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Chimeric RNA and Exosomes-Based Liquid Biopsy

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Chimeric RNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2079))

Abstract

Exosomes are considered as sources of disease biomarkers since they are stable carriers of genetic material and proteins. We recently demonstrated that chimeric RNA in exosomes derived from patient fluids can be detected and further used for disease diagnosis. Here we describe a systematic method to obtain exosomes from body fluids for detecting expression of specific chimeric RNA based on a RT-qPCR strategy.

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References

  1. Shi Y (2017) Mechanistic insights into precursor messenger RNA splicing by the spliceosome. Nat Rev Mol Cell Biol 18(11):655–670. https://doi.org/10.1038/nrm.2017.86

    Article  CAS  PubMed  Google Scholar 

  2. Jia Y, Xie Z, Li H (2016) Intergenically spliced chimeric RNAs in cancer. Trends Cancer 2(9):475–484. https://doi.org/10.1016/j.trecan.2016.07.006

    Article  PubMed  PubMed Central  Google Scholar 

  3. Zhang Y, Gong M, Yuan H et al (2012) Chimeric transcript generated by cis-splicing of adjacent genes regulates prostate cancer cell proliferation. Cancer Discov 2(7):598–607. https://doi.org/10.1158/2159-8290.CD-12-0042

    Article  CAS  PubMed  Google Scholar 

  4. Lopez-Bigas N, Audit B, Ouzounis C et al (2005) Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett 579(9):1900–1903. https://doi.org/10.1016/j.febslet.2005.02.047

    Article  CAS  PubMed  Google Scholar 

  5. Singh RK, Cooper TA (2012) Pre-mRNA splicing in disease and therapeutics. Trends Mol Med 18(8):472–482. https://doi.org/10.1016/j.molmed.2012.06.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Daguenet E, Dujardin G, Valcarcel J (2015) The pathogenicity of splicing defects: mechanistic insights into pre-mRNA processing inform novel therapeutic approaches. EMBO Rep 16(12):1640–1655. https://doi.org/10.15252/embr.201541116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Wang Y, Chen D, Qian H et al (2014) The splicing factor RBM4 controls apoptosis, proliferation, and migration to suppress tumor progression. Cancer Cell 26(3):374–389. https://doi.org/10.1016/j.ccr.2014.07.010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Zhang H, Lin W, Kannan K et al (2013) Aberrant chimeric RNA GOLM1-MAK10 encoding a secreted fusion protein as a molecular signature for human esophageal squamous cell carcinoma. Oncotarget 4(11):2135–2143. https://doi.org/10.18632/oncotarget.1465

    Article  PubMed  PubMed Central  Google Scholar 

  9. Tkach M, Thery C (2016) Communication by extracellular vesicles: where we are and where we need to go. Cell 164(6):1226–1232. https://doi.org/10.1016/j.cell.2016.01.043

    Article  CAS  PubMed  Google Scholar 

  10. Thery C, Zitvogel L, Amigorena S (2002) Exosomes: composition, biogenesis and function. Nat Rev Immunol 2(8):569–579. https://doi.org/10.1038/nri855

    Article  CAS  PubMed  Google Scholar 

  11. Siravegna G, Marsoni S, Siena S et al (2017) Integrating liquid biopsies into the management of cancer. Nat Rev Clin Oncol 14(9):531–548. https://doi.org/10.1038/nrclinonc.2017.14

    Article  CAS  PubMed  Google Scholar 

  12. Barile L, Vassalli G (2017) Exosomes: therapy delivery tools and biomarkers of diseases. Pharmacol Ther 174:63–78. https://doi.org/10.1016/j.pharmthera.2017.02.020

    Article  CAS  PubMed  Google Scholar 

  13. Xu R, Rai A, Chen M et al (2018) Extracellular vesicles in cancer - implications for future improvements in cancer care. Nat Rev Clin Oncol 15(10):617–638. https://doi.org/10.1038/s41571-018-0036-9

    Article  CAS  PubMed  Google Scholar 

  14. Mathivanan S, Fahner CJ, Reid GE et al (2012) ExoCarta 2012: database of exosomal proteins, RNA and lipids. Nucleic Acids Res 40. (Database issue:D1241–D1244. https://doi.org/10.1093/nar/gkr828

    Article  CAS  PubMed  Google Scholar 

  15. Melo SA, Sugimoto H, O’Connell JT et al (2014) Cancer exosomes perform cell-independent microRNA biogenesis and promote tumorigenesis. Cancer Cell 26(5):707–721. https://doi.org/10.1016/j.ccell.2014.09.005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Li S, Li Y, Chen B et al (2018) exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes. Nucleic Acids Res 46(D1):D106–D112. https://doi.org/10.1093/nar/gkx891

    Article  CAS  PubMed  Google Scholar 

  17. Cocucci E, Racchetti G, Meldolesi J (2009) Shedding microvesicles: artefacts no more. Trends Cell Biol 19(2):43–51. https://doi.org/10.1016/j.tcb.2008.11.003

    Article  CAS  PubMed  Google Scholar 

  18. Lin Y, Dong H, Deng W et al (2019) Evaluation of salivary exosomal chimeric GOLM1-NAA35 RNA as a potential biomarker in esophageal carcinoma. Clin Cancer Res 25:3035–3045. https://doi.org/10.1158/1078-0432.CCR-18-3169

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported in part by National Natural Science Foundation of China (81572876, 81773087, 81071736, and 30973508 to H.Z.).

Author information

Authors and Affiliations

  1. Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China

    Xiurong Ke, Xiao Xiong & Yusheng Lin

  2. Laboratory for Translational Surgical Oncology, Department of Surgery, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands

    Xiurong Ke

  3. Department of Hematology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands

    Yusheng Lin

  4. Institute of Precision Cancer and Pathology, Jinan University Medical College, Guangzhou, Guangdong, China

    Hao Zhang

  5. Department of Pathology, Jinan University Medical College, Guangzhou, Guangdong, China

    Hao Zhang

Authors
  1. Xiurong Ke
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  2. Xiao Xiong
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  3. Yusheng Lin
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  4. Hao Zhang
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Corresponding author

Correspondence to Hao Zhang .

Editor information

Editors and Affiliations

  1. Department of Paathology, School of Medicine, University of Virginia, Charlottesville, VA, USA, Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA

    Hui Li

  2. Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA

    Justin Elfman

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Ke, X., Xiong, X., Lin, Y., Zhang, H. (2020). Chimeric RNA and Exosomes-Based Liquid Biopsy. In: Li, H., Elfman, J. (eds) Chimeric RNA. Methods in Molecular Biology, vol 2079. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9904-0_16

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  • DOI: https://doi.org/10.1007/978-1-4939-9904-0_16

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9903-3

  • Online ISBN: 978-1-4939-9904-0

  • eBook Packages: Springer Protocols

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