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Arshad S, Ishaque I, Mumtaz S, Rashid MU, Malkani N. In-Silico Analyses of Nonsynonymous Variants in the BRCA1 Gene. Biochem Genet 2021; 59:1506-1526. [PMID: 33945048 DOI: 10.1007/s10528-021-10074-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 04/22/2021] [Indexed: 10/21/2022]
Abstract
BReast CAncer gene 1 (BRCA1)-a tumor suppressor gene plays an important role in the DNA repair mechanism. Several BRCA1 variants perturb its structure and function, including synonymous and nonsynonymous single nucleotide polymorphisms (SNPs). In the present study, we performed in-silico analyses of nonsynonymous SNPs (nsSNPs) of the BRCA1 gene. In total, 122 nsSNPs were retrieved from the NCBI SNP database and in-silico analyses were performed using computational prediction tools: SIFT, PROVEAN, Mutation Taster, PolyPhen-2, MutPred, and ConSurf. Of these tools, SIFT, PROVEAN, and Mutation Taster predicted 61 out of 122 nsSNPs as "damaging", based on structural homology analysis. PolyPhen-2 classified 22 nsSNPs as "probably damaging". These nsSNPs were further analyzed by MutPred to predict basic molecular mechanisms of amino acid alteration. ConSurf analysis predicted eleven conserved amino acid residues with structural and functional consequences. We identified five amino acid residues in the RING finger domain (L22, C39, H41, C44, and C47) and two in the BRCT domain (P1771 and I1707) with the potential to deter the BRCA1 protein function. This study provides insights into the effect of nsSNPs and amino acid substitutions in BRCA1.
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Affiliation(s)
- Sidra Arshad
- Department of Zoology, GC University, Lahore, Pakistan
| | - Irfan Ishaque
- Department of Zoology, GC University, Lahore, Pakistan
| | - Sidra Mumtaz
- Department of Zoology, GC University, Lahore, Pakistan
| | - Muhammad Usman Rashid
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Naila Malkani
- Department of Zoology, GC University, Lahore, Pakistan.
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Kowalski TW, Fraga LR, Tovo-Rodrigues L, Sanseverino MTV, Hutz MH, Schuler-Faccini L, Vianna FSL. Angiogenesis-related genes and thalidomide teratogenesis in humans: an approach on genetic variation and review of past in vitro studies. Reprod Toxicol 2017; 70:133-140. [PMID: 28161597 DOI: 10.1016/j.reprotox.2017.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/19/2017] [Accepted: 01/30/2017] [Indexed: 12/13/2022]
Abstract
Thalidomide embryopathy (TE) has affected more than 10,000 babies worldwide. The hypothesis of antiangiogenesis as the teratogenic mechanism of thalidomide has been investigated in several experimental models; but, in humans, it has only been accessed by in vitro studies. Here, we hypothesized the effect of thalidomide upon angiogenesis-related molecules or proteins, previously identified in human embryonic cells, through the in silico STRING-tool. We also investigated ten polymorphisms in angiogenesis-related genes in 38 Brazilian TE individuals and 136 non-affected Brazilians. NOS2, PTGS2, and VEGFA polymorphisms were chosen for genotyping. The STRING-tool suggested nitric oxide and β-catenin as the central angiogenesis-related molecules affected by thalidomide's antiangiogenic property. We did not identify a significant difference of allelic, genotypic or haplotypic frequencies between the groups. We could not predict a risk allele or a protective one for TE in NOS2, PTGS2, or VEGFA, although other genes should be analyzed in larger samples. The role of nitric oxide and β-catenin must be further evaluated, regarding thalidomide teratogenesis complex etiology.
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Affiliation(s)
- Thayne Woycinck Kowalski
- INAGEMP-Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- INAGEMP-Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luciana Tovo-Rodrigues
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Post-Graduate Program of Epidemiology, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Maria Teresa Vieira Sanseverino
- INAGEMP-Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Brazil
| | - Mara Helena Hutz
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lavínia Schuler-Faccini
- INAGEMP-Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- INAGEMP-Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Brazil; Service of Experimental Research, Genomics Medicine Laboratory, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.
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