Abstract
Specific and sensitive noninvasive biofluid-based biomarkers are always needed in the laboratory diagnosis of diseases. Biomarkers are applied not only for diagnostic purposes but for stratifying a disease and for assessing the therapy response or disease progression. MicroRNAs (miRNAs) are short noncoding RNA molecules regulating gene expression posttranscriptionally. They are frequently dysregulated in many physiological and pathophysiological conditions. miRNAs are present in the circulation and in other biofluids that are common matrices for clinical laboratory testing that has raised the possibility that miRNAs may serve as novel biomarkers. Their excellent stability also supports the possibility that miRNAs once will be routinely used biomarkers in clinical practice. From an analytical point of view, there are many factors (starting material, sample storage and processing, different RNA extraction and detection methods, intra- and interassay variability, and assay interferences) to consider if a miRNA as biomarker is aimed to be introduced as a clinical laboratory test. Despite several pre-analytical and analytical factors that still need standardization, a significant number of studies have been published about the potential role of circulating miRNAs as biomarkers. Due to the lack of standardization of methods, there are a lot of discrepancies among results. In this chapter, we aimed to summarize the current findings about circulating miRNAs focusing on the analytical points related to miRNAs measurements from biofluids.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Akane A, Matsubara K, Nakamura H et al (1994) Identification of the heme compound copurified with deoxyribonucleic acid (DNA) from bloodstains, a major inhibitor of polymerase chain reaction (PCR) amplification. J Forensic Sci 39:362–372
Al-Soud WA, Rådström P (2001) Purification and characterization of PCR-inhibitory components in blood cells. J Clin Microbiol 39:485–493
Al-Soud WA, Jönsson LJ, Râdström P (2000) Identification and characterization of immunoglobulin G in blood as a major inhibitor of diagnostic PCR. J Clin Microbiol 38:345–350
Arroyo JD, Chevillet JR, Kroh EM et al (2011) Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci USA 108:5003–5008
Benz F, Roderburg C, Vargas Cardenas D et al (2013) U6 is unsuitable for normalization of serum miRNA levels in patients with sepsis or liver fibrosis. Exp Mol Med 45, e42
Brase JC, Wuttig D, Kuner R et al (2010) Serum microRNAs as non-invasive biomarkers for cancer. Mol Cancer 9:306
Bryant RJ, Pawlowski T, Catto JW et al (2012) Changes in circulating microRNA levels associated with prostate cancer. Br J Cancer 106:768–774
Castoldi M, Schmidt S, Benes V et al (2006) A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). RNA 12:913–920
Chen X, Ba Y, Ma L et al (2008) Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18:997–1006
Cheng G (2015) Circulating miRNAs: roles in cancer diagnosis, prognosis and therapy. Adv Drug Deliv Rev 81:75–93
Cheng Y, Zhang X, Li Z et al (2009) Highly sensitive determination of microRNA using target-primed and branched rolling-circle amplification. Angew Chem Int Ed Engl 48:3268–3272
Chevillet JR, Lee I, Briggs HA et al (2014) Issues and prospects of microRNA-based biomarkers in blood and other body fluids. Molecules 19:6080–6105
Cissell KA, Rahimi Y, Shrestha S et al (2008) Bioluminescence-based detection of microRNA, miR21 in breast cancer cells. Anal Chem 80:2319–2325
Cortez MA, Bueso-Ramos C, Ferdin J et al (2011) MicroRNAs in body fluids--the mix of hormones and biomarkers. Nat Rev Clin Oncol 8:467–477
Duygu B, de Windt LJ, da Costa Martins PA (2015) Targeting microRNAs in heart failure. Trends Cardiovasc Med. doi:10.1016/j.tcm.2015.05.008 [Epub ahead of print]
Farazi TA, Hoell JI, Morozov P et al (2013) MicroRNAs in human cancer. Adv Exp Med Biol 774:1–20
Farina NH, Wood ME, Perrapato SD et al (2014) Standardizing analysis of circulating microRNA: clinical and biological relevance. J Cell Biochem 115:805–811
Gadelha MR, Kasuki L, Dénes J et al (2013) MicroRNAs: suggested role in pituitary adenoma pathogenesis. J Endocrinol Invest 36:889–895
Git A, Dvinge H, Salmon-Divon M et al (2010) Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 16:991–1006
Grasedieck S, Sorrentino A, Langer C et al (2013) Circulating microRNAs in hematological diseases: principles, challenges, and perspectives. Blood 121:4977–4984
