Concordant gene expression in leukemia cells and normal leukocytes is associated with germline cis-SNPs.
The degree to which gene expression covaries between different primary tissues within an individual is not well defined. We hypothesized that expression that is concordant across tissues is more likely influenced by genetic variability than gene expression which is discordant between tissues. We quantified expression of 11,873 genes in paired samples of primary leukemia cells and normal leukocytes from 92 patients with acute lymphoblastic leukemia (ALL). Genetic variation at >500,000 single nucleotide polymorphisms (SNPs) was also assessed. The expression of only 176/11,783 (1.5%) genes was correlated (p<0.008, FDR = 25%) in the two tissue types, but expression of a high proportion (20 of these 176 genes) was significantly related to cis-SNP genotypes (adjusted p<0.05). In an independent set of 134 patients with ALL, 14 of these 20 genes were validated as having expression related to cis-SNPs, as were 9 of 20 genes in a second validation set of HapMap cell lines. Genes whose expression was concordant among tissue types were more likely to be associated with germline cis-SNPs than genes with discordant expression in these tissues; genes affected were involved in housekeeping functions (GSTM2, GAPDH and NCOR1) and purine metabolism.
French
Deborah
D
Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America.
Yang
Wenjian
W
Hamilton
Leo H
LH
Neale
Geoffrey
G
Fan
Yiping
Y
Downing
James R
JR
Cox
Nancy J
NJ
Pui
Ching-Hon
CH
Evans
William E
WE
Relling
Mary V
MV
D002648:Child; D020869:Gene Expression Profiling; D015973:Gene Expression Regulation, Leukemic; D005838:Genotype; D018095:Germ-Line Mutation; D006801:Humans; D007962:Leukocytes / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics* / Q000473:pathology