Research article

Improved Methodology for Assessment of mRNA Levels in Blood of Patients with FMR1 Related Disorders

David E Godler¹ , Danuta Z Loesch^1,2 , Richard Huggins³ , Lavinia Gordon⁴ , Howard R Slater^5,6 , Freya Gehling¹ , Trent Burgess⁵ and KH Andy Choo^1,6

¹Chromosome and Chromatin Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia

²School of Psychological Science, La Trobe University, Melbourne, Australia

³Department of Mathematics and Statistics, University of Melbourne, Melbourne, Australia

⁴The Bioinformatics Unit, Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia

⁵VCGS Cytogenetics Laboratory, Murdoch Research Institute, Royal Children's Hospital, Melbourne, Australia

⁶Department of Pediatrics, University of Melbourne, Melbourne, Australia

author email corresponding author email

BMC Clinical Pathology 2009, 9:5doi:10.1186/1472-6890-9-5

Published:	9 June 2009

Abstract

Background

Elevated levels of FMR1 mRNA in blood have been implicated in RNA toxicity associated with a number of clinical conditions. Due to the extensive inter-sample variation in the time lapse between the blood collection and RNA extraction in clinical practice, the resulting variation in mRNA quality significantly confounds mRNA analysis by real-time PCR.

Methods

Here, we developed an improved method to normalize for mRNA degradation in a sample set with large variation in rRNA quality, without sample omission. Initially, RNA samples were artificially degraded, and analyzed using capillary electrophoresis and real-time PCR standard curve method, with the aim of defining the best predictors of total RNA and mRNA degradation.

Results

We found that: (i) the 28S:18S ratio and RNA quality indicator (RQI) were good predictors of severe total RNA degradation, however, the greatest changes in the quantity of different mRNAs (FMR1, DNMT1, GUS, B2M and GAPDH) occurred during the early to moderate stages of degradation; (ii) chromatographic features for the 18S, 28S and the inter-peak region were the most reliable predictors of total RNA degradation, however their use for target gene normalization was inferior to internal control genes, of which GUS was the most appropriate. Using GUS for normalization, we examined in the whole blood the relationship between the FMR1 mRNA and CGG expansion in a non-coding portion of this gene, in a sample set (n = 30) with the large variation in rRNA quality. By combining FMR1 3' and 5' mRNA analyses the confounding impact of mRNA degradation on the correlation between FMR1 expression and CGG size was minimized, and the biological significance increased from p = 0.046 for the 5' FMR1 assay, to p = 0.018 for the combined FMR1 3' and 5' mRNA analysis.

Conclusion

Our observations demonstrate that, through the use of an appropriate internal control and the direct analysis of multiple sites of target mRNA, samples that do not conform to the conventional rRNA criteria can still be utilized to obtain biologically/clinically relevant data. Although, this strategy clearly has application for improved assessment of FMR1 mRNA toxicity in blood, it may also have more general implications for gene expression studies in fresh and archival tissues.