Heegaard NH, Schetter AJ, Welsh JA et al (2012) Circulating micro-RNA expression profiles in early stage nonsmall cell lung cancer. Int J Cancer 130:1378–1386
Hindson CM, Chevillet JR, Briggs HA et al (2013) Absolute quantification by droplet digital PCR versus analog real-time PCR. Nat Methods 10:1003–1005
Hong CY, Chen X, Liu T et al (2013) Ultrasensitive electrochemical detection of cancer-associated circulating microRNA in serum samples based on DNA concatamers. Biosens Bioelectron 50:132–136
Hossain MM, Sohel MM, Schellander K et al (2012) Characterization and importance of microRNAs in mammalian gonadal functions. Cell Tissue Res 349:679–690
Hu J, Wang Z, Liao BY et al (2014) Human miR-1228 as a stable endogenous control for the quantification of circulating microRNAs in cancer patients. Int J Cancer 135:1187–1194
Huang X, Yuan T, Tschannen M et al (2013) Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genomics 14:319
Jia H, Li Z, Liu C et al (2010) Ultrasensitive detection of microRNAs by exponential isothermal amplification. Angew Chem Int Ed Engl 49:5498–5501
Jiang Z, Song Q, Yang S et al (2015) Serum microRNA-218 is a potential biomarker for esophageal cancer. Cancer Biomark. doi:10.3233/CBM-150480 [Epub ahead of print]
Kim DJ, Linnstaedt S, Palma J et al (2012a) Plasma components affect accuracy of circulating cancer-related microRNA quantitation. J Mol Diagn 14:71–80
Kim YK, Yeo J, Kim B et al (2012b) Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells. Mol Cell 46:893–895
Köberle V, Pleli T, Schmithals C et al (2013) Differential stability of cell-free circulating microRNAs: implications for their utilization as biomarkers. PLoS ONE 8, e75184
Kriebel S, Schmidt D, Holdenrieder S et al (2015) Analysis of tissue and serum microRNA expression in patients with upper urinary tract urothelial cancer. PLoS ONE 10, e0117284
Lagos-Quintana M, Rauhut R, Lendeckel W et al (2001) Identification of novel genes coding for small expressed RNAs. Science 294:853–858
Lawrie CH, Gal S, Dunlop HM et al (2008) Detection of elevated levels of tumour-associated microRNAs in serum of patients with diffuse large B-cell lymphoma. Br J Haematol 141:672–675
Leone V, D’Angelo D, Ferraro A et al (2011) A TSH-CREB1-microRNA loop is required for thyroid cell growth. Mol Endocrinol 10:1819–1830
Li X (2014) MiR-375, a microRNA related to diabetes. Gene 533:1–4
Li A, Yu J, Kim H et al (2013) MicroRNA array analysis finds elevated serum miR-1290 accurately distinguishes patients with low-stage pancreatic cancer from healthy and disease controls. Clin Cancer Res 19:3600–3610
Lisse TS, Adams JS, Hewison M (2013) Vitamin D and microRNAs in bone. Crit Rev Eukaryot Gene Expr 23:195–214
McDonald JS, Milosevic D, Reddi HV et al (2011) Analysis of circulating microRNA: preanalytical and analytical challenges. Clin Chem 57:833–840
Mestdagh P, Hartmann N, Baeriswyl L et al (2014) Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study. Nat Methods 11:809–815
Meyer SU, Pfaffl MW, Ulbrich SE (2010) Normalization strategies for microRNA profiling experiments: a ‘normal’ way to a hidden layer of complexity? Biotechnol Lett 32:1777–1788
Mishra PJ, Bertino JR (2009) MicroRNA polymorphisms: the future of pharmacogenomics, molecular epidemiology and individualized medicine. Pharmacogenomics 10:399–416
Mishra PJ, Merlino G (2009) MicroRNA reexpression as differentiation therapy in cancer. J Clin Invest 119:2119–2123
Mishra PJ, Humeniuk R, Mishra PJ et al (2007) A miR-24 microRNA binding-site polymorphism in dihydrofolate reductase gene leads to methotrexate resistance. Proc Natl Acad Sci USA 104:13513–13518
Mishra PJ, Song B, Mishra PJ et al (2009) MiR-24 tumor suppressor activity is regulated independent of p53 and through a target site polymorphism. PLoS ONE 4, e8445
Mitchell PS, Parkin RK, Kroh EM et al (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA 105:10513–10518
Nelson PT, Baldwin DA, Scearce LM et al (2004) Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods 1:155–161
Orom UA, Nielsen FC, Lund AH (2008) MicroRNA-10a binds the 5′UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 30:460–471
Page K, Guttery DS, Zahra N et al (2013) Influence of plasma processing on recovery and analysis of circulating nucleic acids. PLoS ONE 8, e77963
Pallante P, Battista S, Pierantoni GM et al (2014) Deregulation of microRNA expression in thyroid neoplasias. Nat Rev Endocrinol 10:88–101
Place RF, Li LC, Pookot D et al (2008) MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci USA 105:1608–1613
