The power of genome-wide SNP association studies is limited, among others, by the large number of false positive test results. To provide a remedy, we combined SNP association analysis with the pathway-driven gene set enrichment analysis (GSEA), recently developed to facilitate handling of genome-wide gene expression data. The resulting GSEA-SNP method rests on the assumption that SNPs underlying a disease phenotype are enriched in genes constituting a signaling pathway or those with a common regulation. Besides improving power for association mapping, GSEA-SNP may facilitate the identification of disease-associated SNPs and pathways, as well as the understanding of the underlying biological mechanisms. GSEA-SNP may also help to identify markers with weak effects, undetectable in association studies without pathway consideration. The program is freely available and can be downloaded from our website.

BackgroundThe bisdioxopiperazine dexrazoxane (DRZ) prevents anthracycline-induced heart failure, but its clinical use is limited by uncertain cardioprotective mechanism and by concerns of interference with cancer response to anthracyclines and of long-term safety.MethodsWe investigated the effects of DRZ on the stability of topoisomerases IIα (TOP2A) and IIβ (TOP2B) and on the DNA damage generated by poisoning these enzymes by the anthracycline doxorubicin (DOX).ResultsDRZ given i.p. transiently depleted in mice the predominant cardiac isoform Top2b. The depletion was also seen in H9C2 cardiomyocytes and it was attenuated by mutating the bisdioxopiperazine binding site of TOP2B. Consistently, the accumulation of DOX-induced DNA double strand breaks (DSB) by wild-type, although not by mutant TOP2B, was reduced by DRZ. In contrast, the DRZ analogue ICRF-161, which is capable of iron chelation but not of TOP2B binding and cardiac protection, did not deplete TOP2B and did not prevent the accumulation of DOX-induced DSB. TOP2A, re-expressed in cultured cardiomyocytes by fresh serum, was depleted by DRZ along with TOP2B. DRZ depleted TOP2A also from fibrosarcoma-derived cells, but not from lung cancer-derived and human embryo-derived cells. DRZ-mediated TOP2A depletion reduced the accumulation of DOX-induced DSB.ConclusionsTaken together, our data support a model of anthracycline-induced heart failure caused by TOP2B-mediated DSB and of its prevention by DRZ via TOP2B degradation rather than via iron chelation. The depletion of TOP2B and TOP2A suggests an explanation for the reported DRZ interference with cancer response to anthracyclines and for DRZ side-effects.

No abstract