A comparative analysis of high-throughput platforms for validation of a circulating microRNA signature in diabetic retinopathy

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Farr, Ryan J ^a   Januszewski, Andrzej S ^b   Joglekar, Mugdha V ^a   Liang, Helena ^c   McAulley, Annie K ^c   Hewitt, Alex W ^c   Thomas, Helen E ^d   Loudovaris, Tom ^d   Kay, Thomas W H ^d   Jenkins, Alicia ^b   Hardikar, Anandwardhan A ^a  

^a University of Sydney   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

^c UNIVERSITY OF MELBOURNE   (Australia)

^d ST VINCENT'S INSTITUTE OF MEDICAL RESEARCH   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; MICRORNA;

BLOOD; CLUSTER ANALYSIS; DIABETIC RETINOPATHY; FLUORESCENCE ANGIOGRAPHY; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; PATHOLOGY;

BIOMARKERS; CLUSTER ANALYSIS; DIABETIC RETINOPATHY; FLUORESCEIN ANGIOGRAPHY; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICRORNAS;

EID: 84934882204     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep10375     Document Type: Article

References (30)

1. Kim, V. N., Han, J. & Siomi, M. C. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol. 10, 126-139, doi:10.1038/nrm2632 (2009).
2. Joglekar, M. V., Parekh, V. S. & Hardikar, A. A. New pancreas from old: microregulators of pancreas regeneration. Trends Endocrinol Metab 18, 393-400, doi:10.1016/j.tem.2007.10.001 (2007).
3. Joglekar, M. V., Parekh, V. S., Mehta, S., Bhonde, R. R. & Hardikar, A. A. MicroRNA profiling of developing and regenerating pancreas reveal post-transcriptional regulation of neurogenin3. Dev Biol 311, 603-612, doi:10.1016/j.ydbio.2007.09.008 (2007).
4. Gauthier, B. R. & Wollheim, C. B. MicroRNAs: 'ribo-regulators' of glucose homeostasis. Nat Medicine 12, 36-38, doi:10.1038/nm0106-36 (2006).
5. Poy, M. N. et al. A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432, 226-230, doi:10.1038/nature03076 (2004).
6. Poy, M. N. et al. miR-375 maintains normal pancreatic alpha- and beta-cell mass. Proc Nat Acad Sci USA 106, 5813-5818, doi:10.1073/pnas.0810550106 (2009).
7. Lynn, F. C. Meta-regulation: microRNA regulation of glucose and lipid metabolism. Trends Endocrinol Metab 20, 452-459, doi:10.1016/j.tem.2009.05.007 (2009).
8. Asaga, S. et al. Direct serum assay for microRNA-21 concentrations in early and advanced breast cancer. Clinical Chem 57, 84-91, doi:10.1373/clinchem.2010.151845 (2011).
9. Hayes, J., Peruzzi, P. P. & Lawler, S. MicroRNAs in cancer: biomarkers, functions and therapy. Trends Mol Med 20, 460-469, doi:10.1016/j.molmed.2014.06.005 (2014).
10. Liu, R. et al. Serum microRNA expression profile as a biomarker in the diagnosis and prognosis of pancreatic cancer. Clinical Chem 58, 610-618, doi:10.1373/clinchem.2011.172767 (2012).
11. Murray, M. J. et al. Identification of microRNAs from the miR-371~373 and miR-302 clusters as potential serum biomarkers of malignant germ cell tumors. Am J Clin Path 135, 119-125, doi:10.1309/AJCPOE11KEYZCJHT (2011).
12. Zhang, C. et al. Expression profile of microRNAs in serum: a fingerprint for esophageal squamous cell carcinoma. Clinical Chem 56, 1871-1879, doi:10.1373/clinchem.2010.147553 (2010).
13. Erener, S., Mojibian, M., Fox, J. K., Denroche, H. C. & Kieffer, T. J. Circulating miR-375 as a biomarker of beta-cell death and diabetes in mice. Endocrinology 154, 603-608, doi:10.1210/en.2012-1744 (2013).
14. Farr, R. J., Joglekar, M. V., Taylor, C. J. & Hardikar, A. A. Circulating non-coding RNAs as biomarkers of beta cell death in diabetes. Pediatr Endocrinol Rev: PER 11, 14-20 (2013).
15. Farr, R. J., Taylor, C. J., Satoor, S. N., Williams, M. D. & Joglekar, M. V. From Cradle to the Grave: Tissue-specific microRNA signatures in detecting clinical progression of diabetes. ncRNAs Endocrinol 1, 16-27 (2013).
16. Guay, C. & Regazzi, R. Circulating microRNAs as novel biomarkers for diabetes mellitus. Nature reviews. Endocrinology 9, 513-521, doi:10.1038/nrendo.2013.86 (2013).
17. Joglekar, M. V., Joglekar, V. M. & Hardikar, A. A. Expression of islet-specific microRNAs during human pancreatic development. Gene Exp Patt 9, 109-113, doi:10.1016/j.gep.2008.10.001 (2009).
18. Rosero, S. et al. MicroRNA signature of the human developing pancreas. BMC Genomics 11, 509, doi:10.1186/1471-2164-11-509 (2010).
19. Kalis, M. et al. Beta-cell specific deletion of Dicer1 leads to defective insulin secretion and diabetes mellitus. PloS one 6, e29166, doi:10.1371/journal.pone.0029166 (2011).
20. Melkman-Zehavi, T. et al. miRNAs control insulin content in pancreatic beta-cells via downregulation of transcriptional repressors. EMBO J 30, 835-845, doi:10.1038/emboj.2010.361 (2011).
21. Git, A. et al. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 16, 991-1006, doi:10.1261/rna.1947110 (2010).
22. Redshaw, N. et al. A comparison of miRNA isolation and RT-qPCR technologies and their effects on quantification accuracy and repeatability. BioTechniques 54, 155-164, doi:10.2144/000114002 (2013).
23. Mestdagh, P. et al. Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study. Nat Methods 11, 809-815, doi:10.1038/nmeth.3014 (2014).
24. Joglekar, M. V., Wei, C. & Hardikar, A. A. Quantitative estimation of multiple miRNAs and mRNAs from a single cell. Cold Spring Harb Protoc 2010, pdb prot5478, doi:10.1101/pdb.prot5478 2010/8/pdb.prot5478 (2010).
25. Fedick, A. et al. High-throughput carrier screening using TaqMan allelic discrimination. PloS one 8, e59722, doi:10.1371/journal. pone.0059722 (2013).
26. Morrison, T. et al. Nanoliter high throughput quantitative PCR. Nucleic Acids Res 34, e123, doi:gkl63910.1093/nar/gkl639 (2006).
27. Qin, J., Jones, R. C. & Ramakrishnan, R. Studying copy number variations using a nanofluidic platform. Nucleic Acids Res 36, e116, doi:10.1093/nar/gkn518gkn518 (2008).
28. Hardikar, A. A., Farr, R. J. & Joglekar, M. V. Circulating microRNAs: Understanding the limits for quantitative measurement by real-time PCR. J Am Heart Assoc 26; 3(1):e000792. doi: 10.1161/JAHA.113.000792.
29. Wong, W., Farr, R. J., Joglekar, M. V., Januszewski, A. S. & Hardikar, A.A. Probe-based real-time PCR approaches for quantitative measurement of microRNAs. J Vis Exp (in Press).
30. Taylor, C. J., Satoor, S. N., Ranjan, A. K., Pereira e Cotta, M. V. & Joglekar, M. V. A protocol for measurement of noncoding RNA in human serum. Exp Diabetes Res 2012, 2012:168368. doi: 10.1155/2012/168368.