Pritchard CC, Cheng HH, Tewari M (2012a) MicroRNA profiling: approaches and considerations. Nat Rev Genet 13:358–369
Pritchard CC, Kroh E, Wood B et al (2012b) Blood cell origin of circulating microRNAs: a cautionary note for cancer biomarker studies. Cancer Prev Res 5:492–497
Redova M, Poprach A, Nekvindova J et al (2012) Circulating miR-378 and miR-451 in serum are potential biomarkers for renal cell carcinoma. J Transl Med 10:55
Rottiers V, Naar AM (2012) MicroRNAs in metabolism and metabolic disorders. Nat Rev Mol Cell Biol 13:239–250
Sanders I, Holdenrieder S, Walgenbach-Brünagel G et al (2012) Evaluation of reference genes for the analysis of serum miRNA in patients with prostate cancer, bladder cancer and renal cell carcinoma. Int J Urol 19:1017–1025
Schopman NC, Heynen S, Haasnoot J et al (2010) A miRNA-tRNA mix-up: tRNA origin of proposed miRNA. RNA Biol 7:573–576
Shende VR, Goldrick MM, Ramani S et al (2011) Expression and rhythmic modulation of circulating microRNAs targeting the clock gene Bmal1 in mice. PLoS ONE 6, e22586
Silva J, García V, Zaballos Á et al (2010) Vesicle-related microRNAs in plasma of nonsmall cell lung cancer patients and correlation with survival. Eur Respir J 37:617–623
Singh P, Soon PS, Feige JJ et al (2011) Dysregulation of microRNAs in adrenocortical tumors. Mol Cell Endocrinol 351:118–128
Sivapragasam M, Rotondo F, Lloyd RV et al (2011) MicroRNAs in the human pituitary. Endocr Pathol 22:134–143
Song J, Bai Z, Han W et al (2011) Identification of suitable reference genes for qPCR analysis of serum microRNA in gastric cancer patients. Dig Dis Sci 57:897–904
Szabó PM, Butz H, Igaz P et al (2013) Minireview: miRomics in endocrinology: a novel approach for modeling endocrine diseases. Mol Endocrinol 274:573–585
Turchinovich A, Weiz L, Langheinz A et al (2011) Characterization of extracellular circulating microRNA. Nucleic Acids Res 39:7223–7233
Turchinovich A, Weiz L, Burwinkel B (2012) Extracellular miRNAs: the mystery of their origin and function. Trends Biochem Sci 37:460–465
Van Ness J, Van Ness LK, Galas DJ (2003) Isothermal reactions for the amplification of oligonucleotides. Proc Natl Acad Sci USA 100:4504–4509
Vlassov AV, Magdaleno S, Setterquist R et al (2012) Exosomes: current knowledge of their composition, biological functions, and diagnostic and therapeutic potentials. Biochim Biophys Acta 1820:940–948
von Brandenstein M, Pandarakalam JJ, Kroon L et al (2012) MicroRNA 15a, inversely correlated to PKCα, is a potential marker to differentiate between benign and malignant renal tumors in biopsy and urine samples. Am J Pathol 180:1787–1797
Wang B, Howel P, Bruheim S et al (2011) Systematic evaluation of three microRNA profiling platforms: microarray, beads array, and quantitative real-time PCR array. PLoS ONE 6, e17167
Wang K, Yuan Y, Cho JH et al (2012) Comparing the MicroRNA spectrum between serum and plasma. PLoS ONE 7, e41561
Witwer KW (2015) Circulating microRNA biomarker studies: pitfalls and potential solutions. Clin Chem 61:56–63
Witwer KW, Buzás EI, Bemis LT et al (2013) Standardization of sample collection, isolation and analysis methods in extracellular vesicle research. J Extracell Vesicles 2.doi:10.3402/jev.v2i0.20360
Yamada A, Cox MA, Gaffney KA et al (2014) Technical factors involved in the measurement of circulating microRNA biomarkers for the detection of colorectal neoplasia. PLoS ONE 9, e112481
Zen K, Zhang CY (2012) Circulating microRNAs: a novel class of biomarkers to diagnose and monitor human cancers. Med Res Rev 32:326–348
Zhang J, Guo H, Qian G (2010) MiR-145, a new regulator of the DNA fragmentation factor-45 (DFF45)-mediated apoptotic network. Mol Cancer 9:211
Zhang J, Zhao H, Gao Y et al (2012) Secretory miRNAs as novel cancer biomarkers. Biochim Biophys Acta 1826:32–43
Zheng G, Wang H, Zhang X et al (2013) Identification and validation of reference genes for qPCR detection of serum microRNAs in colorectal adenocarcinoma patients. PLoS ONE 8, e83025
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Butz, H., Patócs, A. (2015). Technical Aspects Related to the Analysis of Circulating microRNAs. In: Igaz, P. (eds) Circulating microRNAs in Disease Diagnostics and their Potential Biological Relevance. Experientia Supplementum, vol 106. Springer, Basel. https://doi.org/10.1007/978-3-0348-0955-9_3
Download citation
DOI: https://doi.org/10.1007/978-3-0348-0955-9_3
Published:
Publisher Name: Springer, Basel
Print ISBN: 978-3-0348-0953-5
Online ISBN: 978-3-0348-0955-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)