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https://www.readbyqxmd.com/read/28440475/a-nine-mirna-signature-as-a-potential-diagnostic-marker-for-breast-carcinoma-an-integrated-study-of-1-110-cases
#1
Dan-Dan Xiong, Jun Lv, Kang-Lai Wei, Zhen-Bo Feng, Ji-Tian Chen, Ke-Cheng Liu, Gang Chen, Dian-Zhong Luo
Growing evidence indicates that microRNAs (miRNAs) play critical roles in the initiation and progression of breast carcinoma (BC) and are promising diagnostic biomarkers. In the present study, we aimed to identify a multi-marker miRNA pool with high diagnostic performance for BC. We collected miRNA expression profiles of BC samples and normal breast tissues from The Cancer Genome Atlas (TCGA) and screened differentially expressed miRNAs by conducting two‑sample t-tests and by calculating log2 fold-change (log2FC) ratios...
April 25, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28440066/elevated-glypican-1-expression-is-associated-with-an-unfavorable-prognosis-in-pancreatic-ductal-adenocarcinoma
#2
Haizhen Lu, Fangfei Niu, Fang Liu, Jiajia Gao, Yulin Sun, Xiaohang Zhao
Pancreatic ductal adenocarcinoma (PDAC) is the most lethal cancer in humans, with a 5-year survival rate of <5%. Recently, glypican-1 (GPC1)-expressing circulating exosomes were found to be a promising diagnostic tool for PDAC. However, the aberrant expression of GPC1 has not been systematically evaluated in large-scale clinical samples of PDAC. Here, we performed a comprehensive analysis of GPC1 mRNA and protein expression features. Included in this study were 178 PDAC patients from the cancer genome atlas (TCGA) and 186 subjects whose tissues were used in immunohistochemical staining assays...
April 24, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28439082/expression-of-nestin-associates-with-brca1-mutations-a-basal-like-phenotype-and-aggressive-breast-cancer
#3
Kristi Krüger, Elisabeth Wik, Gøril Knutsvik, Hawa Nalwoga, Tor A Klingen, Jarle B Arnes, Ying Chen, Monica Mannelqvist, Konstantina Dimitrakopoulou, Ingunn M Stefansson, Even Birkeland, Turid Aas, Nicholas P Tobin, Inge Jonassen, Jonas Bergh, William D Foulkes, Lars A Akslen
We here examined whether Nestin, by protein and mRNA levels, could be a predictor of BRCA1 related breast cancer, a basal-like phenotype, and aggressive tumours. Immunohistochemical staining of Nestin was done in independent breast cancer hospital cohorts (Series I-V, total 1257 cases). Also, TCGA proteomic data (n = 103), mRNA microarray data from TCGA (n = 520), METABRIC (n = 1992), and 6 open access breast cancer datasets (n = 1908) were analysed. Patients with Nestin protein expression in tumour cells more often had BRCA1 germline mutations (OR 8...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28430799/diagnostic-and-prognostic-value-of-long-noncoding-rnas-as-biomarkers-in-urothelial-carcinoma
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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/28423580/procollagen-lysine-2-oxoglutarate-5-dioxygenase-2-promotes-hypoxia-induced-glioma-migration-and-invasion
#16
Yangyang Xu, Lin Zhang, Yuzhen Wei, Xin Zhang, Ran Xu, Mingzhi Han, Bing Huang, Anjing Chen, Wenjie Li, Qing Zhang, Gang Li, Jian Wang, Peng Zhao, Xingang Li
Poor prognosis of glioblastoma multiforme is strongly associated with the ability of tumor cells to invade the brain parenchyma, which is believed to be the major factor responsible for glioblastoma recurrence. Therefore, identifying the molecular mechanisms driving invasion may lead to the development of improved therapies for glioblastoma patients. Here, we investigated the role of procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 (PLOD2), an enzyme catalyzing collagen cross-linking, in the biology of glioblastoma invasion...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423541/rna-sequencing-analysis-reveals-protective-role-of-kruppel-like-factor-3-in-colorectal-cancer
#17
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
#18
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
#19
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
#20
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
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