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https://www.readbyqxmd.com/read/28430799/diagnostic-and-prognostic-value-of-long-noncoding-rnas-as-biomarkers-in-urothelial-carcinoma
#1
Johanna Droop, Tibor Szarvas, Wolfgang A Schulz, Christian Niedworok, Günter Niegisch, Kathrin Scheckenbach, Michèle J Hoffmann
Many long noncoding RNAs (lncRNAs) are deregulated in cancer and contribute to oncogenesis. In urothelial carcinoma (UC), several lncRNAs have been reported to be overexpressed and proposed as biomarkers. As most reports have not been confirmed independently in large tissue sets, we aimed to validate the diagnostic and prognostic value of lncRNA upregulation in independent cohorts of UC patients. Thus, expression of seven lncRNA candidates (GAS5, H19, linc-UBC1, MALAT1, ncRAN, TUG1, UCA1) was measured by RT-qPCR in cell lines and tissues and correlated to clinicopathological parameters including follow-up data (set 1: N n = 10; T n = 106)...
2017: PloS One
https://www.readbyqxmd.com/read/28430373/a-five-mirna-expression-signature-predicts-survival-in-hepatocellular-carcinoma
#2
Gang Liu, Hui Wang, Jin-Dong Fu, Jing-Ying Liu, Ai-Guo Yan, Yan-Yan Guan
The aim of this study was to identify a microRNA (miRNA) expression signature for predicting HCC (hepatocellular carcinoma) survival. A total of 322 HCC patients in The Cancer Genome Atlas (TCGA) database were randomly divided into training and testing set. miRNAs, associated with survival time in the training set, were identified by using univariate Cox regression analysis. The risk score was formulated based on the expression levels of these miRNAs. Then the miRNA signature was validated in testing set through Kaplan-Meier analysis and log-rank test...
April 21, 2017: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
https://www.readbyqxmd.com/read/28428277/immune-gene-expression-is-associated-with-genomic-aberrations-in-breast-cancer
#3
Anton Safonov, Tingting Jiang, Giampaolo Bianchini, Balázs Győrffy, Thomas Karn, Christos Hatzis, Lajos Pusztai
The presence of tumor-infiltrating lymphocytes (TIL) is a favorable prognostic factor in breast cancer, but what drives immune infiltration remains unknown. Here we examine if clonal heterogeneity, total mutation load, neoantigen load, copy number variations (CNV), gene- or pathway-level somatic mutations, or germline polymorphisms (SNP) are associated with immune metagene expression in breast cancer subtypes. Thirteen published immune metagenes correlated separately with genomic metrics in the 3 major breast cancer subtypes...
April 20, 2017: Cancer Research
https://www.readbyqxmd.com/read/28427506/recent-advances-in-genitourinary-tumors-a-review-focused-on-biology-and-systemic-treatment
#4
REVIEW
Aránzazu González Del Alba, José Ángel Arranz, Javier Puente, María José Méndez-Vidal, Enrique Gallardo, Enrique Grande, Begoña Pérez-Valderrama, Enrique González-Billalabeitia, Martín Lázaro-Quintela, Álvaro Pinto, Nuria Lainez, Josep M Piulats, Emilio Esteban, José Pablo Maroto Rey, Jorge A García, Cristina Suárez
Updated information published up to 2016 regarding major advances in renal cancer, bladder cancer, and prostate cancer is here presented. Based on an ever better understanding of the genetic and molecular alterations that govern the initial pathogenic mechanisms of tumor oncogenesis, an improvement in the characterization and treatment of urologic tumors has been achieved in the past year. According to the Cancer Genome Atlas (ATLAS) project, alterations in the MET pathway are characteristics of type 1 papillary renal cell carcinomas, and activation of NRF2-ARE pathway is associated with the biologically distinct type 2...
May 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/28427185/transcriptional-landscape-of-human-cancers
#5
Mengyuan Li, Qingrong Sun, Xiaosheng Wang
The homogeneity and heterogeneity in somatic mutations, copy number alterations and methylation across different cancer types have been extensively explored. However, the related exploration based on transcriptome data is lacking. In this study we explored gene expression profiles across 33 human cancer types using The Cancer Genome Atlas (TCGA) data. We identified consistently upregulated genes (such as E2F1, EZH2, FOXM1, MYBL2, PLK1, TTK, AURKA/B and BUB1) and consistently downregulated genes (such as SCARA5, MYOM1, NKAPL, PEG3, USP2, SLC5A7 and HMGCLL1) across various cancers...
