The 40bp Indel Polymorphism rs150550023 in the MDM2 Promoter is Associated with Intriguing Shifts in Gene Expression in the p53-MDM2 Regulatory Hub

Simple Summary Many naturally occurring variants in the human DNA sequence have an influence on cancer risk, and most of them are located outside the parts of the genome that code for proteins. Presumably, they have an effect on the amount of messenger RNA and protein that is made from genes in their neighborhood. We analyzed one such DNA sequence variant termed rs150550023, which is near a gene termed MDM2 (human homolog of mouse double minute 2). The main function of MDM2 is to negatively regulate another gene termed p53, which is a very important tumor suppressor, i.e., it counteracts cancer. We studied the DNA sequence variant rs150550023 by comparing it in 407 female patients with breast cancer and 254 females without cancer. We found no evidence that rs150550023 plays an important role in the risk of breast cancer, the average age at which patients get breast cancer, how many patients develop breast cancer metastases, or how many patients die of breast cancer. However, we found evidence that rs150550023 may work together with another DNA sequence variant within the MDM2 gene termed SNP309. We also analyzed the tumor tissue of ≈100 breast cancer patients of this study after it had been surgically removed. We measured the amount of messenger RNA (mRNA) which is made from the genes MDM2, p53, and three other genes (termed p21, BAX, and PERP) for which it is known that p53 has an influence on the amount of their mRNA being made. We found that rs150550023 indeed has an influence on the amount of mRNA made from some of these genes. However, since MDM2 is a negative regulator of p53, it is likely that many of these alterations cancel each other out if both p53 and MDM2 is produced at higher levels. Abstract Most low-penetrance genetic risk factors for cancer are located in noncoding regions, presumably altering the regulation of neighboring genes. The poorly characterized Indel polymorphism rs150550023 (rs3730485; del1518) in the promoter of MDM2 (human homolog of mouse double minute 2) is a biologically plausible candidate genetic risk factor, which might influence the expression of MDM2, a key negative regulator of the central tumor suppressor p53. Here, we genotyped rs150550023 in a Central European hospital-based case–control study of 407 breast cancer patients and 254 female controls. mRNA levels of MDM2, p53, and the p53 target genes p21, BAX, and PERP were quantified with qRT-PCR, and p53 protein was assessed with immune histochemistry in ≈100 primary breast tumors with ascertained rs150550023 genotype. We found no evidence for an association of rs150550023 with the risk, age at onset, or prognosis of breast cancer. A possible synergism was observed with SNP309 in promoter P2 of MDM2. Mean mRNA levels of MDM2, p53, p21, and BAX were ≈1.5–3 fold elevated in TP53 wildtype tumors with the minor homozygous Del/Del genotype. However, systematic shifts in p53 protein levels or mutation rates were not observed, suggesting that the elevated p53 mRNA levels are due to regulatory feedback loops that compensate for the effects of rs150550023 on MDM2 expression.