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cancer gene profile ncRNA

Aliaksei Z Holik, Charity W Law, Ruijie Liu, Zeya Wang, Wenyi Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, Gordon K Smyth, Matthew E Ritchie
Carefully designed control experiments provide a gold standard for benchmarking different genomics research tools. A shortcoming of many gene expression control studies is that replication involves profiling the same reference RNA sample multiple times. This leads to low, pure technical noise that is atypical of regular studies. To achieve a more realistic noise structure, we generated a RNA-sequencing mixture experiment using two cell lines of the same cancer type. Variability was added by extracting RNA from independent cell cultures and degrading particular samples...
November 29, 2016: Nucleic Acids Research
Angela E Zou, Hao Zheng, Maarouf A Saad, Mehran Rahimy, Jonjei Ku, Selena Z Kuo, Thomas K Honda, Jessica Wang-Rodriguez, Yinan Xuan, Avinaash Korrapati, Vicky Yu, Pranav Singh, Jennifer R Grandis, Charles C King, Scott M Lippman, Xiao Qi Wang, Andrew Hinton, Weg M Ongkeko
Head and neck squamous cell carcinoma (HNSCC) is an aggressive disease marked by frequent recurrence and metastasis and stagnant survival rates. To enhance molecular knowledge of HNSCC and define a non-coding RNA (ncRNA) landscape of the disease, we profiled the transcriptome-wide dysregulation of long non-coding RNA (lncRNA), microRNA (miRNA), and PIWI-interacting RNA (piRNA) using RNA-sequencing data from 422 HNSCC patients in The Cancer Genome Atlas (TCGA). 307 non-coding transcripts differentially expressed in HNSCC were significantly correlated with patient survival, and associated with mutations in TP53, CDKN2A, CASP8, PRDM9, and FBXW7 and copy number variations in chromosomes 3, 5, 7, and 18...
9, 2016: Oncotarget
Ying Qi, Hong Sain Ooi, Jun Wu, Jian Chen, Xiaoli Zhang, Sheng Tan, Qing Yu, Yuan-Yuan Li, Yani Kang, Hua Li, Zirui Xiong, Tao Zhu, Bingya Liu, Zhifeng Shao, Xiaodong Zhao
EZH2, the catalytic component of polycomb repressive complex 2 (PRC2), is frequently overexpressed in human cancers and contributes to tumor initiation and progression, in part through transcriptional silencing of tumor suppressor genes. A number of noncoding RNAs (ncRNAs) recruit EZH2 to specific chromatin loci, where they modulate gene expression. Here, we used RNA immunoprecipitation sequencing (RIP-seq) to profile EZH2-associated transcripts in human gastric cancer cell lines. We identified 8,256 transcripts, including both noncoding and coding transcripts, some of which were derived from cancer-related loci...
March 15, 2016: Oncotarget
Qixue Wang, Junxia Zhang, Yanwei Liu, Wei Zhang, Junhu Zhou, Ran Duan, Peiyu Pu, Chunsheng Kang, Lei Han
The comprehensive lncRNA expression signature in glioma has not yet been fully elucidated. We performed a high-throughput microarray to detect the ncRNA expression profiles of 220 human glioma tissues. Here, we found that a novel lncRNA, HOXA11-AS, was the antisense transcript of the HOX11 gene. It was shown that HOXA11-AS was closely associated with glioma grade and poor prognosis. Multivariate Cox regression analysis revealed that HOXA11-AS was an independent prognostic factor in glioblastoma multiforme patients, and its expression was correlated with the glioma molecular subtypes of the Cancer Genome Atlas...
