Structural impact, ligand-protein interactions, and molecular phenotypic effects of TGF-ß1 gene variants: In silico analysis with implications for idiopathic pulmonary fibrosis.

BACKGROUND: Idiopathic Pulmonary Fibrosis (IPF) is a chronic interstitial lung disease resulting in progressively deteriorating lung function. Transforming growth factor-ß1 (TGF-ß1) belongs to the TGF superfamily and exerts a profibrotic role in promoting lung fibrosis by facilitating fibroblast infiltration and activity, extracellular matrix deposition, and inhibition of collagen breakdown, thus promoting tissue remodelling and IPF. MATERIALS AND METHODS: We evaluated the link between pathogenic TGF-ß1 SNPs and IPF pathogenesis and the structure-activity functional consequences of those SNPs on the TGF-ß1 protein. Several computational algorithms were merged to address the functional consequences of TGF-ß1 gene mutations to protein stability, putative post-translational modification sites, ligand-protein interactions, and molecular phenotypic effects. These included FATHMM, POLYPHEN2, PROVEAN, and SIFT tools (identifying deleterious nsSNPs in the TGF-ß1 gene), along with Pmut, PhD-SNP, SNAP, MutPred and the related TMHMM, MARCOIL, and DisProt algorithms (predicting structural disorders). INPS-MD was also used to evaluate the mutation-induced TGF-ß1 protein's stability and MODPRED for recognition of post-translational TGF-ß1 modification. RESULTS: In total, 14 major pathogenic variants markedly impact the destabilization of the TGF-ß1 protein, with most of these high-risk mutations associated with decreased stability of the TGF-ß1 protein as per the I-Mutant, MUpro, and INPS-MD tools. R205W, R185W, R180Q, D86Y, and I300T variants were proposed to participate in the post-translational modifications, thus affecting affect protein-ligand interactions. Furthermore, at-risk genetic variants appear to target conserved regions in the alpha helices, random coils, and extracellular loops, resulting in a varied composition of amino acids, charge, hydrophobicity, and spatial architecture. CONCLUSIONS: This study manuscript comprehensively analyzes gene variants within the TGF-ß1 gene, offering novel insights into their structural and functional implications in interacting with target sites. This study is significant for the development of targeted therapeutic strategies and personalized treatment approaches for patients with inflammatory lung diseases such as IPF.

Risk factors in autism spectrum disorder: A Tunisian case-control study.

Background: Autism spectrum disorder (ASD) is a neurodevelopmental condition that causes disability in social interaction, communication, and restrictive and repetitive behaviors. Common environmental factors like prenatal, perinatal, and/or postnatal factors play a key role in ASD etiologies. Moreover, specific metabolic disorders can be associated with ASD. Subjects and methods: We performed a retrospective case-control study in child psychiatry clinics, involving 51 children with ASD and 40 typical development controls (TDC). Results: We found a correlation between children being breastfed for less than 6 months, having fathers more than 40 years old at childbirth in ASD compared to TDC group. Our study also associated low blood cholesterol and low erythrocyte magnesium levels with increased risk for ASD. Conclusion: Findings support the implication of total cholesterol (TC) and erythrocyte magnesium level in defining autism outcome.

The Relationship Between Menopause and Metabolic Syndrome: Experimental and Bioinformatics Analysis.

Menopausal hormonal changes have been associated with the emergence of the metabolic syndrome (MetS) and its consequences such as type 2 diabetes (T2D) and cardiovascular diseases (CVD). The common gene signature and the associated signaling pathways of MetS, T2D, CVD and menopause status have not been widely studied. We analyzed a total of 314 women aged between 35 and 75 years. The sample was divided into two groups: Group I, including women in the premenopausal period and Group II, comprising women in the post-menopausal period. The presence of MetS and its components were evaluated, as well as occurrence of T2D and CVD in both groups. We also exploited the translational bioinformatics approach to choose the common gene signatures for MetS, T2D, CVD and the menopause status. The frequency of the MetS was significantly higher in postmenopausal women than in premenopausal ones (67.1 vs. 27.2%, p < 0.001). Gene mining analysis revealed that a total of 47 genes were commonly associated with MetS, T2D, CVD and the menopausal changes. The gene enrichment analysis showed that these genes were markedly enriched in biological processes, including positive regulation of binding, positive regulation of leukocyte cell-cell adhesion, regulation of lipid localization. Furthermore, P53 signaling pathway, prolactin signaling pathway, parathyroid hormone synthesis, secretion and action were the top enriched pathways. Additionally, network analysis revealed TGFB1, SPP1, MMP2, MMP9, CCL2, IGF1, EGFR, ICAM1, TNF and IL6 as important hub genes with significant interacting partners. These hub genes identified in our study may play key role in menopausal changes and influence the risks of MetS, T2D and CVD.

Potential functions of hsa-miR-155-5p and core genes in chronic myeloid leukemia and emerging role in human cancer: A joint bioinformatics analysis.

