Stem Cell Biology Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India.
PLoS One. 2019 Aug 9;14(8):e0220711. doi: 10.1371/journal.pone.0220711. eCollection 2019.
Nowadays CHK2 mutation is studied frequently in hereditary breast and ovarian cancer patients in addition to BRCA1/BRCA2. CHK2 is a tumor suppressor gene that encodes a serine/threonine kinase, also involved in pathways such as DNA repair, cell cycle regulation and apoptosis in response to DNA damage. CHK2 is a well-studied moderate penetrance gene that correlates with third high risk susceptibility gene with an increased risk for breast cancer. Hence before planning large population study, it is better to scrutinize putative functional SNPs of CHK2 using different computational tools. In this study, we have used various computational approaches to identify nsSNPs which are deleterious to the structure and/or function of CHK2 protein that might be causing this disease. Computational analysis was performed by different in silico tools including SIFT, Align GVGD, SNAP-2, PROVEAN, Poly-Phen-2, PANTHER, PhD-SNP, MUpro, iPTREE-STAB, Consurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, Verify-3D, FT Site, COACH and PyMol. Out of 78 nsSNP of human CHK2 gene, seven nsSNPs were predicted functionally most significant SNPs. Among these seven nsSNP, p.Arg160Gly, p.Gly210Arg and p.Ser415Phe are highly conserved residues with conservation score of 9 and three nsSNP were predicted to be involved in post translational modification. The p.Arg160Gly and p.Gly210Arg may interfere in phosphopeptide binding site on FHA conserved domain. The p.Ser415Phe may interfere in formation of activation loop of protein-kinase domain and might interfere in interactions of CHK2 with ligand. The study concludes that mutation of serine to phenylalanine at position 415 is a major mutation in native CHK2 protein which might contribute to its malfunction, ultimately causing disease. This is the first comprehensive study, where CHK2 gene variants are analyzed using in silico tools hence it will be of great help while considering large scale studies and also in developing precision medicines related to these polymorphisms in the era of personalized medicine.
如今，除了 BRCA1/BRCA2 之外，CHK2 突变也经常在遗传性乳腺癌和卵巢癌患者中进行研究。CHK2 是一种肿瘤抑制基因，编码丝氨酸/苏氨酸激酶，还参与 DNA 修复、细胞周期调控和细胞凋亡等途径，以应对 DNA 损伤。CHK2 是一种研究充分的中等外显率基因，与第三个高风险易感性基因相关，乳腺癌风险增加。因此，在计划大规模人群研究之前，最好使用不同的计算工具仔细研究 CHK2 的假定功能 SNPs。在这项研究中，我们使用了各种计算方法来识别可能导致这种疾病的 CHK2 蛋白结构和/或功能有缺陷的 nsSNP。通过不同的计算工具包括 SIFT、Align GVGD、SNAP-2、PROVEAN、Poly-Phen-2、PANTHER、PhD-SNP、MUpro、iPTREE-STAB、Consurf、InterPro、NCBI Conserved Domain Search tool、ModPred、SPARKS-X、RAMPAGE、Verify-3D、FT Site、COACH 和 PyMol 进行计算分析。在人类 CHK2 基因的 78 个 nsSNP 中，有 7 个被预测为功能上最重要的 SNP。在这 7 个 nsSNP 中，p.Arg160Gly、p.Gly210Arg 和 p.Ser415Phe 是高度保守的残基，保守评分均为 9，其中 3 个 nsSNP 被预测参与翻译后修饰。p.Arg160Gly 和 p.Gly210Arg 可能干扰 FHA 保守结构域上的磷酸肽结合位点。p.Ser415Phe 可能干扰蛋白激酶结构域的激活环的形成，并可能干扰 CHK2 与配体的相互作用。该研究得出结论，丝氨酸到 415 位苯丙氨酸的突变是天然 CHK2 蛋白的主要突变，可能导致其功能失调，最终导致疾病。这是首次使用计算工具对 CHK2 基因变异进行全面分析的研究，因此在考虑大规模研究时，以及在个性化医疗时代开发与这些多态性相关的精准药物时，它将非常有帮助。
