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Xi X, Li T, Huang Y, Sun J, Zhu Y, Yang Y, Lu ZJ. RNA Biomarkers: Frontier of Precision Medicine for Cancer. Noncoding RNA 2017; 3:ncrna3010009. [PMID: 29657281 PMCID: PMC5832009 DOI: 10.3390/ncrna3010009] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/13/2017] [Indexed: 12/15/2022] Open
Abstract
As an essential part of central dogma, RNA delivers genetic and regulatory information and reflects cellular states. Based on high-throughput sequencing technologies, cumulating data show that various RNA molecules are able to serve as biomarkers for the diagnosis and prognosis of various diseases, for instance, cancer. In particular, detectable in various bio-fluids, such as serum, saliva and urine, extracellular RNAs (exRNAs) are emerging as non-invasive biomarkers for earlier cancer diagnosis, tumor progression monitor, and prediction of therapy response. In this review, we summarize the latest studies on various types of RNA biomarkers, especially extracellular RNAs, in cancer diagnosis and prognosis, and illustrate several well-known RNA biomarkers of clinical utility. In addition, we describe and discuss general procedures and issues in investigating exRNA biomarkers, and perspectives on utility of exRNAs in precision medicine.
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Affiliation(s)
- Xiaochen Xi
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Tianxiao Li
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Yiming Huang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Jiahui Sun
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Yumin Zhu
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Yang Yang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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Abstract
The identification of common tumor signatures can discover the shared molecular mechanisms underlying tumorgenesis whereby we can prevent and treat tumors by a system intervention. We identified tumor-associated signatures including pathways, transcription factors, microRNAs and gene ontology categories by analyzing gene sets for differential expression between normal vs. tumor phenotypes classes in various tumor gene expression datasets. We obtained the common tumor signatures based on their identified frequencies for different tumor types. Some shared signatures important for various tumor types were uncovered and discussed. We proposed that the interventions aiming at both the shared tumor signatures and the tissue-specific tumor signatures might be a potential approach to overcoming cancer.
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Affiliation(s)
- Xiaosheng Wang
- Biometric Research Branch, National Cancer Institute, National Institutes of Health, Rockville, MD 20852, USA.
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Zywicki M, Bakowska-Zywicka K, Polacek N. Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis. Nucleic Acids Res 2012; 40:4013-24. [PMID: 22266655 PMCID: PMC3351166 DOI: 10.1093/nar/gks020] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The exploration of the non-protein-coding RNA (ncRNA) transcriptome is currently focused on profiling of microRNA expression and detection of novel ncRNA transcription units. However, recent studies suggest that RNA processing can be a multi-layer process leading to the generation of ncRNAs of diverse functions from a single primary transcript. Up to date no methodology has been presented to distinguish stable functional RNA species from rapidly degraded side products of nucleases. Thus the correct assessment of widespread RNA processing events is one of the major obstacles in transcriptome research. Here, we present a novel automated computational pipeline, named APART, providing a complete workflow for the reliable detection of RNA processing products from next-generation-sequencing data. The major features include efficient handling of non-unique reads, detection of novel stable ncRNA transcripts and processing products and annotation of known transcripts based on multiple sources of information. To disclose the potential of APART, we have analyzed a cDNA library derived from small ribosome-associated RNAs in Saccharomyces cerevisiae. By employing the APART pipeline, we were able to detect and confirm by independent experimental methods multiple novel stable RNA molecules differentially processed from well known ncRNAs, like rRNAs, tRNAs or snoRNAs, in a stress-dependent manner.
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Affiliation(s)
- Marek Zywicki
- Innsbruck Biocenter, Medical University Innsbruck, Division of Genomics and RNomics, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria.
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