March 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28427146/microrna-200c-141-upregulates-serpinb2-to-promote-breast-cancer-cell-metastasis-and-reduce-patient-survival
#6
Tiefeng Jin, Hoe Suk Kim, Sul Ki Choi, Eun Hye Hwang, Jisu Woo, Han Suk Ryu, Kwangsoo Kim, Aree Moon, Woo Kyung Moon
The microRNA-200 (miR-200) family is associated with tumor metastasis and poor patient prognosis. We found that miR-200c/141 cluster overexpression upregulated SerpinB2 in the MDA-MB-231 triple-negative (TN) breast cancer cell line. We observed transcription factor (c-Jun, c-Fos, and FosB) upregulation, nuclear localization of c-Jun, and increased SerpinB2 promoter-directed chloramphenicol acetyltransferase activity in miR-200c/141 cluster-overexpressing cells relative to controls. Additionally, miR-124a and miR-26b, which directly target SepinB2, were downregulated compared to controls...
February 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28426276/integrative-epigenetic-and-genetic-pan-cancer-somatic-alteration-portraits
#7
Lucas A Salas, Kevin C Johnson, Devin C Koestler, Dylan E O'Sullivan, Brock C Christensen
Genetic and epigenetic alterations are required for carcinogenesis and the mutation burden across tumor types has been investigated. Here, we investigate epigenetic alterations with a novel measure of global DNA methylation dysregulation, the methylation dysregulation index (MDI), across 14 cancer types in The Cancer Genome Atlas (TCGA) database. DNA methylation data-obtained using Illumina HumanMethylation450 BeadChip-was accessed from TCGA. We calculated the MDI in 14 tumor types (n = 5,592 tumors), using adjacent normal tissues (n = 701) from each tumor site...
April 20, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28424903/zcchc12-a-novel-oncogene-in-papillary-thyroid-cancer
#8
Ouchen Wang, Zhouci Zheng, Qingxuan Wang, Yixiang Jin, Wenxu Jin, Yinghao Wang, Endong Chen, Xiaohua Zhang
PURPOSE: Thyroid cancer is the most common endocrine malignancy worldwide. The molecular mechanisms underlying thyroid tumorigenesis remain unclear. Some studies suggested that the ZCCHC12 gene correlates with certain diseases. However, the function of ZCCHC12 in thyroid cancer has yet to be determined. This study investigated the role of the ZCCHC12 gene in papillary thyroid cancer (PTC). METHODS: We conducted a comprehensive analysis of massively parallel whole-transcriptome resequencing of matched PTC tumors and normal tissues in 19 patients...
April 19, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28423671/genome-wide-dna-methylation-analysis-reveals-molecular-subtypes-of-pancreatic-cancer
#9
Nitish Kumar Mishra, Chittibabu Guda
Pancreatic cancer (PC) is the fourth leading cause of cancer deaths in the United States with a five-year patient survival rate of only 6%. Early detection and treatment of this disease is hampered due to lack of reliable diagnostic and prognostic markers. Recent studies have shown that dynamic changes in the global DNA methylation and gene expression patterns play key roles in the PC development; hence, provide valuable insights for better understanding the initiation and progression of PC. In the current study, we used DNA methylation, gene expression, copy number, mutational and clinical data from pancreatic patients...
March 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423653/a-novel-microrna-signature-predicts-survival-in-stomach-adenocarcinoma
#10
Bowen Ding, Xujie Gao, Hui Li, Liren Liu, Xishan Hao
Recent microRNA (miRNA) expression profiling studies suggest the clinical use of miRNAs as potential prognostic biomarkers in various malignancies. In this study, aiming to identify microRNAs with prognostic value for overall survival (OS) in stomach adenocarcinoma (STAD) patients, we analyzed the miRNA expression profiles and the associated clinical characteristics in 380 STAD samples from The Cancer Genome Atlas (TCGA) dataset. An eight-miRNA signature for predicting OS in STAD patients was identified and self-validated by survival analysis and semi-supervised principal components method...
March 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423633/novel-lincrna-slinky-is-a-prognostic-biomarker-in-kidney-cancer
#11
Xue Gong, Zurab Siprashvili, Okyaz Eminaga, Zhewei Shen, Yusuke Sato, Haruki Kume, Yukio Homma, Seishi Ogawa, Paul A Khavari, Jonathan R Pollack, James D Brooks
Clear cell renal cell carcinomas (ccRCC) show a broad range of clinical behavior, and prognostic biomarkers are needed to stratify patients for appropriate management. We sought to determine whether long intergenic non-coding RNAs (lincRNAs) might predict patient survival. Candidate prognostic lincRNAs were identified by mining The Cancer Genome Atlas (TCGA) transcriptome (RNA-seq) data on 466 ccRCC cases (randomized into discovery and validation sets) annotated for ~21,000 lncRNAs. A previously uncharacterized lincRNA, SLINKY (Survival-predictive LINcRNA in KidneY cancer), was the top-ranked prognostic lincRNA, and validated in an independent University of Tokyo cohort (P=0...
