www.readbyqxmd.com/read/28922552/an-individualized-gene-expression-signature-for-prediction-of-lung-adenocarcinoma-metastases
#3
Lishuang Qi, Tianhao Li, Gengen Shi, Jiasheng Wang, Xin Li, Sainan Zhang, Libin Chen, Yuan Qin, Yunyan Gu, Wenyuan Zhao, Zheng Guo
Our laboratory previously reported an individual-level signature consisting of nine gene pairs, named 9-GPS. This signature was developed by training on microarray expression data and validated using three independent integrated microarray data sets, with samples of stage I non-small cell lung cancer after complete surgical resection. In this study, we first validated the cross-platform robustness of 9-GPS by demonstrating that 9-GPS could significantly stratify the overall survival of 213 stage I lung adenocarcinoma (LUAD) patients detected with RNA-sequencing platform in The Cancer Genome Atlas (log-rank p = 0...
September 18, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28921531/a-naive-bayes-algorithm-for-tissue-origin-diagnosis-tod-bayes-of-synchronous-multifocal-tumors-in-the-hepatobiliary-and-pancreatic-system
#4
Weiqin Jiang, Yifei Shen, Yongfeng Ding, Chuyu Ye, Yi Zheng, Peng Zhao, Lulu Liu, Zhou Tong, Linfu Zhou, Shuo Sun, Xingchen Zhang, Lisong Teng, Michael P Timko, Longjiang Fan, Weijia Fang
Synchronous multifocal tumors are common in the hepatobiliary and pancreatic system but because of similarities in their histological features, oncologists have difficulty in identifying their precise tissue clonal origin through routine histopathological methods. To address this problem and assist in more precise diagnosis, we developed a computational approach for tissue origin diagnosis based on naive Bayes algorithm (TOD-Bayes) using ubiquitous RNA-Seq data. Massive tissue-specific RNA-Seq data sets were first obtained from The Cancer Genome Atlas (TCGA) and ∼1,000 feature genes were used to train and validate the TOD-Bayes algorithm...
September 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28919992/molecular-and-clinical-characterization-of-tim-3-in-glioma-through-1-024-samples
#5
Guanzhang Li, Zheng Wang, Chuanbao Zhang, Xing Liu, Jinquan Cai, Zhiliang Wang, Huimin Hu, Fan Wu, Zhaoshi Bao, Yanwei Liu, Liang Zhao, Tingyu Liang, Fan Yang, Ruoyu Huang, Wei Zhang, Tao Jiang
Background: Researches on immunotherapy of glioma has been increasing exponentially in recent years. However, autoimmune-like side effects of current immune checkpoint blockade hindered the clinical application of immunotherapy in glioma. The discovery of the TIM-3, a tumor-specific immune checkpoint, has shed a new light on solution of this dilemma. We aimed at investigating the role of TIM-3 at transcriptome level and its relationship with clinical practice in glioma. Methods: A cohort of 325 glioma patients with RNA-seq data from Chinese Glioma Genome Atlas (CGGA project) was analyzed, and the results were well validated in TCGA RNA-seq data of 699 gliomas...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28918459/hla-class-i-expression-predicts-prognosis-and-therapeutic-benefits-from-tyrosine-kinase-inhibitors-in-metastatic-renal-cell-carcinoma-patients
#6
Jiajun Wang, Li Liu, Yang Qu, Wei Xi, Yu Xia, Qi Bai, Ying Xiong, Qilai Long, Jiejie Xu, Jianming Guo
PURPOSE: Classical HLA class I antigen is highly involved in antigen presentation and adaptive immune response against tumor. In this study, we explored its predictive value for treatment response and survival in metastatic renal-cell carcinoma (mRCC) patients. EXPERIMENTAL DESIGN: A TKI cohort of 111 mRCC patients treated with sunitinib or sorafenib and a non-TKI cohort of 160 mRCC patients treated with interleukin-2 or interferon-α-based immunotherapy at a single institution were retrospectively enrolled...
