Selection of reference gene expression in a schizophrenia brain cohort

Cynthia Shannon Weickert, The University of New South Wales
D Sheedy
D A Rothmond
I Dedova, Schizophrenia Research Institute, Darlinghurst
S Fung
T Garrick
Jenny Wong, University of Wollongong
A J Harding
S Sivagnanansundaram
C Hunt
C Duncan
N Sundqvist
S-Y Tsai
J Anand
Daren Draganic, Schizophrenia Research Institute
C Harper

Shannon Weickert, C., Sheedy, D., Rothmond, D., Dedova, I., Fung, S., Garrick, T., Wong, J., Harding, A., Sivagnanansundaram, S., Hunt, C., Duncan, C., Sundqvist, N., Tsai, S., Anand, J., Draganic, D. & Harper, C. (2010). Selection of reference gene expression in a schizophrenia brain cohort. Australian and New Zealand Journal of Psychiatry, 44 (1), 59-70.


Objective: In order to conduct postmortem human brain research into the neuropatho-logical basis of schizophrenia, it is critical to establish cohorts that are well-characterized and well-matched. The aim of the present study was therefore to determine if specimen characteristics including: diagnosis, age, postmortem interval (PMI), brain acidity (pH), and/or the agonal state of the subject at death related to RNA quality, and to determine the most appropriate reference gene mRNAs. Methods: A matched cohort was selected of 74 subjects (schizophrenia/schizoaffective disorder, n 37; controls, n 37). Middle frontal gyrus tissue was pulverized, tissue pH was measured, RNA isolated for cDNA from each case, and RNA integrity number (RIN) measurements were assessed. Using quantitative reverse transcriptionpolymerase chain reaction, nine housekeeper genes were measured and a geomean calculated per case in each diagnostic group. Results: The RINs were very good (mean 7.3) and all nine housekeeper control genes were significantly correlated with RIN. Seven of nine housekeeper genes were also correlated with pH; two clinical variables, agonal state and duration of illness, did have an effect on some control mRNAs. No major impact of PMI or freezer time on housekeeper mRNAs was detected. The results show that people with schizophrenia had significantly less PPIA and SDHA mRNA and tended to have less GUSB and B2M mRNA, suggesting that these control genes may not be good candidates for normalization. Conclusions: In the present cohort <10% variability in RINs was detected and the diagnostic groups were well matched overall. The cohort was adequately powered (0.800.90) to detect mRNA differences (25%) due to disease. The study suggests that multiple factors should be considered in mRNA expression studies of human brain tissues. When schizophrenia cases are adequately matched to control cases subtle differences in gene expression can be reliably detected. © 2010 The Royal Australian and New Zealand College of Psychiatrists.