Systematic Analysis of MicroRNA Expression of RNA Extracted from Fresh Frozen and Formalin-fixed Paraffin-embedded Samples

Overview

Journal RNA

Specialty Molecular Biology

Date 2007 Aug 19

PMID 17698639

Citations 268

Authors

Yaguang Xi

Go Nakajima

Elaine Gavin

Chris G Morris

Kenji Kudo

Kazuhiko Hayashi

Jingfang Ju

Affiliations

Soon will be listed here.

Abstract

microRNAs (miRNAs) are noncoding small RNAs that regulate gene expression at the translational level by mainly interacting with 3' UTRs of their target mRNAs. Archived formalin-fixed paraffin-embedded (FFPE) specimens represent excellent resources for biomarker discovery. Currently there is a lack of systematic analysis on the stability of miRNAs and optimized conditions for expression analysis using FFPE samples. In this study, the expression of miRNAs from FFPE samples was analyzed using high-throughput locked nucleic acid-based miRNA arrays. The effect of formalin fixation on the stability of miRNAs was also investigated using miRNA real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis. The stability of miRNAs of archived colorectal cancer FFPE specimens was characterized with samples dating back up to 10 yr. Our results showed that the expression profiles of miRNAs were in good correlation between 1 mug of fresh frozen and 1-5 mug of FFPE samples (correlation coefficient R (2) = 0.86-0.89). Different formalin fixation times did not change the stability of miRNAs based on real-time qRT-PCR analysis. There are no significant differences of representative miRNA expression among 40 colorectal cancer FFPE specimens. This study provides a foundation for miRNA investigation using FFPE samples in cancer and other types of diseases.

Citing Articles

A comprehensive in silico analysis and experimental validation of miRNAs capable of discriminating between lung adenocarcinoma and squamous cell carcinoma.

Javanmardifard Z, Rahmani S, Bayat H, Mirtavoos-Mahyari H, Ghanei M, Mowla S Front Genet. 2024; 15:1419099.

PMID: 39381140 PMC: 11460580. DOI: 10.3389/fgene.2024.1419099.

Research progress on miR-124-3p in the field of kidney disease.

Chen G, Wang Y, Zhang L, Yang K, Wang X, Chen X BMC Nephrol. 2024; 25(1):252.

PMID: 39112935 PMC: 11308398. DOI: 10.1186/s12882-024-03688-7.

MicroRNA biomarkers as next-generation diagnostic tools for neurodegenerative diseases: a comprehensive review.

Azam H, Rossling R, Geithe C, Khan M, Dinter F, Hanack K Front Mol Neurosci. 2024; 17:1386735.

PMID: 38883980 PMC: 11177777. DOI: 10.3389/fnmol.2024.1386735.

MicroRNAs: circulating biomarkers for the early detection of imperceptible cancers via biosensor and machine-learning advances.

Metcalf G Oncogene. 2024; 43(28):2135-2142.

PMID: 38839942 PMC: 11226400. DOI: 10.1038/s41388-024-03076-3.

A Systematic Review and Meta-Analysis of microRNA Profiling Studies in Chronic Kidney Diseases.

Garmaa G, Bunduc S, Koi T, Hegyi P, Csupor D, Ganbat D Noncoding RNA. 2024; 10(3).

PMID: 38804362 PMC: 11130806. DOI: 10.3390/ncrna10030030.

