Identification of novel germline polymorphisms governing capecitabine sensitivity

Abstract

Background: Capecitabine, an oral 5-fluorouracil (5-FU) prodrug, is widely used in the treatment of breast, colorectal, and gastric cancers. To guide the selection of patients with potentially the greatest benefit of experiencing antitumor efficacy, or, alternatively, of developing toxicities, identifying genomic predictors of capecitabine sensitivity could permit its more informed use.

Methods: The objective of this study was to perform capecitabine sensitivity genome-wide association studies (GWAS) using 503 well genotyped human cell lines from individuals representing multiple different world populations. A meta-analysis that included all ethnic populations then enabled the identification of novel germline determinants (single nucleotide polymorphisms [SNPs]) of capecitabine susceptibility.

Results: First, an intrapopulation GWAS of Caucasian individuals identified reference SNP 4702484 (rs4702484) (within adenylate cyclase 2 [ADCY2]) at a level reaching genome-wide significance (P = 5.2 × 10(-8) ). This SNP is located upstream of the 5 methyltetrahydrofolate-homocysteine methyltransferase reductase (MTRR) gene, and it is known that the enzyme for MTRR is involved in the methionine-folate biosynthesis and metabolism pathway, which is the primary target of 5-FU-related compounds, although the authors were unable to identify a direct relation between rs4702484 and MTRR expression in a tested subset of cells. In the meta-analysis, 4 SNPs comprised the top hits, which, again, included rs4702484 and 3 additional SNPs (rs8101143, rs576523, and rs361433) that approached genome-wide significance (P values from 1.9 × 10(-7) to 8.8 × 10(-7) ). The meta-analysis also identified 1 missense variant (rs11722476; serine to asparagine) within switch/sucrose nonfermentable-related, matrix-associated, actin-dependent regulator of chromatin (SMARCAD1), a novel gene for association with capecitabine/5-FU susceptibility.

Conclusions: Toward the goal of individualizing cancer chemotherapy, the current study identified novel SNPs and genes associated with capecitabine sensitivity that are potentially informative and testable in any patient regardless of ethnicity.

Copyright © 2011 American Cancer Society.

Figures

Figure 1. Celluar sensitivity to capecitabine in 503 HapMap lymphoblastoid cell lines

The YRI population was the most sensitive to growth inhibitory effects of 5′DFUR (capecitabine) with a median AUC significantly lower than that of CEU (P=8.5×10−8) and ASN (P=6×10−3) but not significantly different from ASW.

Figure 2. GWAS in Caucasian individuals identified a novel variant, rs4702484, associated with capecitabine sensitivity at a level reaching genome-wide significance (P=5.2×10−8)

(A) Manhattan plot showing capecitabine susceptibility GWAS results in CEU. (B) Zoom-in view of chromosome 5 region around top CEU GWAS SNP, rs4702484. The location within ADCY2 (adenylate cyclase) is shown, in addition to its close proximity (upstream) of MTRR (5-methyltetrahydrofolate-homocysteine methyltransferase reductase). r2 patterns designate LD probabilities with other SNPs in the region.

Figure 3. Manhattan plots of GWAS results for capecitabine sensitivity in different populations

(A): YRI; (B): ASW; (C): ASN.

Figure 4. Meta-anlaysis of individual LCLs from CEU, YRI, ASW and ASN populations

Manhattan plot showing meta-analysis results of capecitabine susceptibility GWA studies including all of the utilized combined world populations (n=503 individuals).

Figure 5. Graphical depiction of the proportion of SNPs identified from each intra-population GWAS that remained strongly significant in the meta-analysis

For example, the ASN-only GWAS identified 200 top SNPs (the sum of 14 + 186), 14 (7%) of which remained significant in the meta-analysis. An arbitrary cutoff of significance of P−4 was used. None of the SNPs from an individual population that remained strongly significantly in the meta-analysis were the same in multiple populations.

Figure 6. Examples of SNPs identified in the meta-analysis

(A) SNP rs8101143 (P=1.9×10−7; ranked #1 in the meta-analysis) illustrates genotype-phenotype associations in the same direction across all six individually evaluated populations; (B) SNP rs576523, which is only polymorphic in the YRI population and, interestingly, was still the second most significant SNP in the overall meta-analysis (P=2.3×10−7) illustrates a SNP with a strong signal in the meta-analysis despite having a genotype-phenotype association only present in one population because the variant was monomorphic in all other populations; (C) SNP rs6971109 illustrates a top hit in the meta-analysis despite the fact that the consensus direction of the genotype-phenotype association for the SNP was opposite in one or more of the ethnic populations. The circular symbol indicates that the directionality of the association in that population was opposite that of the other populations (which are all similarly denoted with diamonds). The dashed vertical line in all panels identifies a P value of 0.05.

Figure 7. Meta-analysis of the cross-population GWAS identified rs11722476, a missense SNP within SMARCAD1

(A) Zoom-in view of the genomic region on chromosome 4 around this SNP. The fact that a number of other signals within SMARCAD1 were found is illustrated by the striking number of SNPs which were found at P values smaller than the arbitrary cutoff of P<10−4; (B) Genotype-phenotype association for this SNP in the n=503 individuals.