April 10, 2016: Cancer Letters
Kosuke Hashimoto, Ana Maria Suzuki, Alexandre Dos Santos, Christophe Desterke, Agnese Collino, Serena Ghisletti, Emilie Braun, Alessandro Bonetti, Alexandre Fort, Xian-Yang Qin, Enrico Radaelli, Bogumil Kaczkowski, Alistair R R Forrest, Soichi Kojima, Didier Samuel, Gioacchino Natoli, Marie Annick Buendia, Jamila Faivre, Piero Carninci
An increasing number of noncoding RNAs (ncRNAs) have been implicated in various human diseases including cancer; however, the ncRNA transcriptome of hepatocellular carcinoma (HCC) is largely unexplored. We used CAGE to map transcription start sites across various types of human and mouse HCCs with emphasis on ncRNAs distant from protein-coding genes. Here, we report that retroviral LTR promoters, expressed in healthy tissues such as testis and placenta but not liver, are widely activated in liver tumors. Despite HCC heterogeneity, a subset of LTR-derived ncRNAs were more than 10-fold up-regulated in the vast majority of samples...
December 2015: Genome Research
Giovanni Lavorgna, Fulvio Chiacchiera, Alberto Briganti, Francesco Montorsi, Diego Pasini, Andrea Salonia
We recently identified the long non-coding RNA (ncRNA) TRPM2-AS as a key regulator of survival in prostate cancer [1]. This essential role, coupled to the TRPM2-AS low-expression levels in healthy tissues, makes this ncRNA a suitable therapeutic target for further clinical studies. To get insights into the survival mechanism controlled by this molecule, we ablated its expression in prostate cancer cells and performed a genome-wide analysis of the transcripts differentially regulated in dying cells. Here, we describe in detail the experimental system, methods and quality control for the generation of the microarray data associated with our recent publication [1]...
March 2015: Genomics Data
Qian Wu, Li Guo, Fei Jiang, Lei Li, Zhong Li, Feng Chen
Recently, rapid advances in bioinformatics analysis have expanded our understanding of the transcriptome to a genome-wide level. miRNA-mRNA-lncRNA interactions have been shown to play critical regulatory role in cancer biology. In this study, we discussed the use of an integrated systematic approach to explore new facets of the oestrogen receptor (ER)-regulated transcriptome. The identification of RNAs that are related to the expression status of the ER may be useful in clinical therapy and prognosis. We used a network modelling strategy...
December 2015: Journal of Cellular and Molecular Medicine
Martin C Abba, Ting Gong, Yue Lu, Jaeho Lee, Yi Zhong, Ezequiel Lacunza, Matias Butti, Yoko Takata, Sally Gaddis, Jianjun Shen, Marcos R Estecio, Aysegul A Sahin, C Marcelo Aldaz
Ductal carcinoma in situ (DCIS) is a noninvasive precursor lesion to invasive breast carcinoma. We still have no understanding on why only some DCIS lesions evolve to invasive cancer whereas others appear not to do so during the life span of the patient. Here, we performed full exome (tumor vs. matching normal), transcriptome, and methylome analysis of 30 pure high-grade DCIS (HG-DCIS) and 10 normal breast epithelial samples. Sixty-two percent of HG-DCIS cases displayed mutations affecting cancer driver genes or potential drivers...
September 15, 2015: Cancer Research
Prerana Jha, Rahul Agrawal, Pankaj Pathak, Anupam Kumar, Suvendu Purkait, Supriyo Mallik, Vaishali Suri, Mehar Chand Sharma, Deepak Gupta, Ashish Suri, B S Sharma, P K Julka, Ritu Kulshreshtha, Chitra Sarkar
Pediatric high-grade gliomas (HGGs) are highly malignant tumors that remain incurable and relatively understudied. The crucial role of noncoding RNAs (ncRNAs) has been reported in various cancers. However, the study on miRNAs in pediatric HGGs is scant and there is no report till date on the status of other small ncRNAs. Genome-wide microarray analysis was performed to investigate small ncRNA expression in pediatric HGG (n = 14) and compared to adult glioblastoma (GBM) signature. The validation of miRNAs and small nucleolar RNAs (snoRNAs) was done by real-time polymerase chain reaction...
