Pre-profiling factors influencing serum microRNA levels

BMC Clinical Pathology

Cathie Garnis¹  Stephen Lam²  Calum MacAulay²  Sara A MacLellan² 

[1] Department of Surgery, University of British Columbia, Vancouver, BC, Canada;Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada

关键词: miR-139-5p;    miR-99a-5p;    Serum;    Biomarker;    Cancer;    MicroRNA;   

Others  :  1084622
DOI  :  10.1186/1472-6890-14-27

 received in 2013-10-21, accepted in 2014-06-13,  发布年份 2014

【 摘 要 】

Background

MicroRNAs (miRNAs) are non-coding RNAs that negatively regulate gene expression by preventing the translation of specific mRNA transcripts. Recent studies have shown that miRNAs are stably expressed in human serum samples, making them good candidates for the non-invasive detection of disease. However, before circulating miRNAs can be used reliably as biomarkers of disease, the pre-measurement variables that may affect serum miRNA levels must be assessed.

Methods

In this study we used quantitative RT-PCR to examine the effect of hemolysis, fasting, and smoking on the levels of 742 miRNAs in the serum of healthy individuals. We also compared serum miRNA profiles of samples taken from healthy individuals over different time periods to assess normal serum miRNA fluctuations.

Results

We have found that mechanical hemolysis of blood samples can significantly alter serum miRNA quantification and have identified 162 miRNAs that are significantly up-regulated in hemolysed serum samples. Conversely, fasting and smoking were demonstrated to not have a significant effect on the overall serum miRNA profiles of healthy individuals. The serum miRNA profiles of matched samples taken from individuals over varying time periods showed a high correlation and no miRNAs were significantly differentially expressed in these samples further suggesting the utility of serum miRNAs as biomarkers of disease. Taking the above results into consideration, we have identified miR-99a-5p and miR-139-5p as novel endogenous controls for serum miRNA studies due to their consistency across all sample sets.

Conclusion

These results identify important pre-profiling factors that should be taken into consideration when identifying endogenous controls and candidate biomarkers for circulating miRNA studies.

