Predicting Associations of miRNAs and Candidate Gastric Cancer Genes for Nanomedicine

Akimniyazova, Aigul; Pyrkova, Anna; Uversky, Vladimir N.; Иващенко, А. Т.

doi:10.3390/nano11030691

Cited by 7 publications

(9 citation statements)

References 51 publications

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“…In recent years, quantitative characteristics of miRNA interactions with the mRNA of target genes have been established and the features of the organization of miRNA BS in mRNA of target genes have been revealed. This opens up new possibilities for regulating gene expression using miRNA ( Aisina et al, 2019 ; Mukushkina et al, 2020 ; Akimniyazova et al, 2021 ; Kamenova et al, 2021 ). In particular, data on fully complementary miRNA and mRNA interactions raise questions about the function of such associations as they are similar to siRNA ( Table 2 ).…”

Section: Resultsmentioning

confidence: 99%

“…The high predictive advantage of the MirTarget program lies in the fact that it finds BSs for the entire nucleotide sequence of miRNA and determines important quantitative characteristics of the interaction of miRNA with mRNA. This approach in determining the properties of the interaction of exosomal miRNA with mRNA made it possible to reveal fundamentally new properties of miRNA forming in mRNA clusters to reduce the length of the 5′UTR and CDS regions ( Kondybayeva et al, 2018 ; Aisina et al, 2019 ; Mukushkina et al, 2020 ; Akimniyazova et al, 2021 ; Kamenova et al, 2021 ). Studying the interaction of exogenous miRNAs with mRNA genes of humans in silico makes it possible to significantly reduce the material and time costs for determining effective associations of miRNAs and their target genes.…”

Section: Discussionmentioning

confidence: 99%

“…Breast milk is the main source of nutrition and supply of the child, containing the biologically active substances that regulate the development of the body ( Kim et al, 2020 ; McNeill and Hirschi, 2020 ) . A significant part of regulatory molecules, including miRNAs, is transported in exosomes that are resistant to the conditions of the gastrointestinal tract, enter the bloodstream and spread throughout the recipient’s body ( Reif et al, 2020 ; Akimniyazova et al, 2021 ; Melnik B., 2021 ; Billa et al, 2021 ; Melnik B. C., 2021 ; Wang X. et al, 2021 ; Jiang et al, 2021 ; Leroux et al, 2021 ; Lowry et al, 2021 ; Xia et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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Identification of Bovine miRNAs with the Potential to Affect Human Gene Expression

et al. 2022

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Milk and other products from large mammals have emerged during human evolution as an important source of nutrition. Recently, it has been recognized that exogenous miRNAs (mRNA inhibited RNA) contained in milk and other tissues of the mammalian body can enter the human body, which in turn have the ability to potentially regulate human metabolism by affecting gene expression. We studied for exogenous miRNAs from Bos taurus that are potentially contain miRNAs from milk and that could act postprandially as regulators of human gene expression. The interaction of 17,508 human genes with 1025 bta-miRNAs, including 245 raw milk miRNAs was studied. The milk bta-miR-151-5p, bta-miR-151-3p, bta-miRNA-320 each have 11 BSs (binding sites), and bta-miRNA-345-5p, bta-miRNA-614, bta-miRNA-1296b and bta-miRNA-149 has 12, 14, 15 and 26 BSs, respectively. The bta-miR-574-5p from cow’s milk had 209 human genes in mRNAs from one to 25 repeating BSs. We found 15 bta-miRNAs that have 100% complementarity to the mRNA of 13 human target genes. Another 12 miRNAs have BSs in the mRNA of 19 human genes with 98% complementarity. The bta-miR-11975, bta-miR-11976, and bta-miR-2885 BSs are located with the overlap of nucleotide sequences in the mRNA of human genes. Nucleotide sequences of BSs of these miRNAs in 5′UTR mRNA of human genes consisted of GCC repeats with a total length of 18 nucleotides (nt) in 18 genes, 21 nt in 11 genes, 24 nt in 14 genes, and 27–48 nt in nine genes. Nucleotide sequences of BSs of bta-miR-11975, bta-miR-11976, and bta-miR-2885 in CDS mRNA of human genes consisted of GCC repeats with a total length of 18 nt in 33 genes, 21 nt in 13 genes, 24 nt in nine genes, and 27–36 nt in 11 genes. These BSs encoded polyA or polyP peptides. In only one case, the polyR (SLC24A3 gene) was encoded. The possibility of regulating the expression of human genes by exogenous bovine miRNAs is discussed.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification of Bovine miRNAs with the Potential to Affect Human Gene Expression

