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Wei Sun, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M Perou, David Neil Hayes, Mengjie Chen, Dan-Yu Lin
We systematically studied the association between somatic copy number aberration (SCNA), DNA methylation and gene expression using -omic data from The Cancer Genome Atlas (TCGA) on six cancer types: breast cancer, colon cancer, glioblastoma, leukemia, lower-grade glioma and prostate cancer. A major challenge for such integrated study is that the association between DNA methylation and gene expression is severely confounded by tumor purity and cell type composition, which are often unobserved and difficult to estimate...
February 26, 2018: Nucleic Acids Research
Kathrin Oehl, Jelena Kresoja-Rakic, Isabelle Opitz, Bart Vrugt, Walter Weder, Rolf Stahel, Peter Wild, Emanuela Felley-Bosco
Experimental models closely representing in vivo conditions allow investigating mechanisms of resistance. Our aims were to establish a live-cell biobank of malignant pleural mesothelioma (MPM) samples and to obtain proof of principle that primary culture chemoresistant models, mimicking tumor progression observed in patients, can be obtained in vitro , providing a useful tool to investigate underlying mechanisms. Primary mesothelioma cultures were established from 235 samples between 2007 and 2014. Of two MPM patients, primary cultures obtained at different time points: at initial diagnosis, after neoadjuvant treatment at surgery and/or after tumor recurrence, were deeply investigated...
2018: Frontiers in Oncology
Xiaogang Mao, Xiaomin Qin, Lin Li, Jinting Zhou, Min Zhou, Xianxian Li, Ying Xu, Liyun Yuan, Qiong-Na Liu, Hui Xing
Long non-coding RNAs (lncRNAs), which have little or no protein-coding capacity, caught a particular interest since their potential roles in the cancer paradigm. As the most common cancer in women, cervical squamous cell carcinoma remains one of the leading causes of deaths from cancer. However, limited evidence is available to determine the role of lncRNAs in the prognosis of cervical squamous cell carcinoma. In this study, we collected lncRNA expression profiling to identify prognosis related lncRNAs for cervical squamous cell carcinoma from TCGA database...
March 7, 2018: Gynecologic Oncology
Victoria Peyret, Magalí Nazar, Mariano Martin, Amado A Quintar, Elmer A Fernandez, Romina C Geysels, Cesar Fuziwara, María M Montesinos, Cristina A Maldonado, Pilar Santisteban, Edna T Kimura, Claudia G Pellizas, Juan P Nicola, Ana M Masini-Repiso
Emerging evidence suggests that unregulated Toll-like receptors (TLRs) signaling promotes tumor survival signals, thus favoring tumor progression. Here, the mechanism underlying TLR4 overexpression in papillary thyroid carcinomas (PTCs) mainly harboring the BRAFV600E mutation was studied. TLR4 was overexpressed in PTCs compared to non-neoplastic thyroid tissue. Moreover, paired clinical specimens of primary PTC and its lymph node metastasis showed a significant upregulation of TLR4 levels in the metastatic tissues...
March 9, 2018: Molecular Cancer Research: MCR
Mengdi Yang, Yi Sun, Jing Sun, Zhiyu Wang, Yiyi Zhou, Guangyu Yao, Yifeng Gu, Huizhen Zhang, Hui Zhao
Despite recent advances in targeted and immune-based therapies, the poor prognosis of lung adenocarcinoma (LUAD) with bone metastasis (BM) remains a challenge. First, two-dimensional gel electrophoresis (2-DE) was used to identify proteins that were differentially expressed in LUAD with BM, and then matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) was used to identify these proteins. Second, the Cancer Genome Atlas (TCGA) was used to identify mutations in these differentially expressed proteins and Kaplan-Meier plotter (KM Plotter) was used to generate survival curves for the analyzed cases...
March 9, 2018: Cancer Medicine
Li-Ou Han, Xin-Yu Li, Ming-Ming Cao, Yan Cao, Li-Hong Zhou
New molecular signatures are needed to improve the diagnosis of thyroid cancer (TC) and avoid unnecessary surgeries. In this study, we aimed to develop a robust and individualized diagnostic signature in TC. Gene expression profiles of tumor and nontumor samples were from 13 microarray datasets of Gene Expression Omnibus (GEO) database and one RNA-sequencing dataset of The Cancer Genome Atlas (TCGA). A total of 1246 samples were divided into a training set (N = 435), a test set (N = 247), and one independent validation set (N = 564)...
March 9, 2018: Cancer Medicine
Antonin Dréan, Shai Rosenberg, François-Xavier Lejeune, Larissa Goli, Aravindan Arun Nadaradjane, Jérémy Guehennec, Charlotte Schmitt, Maïté Verreault, Franck Bielle, Karima Mokhtari, Sanson Marc, Alexandre Carpentier, Delattre Jean-Yves, Ahmed Idbaih
ATP-binding cassette transporters (ABC transporters) regulate traffic of multiple compounds, including chemotherapeutic agents, through biological membranes. They are expressed by multiple cell types and have been implicated in the drug resistance of some cancer cells. Despite significant research in ABC transporters in the context of many diseases, little is known about their expression and clinical value in glioblastoma (GBM). We analyzed expression of 49 ABC transporters in both commercial and patient-derived GBM cell lines as well as from 51 human GBM tumor biopsies...