References

Wang H, Ach R, Curry B . Direct and sensitive miRNA profiling from low-input total RNA. RNA. 2006; 13(1):151-9. PMC: 1705746. DOI: 10.1261/rna.234507. View

Xi Y, Shalgi R, Fodstad O, Pilpel Y, Ju J . Differentially regulated micro-RNAs and actively translated messenger RNA transcripts by tumor suppressor p53 in colon cancer. Clin Cancer Res. 2006; 12(7 Pt 1):2014-24. DOI: 10.1158/1078-0432.CCR-05-1853. View

Xi Y, Formentini A, Chien M, Weir D, Russo J, Ju J . Prognostic Values of microRNAs in Colorectal Cancer. Biomark Insights. 2007; 2:113-121. PMC: 2134920. View

Tarasov V, Jung P, Verdoodt B, Lodygin D, Epanchintsev A, Menssen A . Differential regulation of microRNAs by p53 revealed by massively parallel sequencing: miR-34a is a p53 target that induces apoptosis and G1-arrest. Cell Cycle. 2007; 6(13):1586-93. DOI: 10.4161/cc.6.13.4436. View

Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J . The nuclear RNase III Drosha initiates microRNA processing. Nature. 2003; 425(6956):415-9. DOI: 10.1038/nature01957. View

Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk R, Cuppen E . Phylogenetic shadowing and computational identification of human microRNA genes. Cell. 2005; 120(1):21-4. DOI: 10.1016/j.cell.2004.12.031. View

Cummins J, He Y, Leary R, Pagliarini R, Diaz Jr L, Sjoblom T . The colorectal microRNAome. Proc Natl Acad Sci U S A. 2006; 103(10):3687-92. PMC: 1450142. DOI: 10.1073/pnas.0511155103. View

Chang T, Wentzel E, Kent O, Ramachandran K, Mullendore M, Lee K . Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Mol Cell. 2007; 26(5):745-52. PMC: 1939978. DOI: 10.1016/j.molcel.2007.05.010. View

Castoldi M, Schmidt S, Benes V, Noerholm M, Kulozik A, Hentze M . A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). RNA. 2006; 12(5):913-20. PMC: 1440900. DOI: 10.1261/rna.2332406. View

10.

Ambros V . The functions of animal microRNAs. Nature. 2004; 431(7006):350-5. DOI: 10.1038/nature02871. View

11.

Reinhart B, Slack F, Basson M, Pasquinelli A, Bettinger J, Rougvie A . The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature. 2000; 403(6772):901-6. DOI: 10.1038/35002607. View

12.

Calin G, Ferracin M, Cimmino A, Di Leva G, Shimizu M, E Wojcik S . A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med. 2005; 353(17):1793-801. DOI: 10.1056/NEJMoa050995. View

13.

Nielsen J, Stein P, Petersen M . NMR structure of an alpha-L-LNA:RNA hybrid: structural implications for RNase H recognition. Nucleic Acids Res. 2003; 31(20):5858-67. PMC: 219478. DOI: 10.1093/nar/gkg800. View

14.

Feinbaum R, Ambros V . The timing of lin-4 RNA accumulation controls the timing of postembryonic developmental events in Caenorhabditis elegans. Dev Biol. 1999; 210(1):87-95. DOI: 10.1006/dbio.1999.9272. View

15.

Lee Y, Jeon K, Lee J, Kim S, Kim V . MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 2002; 21(17):4663-70. PMC: 126204. DOI: 10.1093/emboj/cdf476. View

16.

Lee R, Feinbaum R, Ambros V . The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993; 75(5):843-54. DOI: 10.1016/0092-8674(93)90529-y. View

17.

Brennecke J, Hipfner D, Stark A, Russell R, Cohen S . bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell. 2003; 113(1):25-36. DOI: 10.1016/s0092-8674(03)00231-9. View

18.

He L, He X, Lim L, de Stanchina E, Xuan Z, Liang Y . A microRNA component of the p53 tumour suppressor network. Nature. 2007; 447(7148):1130-4. PMC: 4590999. DOI: 10.1038/nature05939. View

19.

Chen C, Ridzon D, Broomer A, Zhou Z, Lee D, Nguyen J . Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 2005; 33(20):e179. PMC: 1292995. DOI: 10.1093/nar/gni178. View

20.

Sempere L, Sokol N, Dubrovsky E, Berger E, Ambros V . Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broad-Complex gene activity. Dev Biol. 2003; 259(1):9-18. DOI: 10.1016/s0012-1606(03)00208-2. View