November 15, 2015: International Journal of Cancer. Journal International du Cancer
Paloma Del C Monroig, Lu Chen, Shuxing Zhang, George A Calin
One of the most fascinating discoveries in molecular oncology has been that cancer represents a disease in which genetic alterations in protein-coding, but also in non-coding genes complement each other. MicroRNAs (miRNAs) are a type of non-coding RNA (ncRNA) transcripts that can regulate gene expression primarily by disrupting messenger RNA (mRNA) translation and/or stability, or alternatively by modulating the transcription of target mRNAs. For the last decade, miRNAs have shown to be pivotal characters of every single one of the cancer hallmarks...
January 2015: Advanced Drug Delivery Reviews
Heejin Lee, Chongtae Kim, Ja-Lok Ku, Wook Kim, Sungjoo Kim Yoon, Hyo-Jeong Kuh, Jeong-Hwa Lee, Suk Woo Nam, Eun Kyung Lee
Several types of genetic and epigenetic regulation have been implicated in the development of drug resistance, one significant challenge for cancer therapy. Although changes in the expression of non-coding RNA are also responsible for drug resistance, the specific identities and roles of them remain to be elucidated. Long non-coding RNAs (lncRNAs) are a type of ncRNA (> 200 nt) that influence the regulation of gene expression in various ways. In this study, we aimed to identify differentially expressed lncRNAs in 5-fluorouracil-resistant colon cancer cells...
July 2014: Molecules and Cells
Francesco Fazi, Giovanni Blandino
One of the most important advance obtained from transcriptome analysis in recent years is the discovery of a series of noncoding RNA (ncRNA) families, with regulatory roles in several biological processes, that are actively transcribed from the genome of many organisms. Among them microRNAs (miRNAs) are small regulatory, single-stranded, RNA molecules (19-25 nucleotides in length) that are generated from hairpin primary transcripts [1]. In the cytoplasm, the mature miRNA molecule, through a limited base-pairing complementary sequences interaction, destabilizes or blocks the translation of their phylogenetically conserved target mRNAs transcripts [2]...
2013: MicroRNA
Kenji Takahashi, Irene K Yan, Joseph Wood, Hiroaki Haga, Tushar Patel
UNLABELLED: Hepatocellular cancer (HCC) is a highly treatment-refractory cancer and is also highly resistant to adverse cellular stress. Although cell behavior can be modulated by noncoding RNAs (ncRNA) within extracellular vesicles (EV), the contributions of long noncoding RNAs (lncRNAs) are largely unknown. To this end, the involvement and functional roles of lncRNAs contained within EVs during chemotherapeutic stress in human HCC were determined. Expression profiling identified a subset of lncRNAs that were enriched in tumor cell-derived vesicles released from two different cell lines...
October 2014: Molecular Cancer Research: MCR
Piroon Jenjaroenpun, Yuliya Kremenska, Vrundha M Nair, Maksym Kremenskoy, Baby Joseph, Igor V Kurochkin
Exosomes are nanosized (30-100 nm) membrane vesicles secreted by most cell types. Exosomes have been found to contain various RNA species including miRNA, mRNA and long non-protein coding RNAs. A number of cancer cells produce elevated levels of exosomes. Because exosomes have been isolated from most body fluids they may provide a source for non-invasive cancer diagnostics. Transcriptome profiling that uses deep-sequencing technologies (RNA-Seq) offers enormous amount of data that can be used for biomarkers discovery, however, in case of exosomes this approach was applied only for the analysis of small RNAs...
2013: PeerJ
Samuel Peña-Llopis, James Brugarolas
Genomic technologies have revolutionized our understanding of complex Mendelian diseases and cancer. Solid tumors present several challenges for genomic analyses, such as tumor heterogeneity and tumor contamination with surrounding stroma and infiltrating lymphocytes. We developed a protocol to (i) select tissues of high cellular purity on the basis of histological analyses of immediately flanking sections and (ii) simultaneously extract genomic DNA (gDNA), mRNA, noncoding RNA (ncRNA; enriched in miRNA) and protein from the same tissues...
