In silico mutational analysis to identify the role and pathogenicity of BCL-w missense variants – Journal of Genetic Engineering and Biotechnology

BCL-2 family of proteins are associated with mitochondrial-mediated cell death. The proteins of BCL-2 family either inhibits or induces cell death. On the basis of BH domain, members are classified into three groups [1]. The pro-survival proteins possess BH1-4 domains e.g. BCL-2, BCL-XL, MCL1 [2,3,4], BCL-w, and A1/BFL-1. Multi-domain pro-apoptotic proteins contains BH1-3 domains, e.g., BAX and BAK [2,3,4,5], and lastly the BH3 only pro-apoptotic proteins which are further classified as activators or sensitizers. BAD, BIK, BMF are sensitizers and BIM, tBID, and PUMA are activators [2, 6]. Here, sensitizers do not bind to BAK and BAX [2, 7, 8] while the BH3 domain of the activators binds to BAK and BAX and induces conformational change that results in the oligomerization of these proteins in the outer membrane of the mitochondria, this oligomerization results in MOMP formation [2, 9]. In cytosol, cytochrome c (released from mitochondria intermembraned space) with Apaf-1, caspase 9, and ATP [10,11,12] forms a complex also known as apoptosome. This complex cleaves off and activates the caspase 3 that results in apoptosis.

BCL-w is the pro-survival protein in the BCL-2 family. BCL2L2 gene present on chromosome number 14 in humans encodes the BCL-w protein and this protein is 193 amino acids residues in length [2, 13]. BCL-w protein is generally found on the outer membrane of the mitochondria [2, 14]. The BCL-w protein consists of nine α helices with flanking amphipathic helices α1 (10−24 residues), α2 (43−56), α3 (62−68), α4 (76−87), α6 (116−132), α7 (134−141), α8 (144−150), α9 (157−173), and central hydrophobic groove formed by helix, α5 (93−111).

BCL-w is found in the testes, colon, brains, and cells with lymphoid and myeloid origin [2, 13, 15]. Studies suggested that BCL-w is involved in spermatogenesis [2, 15] and is majorly expressed in spermatocytes, Leydig cells, Sertoli cells and spermatogonia, BCL-w also promotes their survival [2, 16, 17]. Experimental studies also suggest that overexpression of this protein might results in spermatocytes degeneracy, decline in the number of spermatogonia and vacuolization of sertoli cells [2, 18]. BCL-w also promotes the survival of gut epithelial cells [2, 15], prevents small intestine cells and mid-colon cells from death [2, 19], it also promotes enterocyte survival and B lymphocyte survival [2, 20]. High level of BCL-w also estimated in some areas of brain such as mature brain, sensory neurons, hippocampus and cerebellum [2, 21, 22]. BCL-w has also been involved in the development of dendrite and it controls the morphogenesis of mitochondria. BCL-w has also been involved in disorders of nervous system such as Alzheimer’s disease and Parkinson’s diseases, the cause of these diseases is the increased level of BCL-w. Overexpression of BCL-w is associated with ischemic brain [2, 23]. Overexpression of the BCL2L2 results in the survival of megakaryocytes and increased platelet formation [2, 24].

Genetic alterations in BCL2L2 contributes to many cancers such as copy number variations in small [2, 25] and non-small [2, 26] lung cancer, high level of BCL-w contributes to gastric carcinomas, and low BCL-w expression contributes to colorectal cancer [2, 27]. Patients with breast cancers significantly have high BCL-w mRNA level [2, 28, 29]. BCL-w has significantly involved with the cancer of urinary system [2, 30]. Overexpression of BCL-w is associated with cervical cancer, prostate cancer, hepatocellular carcinoma (HCC) and leiomyosarcomas. Expression of BCL-w is significantly higher in DLBCL, BL, CML [2, 31], and B-CLL [2, 32].

The interaction of pro-survival protein, i.e., BCL-w with pro-apoptotic proteins initiates the process of apoptosis but any dysregulation in these interactions will block the apoptotic pathway. Any chemical or amino acid alterations in the protein will interrupt the interactions between pro-survival proteins and pro-apoptotic proteins. Understanding of these mutations will help us to understand if the mutation is involved in any disease. This in silico study helps us to define the role of missense variants of BCL-w, which may alter proteins native structure and its function. By examining the role of mutation on biological function, we can determine the correlation between the mutation and the disease. The missense variants retrieved from this study were subjected to some in silico prediction tools such as Polyphen-2, SIFT, Provean, FATHMM, mutation assessor and stability prediction namely I-mutant 2.0, iStable, SAAFEC, SDM, DUET, and mCSM (Table 1).