Abstract
Molecular profiling of normal tissues is a regular and necessary step when developing systems for expression analyses in biological samples, including diagnostic panels for various diseases and conditions. Yet there are still no rigorous criteria to allow precise typing of normal tissues. A main problem is that the methods employed in diagnostic expression testing are difficult to standardize. While various technologies, instruments, and reagents are available, universal protocols of handling biological material are lacking, thus impairing the reproducibility of data from independent studies. The review describes a new approach to standardizing circulating microRNA studies in forensic biology, which has relatively recently (7–8 years ago) come to employ RNA markers in molecular typing of tissues and biological fluids. Forensic biology is now one of the few disciplines where several panels of tissue mRNA markers have been developed within a short period of time and a number of specific microRNA markers have been established and validated for several biological fluids. To allow their successful use, new protocols have been combined with the available, rigidly standardized system of genetic personal identification. Although a ready diagnostic product has still not been obtained with this well-working approach, the apparent efficiency of the standardization methods clearly demonstrates that the problem is possible to solve in other biomedical fields, including those where RNA-based diagnostic protocols are still under development.
Similar content being viewed by others
Abbreviations
- STR:
-
short tandem repeat
References
Keller A., Leidinger P., Gislefoss R., Haugen A., Langseth H., Staehler P., Lenhof H.P., Meese E. 2011. Stable serum miRNA profiles as potential tool for noninvasive lung cancer diagnosis. RNA Biol. 8, 506–516. doi 10.4161/rna.8.3.14994
Oury C., Servais L., Bouznad N., Hego A., Nchimi A., Lancellotti P. 2016. MicroRNAs in valvular heart diseases: potential role as markers and actors of valvular and cardiac remodeling. J. Mol. Sci. 17, 1–17. doi 10.3390/ijms17071120
Sethupathy P. 2016. The promise and challenge of therapeutic microRNA silencing in diabetes and metabolic diseases. Curr. Diab. Rep. 6, 1–6. doi 10.1007/s11892-016-0745-3
Dumache R., Rogobete A.F., Bedreag O.H., Sarandan M., Cradigati A.C., Papurica M., Dumbuleu C.M., Nartita R., Sandesc D. 2015. Use of miRNAs as biomarkers in sepsis. Anal. Cell Pathol. (Amst.). 2015 (186716), 1–9. doi 10.1155/2015/186716
Sun M., Zhou X., Chen L., Huang S., Leung V., Wu N., Pan H., Zhen W., Lu W., Peng S. 2016. The regulatory roles of microRNAs in bone remodeling and perspectives as biomarkers in osteoporosis. Biomed. Res. Int. 2016 (1652417), 1–11. doi 10.1155/2016/1652417
Sanders R., Mason D.J., Foy C.A., Huggett J.F. 2014. Considerations for accurate gene expression measurement by reverse transcription quantitative PCR when analysing clinical samples. Anal. Bioanal. Chem. 406, 6471–6483. doi 10.1007/s00216-014-7857-x
Hwang P.I., Wu H.B., Wang C.D., Lin B.L., Chen C.T., Yuan S., Wu G., Li K.C. 2011. Tissue-specific gene expression templates for accurate molecular characterization of the normal physiological states of multiple human tissues with implication in development and cancer studies. BMC Genomics. 12, 1–13. doi 10.1186/1471-2164-12-439
Bammler T., Beyer R.P., Bhattacharya S., Boorman G.A., Boyles A., Bradford B.U., Bumgarner R.E., Bushel P.R., Chaturvedi K., Choi D., Cunningham M.L., Deng S., Dressman H.K., Fannin R.D., Farin F.M., et al. 2005. Standardizing global gene expression analysis between laboratories and across platforms. Nat. Methods. 2, 351–356.
Aran D., Sirota M., Butte A.J. 2015. Systematic pancancer analysis of tumour purity. Nat. Commun. 6, 1–11. doi 10.1038/ncomms9971
Storey J.D., Madeoy J., Strout J.L., Wurfel M., Ronald J., Akey J.M. 2007. Gene-expression variation within and among human populations. Am. J. Hum. Genet. 80, 502–529.