September 16, 2017: Cancer Immunology, Immunotherapy: CII
https://www.readbyqxmd.com/read/28915554/resistance-to-ctla-4-checkpoint-inhibition-reversed-through-selective-elimination-of-granulocytic-myeloid-cells
#7
Paul E Clavijo, Ellen C Moore, Jianhong Chen, Ruth J Davis, Jay Friedman, Young Kim, Carter Van Waes, Zhong Chen, Clint T Allen
PURPOSE: Local immunosuppression remains a critical problem that limits clinically meaningful response to checkpoint inhibition in patients with head and neck cancer. Here, we assessed the impact of MDSC elimination on responses to CTLA-4 checkpoint inhibition. EXPERIMENTAL DESIGN: Murine syngeneic carcinoma immune infiltrates were characterized by flow cytometry. Granulocytic MDSCs (gMDSCs) were depleted and T-lymphocyte antigen-specific responses were measured...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915052/mass-spectrometric-analysis-of-sox11-binding-proteins-in-head-and-neck-cancer-cells-demonstrates-the-interaction-of-sox11-and-hsp90%C3%AE
#8
Naseim Elzakra, Li Cui, Tong Liu, Hong Li, Junwei Huang, Shen Hu
Deregulated expression of SOX11 has been shown to involve in the progression of various types of cancer. However, the role of SOX11 in head and neck cancer remains largely unknown. In this study, co-immunoprecipitation (Co-IP) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were performed to identify the proteins that binds to SOX11 at significant higher levels in head and neck cancer cells compared to the normal human oral keratinocytes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that many potential SOX11-binding partners were associated with protein synthesis, cell metabolism and cell-cell adhesion...
September 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28914394/bioinformatics-based-identification-of-methylated-differentially-expressed-genes-and-related-pathways-in-gastric-cancer
#9
Hao Li, Jing-Wei Liu, Shuang Liu, Yuan Yuan, Li-Ping Sun
BACKGROUND AND AIMS: The aim of the study was to identify methylated-differentially expressed genes (MDEGs) in gastric cancer and investigate their potential pathways. METHODS: Expression profiling (GSE13911 and GSE29272) and methylation profiling (GSE25869 and GSE30601) data were obtained from GEO DataSets. Differentially expressed genes and differentially methylated genes were identified using GEO2R. Gene ontology and pathway enrichment analyses were performed for the MDEGs...
September 15, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28913902/analysis-of-cancer-gene-expression-data-with-an-assisted-robust-marker-identification-approach
#10
Hao Chai, Xingjie Shi, Qingzhao Zhang, Qing Zhao, Yuan Huang, Shuangge Ma
Gene expression (GE) studies have been playing a critical role in cancer research. Despite tremendous effort, the analysis results are still often unsatisfactory, because of the weak signals and high data dimensionality. Analysis is often further challenged by the long-tailed distributions of the outcome variables. In recent multidimensional studies, data have been collected on GEs as well as their regulators (e.g., copy number alterations (CNAs), methylation, and microRNAs), which can provide additional information on the associations between GEs and cancer outcomes...
September 14, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28912897/genomic-analysis-of-tumor-microenvironment-immune-types-across-14-solid-cancer-types-immunotherapeutic-implications
#11
Yu-Pei Chen, Yu Zhang, Jia-Wei Lv, Ying-Qin Li, Ya-Qin Wang, Qing-Mei He, Xiao-Jing Yang, Ying Sun, Yan-Ping Mao, Jing-Ping Yun, Na Liu, Jun Ma
We performed a comprehensive immuno-genomic analysis of tumor microenvironment immune types (TMITs), which is classified into four groups based on PD-L1+CD8A or PD-L1+cytolytic activity (CYT) expression, across a broad spectrum of solid tumors in order to help identify patients who will benefit from anti- PD-1/PD-L1 therapy. The mRNA sequencing data from The Cancer Genome Atlas (TCGA) of 14 solid cancer types representing 6,685 tumor samples was analyzed. TMIT was classified only for those tumor types that both PD-L1 and CD8A/CYT could prefict mutation and/or neoantigen number...
