Structural impact, ligand-protein interactions, and molecular phenotypic effects of TGF-β1 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-β1 (TGF-β1) 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-β1 SNPs and IPF pathogenesis and the structure-activity functional consequences of those SNPs on the TGF-β1 protein. Several computational algorithms were merged to address the functional consequences of TGF-β1 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-β1 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-β1 protein's stability and MODPRED for recognition of post-translational TGF-β1 modification.

RESULTS

In total, 14 major pathogenic variants markedly impact the destabilization of the TGF-β1 protein, with most of these high-risk mutations associated with decreased stability of the TGF-β1 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-β1 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.

Development of Nanotechnology-Based Drug Delivery Systems for Controlling Clinical Multidrug-Resistant Staphylococcus aureus and Escherichia coli Associated with Aerobic Vaginitis

The growing prevalence of resistance to antibiotics potentially makes Escherichia coli and Staphylococcus aureus serious pathogens, necessitating the development of new antimicrobial agents. We extracted crude biosurfactants from a potential probiotic Bacillus spp. to control pathogenic bacteria associated with aerobic vaginal infection. Using nanotechnology formulations, we developed nanoemulsions based on biosurfactants at different concentrations (1% and 3.33%). The results showed that these nanoemulsions were stable, with a weighted index of 0.3, and demonstrated broad-spectrum antibacterial activity against Escherichia coli and Staphylococcus aureus, with MICs ranging between 1.25 and 4 mg/mL. Additionally, the nanoemulsions exhibited interesting antibiofilm effects. All strains became more sensitive to the antibiotics to which they were resistant because of various biosurfactant formulations combined with antibiotics. Lower concentrations of BNE1% and 3.33% were still more efficient than the crude biosurfactants. Our findings demonstrated that the biosurfactant had a strong antibiofilm effect against all tested pathogens. This antibacterial effect can be explained by their ability to alter cell physiology such as cell hydrophobicity and membrane disintegration. Thus, we can conclude that the use of nanotechnology formulations has improved this effect, and the nanoemulsions developed in this study can be used as a potential anti-infectious therapy against multidrug-resistant bacterial strains of clinical origin.

Human forkhead box protein 3 gene variants associated with altered susceptibility to idiopathic recurrent pregnancy loss: A retrospective case-control study

BACKGROUND

The pathogenesis of recurrent pregnancy loss (RPL) is multifactorial and not completely elucidated. Dysregulated immunity was implicated with RPL, in which regulatory T cells (Tregs) are key. As Tregs development and function are regulated by forkhead box P3 (FOXP3) transcription factor, and as FOXP3 expression is genetically determined, a role for FOXP3 polymorphisms in RPL pathogenesis was suggested.

AIM

To investigate the association of rs2294021, rs2232365, rs3761548, and rs141704699 FOXP3 variants with idiopathic RPL in Lebanese women.

METHODS

This retrospective case-control study included 386 RPL cases and 398 age-matched control women. Logistic odds ratios (OR) were estimated with 95% confidence interval after adjustment; a significance value of P<.05 was set.

RESULTS

Significantly lower rs22944021 and rs2232365 minor allele frequency (MAF) was found in patients with idiopathic RPL in comparison with the control group. Furthermore, statistically significantly lower frequency of heterozygous and homozygous rs2294021 and rs2232365 genotypes was seen in controls, while significantly lower rs3761548 heterozygous genotype frequencies were found in the patient group. Obesity, antihypertension treatment, smoking, positive RPL family history, abortion state, and infertility treatment correlated negatively with rs2294021, while rs2232365 negatively correlated with obesity, and rs3761548 negatively correlated with infertility treatment. Marked linkage disequilibrium (LD) was noted among FOXP3 SNPs, with TGCC and CGAC haplotypes being positive, while CAAC, CACC, and TGAC haplotypes being negatively associated with RPL risk. Except for CGAC, the association of these haplotypes with RPL persisted after adjustment.

CONCLUSION

FOXP3 gene variants and haplotypes are associated with altered incidence of RPL, proposing the role of Treg in RPL pathogenesis.

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.

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.

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.

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-β 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 NF-kB with Susceptibility to Breast Cancer: a Case Control Study

Insofar as altered NF-κB signaling stemming from the presence of specific genetic variants in NF-κB gene contribute to cancer pathogenesis, this study evaluated the association between NF-κB rs147574894/I552V, rs148626207/M860T rs3774937 and rs1598859 variants and breast cancer and associated features and complications. This was a retrospective case-control study, which involved 207 women with breast cancer, and 214 cancer-free women who served as controls. NF-κB genotyping was done by real-time PCR. Significantly higher rs3774937 minor allele frequencies (MAF), and lower rs147574894 MAF were seen among breast cancer patients, thereby imparting disease susceptibility and protective nature to these variants, respectively. Significant association of rs3774937 and rs147574894 genotypes with breast cancer was seen under the dominant model. Histological type and grade, molecular type, Her2 positivity and ER+/Her2- correlated positively, while distant metastasis negatively correlated with rs3774937. On the other hand, rs147574894 negatively correlated with histological type and grade, tumor size, Her2 positivity, molecular type, and ER+/Her2-, while rs148626207 correlated positively with histological grade, but negatively with distant metastasis and triple-negative status. Breast cancer-susceptible and -protective 4-locus haplotypes were also identified. This is the first report that addresses the contribution of NF-κB variants to the pathogenesis of breast cancer in Middle Eastern-North African population, and the first to document positive association of rs3774937 with breast cancer.

Genetic variation in the progesterone receptor gene and susceptibility to recurrent pregnancy loss: a case-control study

OBJECTIVE

To investigate the association of progesterone receptor (PGR) gene variants with susceptibility to recurrent pregnancy loss (RPL).

DESIGN

Retrospective case-control study.

SETTING

Outpatient obstetrics and gynaecology clinics.

POPULATION

Women with RPL (396), defined as three or more consecutive miscarriages of unknown aetiology, and 361 women used as controls.

METHODS

PGR genotyping was performed by the allelic exclusion method (real-time polymerase chain reaction).

MAIN OUTCOME MEASURES

PGR single nucleotide polymorphisms (SNPs) and the distribution of their alleles, genotypes and haplotypes.

RESULTS

Higher minor allele frequencies (MAFs) for rs590688, rs10895068, and rs1942836 were seen in RPL cases than in controls, which remained significant after controlling for multiple comparisons. Significantly higher frequencies of heterozygous (1/2) rs608995, along with heterozygous (1/2) and homozygous (2/2) rs590688, rs10895068, and rs1942836 genotype carriers, were seen between RPL cases versus controls, respectively, which persisted after controlling for age, body mass index (BMI), and menarche. The increased risk of RPL associated with rs590688 and rs1942836 was dependent on the number of minor alleles, thus suggesting a 'dose-dependent' effect associated with both variants. Varied linkage disequilibrium (LD) was noted between rs590688, rs10895068, rs608995, and rs1942836 PGR variants associated with RPL. Haplotypes with an increased frequency of CGTC and reduced frequency of GGAT were noted in women with RPL, compared with controls, thereby indicating these haplotypes as RPL-susceptible and RPL-protective, respectively. This association persisted after controlling for multiple comparisons, and after adjusting for covariates.

CONCLUSIONS

We have confirmed a positive association of specific PGR variants (rs590688, rs10895068, and rs1942836) and PGR haplotypes (ATGCCGTC and ATTCGGTC) with an increased risk of RPL, thereby supporting a role for PGR as an RPL candidate locus.

TWEETABLE ABSTRACT

Genetic variants in progesterone receptor gene are associated with increased risk of recurrent pregnancy loss.