COMPUTATIONAL ANALYSIS OF MUTATIONS IN REALLY INTERESTING NEW GENE FINGER DOMAIN AND BRCA1 C TERMINUS DOMAIN OF BREAST CANCER SUSCEPTIBILITY GENE

Objective: Breast Cancer 1 (BRCA1), Early Onset and Breast Cancer 2, Early Onset (BRCA2) genes are involved in pathways important for DNA damagerecognition, double-strand break repair, checkpoint control, transcription regulation, and chromatin remodeling. These functions are essential andimportant for all cell types. Germline mutations in these genes increase the risk of breast and ovarian cancer in women. In this study, we did ananalysis of the functional and structural impact of all known single nucleotide polymorphisms (SNPs) in BRCA1 and BRCA2 using publicly availablecomputational prediction tools.Methods: We analyzed the mutations using two mutation tolerance prediction approaches: Sorting intolerant from tolerant (SIFT), and polymorphismphenotyping (PolyPhen-2). In addition, stability of the protein was analyzed by I-Mutant. Affinity and stability of really interesting new gene (RING)and BRCA1 C-terminus (BRCT) domains were also analyzed by BioLuminate tool.Results: Out of 486 SNPs in BRCA retrieved from functional SNP, a total of 10 SNPs were found to be deleterious by SIFT and PolyPhen. I-Mutant resultsindicate that C27F, A1708V could increase the stability of protein, whereas other mutations decrease the stability. Predicted changes in stability andaffinity of RING and BRCT domains of BRCA were computed using residue scanning functionality in bioluminate for all 10 SNPs. The mutation C61Rcould affect the stability of RING domain and all mutations in BRCT domain were affecting the inter subunit affinity and stability of the complex.Conclusion: The combination of computational methods provides a way in understanding the impact of deleterious mutations in altering the BRCAprotein stability and affinity. Based on our investigation, we report potential candidate SNPs for future studies of BRCA mutations.Keywords: Breast cancer susceptibility gene, BRCA1 C terminus domain, Zinc finger domain, Sorting intolerant from tolerant, Polymorphismphenotyping, I-mutant, BioLuminate

MOLECULAR MODELLING AND DOCKING STUDIES OF HUMAN ACROSIN BINDING PROTEIN (ACRBP/OY-TES-1)

Objective: We have made an attempt to identify inhibitors that are bound with Acrosin binding protein (ACRBP/OY-TES-1) through In silico molecular docking studies.Methods: Modeling of ACRBP/OY-TES-1 was performed using Iterative Threading Assembly Refinement (I-TASSER) software. Docking calculations were carried out using Glide. Glide Score (GS core) was used to rank the ligands on the basis of their relative binding affinities.Results: Food and Drug Administration (FDA)-approved drugs were docked with ACRBP/OY-TES-1 to identify potent inhibitors. Leuprolide a decapeptide interacts with the protein at residues Tyr116, Gly421, Leu433, Asp480 and Gln483 with Glide score-14.188. Other compounds that showed high affinity to the protein are triptorelin, nafatarelin, goserelin and sincalide.Conclusion: The investigation concluded that these drugs could be used as potential inhibitors against ACRBP/OY-TES-1 in cancer treatment.Â

Identification and validation of genes involved in gastric tumorigenesis

<p>Abstract</p> <p>Background</p> <p>Gastric cancer is one of the common cancers seen in south India. Unfortunately more than 90% are advanced by the time they report to a tertiary centre in the country. There is an urgent need to characterize these cancers and try to identify potential biomarkers and novel therapeutic targets.</p> <p>Materials and methods</p> <p>We used 24 gastric cancers, 20 Paired normal (PN) and 5 apparently normal gastric tissues obtained from patients with non-gastric cancers (Apparently normal - AN) for the microarray study followed by validation of the significant genes (n = 63) by relative quantitation using Taqman Low Density Array Real Time PCR. We then used a custom made Quantibody protein array to validate the expression of 15 proteins in gastric tissues (4 AN, 9 PN and 9 gastric cancers). The same array format was used to study the plasma levels of these proteins in 58 patients with gastric cancers and 18 from patients with normal/non-malignant gastric conditions.</p> <p>Results</p> <p>Seventeen genes (ASPN, CCL15/MIP-1δ, MMP3, SPON2, PRSS2, CCL3, TMEPAI/PMEPAI, SIX3, MFNG, SOSTDC1, SGNE1, SST, IGHA1, AKR1B10, FCGBP, ATP4B, NCAPH2) were shown to be differentially expressed between the tumours and the paired normal, for the first time. EpCAM (p = 0.0001), IL8 (p = 0.0003), CCL4/MIP-1β (p = 0.0026), CCL20/MIP-3α (p = 0.039) and TIMP1 (p = 0.0017) tissue protein levels were significantly different (Mann Whitney U test) between tumours versus AN & PN. In addition, median plasma levels of IL8, CXCL9/MIG, CCL3/MIP-1α, CCL20/MIP-3α, PDGFR-B and TIMP1 proteins were significantly different between the non-malignant group and the gastric cancer group. The post-surgical levels of EpCAM, IGFBP3, IL8, CXCL10/IP10, CXCL9/MIG, CCL3/MIP-1α, CCL20/MIP-3α, SPP1/OPN and PDGFR-B showed a uniform drop in all the samples studied.</p> <p>Conclusions</p> <p>Our study has identified several genes differentially expressed in gastric cancers, some for the first time. Some of these have been confirmed at the protein level, as well. Some of these proteins will need to be evaluated further for their potential as diagnostic biomarkers in gastric cancers and some could be useful as follow-up markers in gastric cancer.</p