Farina N.H., Wood M.E., Perrapato S.D., Francklyn C.S., Stein G.S., Stein J.L., Lian J.B. 2014. Standardizing analysis of circulating microRNA: Clinical and biological relevance. J. Cell Biochem. 115, 805–811. doi 10.1002/jcb.24745
Moldovan L., Batte K.E., Trgovcich J., Wisler J., Marsh C.B., Piper M.J. 2014. Methodological challenges in utilizing miRNAs as circulating biomarkers. J. Cell. Mol. Med. 18, 371–390. doi 10.1111/jcmm.12236
Lindenbergh A., Maaskant P., Sijen T. 2013. Implementation of RNA profiling in forensic casework. Forensic Sci. Int. Genet. 7, 159–166. doi 10.1016/j.fsigen.2012.09.003
Hanson E.K., Lubenow H., Ballantyne J. 2009. Identification of forensically relevant body fluids using a panel of differentially expressed microRNAs. Anal. Biochem. 387, 303–314.
van den Berge M., Carracedo A., Gomes I., Graham E.A., Haas C., Hjort B., Hoff-Olsen P., Maronas O., Mevag B., Morling N., Niederstatter H., Parson W., Schneider P.M., Court D.S., Vidaki A., Sijen T. 2014. A collaborative European exercise on mRNA-based body fluid/skin typing and interpretation of DNA and RNA results. Forensic Sci. Int. Genet. 10, 40–48. doi 10.1016/j.fsigen. 2014.01.006
Silva S.S., Lopes C., Teixeira A.L., Carneiro de Sousa M.J., Medeiros R. 2015. Forensic miRNA: Potential biomarker for body fluids? Forensic Sci. Int. Genet. 14, 1–10. doi 10.1016/j.fsigen.2014.09.002
Dumache R., Ciocan V., Muresan C., Rogobete A.F., Enache A. 2015. Circulating microRNAs as promising biomarkers in forensic body fluids identification. Clin. Lab. 6, 1129–1135.
Zubakov D., Boersma A.W., Choi Y., Van Kuijk P.F., Wiemer E.A., Kayser M. 2010. MicroRNA markers for forensic body fluid identification obtained from microarray screening and quantitative RT-PCR confirmation. Int. J. Legal Med. 124, 217–226.
van der Meer D.J., Williams G.A. 2015. Performing body fluid identification with microRNAs using capillary electrophoresis. Forensic Sci. Int. Genet. Suppl. Ser. 5, e592–e594. http://dx.doi.org/10.1016/j.fsigss.2015.09.234.
He L., Hannon G.J. 2004. MicroRNAs: Small RNAs with a big role in gene regulation. Nat. Rev. Genet. 5, 522–531. doi 10.1038/nrg1379
Kiseleva Ya.Yu., Radko S.P., Bodoev N.V. 2015. Circulating microRNA as diagnostic markers of oncological diseases. Vestn. Ross. Akad. Estestv. Nauk. 5, 79–85.
Vlassov V.V., Rykova E. Yu., Ponomariova A.A., Zaporozhchenko I.A., Morozkin E.S., Cherdyntseva N.V., Laktionov P.P. 2015. Circulating microRNAs in lung cancer: Prospects for diagnosis, prognosis, and prediction of antitumor treatment efficacy. Mol. Biol. (Moscow). 49 (1), 48–57.
Kayser M., de Knijff P. 2011. Improving human forensics through advances in genetics, genomics and molecular biology. Nat. Rev. Genet. 12, 179–192. doi 10.1038/nrg2952
Silvia A. 2015. Extracellular microRNAs in forensic sciences: Potential biomarkers for body fluid identification. Ph. D. Thesis, Abel Salazar Biomedical Sciences Institute, University of Porto, Portugal. https://repositorio-aberto.up.pt/bitstream/10216/81679/2/127803.pdf.