November 2013: Nature Protocols
Shancheng Ren, Zhiyu Peng, Jian-Hua Mao, Yongwei Yu, Changjun Yin, Xin Gao, Zilian Cui, Jibin Zhang, Kang Yi, Weidong Xu, Chao Chen, Fubo Wang, Xinwu Guo, Ji Lu, Jun Yang, Min Wei, Zhijian Tian, Yinghui Guan, Liang Tang, Chuanliang Xu, Linhui Wang, Xu Gao, Wei Tian, Jian Wang, Huanming Yang, Jun Wang, Yinghao Sun
There are remarkable disparities among patients of different races with prostate cancer; however, the mechanism underlying this difference remains unclear. Here, we present a comprehensive landscape of the transcriptome profiles of 14 primary prostate cancers and their paired normal counterparts from the Chinese population using RNA-seq, revealing tremendous diversity across prostate cancer transcriptomes with respect to gene fusions, long noncoding RNAs (long ncRNA), alternative splicing and somatic mutations...
May 2012: Cell Research
Feng Yang, Fan Yi, Zhiguo Zheng, Zhiqiang Ling, Jianv Ding, Jiangfeng Guo, Weimin Mao, Xiongbiao Wang, Xiaoxia Wang, Xianfeng Ding, Zicai Liang, Quan Du
A negative selection strategy was used in the present study to isolate long polyA-minus RNAs from the total transcriptome and a long non-coding RNA named Yiya was identified. Yiya is a 1.9 kb long intergenic ncRNA gene mapped to chromosome 1q41, a well-established cancer susceptibility locus. Expression profiling revealed a general and regulated expression pattern of Yiya in major tissues, and more interestingly, identified elevated mRNA levels in different cancers. Quantitative analysis further demonstrated a dynamic regulation of Yiya expression in cell cycle progression, suggesting that it was involved in cell cycle regulation...
January 2012: RNA Biology
Tetsuro Setoyama, Hui Ling, Shoji Natsugoe, George A Calin
Alterations in microRNA (miRNA) and other short or long non-coding RNA (ncRNA) are involved in the initiation, progression, and metastasis of human cancer. The main molecular alterations result from variations in gene expression, which are usually minor but have consequences for a vast number of target protein-coding genes. The causes of the widespread differential expression of ncRNAs in malignant cells compared with normal cells can be explained by the location of these genes in genomic regions associated with cancer, by epigenetic mechanisms, and by alterations in the processing machinery...
2011: Keio Journal of Medicine
Ewa Dudziec, John R Goepel, James W F Catto
Urothelial carcinoma of the bladder is a common disease that arises from two distinct molecular pathways, and is one of the most expensive malignancies to manage. Accurate biomarkers that could detect tumor recurrence or predict future progression would improve the care of patients and reduce the cost of managing the disease. DNA methylation, histone modification and ncRNA expression are important epigenetic mechanisms that regulate the expression of genes. These regulatory mechanisms are altered with bladder cancer, and therefore, represent potential biomarkers and therapeutic targets owing to the reversible nature of their modification...
February 2011: Epigenomics
Anna B Glinskii, Shuang Ma, Jun Ma, Denise Grant, Chang-Uk Lim, Ian Guest, Stewart Sell, Ralph Buttyan, Gennadi V Glinsky
The mechanistic relevance of intergenic disease-associated genetic loci (IDAGL) containing highly statistically significant disease-linked SNPs remains unknown. Here, we present experimental and clinical evidence supporting the importantance of the role of IDAGL in human diseases. A targeted RT-PCR screen coupled with sequencing of purified PCR products detects widespread transcription at multiple IDAGL and identifies 96 small noncoding trans-regulatory RNAs of ~100-300 nt in length containing SNPs (snpRNAs) associated with 21 common disorders...
October 15, 2011: Cell Cycle
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