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https://www.readbyqxmd.com/read/29221168/diagnosis-prognosis-and-bioinformatics-analysis-of-lncrnas-in-hepatocellular-carcinoma
#1
Meiyu Dai, Siyuan Chen, Xiaomou Wei, Xuan Zhu, Fang Lan, Shengming Dai, Xue Qin
This study aims to comprehensively analyze the diagnosis and prognosis of lncRNAs in hepatocellular carcinoma (HCC). From the Gene Expression Omnibus database, we screened out and analyzed the differently expressed lncRNAs and related mRNAs using bioinformatics methods. The expressions of lncRNAs were validated in tumor tissues, cell lines and the Cancer Genome Atlas database. At the same time, we also conducted an exploratory analysis on the diagnostic and prognostic ability of lncRNAs in HCC. In this study, we found that most of the targeted mRNAs promote the biological process of cell division, cellular component of nucleoplasm, molecular function of protein binding, which were significantly associated with 12 KEGG pathways...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29220078/using-the-seven-bridges-cancer-genomics-cloud-to-access-and-analyze-petabytes-of-cancer-data
#2
Raunaq Malhotra, Isheeta Seth, Erik Lehnert, Jing Zhao, Gaurav Kaushik, Elizabeth H Williams, Anurag Sethi, Brandi N Davis-Dusenbery
Next-generation sequencing has produced petabytes of data, but accessing and analyzing these data remain challenging. Traditionally, researchers investigating public datasets like The Cancer Genome Atlas (TCGA) would download the data to a high-performance cluster, which could take several weeks even with a highly optimized network connection. The National Cancer Institute (NCI) initiated the Cancer Genomics Cloud Pilots program to provide researchers with the resources to process data with cloud computational resources...
December 8, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/29218898/building-trans-omics-evidence-using-imaging-and-omics-to-characterize-cancer-profiles
#3
Arunima Srivastava, Chaitanya Kulkarni, Parag Mallick, Kun Huang, Raghu Machiraju
Utilization of single modality data to build predictive models in cancer results in a rather narrow view of most patient profiles. Some clinical facet s relate strongly to histology image features, e.g. tumor stages, whereas others are associated with genomic and proteomic variations (e.g. cancer subtypes and disease aggression biomarkers). We hypothesize that there are coherent "trans-omics" features that characterize varied clinical cohorts across multiple sources of data leading to more descriptive and robust disease characterization...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218894/mri-to-mgmt-predicting-methylation-status-in-glioblastoma-patients-using-convolutional-recurrent-neural-networks
#4
Lichy Han, Maulik R Kamdar
Glioblastoma Multiforme (GBM), a malignant brain tumor, is among the most lethal of all cancers. Temozolomide is the primary chemotherapy treatment for patients diagnosed with GBM. The methylation status of the promoter or the enhancer regions of the O6-methylguanine methyltransferase (MGMT) gene may impact the efficacy and sensitivity of temozolomide, and hence may affect overall patient survival. Microscopic genetic changes may manifest as macroscopic morphological changes in the brain tumors that can be detected using magnetic resonance imaging (MRI), which can serve as noninvasive biomarkers for determining methylation of MGMT regulatory regions...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218871/extracting-a-biologically-relevant-latent-space-from-cancer-transcriptomes-with-variational-autoencoders
#5
Gregory P Way, Casey S Greene
The Cancer Genome Atlas (TCGA) has profiled over 10,000 tumors across 33 different cancer-types for many genomic features, including gene expression levels. Gene expression measurements capture substantial information about the state of each tumor. Certain classes of deep neural network models are capable of learning a meaningful latent space. Such a latent space could be used to explore and generate hypothetical gene expression profiles under various types of molecular and genetic perturbation. For example, one might wish to use such a model to predict a tumor's response to specific therapies or to characterize complex gene expression activations existing in differential proportions in different tumors...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218652/metastasis-suppressor-1-mtss1-expression-is-associated-with-reduced-in-vivo-metastasis-and-enhanced-patient-survival-in-lung-adenocarcinoma
#6
Matthew D Taylor, Oana Bollt, Soumya C Iyer, Gavin P Robertson
Metastasis suppressor 1 (MTSS1) has been shown to be a metastasis suppressor in a number of cancers. However, its role in lung adenocarcinoma is largely unknown. To evaluate the significance of MTSS1 expression on lung adenocarcinoma metastatic properties, the gain or loss of MTSS1 in in vivo and in vitro experiments were employed. Using an in vivo orthotopic mouse xenograft model mimicking human disease progression, stable overexpression of MTSS1 in lung adenocarcinoma cells resulted in a significant decrease in metastatic burden...
