Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1

Abdominal aortic aneurysm (AAA) is a common cause of morbidity and mortality and has a significant heritability. We carried out a genome-wide association discovery study of 1866 patients with AAA and 5435 controls and replication of promising signals (lead SNP with a p value < 1 × 10-5) in 2871 additional cases and 32,687 controls and performed further follow-up in 1491 AAA and 11,060 controls. In the discovery study, nine loci demonstrated association with AAA (p < 1 × 10-5). In the replication sample, the lead SNP at one of these loci, rs1466535, located within intron 1 of low-density-lipoprotein receptor-related protein 1 (LRP1) demonstrated significant association (p = 0.0042). We confirmed the association of rs1466535 and AAA in our follow-up study (p = 0.035). In a combined analysis (6228 AAA and 49182 controls), rs1466535 had a consistent effect size and direction in all sample sets (combined p = 4.52 × 10-10, odds ratio 1.15 [1.10-1.21]). No associations were seen for either rs1466535 or the 12q13.3 locus in independent association studies of coronary artery disease, blood pressure, diabetes, or hyperlipidaemia, suggesting that this locus is specific to AAA. Gene-expression studies demonstrated a trend toward increased LRP1 expression for the rs1466535 CC genotype in arterial tissues; there was a significant (p = 0.029) 1.19-fold (1.04-1.36) increase in LRP1 expression in CC homozygotes compared to TT homozygotes in aortic adventitia. Functional studies demonstrated that rs1466535 might alter a SREBP-1 binding site and influence enhancer activity at the locus. In conclusion, this study has identified a biologically plausible genetic variant associated specifically with AAA, and we suggest that this variant has a possible functional role in LRP1 expression

Affinity of estrogens for human progesterone receptor A and B monomers and risk of breast cancer: a comparative molecular modeling study

Tarique N Hasan1,4, Leena Grace B2, Tariq A Masoodi3,5, Gowhar Shafi4 , Ali A. Alshatwi4, P Sivashanmugham31Department of Biotechnology, Bharathiar University, Coimbator, TN, India; 2Department of Biotechnology, V. M. K. V. College of Engineering, Salem, TN, India; 3Department of Bioinformatics, Jamal Mohammed College, Bharathidasan University, Tiruchirappalli, India; 4Molecular Cancer Biology Laboratory, Department of Food Science and Nutrition, College of Food and Agricultural Sciences; 5Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Saudi ArabiaBackground: The human progesterone receptor (hPR) belongs to the steroid receptor family. It may be found as monomers (A and B) and or as a dimer (AB). hPR is regarded as the prognostic biomarker for breast cancer. In a cellular dimer system, AB is the dominant species in most cases. However, when a cell coexpresses all three isoforms of hPR, the complexity of the action of this receptor increases. For example, hPR A suppresses the activity of hPR B, and the ratio of hPR A to hPR B may determine the physiology of a breast tumor. Also, persistent exposure of hPRs to nonendogenous ligands is a common risk factor for breast cancer. Hence we aimed to study progesterone and some nonendogenous ligand interactions with hPRs and their molecular docking.Methods and results: A pool of steroid derivatives, namely, progesterone, cholesterol, testosterone, testolectone, estradiol, estrone, norethindrone, exemestane, and norgestrel, was used for this in silico study. Dockings were performed on AutoDock 4.2. We found that estrogens, including estradiol and estrone, had a higher affinity for hPR A and B monomers in comparison with the dimer, hPR AB, and that of the endogenous progesterone ligand. hPR A had a higher affinity to all the docked ligands than hPR B.Conclusion: This study suggests that the exposure of estrogens to hPR A as well as hPR B, and more particularly to hPR A alone, is a risk factor for breast cancer.Keywords: human progesterone receptor, breast cancer, steroid derivatives, estrogens, molecular dockin

Identification of functional SNPs in BARD1 gene and in silico analysis of damaging SNPs: based on data procured from dbSNP database.

The BARD1 gene encodes for the BRCA1-associated RING domain (BARD1) protein. Germ line and somatic mutations in BARD1 are found in sporadic breast, ovarian and uterine cancers. There is a plethora of single nucleotide polymorphisms (SNPs) which may or may not be involved in the onset of female cancers. Hence, before planning a larger population study, it is advisable to sort out the possible functional SNPs. To accomplish this goal, data available in the dbSNP database and different computer programs can be used. To the best of our knowledge, until now there has been no such study on record for the BARD1 gene. Therefore, this study was undertaken to find the functional nsSNPs in BARD1.2.85% of all SNPs in the dbSNP database were present in the coding regions. SIFT predicted 11 out of 50 nsSNPs as not tolerable and PolyPhen assessed 27 out of 50 nsSNPs as damaging. FastSNP revealed that the rs58253676 SNP in the 3' UTR may have splicing regulator and enhancer functions. In the 5' UTR, rs17489363 and rs17426219 may alter the transcriptional binding site. The intronic region SNP rs67822872 may have a medium-high risk level. The protein structures 1JM7, 3C5R and 2NTE were predicted by PDBSum and shared 100% similarity with the BARD1 amino acid sequence. Among the predicted nsSNPs, rs4986841, rs111367604, rs13389423 and rs139785364 were identified as deleterious and damaging by the SIFT and PolyPhen programs. Additionally, I-Mutant showed a decrease in stability for these nsSNPs upon mutation. Finally, the ExPASy-PROSIT program revealed that the predicted deleterious mutations are contained in the ankyrin ring and BRCT domains.Using the available bioinformatics tools and the data present in the dbSNP database, the four nsSNPs, rs4986841, rs111367604, rs13389423 and rs139785364, were identified as deleterious, reducing the protein stability of BARD1. Hence, these SNPs can be used for the larger population-based studies of female cancers

A comparison of amino acid substitutions due to nsSNPs, rs4986841 (Ile653Phe), rs111367604 (Val695Leu), rs13389423 (Ser728FPhe) and rs139785364 (Arg751Trp).

<p>Figure shows the differences of structure and electron cloud density between native and mutant models BARD1 Protein (PDB ID: 2NTE). Models were generated by using SPDBV (v4.0).</p

A graphical representation of distribution of nonsynonymous, 5′UTR and 3′ UTR SNPs for <i>BARD1</i> gene (based on the dbSNP database).

<p>A graphical representation of distribution of nonsynonymous, 5′UTR and 3′ UTR SNPs for <i>BARD1</i> gene (based on the dbSNP database).</p

Sequence homology-based results from Sorting Intolerant from Tolerant (SIFT) server for SNPs (SIFT output is modified and depicted only the intolerant amino acid substitutions).

<p>Sequence homology-based results from Sorting Intolerant from Tolerant (SIFT) server for SNPs (SIFT output is modified and depicted only the intolerant amino acid substitutions).</p

List of nsSNPs predicted by SIFT as Not Tolerated.

<p>List of nsSNPs predicted by SIFT as Not Tolerated.</p

The available PDB structure for the BARD1 gene with a similarity (100%) with BARD1 FASTA sequence at PDBsum.

<p>The available PDB structure for the BARD1 gene with a similarity (100%) with BARD1 FASTA sequence at PDBsum.</p