Evaluation of EZH2 SNPs in cholangiocarcinoma patients.

Background: Breast cancer (BC) remains one of the leading causes of death in women worldwide. The BRCA1 deleterious mutation has a significant role in developing BC, and the risk has been estimated to be 46–87%. Many studies emphasize the need for mining BRCA1 gene mutations that might have a role in BC pathogenesis and could affect early disease onset. This study was conducted to screen for possible pathogenic single nucleotide polymorphisms (SNPs) in BRCA1, targeting three regions: two in exon 11 and the third in exon 20. Methods: 45 blood samples were collected from patients diagnosed with BC. DNA was extracted and selected regions were amplified by PCR using three sets of primers - two within exon 11 and one within exon 20 of BRCA1. Subsets of 10 samples were selected for each primer set (30 PCR products) and sequenced. Sequences were analyzed using various bioinformatics tools. Results: Two missense mutations were found, Q356R (rs1799950) in one patient (27 years old) and a novel SNP, V1736D, in three premenopausal patients (≤45 years), which were located within exons 11 and 20, respectively. Both detected variants were heterozygous, a status found in all patients detected with such monoallelic variation. Both missense variants underwent in silico analysis. The well-known mutation, rs1799950, was predicted to alter the protein activity, conferred by a mutant residue (R-Arg), owing to the position with a bigger size and positive charge. The novel SNP, V1736D, was predicted to play a role in the pathogenesis of BC. Conclusion: Both variants require further investigation, firstly to assess their contribution to BC and secondly to determine their potential diagnostic value when assessed in a larger population.

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Investigating the Inhibitory Aspects of Metformin/Curcumin Co-Treatment through Convergence of In-Silico and In-Vitro Approaches

10.1101/568634 ◽

2019 ◽

Author(s):

Farzaneh Afzali ◽

Zahra Nayeri ◽

Zarrin Minuchehr ◽

Mossa Gardaneh

Keyword(s):

Treatment Strategy ◽

In Silico ◽

Treatment Optimization ◽

Risk Of Death ◽

Viability Assay ◽

Mcf7 Cell Line ◽

Underlying Mechanisms ◽

Pathway Analyses ◽

Functional Mechanisms

ABSTRACTNearly 16% of people with breast cancer (BC) have Diabetes Mellitus type 2 (DM2) and are at a higher risk of death worldwide. Their common regulatory factors and functional mechanisms can be targeted applying multi-target drugs including Metformin (MTFN) and Curcumin (CURC). In this study, we used in-silico approaches to study the potential underlying mechanisms of this co-treatment strategy on BC and DM2 in order to introduce novel therapeutic targets.The total number of 48 shared differentially expressed genes (17 up-regulated and 31 down-regulated) were identified through establishing diseases’ protein-protein network and BC RNA-sequencing expression data. The integration of functional clustering and pathway analyses revealed that the most involved cellular pathways and processes are regard to cells’ proliferation, death, migration, and response to external stimulus. Afterwards, the MTFN/CURC correlation and co-treatment optimization was probed through response surface methodology (RSM) based on MCF7 cell line and confirmed by MDA-MB-231. Combination index calculation by MTT viability assay proved supportive effects on both cell lines. The superior apoptotic potential of co-treatment compared to single treatments was shown on inhibition of MCF7 proliferation and induction of cell death demonstrated by cell body co-staining and flow cytometry as well as gene expression analysis via RT-PCR. Furthermore, wound-healing scratch assay showed that this co-treatment has a slightly higher effect on migration inhibition compared to single treatments.In conclusion, our study used in-silico and in-vitro approaches and introduced a potential regulatory panel between BC and DM2. We also provided a linear model and equation that show the positive relation of drugs’ co-treatment. The proposed co-treatment strategy successfully controlled the biological processes under investigation.

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BRCA1 novel mutation V1736D and in silico analysis of SNP Q356R in Sudanese patients with breast cancer

F1000Research ◽

10.12688/f1000research.11395.3 ◽

2017 ◽

Vol 6 ◽

pp. 1461

Author(s):

Mohamed Elmogtba Mouaweia Mohamed Aabdein ◽

Alsmawal Awad Mohammed Elimam ◽

Hisham N. Altayb ◽

Mohamed El-Fatih Mohy Eldeen ◽

Mosab Mohamed Gasemelseed ◽

...

Keyword(s):

Breast Cancer ◽

In Silico ◽

Novel Mutation ◽

Disease Onset ◽

Missense Mutations ◽

Nucleotide Polymorphisms ◽

Protein Activity ◽

Exon 11 ◽

Exon 20 ◽

Novel Snp

Background: Breast cancer (BC) remains one of the leading causes of death in women worldwide. The BRCA1 deleterious mutation has a significant role in developing BC, and the risk has been estimated to be 46–87%. Many studies emphasize the need for mining BRCA1 gene mutations that might have a role in BC pathogenesis and could affect early disease onset. This study was conducted to screen for possible pathogenic single nucleotide polymorphisms (SNPs) in BRCA1, targeting three regions: two in exon 11 and the third in exon 20. Methods: 45 blood samples were collected from patients diagnosed with BC. DNA was extracted and selected regions were amplified by PCR using three sets of primers - two within exon 11 and one within exon 20 of BRCA1. Subsets of 10 samples were selected for each primer set (30 PCR products) and sequenced. Sequences were analyzed using various bioinformatics tools. Results: Two missense mutations were found, Q356R (rs1799950) in one patient (27 years old) and a novel SNP, V1736D, in three premenopausal patients (≤45 years), which were located within exons 11 and 20, respectively. Both detected variants were heterozygous, a status found in all patients detected with such monoallelic variation. Both missense variants underwent in silico analysis. The well-known mutation, rs1799950, was predicted to alter the protein activity, conferred by a mutant residue (R-Arg), owing to the position with a bigger size and positive charge. The novel SNP, V1736D, was predicted to play a role in the pathogenesis of BC. Conclusion: Both variants require further investigation, firstly to assess their contribution to BC and secondly to determine their potential diagnostic value when assessed in a larger population.