December 7, 2017: Clinical & Experimental Metastasis
https://www.readbyqxmd.com/read/29212269/low-neighbor-of-brca1-gene-expression-predicts-poor-clinical-outcome-and-resistance-of-sunitinib-in-clear-cell-renal-cell-carcinoma
#7
Wen Xiao, Zhiyong Xiong, Changfei Yuan, Lin Bao, Di Liu, Xiong Yang, Wencheng Li, Junwei Tong, Yan Qu, Lei Liu, Haibing Xiao, Hongmei Yang, Xiaoping Zhang, Ke Chen
Objective: To study the expression of Neighbor of Brca1 gene (NBR1) in clear cell renal cell carcinoma (ccRCC), renal cancer cells and the chemoresistance cells and to elucidate its clinical prognostic and chemoresistance value. Materials and Methods: We screened the NBR1 mRNA in ccRCC from The Cancer Genome Atlas (TCGA) database and examined expression levels of NBR1 mRNA in 48 cases of ccRCC tissues, renal cancer cell lines and chemoresistance cells by qRT-PCR...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29212211/setd7-is-a-prognosis-predicting-factor-of-breast-cancer-and-regulates-redox-homeostasis
#8
Run Huang, Xiaolin Li, Yang Yu, Lisi Ma, Sixuan Liu, Xiangyun Zong, Qi Zheng
SETD7 is a methyltransferase that specifically catalyzes the monomethylation of lysine 4 on histone H3. A variety of studies has revealed the role of SETD7 in posttranslational modifications of non-histone proteins. However, the prognostic value of SETD7 on breast cancer and the ability of SETD7 of regulating intrinsic redox homeostasis has never been investigated. In this study, using The Cancer Genome Atlas (TCGA) database, we revealed that SETD7 was a potential prognostic marker of breast cancer. Median survival time of patients with low SETD7 expression (18...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29212036/%C3%AE-np63-inhibits-oxidative-stress-induced-cell-death-including-ferroptosis-and-cooperates-with-the-bcl-2-family-to-promote-clonogenic-survival
#9
Gary X Wang, Ho-Chou Tu, Yiyu Dong, Anders Jacobsen Skanderup, Yufeng Wang, Shugaku Takeda, Yogesh Tengarai Ganesan, Song Han, Han Liu, James J Hsieh, Emily H Cheng
The BCL-2 family proteins are central regulators of apoptosis. However, cells deficient for BAX and BAK or overexpressing BCL-2 still succumb to oxidative stress upon DNA damage or matrix detachment. Here, we show that ΔNp63α overexpression protects cells from oxidative stress induced by oxidants, DNA damage, anoikis, or ferroptosis-inducing agents. Conversely, ΔNp63α deficiency increases oxidative stress. Mechanistically, ΔNp63α orchestrates redox homeostasis through transcriptional control of glutathione biogenesis, utilization, and regeneration...
December 5, 2017: Cell Reports
https://www.readbyqxmd.com/read/29209625/prediction-and-validation-of-hub-genes-associated-with-colorectal-cancer-by-integrating-ppi-network-and-gene-expression-data
#10
Yongfu Xiong, Wenxian You, Rong Wang, Linglong Peng, Zhongxue Fu
Although hundreds of colorectal cancer- (CRC-) related genes have been screened, the significant hub genes still need to be further identified. The aim of this study was to identify the hub genes based on protein-protein interaction network and uncover their clinical value. Firstly, 645 CRC patients' data from the Tumor Cancer Genome Atlas were downloaded and analyzed to screen the differential expression genes (DEGs). And then, the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed, and PPI network of the DEGs was constructed by Cytoscape software...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29209123/prediction-of-early-stage-hepatocellular-carcinoma-using-oncoscan-chromosomal-copy-number-aberration-data
#11
Ming-Chin Yu, Chao-Wei Lee, Yun-Shien Lee, Jang-Hau Lian, Chia-Lung Tsai, Yi-Ping Liu, Chun-Hsing Wu, Chi-Neu Tsai
AIM: To identify chromosomal copy number aberrations (CNAs) in early-stage hepatocellular carcinoma (HCC) and analyze whether they are correlated with patient prognosis. METHODS: One hundred and twenty patients with early-stage HCC were enrolled in our study, with the collection of formalin fixed, paraffin-embedded (FFPE) specimens and clinicopathological data. Tumor areas were marked by certified pathologists on a hematoxylin and eosin-stained slide, and cancer and adjacent non-cancerous tissues underwent extraction of DNA, which was analyzed with the Affymetrix OncoScan platform to assess CNAs and loss of heterozygosity (LOH)...
