keyword
MENU ▼
Read by QxMD icon Read
search

RNA sequencing Cancer

keyword
https://www.readbyqxmd.com/read/28346474/the-microrna-205-5p-is-correlated-to-metastatic-potential-of-21t-series-a-breast-cancer-progression-model
#1
L Stankevicins, A Barat, P Dessen, Y Vassetzky, C V de Moura Gallo
MicroRNA is a class of noncoding RNAs able to base pair with complementary messenger RNA sequences, inhibiting their expression. These regulatory molecules play important roles in key cellular processes including cell proliferation, differentiation and response to DNA damage; changes in miRNA expression are a common feature of human cancers. To gain insights into the mechanisms involved in breast cancer progression we conducted a microRNA global expression analysis on a 21T series of cell lines obtained from the same patient during different stages of breast cancer progression...
2017: PloS One
https://www.readbyqxmd.com/read/28346055/a-to-i-editing-in-disease-is-not-fake-news
#2
Prajakta Bajad, Michael F Jantsch, Liam Keegan, Mary O'Connell
Adenosine deaminases acting on RNA (ADARs) are zinc-containing enzymes that deaminate adenosine bases to inosines within dsRNA regions in transcripts. In short, structured dsRNA hairpins individual adenosine bases may be targeted specifically and edited with up to one hundred percent efficiency, leading to the production of alternative protein variants. However, the majority of editing events occur within longer stretches of dsRNA formed by pairing of repetitive sequences. Here, many different adenosine bases are potential targets but editing efficiency is usually much lower...
March 27, 2017: RNA Biology
https://www.readbyqxmd.com/read/28345805/promoter-hypermethylation-mediated-downregulation-of-mir-770-and-its-host-gene-meg3-a-long-non-coding-rna-in-the-development-of-gastric-cardia-adenocarcinoma
#3
Wei Guo, Zhiming Dong, Shengnan Liu, Yiling Qiao, Gang Kuang, Yanli Guo, Supeng Shen, Jia Liang
Maternally expressed gene 3 (MEG3) is an imprinted gene located at 14q32 which encodes an lncRNA and is downregulated in an expanding list of cancer cell lines and primary human cancers. The miR-770 is transcribed from the intronic sequence of MEG3 and MEG3 may be the host gene for miR-770. However, the biological role of MEG3 and miR-770 in gastric cardia adenocarcinoma (GCA) development and prognosis is poorly defined. The present study was to investigate the function and methylation status of MEG3 in GCA, and further to detect the functional association of miR-770 and its host gene MEG3 in GCA carcinogenesis and prognosis...
March 27, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28345687/recent-advances-in-high-performance-fluorescent-and-bioluminescent-rna-imaging-probes
#4
REVIEW
Yuqiong Xia, Ruili Zhang, Zhongliang Wang, Jie Tian, Xiaoyuan Chen
RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment...
March 27, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28344865/identification-of-genetic-determinants-of-breast-cancer-immune-phenotypes-by-integrative-genome-scale-analysis
#5
Wouter Hendrickx, Ines Simeone, Samreen Anjum, Younes Mokrab, François Bertucci, Pascal Finetti, Giuseppe Curigliano, Barbara Seliger, Luigi Cerulo, Sara Tomei, Lucia Gemma Delogu, Cristina Maccalli, Ena Wang, Lance D Miller, Francesco M Marincola, Michele Ceccarelli, Davide Bedognetti
Cancer immunotherapy is revolutionizing the clinical management of several tumors, but has demonstrated limited activity in breast cancer. The development of more effective treatments is hindered by incomplete knowledge of the genetic determinant of immune responsiveness. To fill this gap, we mined copy number alteration, somatic mutation, and expression data from The Cancer Genome Atlas (TCGA). By using RNA-sequencing data from 1,004 breast cancers, we defined distinct immune phenotypes characterized by progressive expression of transcripts previously associated with immune-mediated rejection...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28342987/circular-rnas-and-cancer
#6
Jun He, Qichao Xie, Hailin Xu, Jiantian Li, Yongsheng Li
Circular RNAs (circRNAs) are a type of non-coding RNA molecules that lack a 5'-terminal cap and 3'-terminal poly A tail. A large number of circRNAs have been identified through biological experiments, computational methods and high-throughput sequencing. CircRNA sequence composition determines if a given circRNA is exonic, intronic or retained-intronic. CircRNAs are more abundant and stable than linear mRNAs, and their expression is both step- and location-specific. CircRNAs mediate transcriptional and post-transcriptional regulation of gene and protein expression...
