Variability of gene expression profiles in human blood and lymphoblastoid cell lines.
BACKGROUND
Readily accessible samples such as peripheral blood or cell lines are increasingly being used in large cohorts to characterise gene expression differences between a patient group and healthy controls. However, cell and RNA isolation procedures and the variety of cell types that make up whole blood can affect gene expression measurements. We therefore systematically investigated global gene expression profiles in peripheral blood from six individuals collected during two visits by comparing five of the following cell and RNA isolation methods: whole blood (PAXgene), peripheral blood mononuclear cells (PBMCs), lymphoblastoid cell lines (LCLs), CD19 and CD20 specific B-cell subsets.


RESULTS
Gene expression measurements were clearly discriminated by isolation method although the reproducibility was high for all methods (range rho = 0.90-1.00). The PAXgene samples showed a decrease in the number of expressed genes (P < 1*10(-16)) with higher variability (P < 1*10(-16)) compared to the other methods. Differentially expressed probes between PAXgene and PBMCs were correlated with the number of monocytes, lymphocytes, neutrophils or erythrocytes. The correlations (rho = 0.83; rho = 0.79) of the expression levels of detected probes between LCLs and B-cell subsets were much lower compared to the two B-cell isolation methods (rho = 0.98). Gene ontology analysis of detected genes showed that genes involved in inflammatory responses are enriched in B-cells CD19 and CD20 whereas genes involved in alcohol metabolic process and the cell cycle were enriched in LCLs.


CONCLUSIONS
Gene expression profiles in blood-based samples are strongly dependent on the predominant constituent cell type(s) and RNA isolation method. It is crucial to understand the differences and variability of gene expression measurements between cell and RNA isolation procedures, and their relevance to disease processes, before application in large clinical studies.
Min
Josine L
JL
Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, Oxford, UK. jlmin@well.ox.ac.uk
Barrett
Amy
A
Watts
Tim
T
Pettersson
Fredrik H
FH
Lockstone
Helen E
HE
Lindgren
Cecilia M
CM
Taylor
Jennifer M
JM
Allen
Maxine
M
Zondervan
Krina T
KT
McCarthy
Mark I
MI
D016175:B-Lymphocyte Subsets / Q000378:metabolism*; D002460:Cell Line; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000378:metabolism*; D012313:RNA / Q000097:blood* / Q000302:isolation & purification; D015203:Reproducibility of Results
D012313:RNA