et al. 2022

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“…The chosen selection criteria for piRNAs strongly interacting with gRNA made it possible to identify the gRNA regions to which two or more piRNAs bound with overlapping nucleotide sequences of BSs. Such regions, which we called clusters of miRNA and piRNA BSs, indicate that the corresponding piRNAs can more effectively suppress both protein synthesis on mRNA and gRNA and gRNA replication [58][59][60][61][62][63]. The strong interaction of several piRNAs in the gRNA BSs cluster makes it possible to more reliably suppress the reproduction of the coronavirus, since a decrease in the concentration of one of the piRNAs will not significantly affect the inhibitory effect of the piRNAs group.…”

Section: Discussionmentioning

confidence: 99%

Endogenous piRNAs Can Interact with Omicron Variant of the SARS-CoV-2 Genome

Rakhmetullina¹,

Akimniyazova²,

Niyazova³

et al. 2023

Preprint

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that caused the COVID-19 pandemic still able to infect the population in many countries. The Omicron strain is the most mutated variant of SARS-CoV-2. The high transmissibility of the strain and the ability to evade immunity require a priority study of its properties in order to quickly create effective means of preventing it. The present work is devoted to the study of in silico interaction of piRNAs with the genome of the SARS-CoV-2 (gRNA) in order to identify endogenous piRNAs and propose synthetic piRNAs with high antiviral activity for drug development. The studies were carried out using proven bioinformatic methods of interaction of the entire SARS-CoV-2 genome with more than eight million piRNAs. Binding sites (BSs) of piRNAs in the 5'UTR were located with overlapping nucleotide sequences called clusters of BSs. Several clusters of BSs were found in the nsp3, nsp7, RNA-dependent RNA polymerase, endoRNAse, S surface glycoprotein, ORF7a and nucleocapsid. 16 synthetic piRNAs have been proposed that interact with gRNA with free binding energy from -170 kJ/mol to -175 kJ/mol, which can be used to create drugs that suppress the reproduction of SARS-CoV-2.

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“…The MirTarget program has proven itself useful in the search for associations of miRNAs and target genes in various diseases [ 37 , 38 , 39 , 40 , 41 , 42 ]. This program makes it possible to determine the quantitative characteristics of these miRNAs with mRNAs, which is very difficult to establish in wet experiments.…”

Section: Methodsmentioning

confidence: 99%

piRNA and miRNA Can Suppress the Expression of Multiple Sclerosis Candidate Genes

et al. 2022

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Multiple sclerosis (MS) is a common inflammatory demyelinating disease with a high mortality rate. MS is caused by many candidate genes whose specific involvement has yet to be established. The aim of our study was to identify endogenous miRNAs and piRNAs involved in the regulation of MS candidate gene expression using bioinformatic methods. A program was used to quantify the interaction of miRNA and piRNA nucleotides with mRNA of the target genes. We used 7310 miRNAs from three databases and 40,000 piRNAs. The mRNAs of the candidate genes revealed miRNA binding sites (BSs), which were located separately or formed clusters of BSs with overlapping nucleotide sequences. The miRNAs from the studied databases were generally bound to mRNAs in different combinations, but miRNAs from only one database were bound to the mRNAs of some genes. For the first time, a direct interaction between the complete sequence of piRNA nucleotides and the nucleotides of their mRNA BSs of target genes was shown. One to several clusters of BSs of miRNA and piRNA were identified in the mRNA of ADAM17, AHI1, CD226, EOMES, EVI5, IL12B, IL2RA, KIF21B, MGAT5, MLANA, SOX8, TNFRSF1A, and ZBTB46 MS candidate genes. These piRNAs form the expression regulation system of the MS candidate genes to coordinate the synthesis of their proteins. Based on these findings, associations of miRNAs, piRNAs, and candidate genes for MS diagnosis are recommended.

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Predicting Associations of miRNAs and Candidate Gastric Cancer Genes for Nanomedicine

Cited by 7 publications

References 51 publications

Identification of Bovine miRNAs with the Potential to Affect Human Gene Expression

Identification of Bovine miRNAs with the Potential to Affect Human Gene Expression

Endogenous piRNAs Can Interact with Omicron Variant of the SARS-CoV-2 Genome

piRNA and miRNA Can Suppress the Expression of Multiple Sclerosis Candidate Genes

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