In Silico Prediction of Functional SNPs Interrupting Antioxidant Defense Genes in Relation to COVID-19 Progression

The excessive production of reactive oxygen species and weakening of antioxidant defense system play a pivotal role in the pathogenesis of different diseases. Extensive differences observed among individuals in terms of affliction with cancer, cardiovascular disorders, diabetes, bacterial, and viral infections, as well as response to treatments can be partly due to their genomic variations. In this work, we attempted to predict the effect of SNPs of the key genes of antioxidant defense system on their structure, function, and expression in relation to COVID-19 pathogenesis using in silico tools. In addition, the effect of SNPs on the target site binding efficiency of SNPs was investigated as a factor with potential to change drug response or susceptibility to COVID-19. According to the predicted results, only six missense SNPs with minor allele frequency (MAF) ≥ 0.1 in the coding region of genes GPX7, GPX8, TXNRD2, GLRX5, and GLRX were able to strongly affect their structure and function. Our results predicted that 39 SNPs with MAF ≥ 0.1 led to the generation or destruction of miRNA-binding sites on target antioxidant genes from GPX, PRDX, GLRX, TXN, and SOD families. The results obtained from comparing the expression profiles of mild vs. severe COVID-19 patients using GEO2R demonstrated a significant change in the expression of approximately 250 miRNAs. The binding efficiency of 21 of these miRNAs was changed due to the elimination or generation of target sites in these genes. Altogether, this study reveals the fundamental role of the SNPs of antioxidant defense genes in COVID-19 progression and susceptibility of individuals to this virus. In addition, different responses of COVID-19 patients to antioxidant defense system enhancement drugs may be due to presence of these SNPs in different individuals.

Identification of ITPR1 gene as a novel target for hsa-miR-34b-5p in non-obstructive azoospermia: a Ca2+/apoptosis pathway cross-talk

MiR-34b-5p has been reported as a non-invasive diagnostic biomarker for infertility. However, no gene targets regulating the mechanism of cation of this miRNA are known. In this study, using gene set enrichment analysis the Inositol 1,4,5-Trisphosphate Receptor Type 1 (ITPR1) gene was identified as the sole target for hsa-miR-34b-5p, and found significantly overexpressed in non-obstructive azoospermia (NOA) patients. This finding was confirmed by qRT-PCR on fresh testicular tissues from NOA patients. Then, pathway enrichment analysis as well as the diagnostic value analysis of hsa-miR-34b-5p/ITPR1 indicated ITPR1 as a hub gene in the calcium (Ca2+)-apoptosis pathway, and a valuable predictive biomarker for NOA. Moreover, gene expression and histological assays showed the association of the effects of ITPR1's increased expression on spermatogenesis failure through induction of apoptosis in NOA patients. These data suggested that the hsa-miR-34b-5p/ITPR1 axis could serve as a potential regulatory predictive biomarker for human spermatogenesis through the Ca2+-apoptosis pathway cross-talk.

Meta-analysis of microarray data to determine gene indicators involved in the cisplatin resistance in ovarian cancer

BACKGROUND

Significant miss-expressed gene indicators contributing to cisplatin resistance in ovarian cancer have not been completely understood. It seems that several regulatory genes and signaling pathways are associated with the emergence of the chemo-resistant phenotype.

AIMS

Here, a meta-analysis approach was adopted to assess deregulated genes involved in relapse after the first line of chemotherapy (cisplatin).

METHODS AND RESULTS

To do so, six ovarian cancer libraries were gathered from GEO repository. Batch effect removal and quality assessment, and boxplots and PCA were performed using SVA and ggplot2 packages in R, respectively. Cisplatin-resistant and -sensitive ovarian cancer groups were compared with find genes with significant expression changes using linear regression models in the LIMMA R package. The significance threshold for DEGs was taken as adj p-value < .05 and - 1 > logFC > 1. A total of 261 genes were identified to have significant differential expression levels in the cisplatin-resistant versus cisplatin-sensitive group. Among the 10 top up-regulated and down-regulated genes, PITX2, SNCA, and EPHA7 (up), as well as TMEM98 (down) are indirect upstream regulators of PI3K/AKT signaling pathway, contributing greatly to the development of chemo-resistance in cancer via promoting cell proliferation, survival, and cell cycle progression as well as inhibiting apoptosis. Moreover, a comprehensive assessment of DEGs revealed the dysregulation of not only membrane ion channels KCa1.1, Kv4, and CACNB4, affecting cell excitability, proliferation, and apoptosis but also cell adhesion proteins COL4A6, EPHA3, and CD9, affecting the attachment of normal cells to ECM and apoptosis, introducing good options to reverse cisplatin resistance.

CONCLUSION

Our results predict and suggest that upstream regulators of PI3K/AKT signaling pathway, ion channels, and cell adhesion proteins play important roles in cisplatin resistance development in ovarian cancer.