2017: Theranostics
https://www.readbyqxmd.com/read/28912488/gene-expression-and-methylation-analyses-suggest-dctd-as-a-prognostic-factor-in-malignant-glioma
#12
Huimin Hu, Zheng Wang, Mingyang Li, Fan Zeng, Kuanyu Wang, Ruoyu Huang, Haoyuan Wang, Fan Yang, Tingyu Liang, Hua Huang, Tao Jiang
Malignant glioma is the most common brain cancer with dismal outcomes. Individual variation of the patients' survival times is remarkable. Here, we investigated the transcriptome and promoter methylation differences between patients of malignant glioma with short (less than one year) and the patients with long (more than three years) survival in CGGA (Chinese Glioma Genome Atlas), and validated the differences in TCGA (The Cancer Genome Atlas) to identify the genes whose expression levels showed high concordance with prognosis of glioma patients, as well as played an important role in malignant progression...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28912426/deconvolution-of-dna-methylation-identifies-differentially-methylated-gene-regions-on-1p36-across-breast-cancer-subtypes
#13
Alexander J Titus, Gregory P Way, Kevin C Johnson, Brock C Christensen
Breast cancer is a complex disease consisting of four distinct molecular subtypes. DNA methylation-based (DNAm) studies in tumors are complicated further by disease heterogeneity. In the present study, we compared DNAm in breast tumors with normal-adjacent breast samples from The Cancer Genome Atlas (TCGA). We constructed models stratified by tumor stage and PAM50 molecular subtype and performed cell-type reference-free deconvolution to control for cellular heterogeneity. We identified nineteen differentially methylated gene regions (DMGRs) in early stage tumors across eleven genes (AGRN, C1orf170, FAM41C, FLJ39609, HES4, ISG15, KLHL17, NOC2L, PLEKHN1, SAMD11, WASH5P)...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28912017/indoleamine-2-3-dioxygenase-1-increased-in-human-gastric-pre-neoplasia-promotes-inflammation-and-metaplasia-in-mice-and-is-associated-with-type-ii-hypersensitivity-autoimmunity
#14
Mohamad El-Zaatari, Adam J Bass, Reanne Bowlby, Min Zhang, Li-Jyun Syu, Yitian Yang, Helmut Grasberger, Andrew Shreiner, Bei Tan, Shrinivas Bishu, Wai K Leung, Andrea Todisco, Nobuhiko Kamada, Marilia Cascalho, Andrzej A Dlugosz, John Y Kao
BACKGROUND & AIMS: Chronic gastrointestinal inflammation increases the risk of cancer by mechanisms that are not well understood. Indoleamine-2,3-dioxygenase 1 (IDO1) is a heme-binding enzyme that regulates the immune response via catabolization and regulation of tryptophan availability for immune cell uptake. IDO1 expression is increased during the transition from chronic inflammation to gastric metaplasia. We investigated whether IDO1 contributes to the inflammatory response that mediates loss of parietal cells leading to metaplasia...
September 11, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28911108/the-third-restriction-modification-system-from-thermus-aquaticus-yt-1-solving-the-riddle-of-two-taqii-specificities
#15
Piotr M Skowron, Brian P Anton, Edyta Czajkowska, Joanna Zebrowska, Ewa Sulecka, Daria Krefft, Joanna Jezewska-Frackowiak, Olga Zolnierkiewicz, Malgorzata Witkowska, Richard D Morgan, Geoffrey G Wilson, Alexey Fomenkov, Richard J Roberts, Agnieszka Zylicz-Stachula
Two restriction-modification systems have been previously discovered in Thermus aquaticus YT-1. TaqI is a 263-amino acid (aa) Type IIP restriction enzyme that recognizes and cleaves within the symmetric sequence 5'-TCGA-3'. TaqII, in contrast, is a 1105-aa Type IIC restriction-and-modification enzyme, one of a family of Thermus homologs. TaqII was originally reported to recognize two different asymmetric sequences: 5'-GACCGA-3' and 5'-CACCCA-3'. We previously cloned the taqIIRM gene, purified the recombinant protein from Escherichia coli, and showed that TaqII recognizes the 5'-GACCGA-3' sequence only...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28911005/ociad2-suppressed-tumor-growth-and-invasion-via-akt-pathway-in-hepatocelluar-carcinoma
#16
Dan Wu, Xufang Yang, Huiming Peng, Dongmin Guo, Weiling Zhao, Chen Zhao, Xiaobo Zhou
Hepatocellular carcinoma (HCC) is an aggressive tumor and the third leading cause of cancer-related death worldwide. Ovarian carcinoma immunoreactive antigen-like protein 2 (OCIAD2) has been found frequently methylated in various cancers, including HCC. The aim of the present study was to investigate the role of OCIAD2 in HCC progression. We analyzed liver hepatocellular carcinoma patients' data from the Cancer Genome Atlas (TCGA), including data extracted from 371 HCC tissues and 50 adjacent normal liver tissues...