March 8, 2018: Journal of Neuro-oncology
Bin Xiao, Weiyun Zhang, Lidan Chen, Jianfeng Hang, Lizhi Wang, Rong Zhang, Yang Liao, Jianyun Chen, Qiang Ma, Zhaohui Sun, Linhai Li
Estrogen receptor-positive (ER+ ) and ER-negative (ER- ) subtypes of breast cancer have distinct clinical outcomes because they respond differentially to endocrine therapies. We aimed to comprehensively analyze differentially expressed microRNA (miRNAs), long non-coding RNAs (lncRNAs) and mRNAs in different ER subtypes as well as to identify prognosis-related RNAs. The expression levels of miRNAs, lncRNAs, and mRNAs between breast cancer and normal samples were compared using data from The Cancer Genome Atlas database...
March 5, 2018: Gene
Constantinos Roufas, Dimitrios Chasiotis, Anestis Makris, Christodoulos Efstathiades, Christos Dimopoulos, Apostolos Zaravinos
Background: Recently, immune-checkpoint blockade has shown striking clinical results in different cancer patients. However, a significant inter-individual and inter-tumor variability exists among different cancers. The expression of the toxins granzyme A (GZMA) and perforin 1 (PRF1), secreted by effector cytotoxic T cells and natural killer (NK) cells, were recently used as a denominator of the intratumoral immune cytolytic activity (CYT). These levels are significantly elevated upon CD8+ T-cell activation as well as during a productive clinical response against immune-checkpoint blockade therapies...
2018: Frontiers in Oncology
Shi-Tong Yu, Qian Zhong, Ren-Hui Chen, Ping Han, Shi-Bing Li, Hua Zhang, Li Yuan, Tian-Liang Xia, Mu-Sheng Zeng, Xiao-Ming Huang
Papillary thyroid carcinoma (PTC) is the one of the most common types of endocrine cancer and has a heterogeneous prognosis. Tumors from patients with poor prognosis may differentially express specific genes. Therefore, an analysis of The Cancer Genome Atlas (TCGA) database was performed and revealed that cytokine receptor-like factor 1 (CRLF1) may be a potential novel target for PTC treatment. The objective of the current study was to explore the expression of CRLF1 in PTC and to investigate the main functions and mechanisms of CRLF1 in PTC...
March 7, 2018: Cell Death & Disease
Hangcheng Fu, Yu Zhu, Yiwei Wang, Zheng Liu, Junyu Zhang, Huyang Xie, Qiang Fu, Bo Dai, Dingwei Ye, Jiejie Xu
PURPOSE: This study aims to construct the stromal immunotype which could improve prediction of postsurgical survival and adjuvant platinum-based chemotherapy in muscle-invasive bladder cancer (MIBC). PATIENTS AND METHODS: A total of 118 MIBC patients from Shanghai Cancer Center, 140 MIBC patients from Zhongshan hospital and 287 MIBC patients from TCGA cohort were included in the study. Immune cell infiltration was evaluated by immunohistochemical staining or CIBERSORT method...
March 7, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Shannon E Ellis, Leonardo Collado-Torres, Andrew Jaffe, Jeffrey T Leek
Publicly available genomic data are a valuable resource for studying normal human variation and disease, but these data are often not well labeled or annotated. The lack of phenotype information for public genomic data severely limits their utility for addressing targeted biological questions. We develop an in silico phenotyping approach for predicting critical missing annotation directly from genomic measurements using well-annotated genomic and phenotypic data produced by consortia like TCGA and GTEx as training data...
March 5, 2018: Nucleic Acids Research
Chengbin Ma, Wenying Zhang, Qiongwei Wu, Yu Liu, Chao Wang, Guoying Lao, Longtao Yang, Ping Liu
BACKGROUND: The aim of this study is to find the potential miRNA expression signature capable of predicting survival time for cervical squamous cell carcinoma (CSCC) patients. METHODS: The expression of 332 miRNAs was measured in 131 (Training cohort) and 130 (Validation cohort) patients with CSCC in the Cancer Genome Atlas (TCGA) data portal. The miRNA expression signature was identified by Cox Proportion Hazard regression model to the Training data set, and subsequently validated in an independent Validation set...
2018: PloS One
Yu Geng, Zhongmeng Zhao, Xuanping Zhang, Wenke Wang, Xingjian Cui, Kai Ye, Xiao Xiao, Jiayin Wang
BACKGROUND: Identifying rare germline and somatic variants associated with cancer progression is an important research topic in cancer genomics. Although many approaches are proposed for rare variant association study, they are not fit for cancer sequencing data due to multiple issues, such as overly relying on pre-selection, losing sight of interacting hotspots, etc. RESULTS: In this article, we propose an improved pipeline to identify germline variant and somatic mutation interactions influencing cancer susceptibility from pair-wise cancer sequencing data...