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Polycomb Group Protein EZH2 is Frequently Expressed in Inflammatory Breast Cancer and is Predictive of Worse Clinical Outcome

Breast Diseases A Year Book Quarterly ◽

10.1016/j.breastdis.2012.06.029 ◽

2012 ◽

Vol 23 (3) ◽

pp. 248-250

Author(s):

L.Y. Dirix

Keyword(s):

Breast Cancer ◽

Clinical Outcome ◽

Inflammatory Breast Cancer ◽

Polycomb Group ◽

Polycomb Group Protein ◽

Group Protein

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In Silico Analysis of Missense Mutations as a First Step in Functional Studies: Examples from Two Sphingolipidoses

International Journal of Molecular Sciences ◽

10.3390/ijms19113409 ◽

2018 ◽

Vol 19 (11) ◽

pp. 3409 ◽

Cited By ~ 2

Author(s):

Ana Duarte ◽

Diogo Ribeiro ◽

Luciana Moreira ◽

Olga Amaral

Keyword(s):

Amino Acid ◽

Protein Level ◽

In Silico ◽

In Silico Analysis ◽

Amino Acid Substitutions ◽

Missense Mutations ◽

Nucleotide Polymorphisms ◽

Functional Studies ◽

Analysis System ◽

Silico Analysis

In order to delineate a better approach to functional studies, we have selected 23 missense mutations distributed in different domains of two lysosomal enzymes, to be studied by in silico analysis. In silico analysis of mutations relies on computational modeling to predict their effects. Various computational platforms are currently available to check the probable causality of mutations encountered in patients at the protein and at the RNA levels. In this work we used four different platforms freely available online (Protein Variation Effect Analyzer- PROVEAN, PolyPhen-2, Swiss-model Expert Protein Analysis System—ExPASy, and SNAP2) to check amino acid substitutions and their effect at the protein level. The existence of functional studies, regarding the amino acid substitutions, led to the selection of the distinct protein mutants. Functional data were used to compare the results obtained with different bioinformatics tools. With the advent of next-generation sequencing, it is not feasible to carry out functional tests in all the variants detected. In silico analysis seems to be useful for the delineation of which mutants are worth studying through functional studies. Therefore, prediction of the mutation impact at the protein level, applying computational analysis, confers the means to rapidly provide a prognosis value to genotyping results, making it potentially valuable for patient care as well as research purposes. The present work points to the need to carry out functional studies in mutations that might look neutral. Moreover, it should be noted that single nucleotide polymorphisms (SNPs), occurring in coding and non-coding regions, may lead to RNA alterations and should be systematically verified. Functional studies can gain from a preliminary multi-step approach, such as the one proposed here.

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BRCA1 novel mutation V1736D and in silico analysis of SNP Q356R in Sudanese patients with breast cancer

F1000Research ◽

10.12688/f1000research.11395.2 ◽

2017 ◽

Vol 6 ◽

pp. 1461

Author(s):

Mohamed Elmogtba Mouaweia Mohamed Aabdein ◽

Alsmawal Awad Mohammed Elimam ◽

Hisham N. Altayb ◽

Mohamed El-Fatih Mohy Eldeen ◽

Mosab Mohamed Gasemelseed ◽

...

Keyword(s):

Breast Cancer ◽

In Silico ◽

Novel Mutation ◽

Disease Onset ◽

Missense Mutations ◽

Nucleotide Polymorphisms ◽

Protein Activity ◽

Exon 11 ◽

Exon 20 ◽

Novel Snp

Background: Breast cancer (BC) remains one of the leading causes of death in women worldwide. The BRCA1 deleterious mutation has a significant role in developing BC, and the risk has been estimated to be 46–87%. Many studies emphasize the need for mining BRCA1 gene mutations that might have a role in BC pathogenesis and could affect early disease onset. This study was conducted to screen for possible pathogenic single nucleotide polymorphisms (SNPs) in BRCA1, targeting three regions: two in exon 11 and the third in exon 20. Methods: 45 blood samples were collected from patients diagnosed with BC. DNA was extracted and selected regions were amplified by PCR using three sets of primers - two within exon 11 and one within exon 20 of BRCA1. Subsets of 10 samples were selected for each primer set (30 PCR products) and sequenced. Sequences were analyzed using various bioinformatics tools. Results: Two missense mutations were found, Q356R (rs1799950) in one patient (27 years old) and a novel SNP, V1736D, in three premenopausal patients (≤45 years), which were located within exons 11 and 20, respectively. Both detected variants were heterozygous, a status found in all patients detected with such monoallelic variation. Both missense variants underwent in silico analysis. The well-known mutation, rs1799950, was predicted to alter the protein activity, conferred by a mutant residue (R-Arg), owing to the position with a bigger size and positive charge. The novel SNP, V1736D, was predicted to play a role in the pathogenesis of BC. Conclusion: Both variants require further investigation, firstly to assess their contribution to BC and secondly to determine their potential diagnostic value when assessed in a larger population.

Download Full-text