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Blood, Vol. 113, Issue 19, 4512-4520, May 7, 2009
Acquired variation outweighs inherited variation in whole genome analysis of methotrexate polyglutamate accumulation in leukemia
Blood French et al.
113: 4512
Supplemental materials for: French et al
Files in this Data Supplement:
- Figure S1. Patient enrollment and evaluability for pharmacologic, biologic, and genomic parameters (JPG, 74.2 KB)
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HDMTX = methotrexate at 1 g/m2; MTXPG = methotrexate polyglutamates measured in vivo in bone marrow samples; SNP = single nucleotide polymorphisms evaluated via genome-wide interrogations.
- Figure S2. Correlation between HPLC-fluorescence measured and HPLC-REA–measured MTXPGs, based on paired assays of Nalm6 lysates spiked with various concentrations of MTXPG1 to MTXPG7 (JPG, 27.6 KB)
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- Figure S3 (JPG, 44.1 KB)
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(A) The methotrexate polyglutamate accumulation in 248 acute lymphoblastic leukemia patients shows normal distribution but wide inter-individual variation (CV=93%; median = 2180 pmol/109 cells). (B) There is wide inter-cell line variability in MTXPG accumulation in the CEU and YRI HapMap cell lines (n=176; CV=51%; median = 3718.953 pmols/109 cells) and it shows normal distribution.
- Figure S4 (JPG, 59.9 KB)
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(A) There is an over representation of low p-values (x-axis) for the association between patient leukemia cell gene expression (y-axis; frequency of associations) and MTXPG accumulation in patient leukemia cells (n=145). (B) There is a small over representation of low p-values (x-axis) for the association between inherited SNP genotypes (y-axis; frequency of associations) and MTXPG accumulation in patient leukemia cells (n=144).
- Figure S5. The percentage of total inherited SNP genotypes associated with leukemia cell MTXPG accumulation on each chromosome was similar for the patients, except chromosome 21 that was under represented (n=144; p=1.283 × 10−8) (JPG, 30.5 KB)
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- Figure S6 (JPG, 53.6 KB)
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(A) Copy number of chromosome 18 determined cytogenetically (n=213) was significantly associated (p=1.03 × 10−9, Wilcoxon rank sum test) with MTXPG accumulation in patient leukemia cells. (B) Copy number of chromosome 10 determined cytogenetically (n=213) was significantly associated (p=1.88 × 10−8, Wilcoxon rank sum test) with methotrexate polyglutamate accumulation in patient leukemia cells. (C) Copy number of chromosome 17 determined cytogenetically (n=213) was significantly associated (p=1.84 × 10−6, Wilcoxon rank sum test) with methotrexate polyglutamate accumulation in patient leukemia cells.
- Figure S7. Association of SNP chip-defined somatic leukemia cell chromosome copy number with leukemia cell MTXPG accumulation (n=82) (JPG, 70.8 KB)
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Gain of copy number for chromosomes 4, 5, 6, 10, 14, 18 and 21 were significantly associated with MTXPG accumulation in a univariate analysis (p=7 × 10−4, p=0.0060, p=0.0016, p=1.08 × 10−5, p=1.25 × 10−6, p=3.16 × 10−8, and p=4 × 10−8 respectively). When the association analysis was adjusted for ALL subtype, there was still a significant association for chromosomes 10 and 18 (p=0.0362 and p=0.0019 respectively) but there was no longer a significant association for chromosomes 4, 5, 6, 14 and 21 (p=0.38, p=0.97 p=0.50, p=0.22 and p=0.94 respectively).
- Figure S8. Association of cytogenetically-defined somatic leukemia cell chromosome copy number with leukemia cell MTXPG accumulation (n=213) (JPG, 39.9 KB)
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Gain of copy number for chromosomes 4 and 21 were significantly associated with MTXPG accumulation (p=5.06 × 10−8 and p=6.42 × 10−10,respectively). When the association analysis was adjusted for ALL subtype, there was no longer a significant association (p=0.62 and p=0.31 respectively).
- Figure S9. Association between expression of genes on chromosome 18 with methotrexate polyglutamate accumulation in normal lymphoblastoid cell lines (JPG, 43.9 KB)
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There was a significant positive correlation between IMPA2 expression (p=0.033, Pearson’s correlation) and PHLPP expression (p=0.041, Pearson’s correlation) and methotrexate polyglutamate accumulation in the CEU (n=87) and YRI (n=89) populations of the HapMap cell lines.
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