March 22, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28342451/tert-promoter-mutations-in-telomere-biology
#7
REVIEW
Barbara Heidenreich, Rajiv Kumar
Telomere repeats at chromosomal ends, critical to genome integrity, are maintained through an elaborate network of proteins and pathways. Shelterin complex proteins shield telomeres from induction of DNA damage response to overcome end protection problem. A specialized ribonucleic protein, telomerase, maintains telomere homeostasis through repeat addition to counter intrinsic shortcomings of DNA replication that leads to gradual sequence shortening in successive mitoses. The biogenesis and recruitment of telomerase composed of telomerase reverse transcriptase (TERT) subunit and an RNA component, takes place through the intricate machinery that involves an elaborate number of molecules...
January 2017: Mutation Research
https://www.readbyqxmd.com/read/28341852/profiling-of-long-non-coding-rnas-identifies-linc00958-and-linc01296-as-candidate-oncogenes-in-bladder-cancer
#8
Anna Katharina Seitz, Lise Lotte Christensen, Emil Christensen, Kasper Faarkrog, Marie Stampe Ostenfeld, Jakob Hedegaard, Iver Nordentoft, Morten Muhlig Nielsen, Johan Palmfeldt, Michelle Thomson, Michael Theis Solgaard Jensen, Roman Nawroth, Tobias Maurer, Torben Falck Ørntoft, Jørgen Bjerggaard Jensen, Christian Kroun Damgaard, Lars Dyrskjøt
Aberrant expression of long non-coding RNAs (lncRNAs) has been regarded as a critical component in bladder cancer (BC) and lncRNAs have been associated with BC development and progression although their overall expression and functional significance is still unclear. The aim of our study was to identify novel lncRNAs with a functional role in BC carcinogenesis. RNA-sequencing was used to identify aberrantly expressed lncRNAs in 8 normal and 72 BC samples. We identified 89 lncRNAs that were significantly dys-regulated in BC...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28340574/myocyte-enhancer-factor-2d-provides-a-cross-talk-between-chronic-inflammation-and-lung-cancer
#9
Hai-Xing Zhu, Lin Shi, Yong Zhang, Yi-Chun Zhu, Chun-Xue Bai, Xiang-Dong Wang, Jie-Bai Zhou
BACKGROUND: Lung cancer is the leading cause of cancer-related morbidity and mortality worldwide. Patients with chronic respiratory diseases, such as chronic obstructive pulmonary disease (COPD), are exposed to a higher risk of developing lung cancer. Chronic inflammation may play an important role in the lung carcinogenesis among those patients. The present study aimed at identifying candidate biomarker predicting lung cancer risk among patients with chronic respiratory diseases. METHODS: We applied clinical bioinformatics tools to analyze different gene profile datasets with a special focus on screening the potential biomarker during chronic inflammation-lung cancer transition...
March 24, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28339459/functional-classification-of-dna-variants-by-hybrid-minigenes-identification-of-30-spliceogenic-variants-of-brca2-exons-17-and-18
#10
Eugenia Fraile-Bethencourt, Beatriz Díez-Gómez, Valeria Velásquez-Zapata, Alberto Acedo, David J Sanz, Eladio A Velasco
Mutation screening of the breast cancer genes BRCA1 and BRCA2 identifies a large fraction of variants of uncertain clinical significance (VUS) whose functional and clinical interpretations pose a challenge for genomic medicine. Likewise, an increasing amount of evidence indicates that genetic variants can have deleterious effects on pre-mRNA splicing. Our goal was to investigate the impact on splicing of a set of reported variants of BRCA2 exons 17 and 18 to assess their role in hereditary breast cancer and to identify critical regulatory elements that may constitute hotspots for spliceogenic variants...
