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Chimeric RNA pp 211-218 | Cite as

Chimeric RNA and Exosomes-Based Liquid Biopsy

  • Xiurong Ke
  • Xiao Xiong
  • Yusheng Lin
  • Hao ZhangEmail author
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Exosomal chimeric RNA Liquid biopsy Disease diagnosis Exosome extraction and purification RT-qPCR 

Notes

Acknowledgments

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

References

  1. 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.2017.86CrossRefPubMedGoogle Scholar
  2. 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.2016.07.006CrossRefPubMedPubMedCentralGoogle Scholar
  3. 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-12-0042CrossRefPubMedGoogle Scholar
  4. 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.2005.02.047CrossRefPubMedGoogle Scholar
  5. 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.2012.06.006CrossRefPubMedPubMedCentralGoogle Scholar
  6. 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.201541116CrossRefPubMedPubMedCentralGoogle Scholar
  7. 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.2014.07.010CrossRefPubMedPubMedCentralGoogle Scholar
  8. 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.1465CrossRefPubMedPubMedCentralGoogle Scholar
  9. 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.2016.01.043CrossRefPubMedGoogle Scholar
  10. 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/nri855CrossRefPubMedGoogle Scholar
  11. 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.2017.14CrossRefPubMedGoogle Scholar
  12. 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.2017.02.020CrossRefPubMedGoogle Scholar
  13. 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/s41571-018-0036-9CrossRefPubMedGoogle Scholar
  14. 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/gkr828CrossRefPubMedGoogle Scholar
  15. 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.2014.09.005CrossRefPubMedPubMedCentralGoogle Scholar
  16. 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/gkx891CrossRefPubMedGoogle Scholar
  17. 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.2008.11.003CrossRefPubMedGoogle Scholar
  18. 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-18-3169CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Xiurong Ke
    • 1
    • 2
  • Xiao Xiong
    • 1
  • Yusheng Lin
    • 1
    • 3
  • Hao Zhang
    • 4
    • 5
    Email author
  1. 1.Cancer Research CenterShantou University Medical CollegeShantouChina
  2. 2.Laboratory for Translational Surgical Oncology, Department of Surgery, University Medical Center Groningen (UMCG)University of GroningenGroningenThe Netherlands
  3. 3.Department of Hematology, University Medical Center Groningen (UMCG)University of GroningenGroningenThe Netherlands
  4. 4.Institute of Precision Cancer and PathologyJinan University Medical CollegeGuangzhouChina
  5. 5.Department of PathologyJinan University Medical CollegeGuangzhouChina

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