March 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423619/cdca2-promotes-lung-adenocarcinoma-cell-proliferation-and-predicts-poor-survival-in-lung-adenocarcinoma-patients
#12
Run Shi, Chunrong Zhang, Yaqin Wu, Xin Wang, Qi Sun, Jing Sun, Wenjie Xia, Gaochao Dong, Anpeng Wang, Feng Jiang, Lin Xu
Cell division cycle associated 2(CDCA2) is overexpressed in neuroblastoma and oral squamous cell carcinoma, and its overexpression positively correlates to tumor progression. However, the biological and clinical significance of CDCA2 in lung adenocarcinoma(LAC) has never been investigated. We determined the expression profile and clinical significance of CDCA2 using The Cancer Genome Atlas(TCGA) and tissue microarray(TMA). Furthermore, we explored the biological function of CDCA2 both in vitro and in vivo. A great upregulation of CDCA2 was observed in LAC tissues compared with adjacent normal tissues...
March 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423541/rna-sequencing-analysis-reveals-protective-role-of-kruppel-like-factor-3-in-colorectal-cancer
#13
Xiaohong Wang, Zhonghua Jiang, Yu Zhang, Xiang Wang, Li Liu, Zhining Fan
The Kruppel-like factor (KLF) family of transcription factors plays an important role in embryonic formation and cancer progression. This study was performed to determine the clinical importance of the KLF family in colorectal cancer (CRC). In total, 361 patients with CRC from The Cancer Genome Atlas (TCGA) cohort were used to comprehensively study the role of the KLF family in CRC. The results were then further validated using an in-house cohort (n=194). Univariate and multivariate Cox proportional hazards models were used to assess the risk factors for survival...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423523/mir-106b-5p-promotes-renal-cell-carcinoma-aggressiveness-and-stem-cell-like-phenotype-by-activating-wnt-%C3%AE-catenin-signalling
#14
Jun Lu, Jin-Huan Wei, Zi-Hao Feng, Zhen-Hua Chen, Yong-Qian Wang, Yong Huang, Yong Fang, Yan-Ping Liang, Jun-Jie Cen, Yi-Hui Pan, Bing Liao, Wen-Fang Chen, Wei Chen, Jun-Hang Luo
PURPOSE: To examine the role of miR-106b-5p in regulating the cancer stem-cell-like phenotype in clear cell renal cell carcinomas (ccRCC). EXPERIMENTAL DESIGN: Real-time PCR was performed to evaluate miR-106b-5p levels in ccRCC cell lines and patients specimens. A series of in vivo and in vitro assays were performed to confirm the effect of miR-106b-5p on ccRCC stemness phenotype. RESULTS: ccRCC cells and tissues expressed more miR-106b-5p than normal controls...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423358/characterization-of-fusion-genes-in-common-and-rare-epithelial-ovarian-cancer-histologic-subtypes
#15
Madalene A Earp, Rama Raghavan, Qian Li, Junqiang Dai, Stacey J Winham, Julie M Cunningham, Yanina Natanzon, Kimberly R Kalli, Xiaonan Hou, S John Weroha, Paul Haluska, Kate Lawrenson, Simon A Gayther, Chen Wang, Ellen L Goode, Brooke L Fridley
Gene fusions play a critical role in some cancers and can serve as important clinical targets. In epithelial ovarian cancer (EOC), the contribution of fusions, especially by histological type, is unclear. We therefore screened for recurrent fusions in a histologically diverse panel of 220 EOCs using RNA sequencing. The Pipeline for RNA-Sequencing Data Analysis (PRADA) was used to identify fusions and allow for comparison with The Cancer Genome Atlas (TCGA) tumors. Associations between fusions and clinical prognosis were evaluated using Cox proportional hazards regression models...