September 1, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28910345/circulating-mrnas-and-mirnas-as-candidate-markers-for-the-diagnosis-and-prognosis-of-prostate-cancer
#17
Marilesia Ferreira de Souza, Hellen Kuasne, Mateus de Camargo Barros-Filho, Heloísa Lizotti Cilião, Fabio Albuquerque Marchi, Paulo Emilio Fuganti, Alexandre Rossi Paschoal, Silvia Regina Rogatto, Ilce Mara de Syllos Cólus
Circulating nucleic acids are found in free form in body fluids and may serve as minimally invasive tools for cancer diagnosis and prognosis. Only a few studies have investigated the potential application of circulating mRNAs and microRNAs (miRNAs) in prostate cancer (PCa). The Cancer Genome Atlas (TCGA) database was used for an in silico analysis to identify circulating mRNA and miRNA as potential markers of PCa. A total of 2,267 genes and 49 miRNAs were differentially expressed between normal and tumor samples...
2017: PloS One
https://www.readbyqxmd.com/read/28903422/cdk4-6-inhibition-is-more-active-against-the-glioblastoma-proneural-subtype
#18
Ming Li, Aizhen Xiao, Desiree Floyd, Inan Olmez, Jeongwu Lee, Jakub Godlewski, Agnieszka Bronisz, Krishna P L Bhat, Erik P Sulman, Ichiro Nakano, Benjamin Purow
Glioblastoma (GBM) is the most common and lethal brain tumor. Gene expression profiling has classified GBM into distinct subtypes, including proneural, mesenchymal, and classical, and identifying therapeutic vulnerabilities of these subtypes is an extremely high priority. We leveraged The Cancer Genome Atlas (TCGA) data, in particular for microRNA expression, to seek druggable core pathways in GBM. The E2F1-regulated miR-17˜92 cluster and its analogs are shown to be highly expressed in proneural GBM and in GSC lines, suggesting the E2F cell cycle pathway might be a key driver in proneural GBM...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28903341/apobec3g-acts-as-a-therapeutic-target-in-mesenchymal-gliomas-by-sensitizing-cells-to-radiation-induced-cell-death
#19
Yu Wang, Shaofang Wu, Siyuan Zheng, Shuzhen Wang, Arjun Wali, Ravesanker Ezhilarasan, Erik P Sulman, Dimpy Koul, W K Alfred Yung
Genomic, transcriptional, and proteomic analyses of brain tumors reveal that subtypes differ in their pathway activity, progression, and response to therapy. We performed an expression profiling of Glioma Initiating Cells (GICs) and comparative analysis between different groups of GICs indicates major variations in gene expression. Hierarchical clustering analysis revealed groups of GICs reflecting their heterogeneity, and among some of the genes as major regulators of mesenchymal phenotype, we identified ABOBEC3G as one of the most discriminating genes in mesenchymal group...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28902365/appl1-promotes-the-migration-of-gastric-cancer-cells-by-regulating-akt2-phosphorylation
#20
Yingxun Liu, Chunli Zhang, Lingyu Zhao, Ning Du, Ni Hou, Tusheng Song, Chen Huang
As a multifunctional adaptor protein, APPL1 (adaptor protein containing pleckstrin homology domain, phosphotyrosine binding domain and a leucine zipper motif 1) is overexpressed in many cancers, and has been implicated in tumorigenesis and tumor progression. The present study investigated the expression of APPL1 in gastric carcinoma and the function in regulating cell migration. We investigated the expression of APPL1 in gastric carcinoma based upon The Cancer Genome Atlas (TCGA) database. The expression of APPL1 in collected gastric carcinoma tissues and cultured cells was measured by qRT-PCR and western blot analysis...
September 5, 2017: International Journal of Oncology
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