Bentwich I., Avniel A., Karov Y., Aharonov R., Gilad S., Barad O., Barzilai A., Einat P., Einav U., Meiri E., Sharon E., Spector Y., Bentwich Z. 2005. Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 37, 766–770. doi 10.1038/ng1590
Williams G., Uchimoto M.L., Coult N., World D., Beasley E. 2013. Body fluid mixtures: Resolution using forensic microRNA analysis. Forensic Sci. Int.: Genet. Suppl. Ser. 4, 292–293. doi 10.1016/j.fsigss.2013.10.149
Wang Z., Zhang J., Wei W., Zhou D., Luo H., Chen X., Hou Y. 2015. Identification of saliva using microRNA biomarkers for forensic purpose. J. Forensic Sci. 60, 702–706. doi 10.1111/1556-4029.12730
Courts C., Madea B. 2011. Specific micro-RNA signatures for the detection of saliva and blood in forensic body-fluid identification. J. Forensic Sci. 56, 1464–1470. doi 10.1111/j.1556-4029.2011.01894.x
Sauer E., Reinke A.K., Courts C. 2016. Differentiation of five body fluids from forensic samples by expression analysis of four microRNAs using quantitative PCR. Forensic Sci. Int. Genet. 22, 89–99. doi 10.1016/j.fsigen. 2016.01.018
Wang Z., Luo H., Pan X., Liao M., Hou Y. 2012. A model for data analysis of microRNA expression in forensic body fluid identification. Forensic Sci. Int. Genet. 6, 419–423. doi 10.1016/j.fsigen.2011.08.008
Wang Z., Zhang J., Luo H., Ye Y., Yan J., Hou Y. 2013. Screening and confirmation of microRNA markers for forensic body fluid identification. Forensic Sci. Int. Genet. 1, 116–123. doi 10.1016/j.fsigen.2012.07.006
de Waele J. 2011. Evaluation of factors affecting the identification of body fluids using mRNA in forensic case samples. Univ. Amsterdam Res. Project (36 EC). UvA Scripties Online. http://dare.uva.nl/cgi/arno/show.cgi?fid=333666.
Lindenbergh A., de Pagter M., Ramdayal G., Visser M., Zubakov D., Kayser M., Sijen T. A. 2012. Multiplex (m)RNA-profiling system for the forensic identification of body fluids and contact traces. Forensic Sci. Int. Genet. 6, 565–577. doi 10.1016/j.fsigen.2012.01.009
van den Berge M., Bhoelai B., Harteveld J., Matai A., Sijen T. 2016. Advancing forensic RNA typing: On non-target secretions, a nasal mucosa marker, a differential co-extraction protocol and the sensitivity of DNA and RNA profiling. Forensic Sci. Int. Genet. 20, 119–129. doi 10.1016/j.fsigen.2015.10.011
Vennemann M., Koppelkamm A. 2010. mRNA profiling in forensic genetics I: Possibilities and limitations. Forensic Sci. Int. 203, 71–75. doi 10.1016/j.forsciint.2010.07.006
Uchimoto M.L., Beasley E., Coult N., Omelia E.J., World D., Williams G. 2013. Considering the effect of stem-loop reverse transcription and real-time PCR analysis of blood and saliva specific microRNA markers upon mixed body fluid stains. Forensic Sci. Int. Genet. 7, 418–421. doi 10.1016/j.fsigen.2013.04.006
Bowden A., Fleming R., Harbison S. 2011. A method for DNA and RNA co-extraction for use on forensic samples using the Promega DNA IQ™ system. Forensic Sci. Int. Genet. 5, 64–68. doi 10.1016/j.fsigen.2009.11.007
van der Meer D., Uchimoto M.L., Williams G. 2013. Simultaneous analysis of micro-RNA and DNA for determining the body fluid origin of DNA profiles. J. Forensic Sci. 58, 967–971. doi 10.1111/1556-4029.12160
Sijen T. 2014. Molecular approaches for forensic cell type identification: On mRNA, miRNA, DNA methylation and microbial markers. Forensic Sci. Int. Genet. 18, 21–32. doi 10.1016/j.fsigen.2014.11.015
Wegman D.W., Ghasemi F., Khorshidi A., Yang B.B., Liu S.K., Yousef G.M., Krylov S.N. 2015. Highly-sensitive amplification-free analysis of multiple miRNAs by capillary electrophoresis. Anal. Chem. 87, 1404–1410. doi 10.1021/ac504406s
Li Y., Zhang J., Wei W., Wang Z., Prinz M., Hou Y. 2014. A strategy for co-analysis of microRNAs and DNA. Forensic Sci. Int. Genet. 12, 24–29. doi 10.1016/j.fsigen.2014.04.011
Williams G., Uchimoto M.L., Coult N., World D., Beasley E., Avenell P. 2013. Characterisation of body fluid specific microRNA markers by capillary electrophoresis. Forensic Sci. Int. Gen. Suppl. Ser. 4, 274–275. http://dx.doi.org/10.1016/j.fsigss.2013.10.140.