November 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29208006/identification-and-validation-of-a-44-gene-expression-signature-for-the-classification-of-renal-cell-carcinomas
#12
Qifeng Wang, Hualei Gan, Chengshu Chen, Yifeng Sun, Jinying Chen, Midie Xu, Weiwei Weng, Liyu Cao, Qinghua Xu, Jian Wang
BACKGROUND: Renal cancers account for more than 3% of all adult malignancies and cause more than 23,400 deaths per year in China alone. The four most common types of kidney tumours include clear cell, papillary, chromophobe and benign oncocytoma. These histological subtypes vary in their clinical course and prognosis, and different clinical strategies have been developed for their management. Some kidney tumours can be very difficult to distinguish based on the pathological assessment of morphology and immunohistochemistry...
December 6, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29207133/potential-role-of-microrna%C3%A2-223%C3%A2-3p-in-the-tumorigenesis-of-hepatocellular-carcinoma-a-comprehensive-study-based-on-data-mining-and-bioinformatics
#13
Rui Zhang, Li-Jie Zhang, Mei-Ling Yang, Lan-Shan Huang, Gang Chen, Zhen-Bo Feng
The aims of the present study were to examine the potential role of microRNA‑233‑3p (miR)‑223‑3p in the tumorigenesis of hepatocellular carcinoma (HCC), and to investigate its diagnostic accuracy and potential molecular mechanisms. The expression data of miR‑223‑3p in HCC were obtained from the Gene Expression Omnibus (GEO). Data for the precursor miR‑223 were obtained from The Cancer Genome Atlas (TCGA). The diagnostic role of miR‑223‑3p was identified by the receiver operating curve (ROC), and the diagnostic value of miR‑223‑3p in HCC was calculated from qualified reports in the literature...
November 27, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29207095/upregulation-of-zbtb7a-exhibits-a-tumor-suppressive-role-in-gastric-cancer-cells
#14
Guang Sun, Bo Peng, Quan Xie, Jianwen Ruan, Xianwen Liang
Gastric cancer presents as a complex solid tumor and is the third leading cause of global cancer‑associated mortality. The genetic alterations in gastric cancer remain unclear and deserve further investigation. Mining The Cancer Genome Atlas gastric adenocarcinoma dataset identified a frequent loss of the zinc finger and BTB domain containing 7A (ZBTB7A) gene locus and a significant correlation between low ZBTB7A expression and poor patient survival. ZBTB7A belongs to the POZ/BTB and Kruppel transcription factor family...
November 20, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29207053/diagnostic-significance-and-potential-function-of-mir-338-5p-in-hepatocellular-carcinoma-a-bioinformatics-study-with-microarray-and-rna-sequencing-data
#15
Liang Liang, Li Gao, Xiao-Ping Zou, Meng-Lan Huang, Gang Chen, Jian-Jun Li, Xiao-Yong Cai
MicroRNA (miR)-338-5p has been studied in hepatocellular carcinoma (HCC); however, the diagnostic value and molecular mechanism underlying its actions remains to be elucidated. The present study aimed to validate the diagnostic ability of miR‑338‑5p and further explore the underlying molecular mechanism. Data from eligible studies, Gene Expression Omnibus (GEO) chips and The Cancer Genome Atlas (TCGA) datasets were gathered in the data mining and the integrated meta‑analysis, to evaluate the significance of miR‑338‑5p in diagnosing HCC comprehensively...
