Methodological considerations for gene expression profiling of human brain

Abstract

Gene expression profiles of postmortem brain tissue represent important resources for understanding neuropsychiatric illnesses. The impact(s) of quality covariables on the analysis and results of gene expression studies are important questions. This paper addressed critical variables which might affect gene expression in two brain regions. Four broad groups of quality indicators in gene expression profiling studies (clinical, tissue, RNA, and microarray quality) were identified. These quality control indicators were significantly correlated, however one quality variable did not account for the total variance in microarray gene expression. The data showed that agonal factors and low pH correlated with decreased integrity of extracted RNA in two brain regions. These three parameters also modulated the significance of alterations in mitochondrial-related genes. The average F-ratio summaries across all transcripts showed that RNA degradation from the AffyRNAdeg program accounted for higher variation than all other quality factors. Taken together, these findings confirmed prior studies, which indicated that quality parameters including RNA integrity, agonal factors, and pH are related to differences in gene expression profiles in postmortem brain. Individual candidate genes can be evaluated with these quality parameters in post hoc analysis to help strengthen the relevance to psychiatric disorders. We find that clinical, tissue, RNA, and microarray quality are all useful variables for collection and consideration in study design, analysis, and interpretation of gene expression results in human postmortem studies.

Sex-specific differences in the dynamics of cocaine- and amphetamine-regulated transcript and nesfatin-1 expressions in the midbrain of depressed suicide victims vs. controls

“…As to agonal state, gene expression profiles in the post mortem brain are influenced by asphyxia/ ischemia during agony (e.g. Atz et al, 2007;Ervin et al, 2007;Vawter et al, 2006). Recently, Li et al (2004) found that individuals who suffered prolonged agonal states exhibited a consistent change in expression of various genes, whereas those who experienced brief deaths caused by accidents, acute cardio-respiratory events or asphyxia, generally did not (Li et al, 2004).…”

“…Furthermore, since post-mortem delay can significantly alter gene expression profiles (Atz et al, 2007;Ervin et al, 2007;Vawter et al, 2006), subjects with a post-mortem delay longer than 12 h were also excluded from the present account. Brains from suicide victims with MDD (5 males and 3 females) and from controls (8 males and 8 females) were studied.…”

Mitochondrial involvement in psychiatric disorders

“…One method is to develop animal and cellular models that have profiles similar to BPD and SZ gene expression profiles and to show that the pathophysiology involves mitochondrial-related gene expression. The other method is to perform rigorously controlled studies of covariates and gene expression (62,69,(79)(80)(81) which we further comment upon below.…”

Shared Gene Expression Alterations in Schizophrenia and Bipolar Disorder

“…This ANCOVA was restricted to subjects above the median pH of 6.57 and with the covariates of pH and age. Although covariate analysis approach might be useful with the strong effect of pH, it may not be linear through the lower pH range, when subjects may show a ceiling or floor effect depending on the direction of association (7)(8)(9)(16)(17)(18)(19). Therefore, we attempted to use subjects with above-median pH as an indicator of fewer residual agonal effects.…”