【 授权许可】

   
2014 MacLellan et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116(2):281-297.
• [2]Lewis BP, Burge CB, Bartel DP: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120(1):15-20.
• [3]Brennecke J, Cohen SM: Towards a complete description of the microRNA complement of animal genomes. Genome Biol 2003, 4(9):228.
• [4]Chen CZ, Li L, Lodish HF, Bartel DP: MicroRNAs modulate hematopoietic lineage differentiation. Science 2004, 303(5654):83-86.
• [5]Dostie J, Mourelatos Z, Yang M, Sharma A, Dreyfuss G: Numerous microRNPs in neuronal cells containing novel microRNAs. RNA 2003, 9(2):180-186.
• [6]Ioshikhes I, Roy S, Sen CK: Algorithms for mapping of mRNA targets for microRNA. DNA Cell Biol 2007, 26(4):265-272.
• [7]Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G: The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000, 403(6772):901-906.
• [8]Xu P, Vernooy SY, Guo M, Hay BA: The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr Biol 2003, 13(9):790-795.
• [9]Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, Peterson A, Noteboom J, O’Briant KC, Allen A, Lin DW, Urban N, Drescher CW, Knudsen BS, Stirewalt DL, Gentleman R, Vessella RL, Nelson PS, Martin DB, Tewari M: Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A 2008, 105(30):10513-10518.
• [10]Hsu SD, Chu CH, Tsou AP, Chen SJ, Chen HC, Hsu PW, Wong YH, Chen YH, Chen GH, Huang HD: miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res 2008, 36(Database issue):D165-D169.
• [11]Wang K, Zhang S, Marzolf B, Troisch P, Brightman A, Hu Z, Hood LE, Galas DJ: Circulating microRNAs, potential biomarkers for drug-induced liver injury. Proc Natl Acad Sci U S A 2009, 106(11):4402-4407.
• [12]Ai J, Zhang R, Li Y, Pu J, Lu Y, Jiao J, Li K, Yu B, Li Z, Wang R, Wang L, Li Q, Wang N, Shan H, Li Z, Yang B: Circulating microRNA-1 as a potential novel biomarker for acute myocardial infarction. Biochem Biophys Res Commun 2010, 391(1):73-77.
• [13]Tsujiura M, Ichikawa D, Komatsu S, Shiozaki A, Takeshita H, Kosuga T, Konishi H, Morimura R, Deguchi K, Fujiwara H, Okamoto K, Otsuji E: Circulating microRNAs in plasma of patients with gastric cancers. Br J Cancer 2010, 102(7):1174-1179.
• [14]Zhu W, Qin W, Atasoy U, Sauter ER: Circulating microRNAs in breast cancer and healthy subjects. BMC Res Notes 2009, 2:89.
• [15]Lawrie CH, Gal S, Dunlop HM, Pushkaran B, Liggins AP, Pulford K, Banham AH, Pezzella F, Boultwood J, Wainscoat JS, Hatton CS, Harris AL: Detection of elevated levels of tumour-associated microRNAs in serum of patients with diffuse large B-cell lymphoma. Br J Haematol 2008, 141(5):672-675.
• [16]Bianchi F, Nicassio F, Marzi M, Belloni E, Dall’olio V, Bernard L, Pelosi G, Maisonneuve P, Veronesi G, Di Fiore PP: A serum circulating miRNA diagnostic test to identify asymptomatic high-risk individuals with early stage lung cancer. EMBO Mol Med 2011, 3(8):495-503.
• [17]Brase JC, Wuttig D, Kuner R, Sultmann H: Serum microRNAs as non-invasive biomarkers for cancer. Mol Cancer 2010, 9:306.
• [18]Hunter MP, Ismail N, Zhang X, Aguda BD, Lee EJ, Yu L, Xiao T, Schafer J, Lee ML, Schmittgen TD, Nana-Sinkam SP, Jarjoura D, Marsh CB: Detection of microRNA expression in human peripheral blood microvesicles. PLoS One 2008, 3(11):e3694.
• [19]Duttagupta R, Jiang R, Gollub J, Getts RC, Jones KW: Impact of cellular miRNAs on circulating miRNA biomarker signatures. PLoS One 2011, 6(6):e20769.
• [20]McDonald JS, Milosevic D, Reddi HV, Grebe SK, Algeciras-Schimnich A: Analysis of circulating microRNA: preanalytical and analytical challenges. Clin Chem 2011, 57(6):833-840.
• [21]Pritchard CC, Kroh E, Wood B, Arroyo JD, Dougherty KJ, Miyaji MM, Tait JF, Tewari M: Blood cell origin of circulating microRNAs: a cautionary note for cancer biomarker studies. Cancer Prev Res (Phila) 2012, 5(3):492-497.
• [22]Blondal T, Jensby Nielsen S, Baker A, Andreasen D, Mouritzen P, Wrang Teilum M, Dahlsveen IK: Assessing sample and miRNA profile quality in serum and plasma or other biofluids. Methods 2012.
