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Correlation of long non-coding RNA expression with metastasis, drug resistance and clinical outcome in cancer

Ehsan Malek, Sajjeev Jagannathan, James J. Driscoll
2014 OncoTarget  
Non-coding RNAs (ncRNAs) are recently discovered molecules that regulate eukaryotic gene expression and represent a significant advance towards a better understanding of the mechanisms that govern cellular  ...  NcRNAs are essential for the proper regulation of cell proliferation and survival under physiologic conditions and are deregulated in many pathologies, e.g., human cancers.  ...  (B) Distribution of RNA types within the human genome. (C) Distribution of non-coding RNA types within the human genome.  ... 
doi:10.18632/oncotarget.2469 pmid:25275300 pmcid:PMC4226665 fatcat:xbxyk3zygfevpjea5q35rhrowa

A Central Role for Long Non-Coding RNA in Cancer

Sheetal A. Mitra, Anirban P. Mitra, Timothy J. Triche
2012 Frontiers in Genetics  
Long non-coding RNAs (ncRNAs) have been shown to regulate important biological processes that support normal cellular functions.  ...  We also highlight the possibility of using these unique RNAs as diagnostic and prognostic biomarkers in malignancies.  ...  The human genome has more "dark matter" when compared to that of Drosophila. RNA polymerase II transcribes both protein-coding and non-coding transcripts.  ... 
doi:10.3389/fgene.2012.00017 pmid:22363342 pmcid:PMC3279698 fatcat:ouzer23cqzfate742zry2xb3ua

Genome‑wide analysis reveals the emerging roles of long non‑coding RNAs in cancer (Review)

Xiaoxia Ren
2019 Oncology Letters  
Recently, the general application of microarrays and high-throughput sequencing technology has revealed various important roles of long noncoding RNAs (lncRNAs) in cancer.  ...  Collectively, genome-wide analysis is the inexorable trend of future studies or clinical applications of lncRNAs and offers a novel perspective regarding the prognosis and treatment of cancer.  ...  Djebali et al (2) have also used sequencing technology to reveal that <2% of the human genome encodes proteins, and three-quarters of the human genome is actively transcribed into non-coding RNAs.  ... 
doi:10.3892/ol.2019.11141 pmid:31897174 pmcid:PMC6924088 fatcat:spvyqpff2nebxjh6fue32fqrde

The Functions and Unique Features of LncRNAs in Cancer Development and Tumorigenesis

Kenzui Taniue, Nobuyoshi Akimitsu
2021 International Journal of Molecular Sciences  
Over the past decades, research on cancer biology has focused on the involvement of protein-coding genes in cancer development.  ...  Long noncoding RNAs (lncRNAs), which are transcripts longer than 200 nucleotides that lack protein-coding potential, are an important class of RNA molecules that are involved in a variety of biological  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms22020632 pmid:33435206 fatcat:h3ydfymvtfftpdggbtlre5x2jq

Dysregulated Transcriptional Control in Prostate Cancer

Simon J. Baumgart, Ekaterina Nevedomskaya, Bernard Haendler
2019 International Journal of Molecular Sciences  
The rapid progress made in understanding the influence of the non-coding part of the genome and of transcription dysregulation in prostate cancer could pave the way for the identification of novel treatment  ...  Recent advances in whole-genome and transcriptome sequencing of prostate cancer at different stages indicate that a large number of mutations found in tumors are present in non-protein coding regions of  ...  Conflicts of Interest: The authors are employees and/or own shares of Bayer AG.  ... 
doi:10.3390/ijms20122883 fatcat:qooccjwlwrfldfklifiixtly4i

Cancer whole-genome sequencing: present and future

H Nakagawa, C P Wardell, M Furuta, H Taniguchi, A Fujimoto
2015 Oncogene  
fusion genes, and pathogen detection in cancer genomes remain widely unexplored.  ...  WGS approaches can detect these unexplored mutations, as well as coding mutations and somatic copy number alterations, and help us to better understand the whole landscape of cancer genomes and elucidate  ...  ACKNOWLEDGEMENTS We thank researchers and technical staffs in RIKEN-IMS and Professor Miyano and his fellows in Human Genome Center, Institute of Medical Science, The University of Tokyo for their great  ... 
doi:10.1038/onc.2015.90 pmid:25823020 fatcat:b2mot3e2tzbkjl5g4twehj6ude

CRISPR screen in cancer: status quo and future perspectives

Chenglong He, Siqi Han, Yue Chang, Meijuan Wu, Yulu Zhao, Cheng Chen, Xiaoyuan Chu
2021 American Journal of Cancer Research  
Clustered regularly interspaced short palindromic repeats (CRISPR) system offers a powerful platform for genome manipulation, including protein-coding genes, noncoding RNAs and regulatory elements.  ...  Here, we review the recent advances of CRISPR screen in cancer studies both in vitro and in vivo, with a particular focus on identifying cancer immunotherapy targets, and propose optimizing strategies  ...  Acknowledgements This work was supported by grants from National Natural Science Foundation of China (81872042 and 81972333), Foundation of Jiangsu Province (BK20181238) and Jiangsu  ... 
pmid:33948344 pmcid:PMC8085856 fatcat:a57jlropgvg4zgbgwd4gzc3g34

Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer

Anshika Chowdhary, Venkata Satagopam, Reinhard Schneider
2021 Frontiers in Genetics  
Long non-coding RNAs are diverse class of non-coding RNA molecules >200 base pairs of length having various functions like gene regulation, dosage compensation, epigenetic regulation.  ...  Here we present an comprehensive review the molecular mechanisms and functions, state of the art experimental and computational pipelines and challenges involved in the identification and functional annotation  ...  FUNCTIONS AND MECHANISMS OF LONG NON-CODING RNAS The elucidation of the mechanisms of long non-coding RNAs is mostly based on empirical evidence of the subcellular localization, developmental stage of  ... 
doi:10.3389/fgene.2021.649619 doaj:e24a384c23f94dfd82a6a0212a6f34aa fatcat:hzxn5mjydbbfdfob5ixoit6uxm

8q24.21 Locus: A Paradigm to Link Non-Coding RNAs, Genome Polymorphisms and Cancer

Claire Wilson, Aditi Kanhere
2021 International Journal of Molecular Sciences  
The majority of the human genome is comprised of non-protein-coding genes, but the relevance of non-coding RNAs in complex diseases has yet to be fully elucidated.  ...  One class of non-coding RNAs is long non-coding RNAs or lncRNAs, many of which have been identified to play a range of roles in transcription and translation.  ...  These non-coding RNAs, or ncRNAs, if functional, can explain the mystery of the non-coding human genome.  ... 
doi:10.3390/ijms22031094 pmid:33499210 pmcid:PMC7865353 fatcat:kfhpwjp2vzgnvlztnxolhmbyxi

Next-Generation Sequencing in the Understanding of Kaposi's Sarcoma-Associated Herpesvirus (KSHV) Biology

Roxanne Strahan, Timsy Uppal, Subhash Verma
2016 Viruses  
has improved our understanding of human cancers and cancer-related viruses.  ...  In this review, we have complied the most recent findings about the application of NGS in Kaposi's sarcoma-associated herpesvirus (KSHV) biology, including identification of novel genomic features and  ...  This work was supported from the National Institute of Health (CA174459 and AI105000) and the Research Scholar Grant (124389-RSG-13-230-01-MPC) from the American Cancer Society.  ... 
doi:10.3390/v8040092 pmid:27043613 pmcid:PMC4848587 fatcat:u5ualgt3srd6hma6hyvl6fmkyy

Long noncoding RNAs and viral infections

Quan Zhang, Kuan-Teh Jeang
2013 BioMedicine  
The functional role of long [31] Gutschner T, Diederichs S. The hallmarks of cancer: a long non-coding RNA in human carcinomas.  ...  proteins for the elongation of polypeptide; rRNAs are essential A small portion (less than 2%) of the human genome is used to elements for protein translation [8,9].  ... 
doi:10.1016/j.biomed.2013.01.001 pmid:23645970 pmcid:PMC3641704 fatcat:4bjbp2d66ngqpaj6pmijyikrfa

Long Non-coding RNAs in Gammaherpesvirus Infections: Their Roles in Tumorigenic Mechanisms

Wen Liu, Yan Zhang, Bing Luo
2021 Frontiers in Microbiology  
Long non-coding RNAs (lncRNAs) regulate gene expression at the epigenetic, transcriptional, or posttranscriptional level by interacting with protein, DNA, and RNA.  ...  targets for tumor diagnostics and treatment.  ...  FUNDING This work was supported by the Shandong Provincial Natural Science Foundation (ZR2017BH106) and the China Postdoctoral Science Foundation (2017M610411).  ... 
doi:10.3389/fmicb.2020.604536 pmid:33519750 pmcid:PMC7843584 fatcat:xtxuqqcyprccpi3nfmoyp4jqmm

Decoding human cancer with whole genome sequencing: a review of PCAWG Project studies published in February 2020

Simona Giunta
2021 Cancer Metastasis Review  
In an unprecedented international effort, the Pan-Cancer Analysis of Whole Genomes (PCAWG) of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) sequenced the tumors of  ...  What set this project apart from earlier efforts is the use of whole genome sequencing (WGS) that enabled to explore alterations beyond the coding DNA, into cancer's non-coding genome.  ...  Acknowledgements The author is deeply thankful to Elisa Balzano for critical reading and help with assembling references, tables, and Fig. 1 of this manuscript.  ... 
doi:10.1007/s10555-021-09969-z pmid:34097189 pmcid:PMC8180541 fatcat:qfdyx4qzpzf5zecl7knzbsycsu

Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes

A Sveen, S Kilpinen, A Ruusulehto, R A Lothe, R I Skotheim
2015 Oncogene  
In this review, we provide an overview of aberrant RNA splicing and its regulation in cancer. We then focus on the executors of the splicing process.  ...  In cancer, the splicing process is commonly disrupted, resulting in both functional and non-functional end-products.  ...  ACKNOWLEDGEMENTS This study was supported by the Southern and Eastern Norway Regional Health Authority (Research Grant 'Genome Medicine of Colorectal Cancer', project number 2011024), the Norwegian Cancer  ... 
doi:10.1038/onc.2015.318 pmid:26300000 fatcat:aucunencojeclnlxmate2p6edq

Long Non-Coding RNAs: Tools for Understanding and Targeting Cancer Pathways

Gaurav Kumar Pandey, Chandrasekhar Kanduri
2022 Cancers  
The regulatory nature of long non-coding RNAs (lncRNAs) has been well established in various processes of cellular growth, development, and differentiation.  ...  However, whether these non-coding molecules can work as either key drivers or barriers to cancer development remains unknown.  ...  General Features and Roles of Long Non-Coding RNAs LncRNAs are non-protein-coding RNA species that are around 200 base pair or more in size.  ... 
doi:10.3390/cancers14194760 fatcat:e7f3tf2twbhrfe7pyunzwkk5ua
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