October 16, 2017: BMC Genomics
Tian Liao, Yuan-Jin Wang, Jia-Qian Hu, Yu Wang, Li-Tao Han, Ben Ma, Rong-Liang Shi, Ning Qu, Wen-Jun Wei, Qing Guan, Jun Xiang, Jia-Ying Chen, Guo-Hua Sun, Duan-Shu Li, Xiang-Ming Mu, Qing-Hai Ji
KMT5A (known as PR-Set7/9, SETD8 and SET8), a member of the SET domain containing methyltransferase family specifically targeting H4K20 for methylation, has been implicated in multiple biological processes. In the present study, we identified that KMT5A was elevated in 50 pairs of papillary thyroid cancer tissue samples and in cell lines K1 and TPC-1 by qRT-PCR and western blotting, as well as by immunohistochemical staining. CCK-8 assay and flow cytometric analysis revealed that inhibition of KMT5A attenuated proliferation and induced apoptosis...
March 5, 2018: Oncology Reports
Zhiyuan Zhang, Sen Wang, Dongjian Ji, Wenwei Qian, Qingyuan Wang, Jie Li, Jiou Gu, Wen Peng, Tao Hu, Bing Ji, Yue Zhang, Shijia Wang, Yueming Sun
Competing endogenous RNAs (ceRNAs) render the functions of long non‑coding RNAs (lncRNAs) more complicated during cancer processes. Potential lncRNA biomarkers and their roles as ceRNAs have not been clearly described for rectal adenocarcinoma (READ). In the present study, we extracted data from The Cancer Genome Atlas (TCGA) including data from 167 tumor samples and 10 adjacent non‑tumor samples. A total of 202 lncRNAs, 190 microRNAs (miRNAs) and 1,530 mRNAs were identified as READ‑specific RNAs [log2(fold‑change)>2, FDR<0...
March 5, 2018: Oncology Reports
Zhikui Liu, Yufeng Wang, Changwei Dou, Liankang Sun, Qing Li, Liang Wang, Qiuran Xu, Wei Yang, Qingguang Liu, Kangsheng Tu
BACKGROUND: Accumulating evidence confirm that aberrant microRNAs (miRNAs) expression contributes to hepatocellular carcinoma (HCC) development and progression. Previous study reported that miR-1468 showed an up-regulated tendency and might be a potential prognostic biomarker in HCC samples derived from TCGA database. However, the role of miR-1468 and its underlying mechanisms involved in the growth and metastasis of HCC remain poorly investigated. METHODS: CCK-8, EdU, colony formation and flow cytometry were used to determine proliferation, cell cycle progression and apoptosis of HCC cells in vitro...
March 6, 2018: Journal of Experimental & Clinical Cancer Research: CR
Yang Zhao, Yajing Liu, Li Lin, Qiong Huang, Wanming He, Shuyi Zhang, Shumin Dong, Zhaowei Wen, Jinjun Rao, Wangjun Liao, Min Shi
BACKGROUND: Metabolic plasticity has been increasingly thought to be a determinant of tumor growth and metastasis. MACC1, a transcriptional regulator of MET, was recognized as an oncogene in gastric cancer (GC); however, its transcriptional or post-translational regulation was not clear. We previously reported the metabolic role of MACC1 in glycolysis to promote GC progression. MACC1-AS1 is the antisense lncRNA of MACC1, yet its function was previously unknown. METHODS: We profiled and analyzed the expression of MACC1-AS1 utilizing the TCGA database as well as in situ hybridization using 123 pairs of GC tissues and matched adjacent normal gastric mucosa tissues (ANTs)...
March 6, 2018: Molecular Cancer
Boris Sepesi, David B Nelson, Kyle G Mitchell, Don L Gibbons, John V Heymach, Ara A Vaporciyan, Stephen G Swisher, Jason Roszik
BACKGROUND: Immune checkpoint inhibitors targeting the PD-L1 pathway have shown benefit for the treatment of metastatic non-small cell lung cancer (NSCLC). However, the prognostic value of PD-L1 independent of immunotherapy is still unclear, with conflicting results reported between PD-L1 expression and patient survival. Our aim was to correlate PD-L1 mRNA level with clinical and pathologic factors and to investigative the prognostic value of PD-L1 mRNA in all stages of NSCLC. METHODS: Gene expression and clinical data were obtained from public TCGA repositories from the National Cancer Institute...
March 3, 2018: Annals of Thoracic Surgery
S-H Zou, X Du, F-D Sun, P-C Wang, M Li
OBJECTIVE: To observe the effect of cisplatin-induced autophagy in human ovarian cancer cell lines and explore the correlation between RP11-135L22.1 with cisplatin-induced autophagy. MATERIALS AND METHODS: Genome-wide expression profile and chemotherapy sensitivity data of ovarian cancer were downloaded from TCGA database. It was found that the expression level of lncRNA RP11-135L22.1 differed between chemotherapy-sensitive group and insensitive group. Besides, RP11-135L22...
February 2018: European Review for Medical and Pharmacological Sciences
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