November 21, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29205508/aberrant-methylation-of-mutl-homolog-1-is-associated-with-increased-risk-of-non-small-cell-lung-cancer
#16
Haochang Hu, Xiaoying Chen, Cong Zhou, Bin Li, Yong Yang, Xiuru Ying, Yiyi Mao, Yihan Zhang, Jie Zhong, Jie Dai, Hang Yu, Boyi Wu, Xiaodong Li, Tiangong Wang, Shiwei Duan
BACKGROUND: Non-small cell lung cancer (NSCLC) is a common malignant tumor. DNA hypermethylation in the promoter region has been served as a potential molecular marker for several tumors. The goal of the current study was to assess the diagnostic ability of mutL homolog 1 (MLH1) promoter methylation in NSCLC. METHODS: A total of 111 NSCLC patients' paired tissue samples were obtained to explore the association between MLH1 promoter methylation and NSCLC by methylation-specific polymerase chain reaction (MSP) method...
December 5, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29205011/clinical-correlates-of-subventricular-zone-contacting-glioblastomas-a-meta-analysis
#17
Akshitkumar M Mistry
INTRODUCTION: The clinical and molecular correlates of glioblastomas (GBMs) contacting the subventricular zone (SVZ+ GBM) are unknown. We aimed to reveal any such correlates that may help explain their increased GBM malignancy. EVIDENCE ACQUISITION: A meta-analysis was, therefore, conducted to assess whether tumor's MGMT promoter methylation status, IDH mutation status, volume, and extent of resection as well as patients' age at diagnosis and preoperative Karnofsky performance status score (KPS) correlate with SVZ contact by GBM...
December 4, 2017: Journal of Neurosurgical Sciences
https://www.readbyqxmd.com/read/29204839/prognostic-value-of-a-microrna-signature-as-a-novel-biomarker-in-patients-with-lower-grade-gliomas
#18
Zenghui Qian, Yiming Li, Xing Fan, Chuanbao Zhang, Yinyan Wang, Tao Jiang, Xing Liu
MicroRNAs (miRNAs) may act as prognostic biomarkers in a variety of cancers. The aim of this study was to identify and evaluate a prognostic miRNA signature in patients with lower-grade gliomas (LGGs). miRNA expression profiles and clinical data of patients with LGGs from the Chinese Glioma Genome Atlas (CGGA; the training cohort) and The Cancer Genome Atlas (TCGA; the validation cohort) were analyzed, and the least absolute shrinkage and selection operator Cox regression model was used to identify the miRNA signature, which was combined with clinical prognostic factors to develop an individualized survival prediction model...
December 4, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29204322/diagnosis-value-of-aberrantly-expressed-microrna-profiles-in-lung-squamous-cell-carcinoma-a-study-based-on-the-cancer-genome-atlas
#19
Sheng Yang, Jing Sui, Geyu Liang
Background: Lung cancer is considered as one of the most frequent and deadly cancers with high mortality all around the world. It is critical to find new biomarkers for early diagnosis of lung cancer, especially lung squamous cell carcinoma (LUSC). The Cancer Genome Atlas (TCGA) is a database which provides both cancer and clinical information. This study is a comprehensive analysis of a novel diagnostic biomarker for LUSC, based on TCGA. Methods and Results: The present study investigated LUSC-specific key microRNAs (miRNAs) from large-scale samples in TCGA...
2017: PeerJ
https://www.readbyqxmd.com/read/29199088/a-microrna-signature-associated-with-metastasis-of-t1-colorectal-tumors-to-lymph-nodes
#20
Tsuyoshi Ozawa, Raju Kandimalla, Feng Gao, Hiroaki Nozawa, Keisuke Hata, Hiroshi Nagata, Satoshi Okada, Daisuke Izumi, Hideo Baba, James Fleshman, Xin Wang, Toshiaki Watanabe, Ajay Goel
Most T1 colorectal tumors treated by radical surgery can now be cured by endoscopic submucosal dissection. Although 70%-80% of T1 colorectal tumors are classified as high risk, fewer than 16% of these patients actually have lymph node metastases. Biomarkers are needed to identify patients with T1 tumors with the highest risk of metastasis, to prevent unnecessary radical surgeries. We collected data from the Cancer Genome Atlas and identified 5 microRNAs (MIR32, MIR181B, MIR193B, MIR195, and MIR 411) with significant changes in expression in T1 and T2 colorectal tumors with vs without lymphatic invasion...
November 30, 2017: Gastroenterology
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