Skip to main content

Intracellular and Organic miRNA In Situ Detection

  • Chapter
  • First Online:
MicroRNA Detection and Pathological Functions

Part of the book series: SpringerBriefs in Molecular Science ((BRIEFSMOLECULAR))

  • 949 Accesses

Abstract

The detection methods of miRNA in intracellular or organisms fall into two broad categories: indirect detection and direct analysis. The indirect measurement of the expression levels of miRNAs in cells and tissues involves cells lysis and detection by qRT-PCR, northern blotting, or microarray hybridization. The direct analysis methods are a noninvasive manner for repetitively monitoring and obtaining real-time imaging of the intracellular miRNA by using imaging analysis or in situ hybridization (ISH). Technologies for direct detection of the temporal and spatial expression sequence of specific miRNA in cells or tissues are extremely important for elucidating miRNA biology. The progress of optical imaging techniques with multimodal reporter systems holds great promise for noninvasive and real-time imaging of molecular agent expression in living cell. Recent progress in nanotechnology and imaging detection techniques leads to multifunctional nanoprobe with specific-transfection, tracing, and regulation function in intracellular miRNA detection. ISH holds great promise for visualization of the spatial localization of RNA at the tissue, cellular, and even subcellular level.

Haifeng Dong, Xiangdan Meng and Wenhao Dai contributed together to this chapter.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Sinn P, Sauter S, McCray P (2005) Gene therapy progress and prospects: development of improved lentiviral and retroviral vectors–design, biosafety, and production. Gene Ther 12:1089–1098

    Article  CAS  Google Scholar 

  2. Niidome T, Huang L (2002) Gene therapy progress and prospects: nonviral vectors. Gene Ther 9:1647–1652

    Article  CAS  Google Scholar 

  3. McNamara JO, Andrechek ER, Wang Y, Viles KD, Rempel RE, Gilboa E, Sullenger BA, Giangrande PH (2006) Cell type–specific delivery of siRNAs with aptamer-siRNA chimeras. Nat Biotechnol 24:1005–1015

    Article  CAS  Google Scholar 

  4. Hong R, Bai W, Zhai J, Liu W, Li X, Zhang J, Cui X, Zhao X, Ye X, Deng Q (2013) Novel recombinant hepatitis B virus vectors efficiently deliver protein and RNA encoding genes into primary hepatocytes. J Virol 87:6615–6624

    Article  CAS  Google Scholar 

  5. Karlsen TA, Brinchmann JE (2013) Liposome delivery of microRNA-145 to mesenchymal stem cells leads to immunological off-target effects mediated by RIG-I. Mol Ther 21:1169–1181

    Article  CAS  Google Scholar 

  6. Wang K, Zhang X, Liu Y, Liu C, Jiang B, Jiang Y (2014) Tumor penetrability and anti-angiogenesis using iRGD-mediated delivery of doxorubicin-polymer conjugates. Biomaterials 35:8735–8747

    Article  CAS  Google Scholar 

  7. Dong H, Ding L, Yan F, Ji H, Ju H (2011) The use of polyethylenimine-grafted graphene nanoribbon for cellular delivery of locked nucleic acid modified molecular beacon for recognition of microRNA. Biomaterials 32:3875–3882

    Article  CAS  Google Scholar 

  8. Park K, Lee S, Kang E, Kim K, Choi K, Kwon IC (2009) New generation of multifunctional nanoparticles for cancer imaging and therapy. Adv Funct Mater 19:1553–1566

    Article  CAS  Google Scholar 

  9. Bonanni A, Chua CK, Zhao G, Sofer ZK, Pumera M (2012) Inherently electroactive graphene oxide nanoplatelets as labels for single nucleotide polymorphism detection. ACS nano 6:8546–8551

    Google Scholar 

  10. Neely LA, Patel S, Garver J, Gallo M, Hackett M, McLaughlin S, Nadel M, Harris J, Gullans S, Rooke J (2006) A single-molecule method for the quantitation of microRNA gene expression. Nat Methods 3:41–46

    Article  CAS  Google Scholar 

  11. Erickson K, Erni R, Lee Z, Alem N, Gannett W, Zettl A (2010) Determination of the local chemical structure of graphene oxide and reduced graphene oxide. Adv Mater 22:4467–4472