• [23]Kirschner MB, Edelman JJ, Kao SC, Vallely MP, van Zandwijk N, Reid G: The Impact of Hemolysis on Cell-Free microRNA Biomarkers. Front Genet 2013, 4:94.
• [24]Kroh EM, Parkin RK, Mitchell PS, Tewari M: Analysis of circulating microRNA biomarkers in plasma and serum using quantitative reverse transcription-PCR (qRT-PCR). Methods 2010, 50(4):298-301.
• [25]Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, Li J, Bian Z, Liang X, Cai X, Yin Y, Wang C, Zhang T, Zhu D, Zhang D, Xu J, Chen Q, Ba Y, Liu J, Wang Q, Chen J, Wang J, Wang M, Zhang Q, Zhang J, Zen K, Zhang C: Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res 2012, 22(1):107-126.
• [26]Yuxia M, Zhennan T, Wei Z: Circulating miR-125b is a novel biomarker for screening non-small-cell lung cancer and predicts poor prognosis. J Cancer Res Clin Oncol 2012, 138(12):2045-2050.
• [27]Parkin DM, Pisani P, Lopez AD, Masuyer E: At least one in seven cases of cancer is caused by smoking. Global estimates for 1985. Int J Cancer 1994, 59(4):494-504.
• [28]Roth C, Stuckrath I, Pantel K, Izbicki JR, Tachezy M, Schwarzenbach H: Low levels of cell-free circulating miR-361-3p and miR-625* as blood-based markers for discriminating malignant from benign lung tumors. PLoS One 2012, 7(6):e38248.
• [29]Dimeski G: Effects of hemolysis on the Roche ammonia method for Hitachi analyzers. Clin Chem 2004, 50(5):976-977.
• [30]Harboe M: A method for determination of hemoglobin in plasma by near-ultraviolet spectrophotometry. Scand J Clin Lab Invest 1959, 11:66-70.
• [31]Maclellan SA, Lawson J, Baik J, Guillaud M, Poh CF, Garnis C: Differential expression of miRNAs in the serum of patients with high-risk oral lesions. Cancer Med 2012, 1(2):268-274.
• [32]Mo MH, Chen L, Fu Y, Wang W, Fu SW: Cell-free Circulating miRNA Biomarkers in Cancer. J Cancer 2012, 3:432-448.
• [33]Lippi G, Salvagno GL, Montagnana M, Brocco G, Guidi GC: Influence of hemolysis on routine clinical chemistry testing. Clin Chem Lab Med 2006, 44(3):311-316.
• [34]Bihrer V, Friedrich-Rust M, Kronenberger B, Forestier N, Haupenthal J, Shi Y, Peveling-Oberhag J, Radeke HH, Sarrazin C, Herrmann E, Zeuzem S, Waidmann O, Piiper A: Serum miR-122 as a biomarker of necroinflammation in patients with chronic hepatitis C virus infection. Am J Gastroenterol 2011, 106(9):1663-1669.
• [35]Xu J, Wu C, Che X, Wang L, Yu D, Zhang T, Huang L, Li H, Tan W, Wang C, Lin D: Circulating microRNAs, miR-21, miR-122, and miR-223, in patients with hepatocellular carcinoma or chronic hepatitis. Mol Carcinog 2011, 50(2):136-142.
• [36]Lippi G, Salvagno GL, Favaloro EJ, Guidi GC: Survey on the prevalence of hemolytic specimens in an academic hospital according to collection facility: opportunities for quality improvement. Clin Chem Lab Med 2009, 47(5):616-618.
• [37]Sharp MK, Mohammad SF: Hemolysis in needleless connectors for phlebotomy. ASAIO J 2003, 49(1):128-130.
• [38]Zampetaki A, Mayr M: Analytical challenges and technical limitations in assessing circulating miRNAs. Thromb Haemost 2012, 108(4):592-598.
• [39]Mestdagh P, Van Vlierberghe P, De Weer A, Muth D, Westermann F, Speleman F, Vandesompele J: A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol 2009, 10(6):R64.
• [40]Wong TS, Liu XB, Wong BY, Ng RW, Yuen AP, Wei WI: Mature miR-184 as Potential Oncogenic microRNA of Squamous Cell Carcinoma of Tongue. Clin Cancer Res 2008, 14(9):2588-2592.
• [41]Zhan M, Miller CP, Papayannopoulou T, Stamatoyannopoulos G, Song CZ: MicroRNA expression dynamics during murine and human erythroid differentiation. Exp Hematol 2007, 35(7):1015-1025.
• [42]Witwer KW: XenomiRs and miRNA homeostasis in health and disease: evidence that diet and dietary miRNAs directly and indirectly influence circulating miRNA profiles. RNA Biol 2012, 9(9):1147-1154.
• [43]Huang Y, Dai Y, Zhang J, Wang C, Li D, Cheng J, Lu Y, Ma K, Tan L, Xue F, Qin B: Circulating microRNAs as potential biomarkers for smoking-related interstitial fibrosis. Biomarkers 2012, 17(5):435-440.