Park J.L., Park S.M., Kwon O.H., Lee H.C., Kim J.Y., Seok H.H., Lee W.S., Lee S.H., Kim Y.S., Woo K.M., Kim S.Y. 2014. Microarray screening and qRT-PCR evaluation of microRNA markers for forensic body fluid identification. Electrophoresis. 35, 3062–3068. doi 10.1002/elps.201400075
Etheridge A., Lee I., Hood L., Galas D., Wang K. 2011. Extracellular microRNA: A new source of biomarkers. Mutat. Res. 717, 85–90. doi 10.1016/j.mrfmmm.2011.03.004
Dunnett H., van der Meer D., Williams G.A. 2014. Evaluation of stem-loop reverse transcription and poly-A tail extension in microRNA analysis of body f luids. Microrna. 3, 150–154. doi 10.2174/2211536604666150121000603
Luo X.Y., Li Z.L., Peng D., Wang L., Zhang L., Liang W.B. 2015. MicroRNA markers for forensic body fluid identification obtained from miRCURY™ LNA array. Forensic Sci. Int. Genet. Suppl. Ser. 5, e630–e632. http://dx.doi.org/10.1016/j.fsigss.2015.10.006.
Valencia-Sanchez M.A., Liu J., Hannon G.J., Parker R. 2006. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 20, 515–524. doi 10.1101/gad.1399806
Weber J.A., Baxter D.H., Zhang S., Huang D.Y., Huang K.H., Lee M.J., Galas D.J., Wang K. 2010. The microRNA spectrum in 12 body fluids. Clin. Chem. 56, 1733–1741. doi 10.1373/clinchem.2010.147405
Konishi H., Ichikawa D., Komatsu S., Shiozaki A., Tsujiura M., Takeshita H., Morimura R., Nagata H., Arita T., Kawaguchi T., Hirashima S., Fujiwara H., Okamoto K., Otsuji E. 2012. Detection of gastric cancer- associated microRNAs on microRNA microarray comparing pre- and post-operative plasma. Br. J. Cancer. 106, 740–747. doi 10.1038/bjc.2011.588
Grasedieck S., Schö ler N., Bommer M., Niess J.H., Tumani H., Rouhi A., Bloehdorn J., Liebisch P., Mertens D., Döhner H., Buske C., Langer C., Kuchenbauer F. 2012. Impact of serum storage conditions on microRNA stability. Leukemia. 26, 2414–2416. doi 10.1038/leu.2012.106
Patnaik S.K., Mallick R., Yendamuri S. 2010. Detection of microRNAs in dried serum blots. Anal. Biochem. 407, 147–149. doi 10.1016/j.ab.2010.08.004
Kayser M. 2015. Forensic DNA phenotyping: Predicting human appearance from crime scene material for investigative purposes. Forensic Sci. Int. Genet. 18, 33–48. doi 10.1016/j.fsigen.2015.02.003
Simon L.M., Edelstein L.C., Nagalla S., Woodley A.B., Chen E.S., Kong X., Ma L., Fortina P., Kunapuli S., Holinstat M., McKenzie S.E., Dong J.F, Shaw C.A., Bray P.F. 2014. Human platelet microRNA-mRNA networks associated with age and gender revealed by integrated plateletomics. Blood. 123, e37–e45.
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © A.S. Bavykin, 2017, published in Molekulyarnaya Biologiya, 2017, Vol. 51, No. 4, pp. 573–581.
Rights and permissions
About this article
Cite this article
Bavykin, A.S. Circulating microRNAs in the identification of biological fluids: A new approach to standardization of expression-based diagnostics. Mol Biol 51, 506–513 (2017). https://doi.org/10.1134/S0026893317040045
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0026893317040045