    Article  CAS  Google Scholar 

  12. Gambhir SS, Barrio JR, Herschman HR, Phelps ME (1999) Assays for noninvasive imaging of reporter gene expression. Nucl Med Biol 26:481–490

    Article  CAS  Google Scholar 

  13. Blasberg RG (2003) In vivo molecular-genetic imaging: multi-modality nuclear and optical combinations. Nucl Med Biol 30:879–888

    Article  CAS  Google Scholar 

  14. Wang XL, Rosol M, Ge SD, Peterson D, McNamara G, Pollack H, Kohn DB, Nelson MD, Crooks GM (2003) Dynamic tracking of human hematopoietic stem cell engraftment using in vivo bioluminescence imaging. Blood 102:3478–3482

    Article  CAS  Google Scholar 

  15. Kim KI, Chung J-K, Kang JH, Lee YJ, Shin JH, Oh HJ, Jeong JM, Lee DS, Lee MC (2005) Visualization of endogenous p53-mediated transcription in vivo using sodium iodide symporter. Clin Cancer Res 11:123–128

    Google Scholar 

  16. Ryoo S-R, Lee J, Yeo J, Na H-K, Kim Y-K, Jang H, Lee JH, Han SW, Lee Y, Kim VN, Min D-H (2013) Quantitative and multiplexed microRNA sensing in living cells based on peptide nucleic acid and nano graphene oxide (PANGO). ACS Nano 7:5882–5891

    Article  CAS  Google Scholar 

  17. Zhi F, Dong H, Jia X, Guo W, Lu H, Yang Y, Ju H, Zhang X, Hu Y (2013) Functionalized graphene oxide mediated adriamycin delivery and miR-21 gene silencing to overcome tumor multidrug resistance in vitro. PLoS one 8:e60034

    Article  CAS  Google Scholar 

  18. Zhang P, He Z, Wang C, Chen J, Zhao J, Zhu X, Li C-Z, Min Q, Zhu JJ (2015) In situ amplification of intracellular microRNA with MNAzyme nanodevices for multiplexed imaging, logic operation, and controlled drug release. ACS Nano 9:789–798

    Article  CAS  Google Scholar 

  19. Zhang J, Fu Y, Mei Y, Jiang F, Lakowicz JR (2010) Fluorescent metal nanoshell probe to detect single miRNA in lung cancer cell. Anal Chem 82:4464–4471

    Article  CAS  Google Scholar 

  20. Li H, Mu Y, Qian S, Lu J, Wan Y, Fu G, Liu S (2015) Synthesis of fluorescent dye-doped silica nanoparticles for target-cell-specific delivery and intracellular microRNA imaging. Analyst 140:567–573

    Article  CAS  Google Scholar 

  21. Lin L-S, Cong Z-X, Cao J-B, Ke K-M, Peng Q-L, Gao J, Yang H-H, Liu G, Chen X (2014) Multifunctional Fe3O4@polydopamine core–shell nanocomposites for intracellular mRNA detection and imaging-guided photothermal therapy. ACS Nano 8:3876–3883

    Article  CAS  Google Scholar 

  22. Wu Y, Han J, Xue P, Xu R, Kang Y (2014) Nano metal-organic framework (NMOF)-based strategies for multiplexed microRNA detection in solution and living cancer cells. Nanoscale 7:1753–1759

    Google Scholar 

  23. Dong H, Lei J, Ju H, Zhi F, Wang H, Guo W, Zhu Z, Yan F (2012) Target-cell-specific delivery, imaging, and detection of intracellular MicroRNA with a multifunctional SnO2 nanoprobe. Angew Chem Int Ed 51:4607–4612

    Article  CAS  Google Scholar 

  24. Brasier A, Tate J, Habener J (1988) Optimized use of the firefly luciferase assay as a reporter gene in mammalian cell lines. Biotechniques 7:1116–1122