March 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28339031/p53-inducible-long-non-coding-rna-picart1-mediates-cancer-cell-proliferation-and-migration
#11
Yu Cao, Minglin Lin, Yiwen Bu, Hongyan Ling, Yingchun He, Chenfei Huang, Yi Shen, Bob Song, Deliang Cao
Long non-coding RNAs (lncRNAs) function in the development and progression of cancer, but only a small portion of lncRNAs have been characterized to date. A novel lncRNA transcript, 2.53 kb in length, was identified by transcriptome sequencing analysis, and was named p53-inducible cancer-associated RNA transcript 1 (PICART1). PICART1 was found to be upregulated by p53 through a p53-binding site at -1808 to -1783 bp. In breast and colorectal cancer cells and tissues, PICART1 expression was found to be decreased...
March 20, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28337281/c-myc-induced-upregulation-of-lncrna-snhg12-regulates-cell-proliferation-apoptosis-and-migration-in-triple-negative-breast-cancer
#12
Ouchen Wang, Fan Yang, Yehuan Liu, Lin Lv, Ruimin Ma, Chuanzhi Chen, Jiao Wang, Qiufan Tan, Yue Cheng, Erjie Xia, Yizuo Chen, Xiaohua Zhang
Triple-negative breast cancer (TNBC) is one of the most aggressive subtypes of breast cancer, with a significantly higher recurrence and mortality rate. There is an urgent need to uncover the mechanism underlying TNBC and establish therapeutic targets. Long non-coding RNAs (lncRNAs) are involved in a series of biological functions and provide novel insights into the molecular mechanism of cancer. Based on their expression specificity and large number, lncRNAs are likely to serve as the basis for clinical applications in oncology...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28337072/precision-metagenomics-rapid-metagenomic-analyses-for-infectious-disease-diagnostics-and-public-health-surveillance
#13
Ebrahim Afshinnekoo, Chou Chou, Noah Alexander, Sofia Ahsanuddin, Audrey N Schuetz, Christopher E Mason
Next-generation sequencing (NGS) technologies have ushered in the era of precision medicine, transforming the way we treat cancer patients and diagnose disease. Concomitantly, the advent of these technologies has created a surge of microbiome and metagenomic studies over the last decade, many of which are focused on investigating the host-gene-microbial interactions responsible for the development and spread of infectious diseases, as well as delineating their key role in maintaining health. As we continue to discover more information about the etiology of infectious diseases, the translational potential of metagenomic NGS methods for treatment and rapid diagnosis is becoming abundantly clear...
March 21, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28335559/the-optimization-and-characterization-of-an-rna-cleaving-fluorogenic-dnazyme-probe-for-mda-mb-231-cell-detection
#14
Pengcheng Xue, Shengnan He, Yu Mao, Long Qu, Feng Liu, Chunyan Tan, Yuyang Jiang, Ying Tan
Breast cancer is one of the most frequently diagnosed cancers in females worldwide and lacks specific biomarkers for early detection. In a previous study, we obtained a selective RNA-cleaving Fluorogenic DNAzyme (RFD) probe against MDA-MB-231 cells, typical breast cancer cells, through the systematic evolution of ligands by exponential process (SELEX). To improve the performance of this probe for actual application, we carried out a series of optimization experiments on the pH value of a reaction buffer, the type and concentration of cofactor ions, and sequence minimization...
March 21, 2017: Sensors
https://www.readbyqxmd.com/read/28335433/evaluation-and-adaptation-of-a-laboratory-based-cdna-library-preparation-protocol-for-retrospective-sequencing-of-archived-micrornas-from-up-to-35-year-old-clinical-ffpe-specimens
#15
Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert Greenlee, Deborah Multerer, Stacey Honda, Yihe Daida, Heather Spencer Feigelson, Andrew Glass, Fergus J Couch, Thomas Rohan, Iddo Z Ben-Dov
Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years...
