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cancer gene profile ncRNA

Pui Yan Ho, Zhijian Duan, Neelu Batra, Joseph L Jilek, Mei-Juan Tu, Jing-Xin Qiu, Zihua Hu, Theodore Wun, Primo N Lara, Ralph W DeVere White, Hong-Wu Chen, Ai-Ming Yu
Noncoding RNAs (ncRNAs) produced in live cells may better reflect intracellular ncRNAs for research and therapy. Attempts were made to produce biologic ncRNAs, but at low yield or success rate. Here we first report a new ncRNA bioengineering technology using more stable ncRNA carrier (nCAR) containing a pre-miR-34a derivative identified by rational design and experimental validation. This approach offered a remarkable higher level expression (40%-80% of total RNAs) of recombinant ncRNAs in bacteria and gave an 80% success rate (33 of 42 ncRNAs)...
June 2018: Journal of Pharmacology and Experimental Therapeutics
Elena Magnani, Filippo Macchi, Monica Mancini, Vanessa Lomazzi, Sara Cogliati, Christian Pistore, Martina Mandruzzato, Anne-Catherine Dock-Bregeon, Ian Marc Bonapace
Non-coding RNAs (ncRNAs) transcribed from the promoter and the downstream region can affect the expression of the corresponding coding genes. It has been shown that sense-directed ncRNAs arising from the promoter region of the E-cadherin gene (CDH1) mediate its repression. Here, we show that an antisense-directed ncRNA (paRCDH1-AS) transcribed from the CDH1 promoter is necessary for its expression. paRCDH1-AS acts as a hooking scaffold by recruiting the epigenetic regulators, UHRF1, DNMT3A, SUV39H1 and SUZ12, involved in CDH1 repression...
March 2018: Biochimica et Biophysica Acta
Yu Shi, Peng Ye, Xinghua Long
BACKGROUND/AIMS: As MCF-7 and MDA-MB-231 cells are the typical cell lines of two clinical breast tumour subtypes, the aim of the present study was to elucidate the transcriptome differences between MCF-7 and MDA-MB-231 breast cancer cell lines. METHODS: The mRNA, miRNA (MicroRNA) and lncRNA (Long non-coding RNA) expression profiles were examined using NGS (next generation sequencing) instrument Illumina HiSeq-2500. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed to identify the biological functions of differentially expressed coding RNAs...
2017: Cellular Physiology and Biochemistry
Anna Grimaldi, Mayra Rachele Zarone, Carlo Irace, Silvia Zappavigna, Angela Lombardi, Hiromichi Kawasaki, Michele Caraglia, Gabriella Misso
The current knowledge about non-coding RNAs (ncRNAs) as important regulators of gene expression in both physiological and pathological conditions, has been the main engine for the design of innovative platforms to finalize the pharmacological application of ncRNAs as either therapeutic tools or as molecular biomarkers in cancer. Biochemical alterations of cancer cells are, in fact, largely supported by ncRNA disregulation in the tumor site, which, in turn, reflects the cancer-associated specific modification of circulating ncRNA expression pattern...
July 29, 2017: Seminars in Cell & Developmental Biology
Jesper L V Maag, Oliver M Fisher, Angelique Levert-Mignon, Dominik C Kaczorowski, Melissa L Thomas, Damian J Hussey, David I Watson, Antony Wettstein, Yuri V Bobryshev, Melanie Edwards, Marcel E Dinger, Reginald V Lord
Esophageal adenocarcinoma (EAC) has one of the fastest increases in incidence of any cancer, along with poor five-year survival rates. Barrett's esophagus (BE) is the main risk factor for EAC; however, the mechanisms driving EAC development remain poorly understood. Here, transcriptomic profiling was performed using RNA-sequencing (RNA-seq) on premalignant and malignant Barrett's tissues to better understand this disease. Machine-learning and network analysis methods were applied to discover novel driver genes for EAC development...
July 27, 2017: Molecular Cancer Research: MCR
Amy Makler, Ramaswamy Narayanan
BACKGROUND: Exosomes, cell-derived vesicles encompassing lipids, DNA, proteins coding genes and noncoding RNAs (ncRNAs) are present in diverse body fluids. They offer novel biomarker and drug therapy potential for diverse diseases, including cancer. MATERIALS AND METHODS: Using gene ontology, exosomal genes database and GeneCards metadata analysis tools, a database of cancer-associated protein coding genes and ncRNAs (n=2,777) was established. Variant analysis, expression profiling and pathway mapping were used to identify putative pancreatic cancer exosomal gene candidates...
May 2017: Cancer Genomics & Proteomics
Jing Liu, Tian Liu, Xiaman Wang, Aili He
A new type of RNAs was identified from genes traditionally thought to express messenger or linear ncRNA (noncoding RNA) only. They were subsequently named as circRNAs (circular RNAs) due to the covalently closed structure. Accumulating studies were performed to explore the expression profile of circRNAs in different cell types and diseases, the outcomes totally changed our view of ncRNAs, which was thought to be junk by-products in the process of gene transcription, and enriched our poor understanding of its underlying functions...
March 9, 2017: Molecular Cancer
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...
March 17, 2017: 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...
August 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 (nā€‰=ā€‰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
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