Concordant gene expression in leukemia cells and normal leukocytes is associated with germline cis-SNPs

Deborah French, Wenjian Yang, Leo H Hamilton, Geoffrey Neale, Yiping Fan, James R Downing, Nancy J Cox, Ching-Hon Pui, William E Evans, Mary V Relling, Deborah French, Wenjian Yang, Leo H Hamilton, Geoffrey Neale, Yiping Fan, James R Downing, Nancy J Cox, Ching-Hon Pui, William E Evans, Mary V Relling

Abstract

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.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1. The overall strategy: Left: determination…
Figure 1. The overall strategy: Left: determination of genes whose expression is concordant between diagnostic leukemia cells and normal leukocytes; here the expression of CTSW is depicted as an example.
Middle: discovery of germline cis-SNPs that are significantly related to the level of expression of such concordant genes; here a cis-SNP genotype is related to the expression of an example gene (CTSW). Right: validation of the relationship between these same cis-SNPs and their genes in two independent validation sets; here the same cis-SNP related to the expression of CTSW.
Figure 2
Figure 2
a) At adjusted pcis-SNPs associated with the expression of the concordant genes in the normal leukocytes and the leukemia cells in the discovery set. In the discovery set of normal leukocytes (yellow circle), there are 30 out of 176 genes that have significant cis-SNPs and in the discovery set of leukemia cells (green circle) there are 30 out of 176 genes that have significant cis-SNPs. Additionally, in the validation set of leukemia cells (blue circle) there are 28 out of 176 genes that have significant cis-SNPs. There are 14 out of 176 genes with significant cis-SNPs that are common to all 3 of the populations representing 7.95%* of the 176 genes. b) At adjusted p<0.05, there was no difference in the number of cis-SNPs associated with the expression of all 8853 expressed genes in the normal leukocytes and the leukemia cells in the discovery set. In the discovery set of normal leukocytes (yellow circle), there are 559 genes with significant cis-SNPs and in the discovery set of leukemia cells (green circle), there are 532 genes that have significant cis-SNPs (p = 0.41, Fishers exact test). Additionally, in the validation set of leukemia cells (blue circle), there are 619 genes that have significant cis-SNPs. There are 28 out of 8853 genes with significant cis-SNPs that are common to all 3 populations representing 0.32%* of the 8853 genes.
Figure 3
Figure 3
a) An example of one of the 176 genes (here LRAP) whose expression was concordant between diagnostic leukemia cells and normal leukocytes: Left: expression levels among 92 patients in leukemia cells and normal leukocytes are correlated (p = 1.11×10−14); Middle: expression of this gene (median, quartiles, range) in leukemia cells is associated (adjusted p = 0.0016) with the germline genotype of a particular cis-SNP in this gene; Right: expression of this gene in normal leukocytes is also associated (adjusted p = 0.0016) with the germline genotype at the same cis-SNP. (See Figure S4 for additional examples.) b) An example of one of the 8853 genes (here DST) whose expression was not concordant between diagnostic leukemia cells and normal leukocytes: Left: expression levels among 92 patients in leukemia cells and normal leukocytes are not correlated (p = 0.9384); Middle: expression of this gene in leukemia cells is not associated (adjusted p = 1.0000) with the germline genotype of a particular cis-SNP in this gene; Right: expression of this gene in normal leukocytes is also not associated (adjusted p = 0.9994) with the germline genotype at the same cis-SNP. (See Figure S4 for additional examples.)
Figure 4. The 176 genes (open bars)…
Figure 4. The 176 genes (open bars) whose expression was concordant between diagnostic leukemia cells and normal leukocytes were more likely (p = 3.71×10−18, Fishers exact test) to have cis-SNP genotypes (within 50 Kb of a gene) associated with their gene expression (20/176) than genes (closed bars) whose expression was discordant between the leukemia cells and normal leukocytes (53/8,853).
A high proportion of these 176 genes whose expression was concordant between diagnostic leukemia cells and normal leukocytes in the discovery set also had cis-SNPs affecting gene expression in validation set 1 consisting of leukemia cells (14/20) and in validation set 2 consisting of HapMap lymphoid cell lines (9/20).
Figure 5. Genes whose expression is significantly…
Figure 5. Genes whose expression is significantly associated between two tissue types (diagnostic leukemia cell and normal leukocytes) are overrepresented in specific pathways relative to all genes interrogated on the U133A microarray chip.

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