March 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28330331/identification-and-quantification-of-novel-rna-isoforms-in-horn-cancer-of-bos-indicus-by-comprehensive-rna-seq
#16
Subhash J Jakhesara, Prakash G Koringa, Neelam M Nathani, Chaitanya G Joshi
Horn cancer (HC) is a squamous cell carcinoma of horn, commonly observed in Bos indicus of the Asian countries. To elucidate the complexity of alternative splicing present in the HC, high-throughput sequencing and analysis of HC and matching horn normal (HN) tissue were carried out. A total of 535,067 and 849,077 reads were analysed after stringent quality filtering for HN and HC, respectively. Cufflinks pipeline for transcriptome analysis revealed 4786 novel splice isoforms comprising 2432 exclusively in HC, 2055 exclusively in HN and 298 in both the conditions...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329686/demethylated-hsatii-dna-and-hsatii-rna-foci-sequester-prc1-and-mecp2-into-cancer-specific-nuclear-bodies
#17
Lisa L Hall, Meg Byron, Dawn M Carone, Troy W Whitfield, Gayle P Pouliot, Andrew Fischer, Peter Jones, Jeanne B Lawrence
This study reveals that high-copy satellite II (HSATII) sequences in the human genome can bind and impact distribution of chromatin regulatory proteins and that this goes awry in cancer. In many cancers, master regulatory proteins form two types of cancer-specific nuclear bodies, caused by locus-specific deregulation of HSATII. DNA demethylation at the 1q12 mega-satellite, common in cancer, causes PRC1 aggregation into prominent Cancer-Associated Polycomb (CAP) bodies. These loci remain silent, whereas HSATII loci with reduced PRC1 become derepressed, reflecting imbalanced distribution of UbH2A on these and other PcG-regulated loci...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28329662/the-preneoplastic-genome-transcriptomic-drivers-of-squamous-cell-carcinoma-development
#18
Kenneth Y Tsai
Cutaneous squamous cell carcinoma (cuSCC) comprises 15-20% of all skin cancers, accounting for over 700,000 cases in the U.S. annually. Most cuSCC arise in association with a distinct precancerous lesion, the actinic keratosis (AK). In order to identify potential targets for molecularly targeted chemoprevention, we performed integrated cross-species genomic analysis of cuSCC development through the preneoplastic AK stage using matched human samples and a solar UV- driven Hairless mouse model. We performed RNA-seq and microRNA-seq on samples from both patients undergoing Mohs surgery and the mouse model...
September 15, 2016: Dermatology Online Journal
https://www.readbyqxmd.com/read/28327926/genomic-characterisation-of-her2-positive-breast-cancer-and-response-to-neoadjuvant-trastuzumab-and-chemotherapy-results-from-the-acosog-z1041-alliance-trial
#19
R Lesurf, O L Griffith, M Griffith, J Hundal, L Trani, M A Watson, R Aft, M J Ellis, D Ota, V J Suman, F Meric-Bernstam, A M Leitch, J C Boughey, G Unzeitig, A U Buzdar, K K Hunt, E R Mardis
Background: HER2 ( ERBB2 ) gene amplification and its corresponding overexpression are present in 15-30% of invasive breast cancers. While HER2-targeted agents are effective treatments, resistance remains a major cause of death. The American College of Surgeons Oncology Group Z1041 trial (NCT00513292) was designed to compare the pathologic complete response (pCR) rate of distinct regimens of neoadjuvant chemotherapy and trastuzumab, but ultimately identified no difference [1]. Patients and methods: In supplement to tissues from 37 Z1041 cases, 11 similarly treated cases were obtained from a single institution study (NCT00353483)...
February 21, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28327201/detecting-gene-signature-activation-in-breast-cancer-in-an-absolute-single-patient-manner
#20
E R Paquet, R Lesurf, A Tofigh, V Dumeaux, M T Hallett
BACKGROUND: The ability to reliably identify the state (activated, repressed, or latent) of any molecular process in the tumor of a patient from an individual whole-genome gene expression profile obtained from microarray or RNA sequencing (RNA-seq) promises important clinical utility. Unfortunately, all previous bioinformatics tools are only applicable in large and diverse panels of patients, or are limited to a single specific pathway/process (e.g. proliferation). METHODS: Using a panel of 4510 whole-genome gene expression profiles from 10 different studies we built and selected models predicting the activation status of a compendium of 1733 different biological processes...
March 21, 2017: Breast Cancer Research: BCR
keyword
keyword
94103
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"