Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradationCitation formats

  • External authors:
  • J. S. Hall
  • J. Taylor
  • H. R. Valentine
  • J. J. Irlam
  • A. Eustace
  • P. J. Hoskin
  • C. J. Miller

Standard

Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation. / Hall, J. S.; Taylor, J.; Valentine, H. R.; Irlam, J. J.; Eustace, A.; Hoskin, P. J.; Miller, C. J.; West, C. M L.

In: British Journal of Cancer, Vol. 107, No. 4, 07.08.2012, p. 684-694.

Research output: Contribution to journalArticlepeer-review

Harvard

Hall, JS, Taylor, J, Valentine, HR, Irlam, JJ, Eustace, A, Hoskin, PJ, Miller, CJ & West, CML 2012, 'Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation', British Journal of Cancer, vol. 107, no. 4, pp. 684-694. https://doi.org/10.1038/bjc.2012.294

APA

Hall, J. S., Taylor, J., Valentine, H. R., Irlam, J. J., Eustace, A., Hoskin, P. J., Miller, C. J., & West, C. M. L. (2012). Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation. British Journal of Cancer, 107(4), 684-694. https://doi.org/10.1038/bjc.2012.294

Vancouver

Hall JS, Taylor J, Valentine HR, Irlam JJ, Eustace A, Hoskin PJ et al. Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation. British Journal of Cancer. 2012 Aug 7;107(4):684-694. https://doi.org/10.1038/bjc.2012.294

Author

Hall, J. S. ; Taylor, J. ; Valentine, H. R. ; Irlam, J. J. ; Eustace, A. ; Hoskin, P. J. ; Miller, C. J. ; West, C. M L. / Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation. In: British Journal of Cancer. 2012 ; Vol. 107, No. 4. pp. 684-694.

Bibtex

@article{b8fb45e15ad54ef9b99f1095ca633c71,
title = "Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation",
abstract = "Background: As degradation of formalin-fixed paraffin-embedded (FFPE) samples limits the ability to profile mRNA expression, we explored factors predicting the success of mRNA expression profiling of FFPE material and investigated an approach to overcome the limitation.Methods:Bladder (n140, stored 3-8 years) and cervix (n160, stored 8-23 years) carcinoma FFPE samples were hybridised to Affymetrix Exon 1.0ST arrays. Percentage detection above background (%DABG) measured technical success. Biological signal was assessed by distinguishing cervix squamous cell carcinoma (SCC) and adenocarcinoma (AC) using a gene signature. As miR-205 had been identified as a marker of SCC, precursor mir-205 was measured by Exon array and mature miR-205 by qRT-PCR. Genome-wide microRNA (miRNA) expression (Affymetrix miRNA v2.0 arrays) was compared in eight newer FFPE samples with biological signal and eight older samples without.Results:RNA quality controls (QCs) (e.g., RNA integrity (RIN) number) failed to predict profiling success, but sample age correlated with %DABG in bladder (R0.30, P=0.01) and cervix (R0.69, P=0.01). Biological signal was lost in older samples and neither a signature nor precursor mir-205 separated samples by histology. miR-205 qRT-PCR discriminated SCC from AC, validated by miRNA profiling (26-fold higher in SCC; P1.10 × 10 5). Genome-wide miRNA (R0.95) and small nucleolar RNA (R0.97) expression correlated well in the eight newer vs older FFPE samples and better than mRNA expression (R0.72).Conclusion:Sample age is the best predictor of successful mRNA profiling of FFPE material, and miRNA profiling overcomes the limitation of age and copes well with older samples. {\textcopyright} 2012 Cancer Research UK All rights reserved.",
keywords = "degradation, FFPE, microarray, microRNA, profiling, snoRNA",
author = "Hall, {J. S.} and J. Taylor and Valentine, {H. R.} and Irlam, {J. J.} and A. Eustace and Hoskin, {P. J.} and Miller, {C. J.} and West, {C. M L}",
year = "2012",
month = aug,
day = "7",
doi = "10.1038/bjc.2012.294",
language = "English",
volume = "107",
pages = "684--694",
journal = "BJC",
issn = "0007-0920",
publisher = "Springer Nature",
number = "4",

}

RIS

TY - JOUR

T1 - Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation

AU - Hall, J. S.