Considering the critical roles of hsa-miR-155-5p participated in hematopoietic system, this study aims to clarify the possible pathogenesis of chronic myeloid leukemia (CML) induced by hsa-miR-155-5p.Three different strategies were employed, namely a network-based pipeline, a survival analysis and genetic screening method, and a simulation modeling approach, to assess the oncogenic role of hsa-miR-155-5p in CML. We identified new potential roles of hsa-miR-155-5p in CML, involving the BCR/ABL-mediated leukemogenesis through MAPK signaling. Several promising targets including E2F2, KRAS and FLI1 were screened as candidate diagnostic marker genes. The survival analysis revealed that mRNA expression of E2F2, KRAS and FLI1 was negatively correlated with hsa-miR-155-5p and these targets were significantly associated with poor overall survival. Furthermore, an overlap between CML-related genes and hsa-miR-155-5p target genes was revealed using competing endogenous RNA (ceRNA) networks analysis. Taken together, our results reveal the dynamic regulatory aspect of hsa-miR-155-5p as potential player in CML pathogenesis.

Contribution of ADIPOQ Variants to the Genetic Susceptibility of Recurrent Pregnancy Loss.

Adiponectin is a hormone implicated in regulating energy, lipid, and glucose metabolism and is encoded by the ADIPOQ gene. ADIPOQ variants can regulate the circulating levels of adiponectin. Irregular adiponectin concentrations have been associated with numerous reproductive diseases including recurrent pregnancy loss (RPL). The main objective of this study was to determine whether the 14 selected polymorphisms of the ADIPOQ gene are linked with RPL. The retrospective case-control study comprised a total of 332 women with RPL, adjusted as more than three consecutive abortions of unknown etiology, and 286 healthy controls. They were genotyped for the ADIPOQ variants using allele exclusion method on real-time PCR. Significantly higher rs1501299 minor allele frequencies (MAF) and lower rs2241767 and rs2241766 MAF were seen among RPL women, thereby assigning disease susceptibility and protective aspect to the mentioned variants, respectively. Different associations of ADIPOQ genotypes with RPL were noticed according to the genetic model exploited: rs1501299 and rs2241767 were significantly linked with RPL under the three models, while rs17366568 and rs2241766 were associated with RPL under codominant and dominant models, and rs7649121 was related to RPL under the dominant and recessive models. rs4632532 was linked according to the recessive model only. Based on LD pattern, 2-haplotype blocks were specified. Reduced frequency of AGG and GAGG and increased frequency of TAAG were noted in cases, compared with controls, hence indicating these haplotypes as RPL-protective and RPL-susceptible, respectively. These results support a significant role of ADIPOQ as an RPL candidate locus.

Comprehensive in-silico analysis of damage associated SNPs in hOCT1 affecting Imatinib response in chronic myeloid leukemia.

Non-synonymous single nucleotide polymorphisms (nsSNPs) in hOCT1 (encoded by SLC22A1 gene) are expected to affect Imatinib uptake in chronic myeloid leukemia (CML). In this study, sequence homology-based genetic analysis of a set of 270 coding SNPs identified 18 nsSNPs to be putatively damaging/deleterious using eight different algorithms. Subsequently, based on conservation of amino acid residues, stability analysis, posttranscriptional modifications, and solvent accessibility analysis, the possible structural-functional relationship was established for high-confidence nsSNPs. Furthermore, based on the modeling results, some dissimilarities of mutant type amino acids from wild-type amino acids such as size, charge, interaction and hydrophobicity were revealed. Three highly deleterious mutations consisting of P283L, G401S and R402G in SLC22A1 gene that may alter the protein structure, function and stability were identified. These results provide a filtered data to explore the effect of uncharacterized nsSNP and find their association with Imatinib resistance in CML.

Identification of genes and miRNA associated with idiopathic recurrent pregnancy loss: an exploratory data mining study.

BACKGROUND: Recurrent pregnancy loss (RPL) is a significant adverse pregnancy complication, with an incompletely understood pathology. While many entities were proposed to elucidate the pathogenic basis of RPL, only few were significant enough to warrant investigation in all affected couples.. The aim of this study was to provide novel insights into the biological characteristics and related pathways of differentially expressed miRNA (DEMs) and genes (DEGs), in RPL, and construct a molecular miRNAs-mRNAs network. METHODS: miRNAs and gene expression data were collected, and a number of DEMs and (DEGs) were obtained, and regulatory co-expression network were constructed. Function and enrichment analyses of DEMs were conducted using DIANA-miRPath. DEGs were screened, and were used in generation of protein-protein interaction (PPI) network, using STRING online database. Modularity analysis, and pathway identification operations were used in identifying graph clusters and associated pathways. DEGs were also used for further gene ontology (GO) analysis, followed by analysis of KEGG pathway. RESULTS: A total of 34 DEMs were identified, and were found to be highly enriched in TGF-ß signaling pathway, Fatty acid metabolism and TNF signaling pathway. Hub miRNAs were selected and were found to be involved in several functional pathways including progesterone-mediated oocyte maturation and Thyroid hormone signaling pathway. Five dysregulated feedback loops involving miRNA and TFs were identified and characterized. Most notably, PPI network analysis identified hub-bottleneck protein panel. These appear to offer potential candidate biomarker pattern for RPL diagnosis and treatment. CONCLUSIONS: The present study provides novel insights into the molecular mechanisms underlying RPL.