    Google Scholar 

  25. Gould SJ, Subramani S (1988) Firefly luciferase as a tool in molecular and cell biology. Anal Biochem 175:5–13

    Article  CAS  Google Scholar 

  26. Tannous BA, Kim D-E, Fernandez JL, Weissleder R, Breakefield XO (2005) Codon-optimized Gaussia luciferase cDNA for mammalian gene expression in culture and in vivo. Mol Ther 11:435–443

    Article  CAS  Google Scholar 

  27. Ottobrini L, Ciana P, Biserni A, Lucignani G, Maggi A (2006) Molecular imaging: a new way to study molecular processes in vivo. Mol Cell Endocrinol 246:69–75

    Article  CAS  Google Scholar 

  28. Doubrovin M, Serganova I, Mayer-Kuckuk P, Ponomarev V, Blasberg RG (2004) Multimodality in vivo molecular-genetic imaging. Bioconjugate Chem 15:1376–1388

    Article  CAS  Google Scholar 

  29. Lee JY, Kim S, Jeong JM, Chung J-K, Lee MC, Lee DS (2008) Development of a dual-luciferase reporter system for in vivo visualization of MicroRNA biogenesis and posttranscriptional regulation. J Nucl Med 49:285–294

    Article  CAS  Google Scholar 

  30. Ko HY, Lee DS, Kim S (2009) Noninvasive imaging of microRNA124a-mediated repression of the chromosome 14 ORF 24 gene during neurogenesis. FEBS J 276:4854–4865

    Article  CAS  Google Scholar 

  31. Davies BP, Arenz C (2008) A fluorescence probe for assaying micro RNA maturation. Bioorg Med Chem 16:49–55

    Article  CAS  Google Scholar 

  32. Kim HJ, Kim YH, Lee DS, Chung J-K, Kim S (2008) In vivo imaging of functional targeting of miR-221 in papillary thyroid carcinoma. J Nucl Med 49:1686–1693

    Article  CAS  Google Scholar 

  33. Wessels JT, Yamauchi K, Hoffman RM, Wouters FS (2010) Advances in cellular, subcellular, and nanoscale imaging in vitro and in vivo. Cytometry Part A 77A:667–676

    Article  CAS  Google Scholar 

  34. Kato Y, Miyaki S, Yokoyama S, Omori S, Inoue A, Horiuchi M, Asahara H (2009) Real-time functional imaging for monitoring miR-133 during myogenic differentiation. Int J Biochem Cell Biol 41:2225–2231

    Article  CAS  Google Scholar 

  35. Kato Y, Sawata SY, Inoue A (2010) A lentiviral vector encoding two fluorescent proteins enables imaging of adenoviral infection via adenovirus-encoded miRNAs in single living cells. J Biochem 147:63–71

    Article  CAS  Google Scholar 

  36. Brown BD, Venneri MA, Zingale A, Sergi LS, Naldini L (2006) Endogenous microRNA regulation suppresses transgene expression in hematopoietic lineages and enables stable gene transfer. Nat Med 12:585–591

    Article  CAS  Google Scholar 

  37. Tyagi S, Kramer FR (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol, 303–8

    Google Scholar 

  38. Kang WJ, Cho YL, Chae JR, Lee JD, Choi K-J, Kim S (2011) Molecular beacon-based bioimaging of multiple microRNAs during myogenesis. Biomaterials 32:1915–1922

    Article  CAS  Google Scholar 

  39. Hwang DW, Song IC, Lee DS, Kim S (2010) Smart magnetic fluorescent nanoparticle imaging probes to monitor microRNAs. Small 6:81–88

    Article  CAS  Google Scholar 

  40. Ge J, Zhang LL, Liu SJ, Yu RQ, Chu X (2014) A highly sensitive target-primed rolling circle amplification (TPRCA) method for fluorescent in situ hybridization detection of microRNA in tumor cells. Anal Chem 86:1808–1815

    Article  CAS  Google Scholar 

  41. Deng R, Tang L, Tian Q, Wang Y, Lin L, Li J (2014) Toehold-initiated rolling circle amplification for visualizing individual microRNAs in situ in single cells. Angew Chem Int Ed 53:2389–2393

    Article  CAS  Google Scholar 

  42. Dean ZS, Riahi R, Wong PK (2015) Spatiotemporal dynamics of microRNA during epithelial collective cell migration. Biomaterials 37:156–163