AU - Taylor, J.

AU - Valentine, H. R.

AU - Irlam, J. J.

AU - Eustace, A.

AU - Hoskin, P. J.

AU - Miller, C. J.

AU - West, C. M L

PY - 2012/8/7

Y1 - 2012/8/7

N2 - Background: As degradation of formalin-fixed paraffin-embedded (FFPE) samples limits the ability to profile mRNA expression, we explored factors predicting the success of mRNA expression profiling of FFPE material and investigated an approach to overcome the limitation.Methods:Bladder (n140, stored 3-8 years) and cervix (n160, stored 8-23 years) carcinoma FFPE samples were hybridised to Affymetrix Exon 1.0ST arrays. Percentage detection above background (%DABG) measured technical success. Biological signal was assessed by distinguishing cervix squamous cell carcinoma (SCC) and adenocarcinoma (AC) using a gene signature. As miR-205 had been identified as a marker of SCC, precursor mir-205 was measured by Exon array and mature miR-205 by qRT-PCR. Genome-wide microRNA (miRNA) expression (Affymetrix miRNA v2.0 arrays) was compared in eight newer FFPE samples with biological signal and eight older samples without.Results:RNA quality controls (QCs) (e.g., RNA integrity (RIN) number) failed to predict profiling success, but sample age correlated with %DABG in bladder (R0.30, P=0.01) and cervix (R0.69, P=0.01). Biological signal was lost in older samples and neither a signature nor precursor mir-205 separated samples by histology. miR-205 qRT-PCR discriminated SCC from AC, validated by miRNA profiling (26-fold higher in SCC; P1.10 × 10 5). Genome-wide miRNA (R0.95) and small nucleolar RNA (R0.97) expression correlated well in the eight newer vs older FFPE samples and better than mRNA expression (R0.72).Conclusion:Sample age is the best predictor of successful mRNA profiling of FFPE material, and miRNA profiling overcomes the limitation of age and copes well with older samples. © 2012 Cancer Research UK All rights reserved.

AB - Background: As degradation of formalin-fixed paraffin-embedded (FFPE) samples limits the ability to profile mRNA expression, we explored factors predicting the success of mRNA expression profiling of FFPE material and investigated an approach to overcome the limitation.Methods:Bladder (n140, stored 3-8 years) and cervix (n160, stored 8-23 years) carcinoma FFPE samples were hybridised to Affymetrix Exon 1.0ST arrays. Percentage detection above background (%DABG) measured technical success. Biological signal was assessed by distinguishing cervix squamous cell carcinoma (SCC) and adenocarcinoma (AC) using a gene signature. As miR-205 had been identified as a marker of SCC, precursor mir-205 was measured by Exon array and mature miR-205 by qRT-PCR. Genome-wide microRNA (miRNA) expression (Affymetrix miRNA v2.0 arrays) was compared in eight newer FFPE samples with biological signal and eight older samples without.Results:RNA quality controls (QCs) (e.g., RNA integrity (RIN) number) failed to predict profiling success, but sample age correlated with %DABG in bladder (R0.30, P=0.01) and cervix (R0.69, P=0.01). Biological signal was lost in older samples and neither a signature nor precursor mir-205 separated samples by histology. miR-205 qRT-PCR discriminated SCC from AC, validated by miRNA profiling (26-fold higher in SCC; P1.10 × 10 5). Genome-wide miRNA (R0.95) and small nucleolar RNA (R0.97) expression correlated well in the eight newer vs older FFPE samples and better than mRNA expression (R0.72).Conclusion:Sample age is the best predictor of successful mRNA profiling of FFPE material, and miRNA profiling overcomes the limitation of age and copes well with older samples. © 2012 Cancer Research UK All rights reserved.

KW - degradation

KW - FFPE

KW - microarray

KW - microRNA

KW - profiling

KW - snoRNA

U2 - 10.1038/bjc.2012.294

DO - 10.1038/bjc.2012.294

M3 - Article

C2 - 22805332

VL - 107

SP - 684

EP - 694

JO - BJC

JF - BJC

SN - 0007-0920

IS - 4

ER -