Assessing cellular and circulating miRNA recovery: The impact of the RNA isolation method and the quantity of input material

Scientific Reports

Volumn 6, Issue , 2016, Pages

  El Khoury, Victoria ^a   Pierson, Sandrine ^a   Kaoma, Tony ^a   Bernardin, François ^a   Berchem, Guy ^a,b  

^a LUXEMBOURG INSTITUTE OF HEALTH   (Luxembourg)

^b CENTRE HOSPITALIER DE LUXEMBOURG   (Luxembourg)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; MICRORNA;

BLOOD; BODY FLUID; CHEMISTRY; EXOSOME; GENE EXPRESSION PROFILING; GENETICS; HUMAN; ISOLATION AND PURIFICATION; PROCEDURES; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; TUMOR CELL LINE;

BIOMARKERS; BODY FLUIDS; CELL LINE, TUMOR; EXOSOMES; GENE EXPRESSION PROFILING; HUMANS; MICRORNAS; REAL-TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY;

EID: 84955263452     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep19529     Document Type: Article

References (33)

1. Witwer, K. W. Circulating microRNA biomarker studies: pitfalls and potential solutions. Clinical chemistry 61, 56-63, doi: 10.1373/clinchem.2014.221341 (2015).
2. Olena, A. F., Patton, J. G. Genomic organization of microRNAs. Journal of cellular physiology 222, 540-545, doi: 10.1002/jcp.21993 (2010).
3. Cheng, L., Sharples, R. A., Scicluna, B. J., Hill, A. F. Exosomes provide a protective and enriched source of miRNA for biomarker profiling compared to intracellular and cell-free blood. Journal of extracellular vesicles 3, doi: 10.3402/jev.v3.23743 (2014).
4. Lin, J. et al. Exosomes: novel biomarkers for clinical diagnosis. TheScientificWorldJournal 2015, 657086, doi: 10.1155/2015/657086 (2015).
5. Inns, J., James, V. Circulating microRNAs for the prediction of metastasis in breast cancer patients diagnosed with early stage disease. Breast 24, 364-369, doi: 10.1016/j.breast.2015.04.001 (2015).
6. Qin, X., Xu, H., Gong, W., Deng, W. The Tumor Cytosol miRNAs, Fluid miRNAs, and Exosome miRNAs in Lung Cancer. Frontiers in oncology 4, 357, doi: 10.3389/fonc.2014.00357 (2014).
7. Mitchell, P. S. et al. Circulating microRNAs as stable blood-based markers for cancer detection. Proceedings of the National Academy of Sciences of the United States of America 105, 10513-10518, doi: 10.1073/pnas.0804549105 (2008).
8. Moldovan, L. et al. Methodological challenges in utilizing miRNAs as circulating biomarkers. Journal of cellular and molecular medicine 18, 371-390, doi: 10.1111/jcmm.12236 (2014).
9. Channavajjhala, S. K. et al. Optimizing the purification and analysis of miRNAs from urinary exosomes. Clinical chemistry and laboratory medicine: CCLM/FESCC 52, 345-354, doi: 10.1515/cclm-2013-0562 (2014).
10. Masotti, A. et al. Quantification of small non-coding RNAs allows an accurate comparison of miRNA expression profiles. Journal of biomedicine & biotechnology 2009, 659028, doi: 10.1155/2009/659028 (2009).
11. Sourvinou, I. S., Markou, A., Lianidou, E. S. Quantification of circulating miRNAs in plasma: effect of preanalytical and analytical parameters on their isolation and stability. The Journal of molecular diagnostics: JMD 15, 827-834, doi: 10.1016/j.jmoldx.2013.07.005 (2013).
12. Cheng, L., Sun, X., Scicluna, B. J., Coleman, B. M., Hill, A. F. Characterization and deep sequencing analysis of exosomal and nonexosomal miRNA in human urine. Kidney international 86, 433-444, doi: 10.1038/ki.2013.502 (2014).
13. Kroh, E. M., Parkin, R. K., Mitchell, P. S., Tewari, M. Analysis of circulating microRNA biomarkers in plasma and serum using quantitative reverse transcription-PCR (qRT-PCR). Methods 50, 298-301, doi: 10.1016/j.ymeth.2010.01.032 (2010).
14. McDonald, J. S., Milosevic, D., Reddi, H. V., Grebe, S. K., Algeciras-Schimnich, A. Analysis of circulating microRNA: preanalytical and analytical challenges. Clinical chemistry 57, 833-840, doi: 10.1373/clinchem.2010.157198 (2011).