    Article  CAS  Google Scholar 

  43. Fox MD, Raichle ME (2007) Spontaneous fluctuations in brain activity observed with functional magnetic resonance imaging. Nat Rev Neurosci 8:700–711

    Article  CAS  Google Scholar 

  44. Kang JH, Chung J-K (2008) Molecular-genetic imaging based on reporter gene expression. J Nucl Med 49:164S–179S

    Article  CAS  Google Scholar 

  45. Rutman AM, Kuo MD (2009) Radiogenomics: creating a link between molecular diagnostics and diagnostic imaging. Eur J Radiol 70:232–241

    Article  Google Scholar 

  46. Zinn PO, Majadan B, Sathyan P, Singh SK, Majumder S, Jolesz FA, Colen RR (2011) Radiogenomic mapping of edema/cellular invasion MRI-phenotypes in glioblastoma multiforme. PLoS one 6:e25451

    Article  CAS  Google Scholar 

  47. Thompson RC, Deo M, Turner DL (2007) Analysis of microRNA expression by in situ hybridization with RNA oligonucleotide probes. Methods 43:153–161

    Article  CAS  Google Scholar 

  48. Levsky JM, Shenoy SM, Pezo RC, Singer RH (2002) Single-cell gene expression profiling. Science 297:836–840

    Article  CAS  Google Scholar 

  49. Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S (2008) Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods 5:877–879

    Article  CAS  Google Scholar 

  50. Politz JCR, Zhang F, Pederson T (2006) MicroRNA-206 colocalizes with ribosome-rich regions in both the nucleolus and cytoplasm of rat myogenic cells. Proc Natl Acad Sci 103:18957–18962

    Article  CAS  Google Scholar 

  51. Schneider M, Andersen DC, Silahtaroglu A, Lyngbæk S, Kauppinen S, Hansen JL, Sheikh SP (2011) Cell-specific detection of microRNA expression during cardiomyogenesis by combined in situ hybridization and immunohistochemistry. J Mol Histol 42:289–299

    Article  CAS  Google Scholar 

  52. Raap A, Van de Corput M, Vervenne R, Van Gijlswijk R, Tanke H, Wiegant J (1995) Ultra-sensitive FISH using peroxidase-mediated deposition of biotin-or fluorochrome tyramides. Hum Mol Genet 4:529–534

    Article  CAS  Google Scholar 

  53. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Rådmark O, Kim S (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425:415–419

    Article  CAS  Google Scholar 

  54. Nuovo G (1995) In situ PCR: protocols and applications. Genome Res 4:S151–S167

    Article  CAS  Google Scholar 

  55. Langer PR, Waldrop AA, Ward DC (1981) Enzymatic synthesis of biotin-labeled polynucleotides: novel nucleic acid affinity probes. Proc Natl Acad Sci 78:6633–6637

    Article  CAS  Google Scholar 

  56. Femino AM, Fay FS, Fogarty K, Singer RH (1998) Visualization of single RNA transcripts in situ. Science 280:585–590

    Article  CAS  Google Scholar 

  57. Neely LA, Patel S, Garver J, Gallo M, Hackett M, McLaughlin S, Nadel M, Harris J, Gullans S, Rooke J (2005) A single-molecule method for the quantitation of microRNA gene expression. Nat Methods 3:41–46

    Article  Google Scholar 

  58. Baker MB, Bao G, Searles CD (2012) In vitro quantification of specific microRNA using molecular beacons. Nucleic Acids Res 40:e13

    Article  CAS  Google Scholar 

  59. Obernosterer G, Martinez J, Alenius M (2007) Locked nucleic acid-based in situ detection of microRNAs in mouse tissue sections. Nat Protoc 2:1508–1514

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Xueji Zhang .

Rights and permissions

Reprints and permissions

Copyright information

© 2015 The Author(s)

About this chapter

Cite this chapter

Zhang, X., Dong, H., Tian, Y. (2015). Intracellular and Organic miRNA In Situ Detection. In: MicroRNA Detection and Pathological Functions. SpringerBriefs in Molecular Science. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-47293-4_7

Download citation

Publish with us

Policies and ethics