PMC:5056896 / 15133-21164 JSONTXT

{"project":"2_test","denotations":[{"id":"27729841-20686687-44843596","span":{"begin":512,"end":514},"obj":"20686687"},{"id":"27729841-22008259-44843597","span":{"begin":512,"end":516},"obj":"22008259"},{"id":"27729841-20686687-44843598","span":{"begin":585,"end":587},"obj":"20686687"},{"id":"27729841-22008259-44843599","span":{"begin":585,"end":589},"obj":"22008259"},{"id":"27729841-19536157-44843600","span":{"begin":585,"end":591},"obj":"19536157"},{"id":"27729841-20686687-44843601","span":{"begin":5276,"end":5278},"obj":"20686687"},{"id":"27729841-26175662-44843602","span":{"begin":5276,"end":5280},"obj":"26175662"}],"text":"Discussion\nThe current study focused on in silico identification of genes and their regulation mediated through miRNAs, involved in seven types of solid tumors of colorectal, pancreatic, breast, stomach, lung, prostate, and bladder. miRNAs have a crucial role in gene silencing mechanism observed through the altered expression of certain miRNA molecules in case of neurodegenerative diseases such as Alzheimer and Parkinson suggesting that the association between mRNA-miRNA-AGO, therefore not cancer specific [1665]. The association between mRNA-miRNA-AGO pattern has been reported [166566] in RNA based gene silencing mechanism and their association at atomic level has already been studied in case of leukemia [25]. In this context, molecular association between AGO protein, miRNAs and mRNAs of target genes were studied and analyzed in case of seven types of solid tumor. Sixty-four genes and 23 miRNAs were collected from the literature (Supplementary Table 1), out of which 45 genes and seventeen miRNAs were selected on the basis of their expression pattern (Table 1). The affinity in binding modes between 15 miRNAs and 23 genes was verified, basing on the availability of MFE scores in miRTarbase web server (Supplementary Table 2). Further, different biological activities of selected genes were studied using UniProt database (http://www.uniprot.org/) to screen out important genes and their contribution towards seven types of solid tumors. The observation suggested three genes namely, PTEN, TGFBR2, and VEGFA were involved in different biological activities like angiogenesis, apoptosis, cell cycle, and cell proliferation, are the major contributing factor in oncogenesis (Table 2). However, quite less sequence conservation was observed within the binding site of 23 target genes (Fig. 2A). But, quite well sequence similarity was observed between miR-106a, miR-17-5p, and miR-20a (Fig. 2B) suggesting for possibility of regulation of PTEN gene through these three miRNAs (Table 3), associated in causing colorectal cancer. Again, a strong and energetically binding affinity was proved through good MFE scores –14.3 (kcal/mol), –16.2 (kcal/mol), and –15 (kcal/mol) for PTEN and miR-106a; TGFBR2 and miR-21; and VEGFA and miR-29b-2, respectively, suggested for appropriate miRNAs selection for PTEN, TGFBR2, and VEGFA genes (Table 3), supported by the predicted binding energy scores for miRNA-mRNA duplex structures (Table 4). Furthermore, to study the molecular basis of AGO protein driven miRNAs namely, miR-106a, miR-21, and miR-29b-2 having highest binding affinity towards their regulating genes namely, PTEN, TGFBR2, and VEGFA respectively, the molecular docking study was carried out. Generally, presence of amino acids with aliphatic group namely, alanine (ALA), valine (VAL), leucine (LEU), and isoleucine (ILE), are strongly hydrophobic in nature provides stability during molecular interaction between macro molecules, whereas amino acids namely, phenylalanine (PHE), tyrosine (TYR), tryptophan (TRP), are relatively hydrophobic in nature, but the presence of aromatic ring like structure provides a steadiness towards binding stability within the structural moiety of a protein. The observation of amino acids (miR-106a: LEU 132, ALA 133, VAL 152, LEU 153, ALA 170, ILE 173, LEU 267, LEU 279, ALA 479,VAL 620, VAL 663, VAL 666, and ILE 671; miR-21: ILE 173, VAL 264, LEU 267, LEU 279, ALA 354, ALA 414, ILE 434, ALA 644, ALA 648, and VAL 685; miR-29b-2: VAL 152, LEU 153, ALA 170, LEU 279, ALA 414, ALA 479, LEU 596, VAL 620, ALA 648, LEU 652, ALA 659, LEU 662, and VAL 663) which are strongly hydrophobic in nature and amino acids with aromatic rings (miR-106a: TYR 135, TYR 171, TRP 415, and PHE 487; miR-21: TYR 135, TYR 171, TRP 415, TYR 642, PHE 647, and PHE 649; miR-29b-2: TRP 156, TRP 415, TYR 642, PHE 647, and PHE649) during interaction within a distance of 3.5Å (Table 6, Fig. 4) recognized a strong molecular interaction between AGO protein and miR-106a, miR-21, and miR-29b-2. Again, weak interaction like hydrogen bonding has a major contribution to facilitate the stability of molecules during interaction at atomic level. Here, the amino acids like, LEU 153, PRO 169, TYR 171, GLU 416, PHE 487, ARG 574, and ARG 615; ARG 172, THR 201, LEU 279, ALA 354, GLN355, PRO 412, MET 413, TRP 415, ARG 418, ASN 436, ARG 615, ALA 644, ARG 661, and ARG 668; LYS 101, ARG 114, ASP 159, PRO 412, ALA 414, ASP 478, LYS 575, ARG 580, ARG 580, GLU 597, ASP 598, ARG 615, ALA 648, ASP 660, and ARG 661 are participated in hydrogen bonding interaction with miR-106a, miR-21, and miR-29b-2 respectively in the structural moiety of AGO protein within a distance of 2.5Å (Table 7, Fig. 5), strongly supports for binding stability during assistance of AGO protein for miRNA based gene regulation. Furthermore, presence of commonly participating strong hydrophobic amino acids namely, VAL 663 and amino acid with aromatic rings namely, TYR 43, TRP 415, and TYR 642 during molecular interaction of AGO protein with miR-106a and PTEN, miR-21 and TGFBR2, and miR-29b-2 and VEGFA duplex within a distance of 3.5Å (Table 9, Fig. 6). Although, the evidence at molecular association between mRNA-miRNA-AGO pattern have already been established computationally [1661] the current investigation recommending for AGO protein assistance in regulation of PTEN, TGFBR2, and VEGFA genes by miR-106a, miR-21, and miR-29b-2, respectively, associated in seven types of solid tumor. This report would be helpful in understanding miRNA-based gene silencing mechanisms in seven types of solid cancer like colorectal cancer, pancreatic cancer, breast cancer, stomach cancer, lung cancer, prostate cancer, and bladder cancer. Furthermore, extensive computational study may be carried out for better understanding the mechanism of miRNAs based gene regulation in solid cancer. This methodology would further help us to design suitable miRNAs against respective genes rationally, only after validation through laboratory experiments."}