April 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422739/diagnostic-role-of-wnt-pathway-gene-promoter-methylation-in-non-small-cell-lung-cancer
#16
Shunlin Liu, Xiaoying Chen, Ruhua Chen, Jinzhi Wang, Guoliang Zhu, Jianzhong Jiang, Hongwei Wang, Shiwei Duan, Jianan Huang
Wnt signal pathway genes are known to be involved with cancer development. Here we tested the hypothesis whether DNA methylation of genes part of the Wnt signaling pathway could help the diagnosis of non-small cell lung cancer (NSCLC). The methylation levels of SFRP1, SFRP2, WIF1 and PRKCB in 111 NSCLC patients were evaluated by quantitative methylation-specific PCR (qMSP). Promoter methylation levels of four candidate genes were significantly higher in tumor tissues compared with the adjacent tissues. SFRP1, SFRP2 and PRKCB genes were all shown to be good predictors of NSCLC risk (SFRP1: AUC = 0...
March 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422174/high-expression-of-matrix-metalloproteinases-16-is-associated-with-the-aggressive-malignant-behavior-and-poor-survival-outcome-in-colorectal-carcinoma
#17
Shengwen Wu, Congchao Ma, Shaoyin Shan, Lei Zhou, Wenhui Li
Recent evidence suggested an important role of matrix metalloproteinases 16 (MMP16) in the progression of several cancers. However, the contribution of MMP16 to colorectal cancer (CRC) remains elusive. In this study, we combined analyzed the MMP16 expression in The Cancer Genome Atlas (TCGA), GSE39582 database and in-house database. In TCGA and GSE39584 database, the log-rank test demonstrated that overall survival (OS) for patients with low MMP16 expression in tumor tissues was significantly higher than those with high expression (P < 0...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28419078/targeting-of-ccbe1-by-mir-330-3p-in-human-breast-cancer-promotes-metastasis
#18
Aruz Mesci, Xiaoyong Huang, Samira Taeb, Sahar Jahangiri, Yohan Kim, Emmanouil Fokas, Jeff Bruce, Hon S Leong, Stanley K Liu
BACKGROUND: MicroRNAs (miRs) are involved in the regulation of many processes that contribute to malignancy, including cell proliferation, radiation resistance, invasion and metastasis. The role of miR-330-3p, an miR upregulated in breast cancer, remains unclear. METHODS: We examine the association of miR-330-3p with distant relapse-free survival in the Oxford cohort of breast cancer patients. We also study miR-330-3p function using in vitro invasion and ex ovo metastasis assays...
April 18, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28418882/oncogenic-histone-methyltransferase-ezh2-a-novel-prognostic-marker-with-therapeutic-potential-in-endometrial-cancer
#19
Shinya Oki, Kenbun Sone, Katsutoshi Oda, Ryuji Hamamoto, Masako Ikemura, Daichi Maeda, Makoto Takeuchi, Michihiro Tanikawa, Mayuyo Mori-Uchino, Kazunori Nagasaka, Aki Miyasaka, Tomoko Kashiyama, Yuji Ikeda, Takahide Arimoto, Hiroyuki Kuramoto, Osamu Wada-Hiraike, Kei Kawana, Masashi Fukayama, Yutaka Osuga, Tomoyuki Fujii
The histone methyltransferase EZH2, a key epigenetic modifier, is known to be associated with human tumorigenesis. However, the physiological importance of EZH2 and its clinical relevance in endometrial cancer remain unclear. Hence, in the present study, we investigated the expression and function of EZH2 in endometrial cancer. In a quantitative real-time PCR analysis of 11 endometrial cancer cell lines and 52 clinical endometrial cancer specimens, EZH2 was significantly overexpressed in cancer cells and tissues compared to that in corresponding normal control cells and tissues...
March 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28418867/early-detection-of-gastric-cancer-using-global-genome-wide-and-irf4-elmo1-clip4-and-msc-dna-methylation-in-endoscopic-biopsies
#20
Francesca Pirini, Sassan Noazin, Martha H Jahuira-Arias, Sebastian Rodriguez-Torres, Leah Friess, Christina Michailidi, Jaime Cok, Juan Combe, Gloria Vargas, William Prado, Ethan Soudry, Jimena Pérez, Tikki Yudin, Andrea Mancinelli, Helen Unger, Carmen Ili-Gangas, Priscilla Brebi-Mieville, Douglas E Berg, Masamichi Hayashi, David Sidransky, Robert H Gilman, Rafael Guerrero-Preston
Clinically useful molecular tools to triage gastric cancer patients are not currently available. We aimed to develop a molecular tool to predict gastric cancer risk in endoscopy-driven biopsies obtained from high-risk gastric cancer clinics in low resource settings.We discovered and validated a DNA methylation biomarker panel in endoscopic samples obtained from 362 patients seen between 2004 and 2009 in three high-risk gastric cancer clinics in Lima, Perú, and validated it in 306 samples from the Cancer Genome Atlas project ("TCGA")...
March 16, 2017: Oncotarget
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