Association of genetic variants in Estrogen receptor (ESR)1 and ESR2 with susceptibility to recurrent pregnancy loss in Tunisian women: A case control study.

Estrogen receptor (ER) signaling is key regulator for maintaining successful pregnancy. Several research suggested that genetic variation in ER genes (ESR)1 and ESR2 is associated with the susceptibility to unexplained recurrent pregnancy loss (RPL), often with inconclusive results. In this study, we investigate the relationship between ESR1 and ESR2 polymorphisms and idiopathic RPL. A total of 444 patients with RPL, defined as three or more consecutive pregnancy losses of unknown etiology, and 446 control women were recruited to the study and their genotypes for ESR1-rs2234693, ESR1-rs3020314, and ESR2-rs928554 variants were determined using allelic exclusion method on real-time polymerase chain reaction. Minor allele frequencies (MAF) of tagging SNPs ESR1 rs2234693 and rs3020314, and ESR2 rs928554 were not significantly different between RPL cases and control women. Considerable higher frequencies of homozygous (2/2) ESR1 rs2234693 genotype carriers were seen between patients vs. control women, which maintained after controlling for age, body mass index (BMI), and menarche. ESR1 haplotype analysis demonstrated two common haplotype (rs2234693-rs3020314) with no linkage disequilibrium between both polymorphisms, and no 2-locus haplotype linked with RPL risk was revealed. The present study confirmed a significant association of specific ESR1 variant (rs2234693) with an increased risk of RPL, further supporting a role for ESR1 as an important candidate locus inducing RPL.

Regulatory network analysis of microRNAs and genes in imatinib-resistant chronic myeloid leukemia.

Targeted therapy in the form of selective breakpoint cluster region-abelson (BCR/ABL) tyrosine kinase inhibitor (imatinib mesylate) has successfully been introduced in the treatment of the chronic myeloid leukemia (CML). However, acquired resistance against imatinib mesylate (IM) has been reported in nearly half of patients and has been recognized as major issue in clinical practice. Multiple resistance genes and microRNAs (miRNAs) are thought to be involved in the IM resistance process. These resistance genes and miRNAs tend to interact with each other through a regulatory network. Therefore, it is crucial to study the impact of these interactions in the IM resistance process. The present study focused on miRNA and gene network analysis in order to elucidate the role of interacting elements and to understand their functional contribution in therapeutic failure. Unlike previous studies which were centered only on genes or miRNAs, the prime focus of the present study was on relationships. To this end, three regulatory networks including differentially expressed, related, and global networks were constructed and analyzed in search of similarities and differences. Regulatory associations between miRNAs and their target genes, transcription factors and miRNAs, as well as miRNAs and their host genes were also macroscopically investigated. Certain key pathways in the three networks, especially in the differentially expressed network, were featured. The differentially expressed network emerged as a fault map of IM-resistant CML. Theoretically, the IM resistance process could be prevented by correcting the included errors. The present network-based approach to study resistance miRNAs and genes might help in understanding the molecular mechanisms of IM resistance in CML as well as in the improvement of CML therapy.

Downregulation of miR-451 in Tunisian chronic myeloid leukemia patients: potential implication in imatinib resistance.

OBJECTIVES: Resistance to imatinib has been recognized as a major challenge for the treatment of chronic myeloid leukemia (CML). Aberrant expression of miR-451 has been reported to participate in anticancer drug resistance. However, the role of miR-451 in imatinib resistance has not been investigated. The present study was undertaken to determine the expression of miR-451 in order to find a possible association between the expression of this miRNA and imatinib resistance in Tunisian CML patients. METHODS: First, real-time RT-PCR was performed to identify the expression of miR-451 in peripheral leukocytes of 59 CML patients treated with imatinib. Then, bioinformatics analysis was carried out to understand the regulatory roles of miR-451 in imatinib-resistant process. RESULTS: Downregulated miR-451 was observed in imatinib-resistant CML cases. In silico analysis identified MYC as a potential target of miR-451. We further revealed the existence of an MYC-binding site in MiR-451 promoter region. On the other hand, increased level of MYC was detected in imatinib-resistant CML cases which may explain the causative role of MYC in CML cases and the downregulation of miR-451. CONCLUSION AND DISCUSSION: Taken together, our findings suggest that miR-451 and MYC form together a regulatory loop which may act as a potential therapeutic target, and disruption of suggested regulatory loop could help to improve CML therapy.