Impact of regulatory genetics in the susceptibility to childhood leukemia Free

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Acute lymphoblastic leukemia (ALL), the most frequent cancer affecting children, is a complex genetic disease where the effect of a series of "low penetrance" genes is modulated by external factors, thus modifying the individual’s risk of cancer. Genetic variation plays a significant role in determining individual’s childhood leukemia susceptibility. Indeed, we provided evidence that childhood ALL might originate through the collective contribution of genes controlling the efficiency of carcinogen metabolism, the capacity of maintaining DNA integrity and the response to oxidative stress. This illustrates the importance of thorough genetic studies to define the genetic determinants in this disease. Until recently, most association studies targeted variants in coding regions. Variation in regulatory DNA sequences has been studied less intensively although variants in promoter regions (rSNP) could modify transcription factor binding site (TFBS) and give rise to differences in expression that would modify the risk of disease. Unfortunately, little is known about the nature and the prevalence of rSNPs. Abnormal expression of finely regulated processes such as cell cycle might be particularly sensitive to such variability in gene expression levels. Given the association between cell cycle and cancer, we hypothesized that the susceptibility (or resistance) to childhood ALL is modulated by functional cis-acting regulatory DNA variants in G1/S cell cycle checkpoint genes. The targeted regulatory regions, defined as a 2kb genomic segment upstream of the transcription initiation site, were screened by dHPLC for the presence of rSNPs in a panel of 40 individuals from different ethnic backgrounds. We identified 127 rSNPs in 16 cell cycle checkpoint genes. Their functional impact was assessed by combining in silico analysis and in vitro functional assays: 90 rSNPs have a predicted impact on putative TFBSs; certain rSNPs showed differential DNA-protein binding; and several regulatory haplotypes (rHAP) significantly influenced transcriptional activity in an allele-specific manner. Although, the biological significance of these observations still remain to be demonstrated, the expected variability of expression levels in key cell cycle components might influence individual’s risk of cancer. To evaluate the association between such rSNPs/rHAPs and the risk to childhood ALL, we performed a case-control study (240 ALL, 277 healthy controls) together with a family-based analysis (135 parental trio) targeting cyclin-dependent kinase inhibitor genes. Using both study designs, we showed evidence of association between variants CDKN2A -222A, CDKN2B -593A and CDKN1B -1608A and an increased risk of ALL. These findings suggest that variable expression levels of cell cycle inhibitor genes due to regulatory polymorphisms could indeed influence childhood leukemogenesis.