Screening and Validation of Dinucleotide Repeats in Intron 1 of the Human EGFR Gene and its Paralog in the HER2 Gene

HER2 polymorphisms and breast cancer in Tunisian women

HER2 has been thought to play a critical role in both breast cancer development and progression. Any functional polymorphisms can potentially affect breast cancer risk as well as cancer phenotype and outcome. In our study, we analyzed three polymorphisms in the HER2 gene: the single-nucleotide polymorphism (SNP) HER2 Ile(655)Val as well as another SNP (rs903506) close to it and a new screened dinucleotide repeat H(AC)I4 in intron 4, in a sample of 148 cases and 290 controls from the Tunisian population and investigated their association with breast cancer risk. For the HER2 Ile(655)Val, we found similar allele frequencies between cases and controls (frequency of I allele was 0.92 and 0.91, respectively). The same was observed for the noncoding SNP (rs903506). These two SNPs also showed no association with any clinical parameters, except the association of HER2 Ile(655)Val with tumor size (p = 0.002). But, a significant association was found between the short tandem repeat (STR) [H(AC)I4] and breast cancer risk at both genotypic and allelic levels (p = 0.0004 and p = 0.0001, respectively). Multivariate analysis with binary logistic regression of disease status on genotypes of the three polymorphisms confirmed the association of STR with breast cancer risk (p = 0.016). Therefore, this STR seems to be a promising biomarker in breast cancer and deserves further investigation.

Repeat performance: how do genome packaging and regulation depend on simple sequence repeats?

Non-coding DNA has consistently increased during evolution of higher eukaryotes. Since the number of genes has remained relatively static during the evolution of complex organisms, it is believed that increased degree of sophisticated regulation of genes has contributed to the increased complexity. A higher proportion of non-coding DNA, including repeats, is likely to provide more complex regulatory potential. Here, we propose that repeats play a regulatory role by contributing to the packaging of the genome during cellular differentiation. Repeats, and in particular the simple sequence repeats, are proposed to serve as landmarks that can target regulatory mechanisms to a large number of genomic sites with the help of very few factors and regulate the linked loci in a coordinated manner. Repeats may, therefore, function as common target sites for regulatory mechanisms involved in the packaging and dynamic compartmentalization of the chromatin into active and inactive regions during cellular differentiation.

Investigating the function of three non-synonymous SNPs in EGFR gene: structural modelling and association with breast cancer

Non-synonymous single nucleotide polymorphisms (nsSNPs) represent common genomic variations that alter protein sequence and function. Some nsSNPs affecting conserved amino acids have been reported to be associated with cancer susceptibility. Interestingly, Epidermal Growth Factor Receptor (EGFR) is commonly overexpressed and mutated in many cancers. In this study, we investigated the structural effect of three deleterious nsSNPs: rs17337451 (R962G), rs1140476 (R977C) and rs17290699 (H988P) within EGFR using computational tools. The modelled mutant dimers showed less stability than wild type EGFR dimer. Furthermore, we showed the important role of R962 and H988 residues in the EGFR dimer formation. We also report preliminary experimental data for SNP R977C suggesting that the variant C977 might confer greater risk for breast cancer. These results contribute to an improved understanding of the EGFR dimer stability and provide new elements for understanding the relationship between EGFR and cancer.

Association of polymorphisms in estrogen and thyroid hormone receptors with thyroid cancer risk

The receptors for thyroid hormone (THR) and oestrogen (ESR) are prototypes of nuclear transcription factors that regulate the expression of target genes. Genetic alterations in the genes of these receptors were found to be involved in cancer development. In this study we investigated the association of one SNP (rs2228480, T594T) and one microsatellite marker (D6S440) within the ESR1 gene and a dinucleotide repeat (D17S2189) within the THRA gene, with thyroid cancer risk. A case-control association study was conducted with 299 healthy individuals and 106 patients with thyroid cancer. Genotypic and allelic frequencies for the dinucleotide repeat in the ESR1 gene were similar between thyroid cancer patients and controls. For the AC repeat in the THRA gene, a slightly significant difference was found for the genotype 18/20 between the two groups (P = 0.034), which suggests that alleles with less than 20 repeats might have a protective effect in thyroid cancer risk. For the SNP T594T, the A allele was much more prevalent in patients than in controls and was highly associated with the risk of thyroid cancer (OR: 4,56; IC: 3.23-6.44; P < 10(-18)) and seems to have an additive mode of action. In conclusion, our data suggest that the SNP T594T but not the D6S440 and D17S189 is associated with thyroid cancer risk.