15. Tiberio, P., Callari, M., Angeloni, V., Daidone, M. G., Appierto, V. Challenges in using circulating miRNAs as cancer biomarkers. BioMed research international 2015, 731479, doi: 10.1155/2015/731479 (2015).
16. Monleau, M. et al. Comparison of different extraction techniques to profile microRNAs from human sera and peripheral blood mononuclear cells. BMC genomics 15, 395, doi: 10.1186/1471-2164-15-395 (2014).
17. Gaarz, A. et al. Bead array-based microrna expression profiling of peripheral blood and the impact of different RNA isolation approaches. The Journal of molecular diagnostics : JMD 12, 335-344, doi: 10.2353/jmoldx.2010.090116 (2010).
18. Moret, I. et al. Assessing an improved protocol for plasma microRNA extraction. PloS one 8, e82753, doi: 10.1371/journal. pone.0082753 (2013).
19. Tan, G. W., Khoo, A. S., Tan, L. P. Evaluation of extraction kits and RT-qPCR systems adapted to high-throughput platform for circulating miRNAs. Scientific reports 5, 9430, doi: 10.1038/srep09430 (2015).
20. Selth, L. A., Tilley, W. D., Butler, L. M. Circulating microRNAs: macro-utility as markers of prostate cancer Endocrine-related cancer 19, R99-R113, doi: 10.1530/ERC-12-0010 (2012).
21. McAlexander, M. A., Phillips, M. J., Witwer, K. W. Comparison of Methods for miRNA Extraction from Plasma and Quantitative Recovery of RNA from Cerebrospinal Fluid. Frontiers in genetics 4, 83, doi: 10.3389/fgene.2013.00083 (2013).
22. Page, K. et al. Influence of plasma processing on recovery and analysis of circulating nucleic acids. PloS one 8, e77963, doi: 10.1371/journal.pone.0077963 (2013).
23. Eldh, M., Lotvall, J., Malmhall, C., Ekstrom, K. Importance of RNA isolation methods for analysis of exosomal RNA: evaluation of different methods. Molecular immunology 50, 278-286, doi: 10.1016/j.molimm.2012.02.001 (2012)
24. Moldovan, L., Batte, K., Wang, Y., Wisler, J., Piper, M. Analyzing the circulating microRNAs in exosomes/extracellular vesicles from serum or plasma by qRT-PCR. Methods in molecular biology 1024, 129-145, doi: 10.1007/978-1-62703-453-1-10 (2013).
25. Alvarez, M. L., Khosroheidari, M., Kanchi Ravi, R., DiStefano, J. K. Comparison of protein, microRNA, and mRNA yields using different methods of urinary exosome isolation for the discovery of kidney disease biomarkers. Kidney international 82, 1024-1032, doi: 10.1038/ki.2012.256 (2012).
26. Pisitkun, T., Shen, R. F., Knepper, M. A. Identification and proteomic profiling of exosomes in human urine. Proceedings of the National Academy of Sciences of the United States of America 101, 13368-13373, doi: 10.1073/pnas.0403453101 (2004).
27. Janas, T., Janas, M. M., Sapon, K., Janas, T. Mechanisms of RNA loading into exosomes. FEBS letters 589, 1391-1398, doi: 10.1016/j. febslet.2015.04.036 (2015).
28. Li, M. et al. Analysis of the RNA content of the exosomes derived from blood serum and urine and its potential as biomarkers. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 369, doi: 10.1098/rstb.2013.0502 (2014).
29. Ach, R. A., Wang, H., Curry, B. Measuring microRNAs: comparisons of microarray and quantitative PCR measurements, and of different total RNA prep methods. BMC biotechnology 8, 69, doi:10.1186/1472-6750-8-69 (2008).
30. Kim, Y. K., Yeo, J., Kim, B., Ha, M., Kim, V. N. Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells. Molecular cell 46, 893-895, doi: 10.1016/j.molcel.2012.05.036 (2012).
31. Fichtlscherer, S. et al. Circulating microRNAs in patients with coronary artery disease. Circulation research 107, 677-684, doi: 10.1161/CIRCRESAHA.109.215566 (2010).
32. Fernandez-Llama, P. et al. Tamm-Horsfall protein and urinary exosome isolation. Kidney international 77, 736-742, doi: 10.1038/ki.2009.550 (2010).
33. Zhou, H. et al. Collection, storage, preservation, and normalization of human urinary exosomes for biomarker discovery. Kidney international 69, 1471-1476, doi: 10.1038/sj.ki.5000273 (2006).