In silico identification of potential miRNAs -mRNA inflammatory networks implicated in the pathogenesis of COVID-19

COVID-19 has been found to affect the expression profile of several mRNAs and miRNAs, leading to dysregulation of a number of signaling pathways, particularly those related to inflammatory responses. In the current study, a systematic biology procedure was used for the analysis of high-throughput expression data from blood specimens of COVID-19 and healthy individuals. Differentially expressed miRNAs in blood specimens of COVID-19 vs. healthy specimens were then identified to construct and analyze miRNA-mRNA networks and predict key miRNAs and genes in inflammatory pathways. Our results showed that 171 miRNAs were expressed as outliers in box plot and located in the critical areas according to our statistical analysis. Among them, 8 miRNAs, namely miR-1275, miR-4429, miR-4489, miR-6721-5p, miR-5010-5p, miR-7110-5p, miR-6804-5p and miR-6881-3p were found to affect expression of key genes in NF-KB, JAK/STAT and MAPK signaling pathways implicated in COVID-19 pathogenesis. In addition, our results predicted that 25 genes involved in above-mentioned inflammatory pathways were targeted not only by these 8 miRNAs but also by other obtained miRNAs (163 miRNAs). The results of the current in silico study represent candidate targets for further studies in COVID-19.

Acute Kidney Injury (AKI) in COVID-19: In silico Identification of LncRNA-MiRNA-Gene Networks and Key Transcription Factors

PURPOSE

Acute kidney injury (AKI) accounts for up to 29% of severe COVID-19 cases and increases mortality among these patients. Viral infections participate in the pathogenesis of diseases by changing the expression profile of normal transcriptome. This study attempts to identify LncRNA-miRNA-gene and TF-gene networks as gene expression regulating networks in the kidney tissues of COVID-19 patients.

METHODS

In this analysis, four kidney libraries from the GEO repository were considered. To conduct the preprocessing, Deseq2 software in R was used for the purpose of data normalization and log2 transformation. In addition, pre- and post-normalization, PCA and box plots were developed using ggplot2 software in R for quality control. The expression profiles of the kidney samples of COVID-19 patients and control individuals were compared using DEseq2 software in R. The considered significance thresholds for DEGs were Adj P value < 0.05 and |logFC| >2. Then, to predict molecular interactions in lncRNA-miRNA-gene networks, different databases, including DeepBase v3.0, miRNATissueAtlas2, DIANA-LncBase v3, and miRWalk, were used. Furthermore, by employing ChEA databases, interactions at the TF-Gene level were obtained. Finally, the obtained networks were plotted using Stringdb and Cytoscape v8.

RESULTS

Results obtained from the comparison of the post-mortem kidney tissue samples of the COVID-19 patients with the healthy kidney tissue samples showed significant changes in the expression of more than 2000 genes. In addition, predictions regarding the miRNA-gene interaction network based on DEGs obtained from this meta-analysis showed that 11 miRNAs targeted the obtained DEGs. Interestingly, in the kidney tissue, these 11 miRNAs interacted with LINC01874, LINC01788, and LINC01320, which have high specificity for this tissue. Moreover, four transcription factors of EGR1, SMAD4, STAT3, and CHD1 were identified as key transcription factors regulating DEGs. Taken together, the current study showed several dysregulated genes in the kidney of patients affected with COVID-19.

CONCLUSION

This study suggests lncRNA-miRNA-gene networks and key TFs as new diagnostic and therapeutic targets for experimental and preclinical studies.

An Overview of The Globozoospermia as A Multigenic Identified Syndrome

Acrosome plays an integral role during fertilization and its absence in individuals with globozoospermia leads to failure of in vitro fertilization (IVF) and oocyte activation post-intracytoplasmic sperm injection (ICSI). A variety of processes, organelles and structures are involved in acrosome biogenesis including, trans-golgi network (TGN), acroplaxome and cellular trafficking. This review aims to explain roles of related signals and molecules involved in this process and also describe how their absence in form of mutation, deletion and knockout model may lead to phe- nomenon referred to globozoospermia.

Assessment of DPY19L2 Deletion in Familial and Non-Familial Individuals with Globozoospermia and DPY19L2 Genotyping

Background

Globozoospermia is a rare syndrome with an incidence of less than 0.1% among infertile men. Researchers have recently identified a large deletion, about 200 kbp, encompassing the whole length of DPY19L2 or mutations in SPATA16 and PICK1 genes associated with globozoospermia. The aim of this study was to analyze the DPY19L2 gene deletion using polymerase chain reaction technique for the exons 1, 48, 11 and 22 as well as break point (BP) “a” in globozoospermic men.

Materials and Methods

In this experimental study, genome samples were collected from 27 men with globozoospermia (cases) and 36 fertile individuals (controls), and genomic analysis was carried out on each sample.

Results

Deletion of DPY19L2 gene accounted for 74% of individuals with globozoospermia. DPY19L2 gene deletion was considered as the molecular pathogenic factor for the onset of globozoospermia in infertile men. By quantitative real-time polymerase chain reaction (qPCR), we genotyped DPY19L2 deletion and identified carriers within the population.

Conclusion

This technique may be considered as a method for family counseling and has the potential to be used as a pre-implantation genetic diagnosis, especially in ethnic community with high rate of consanguineous marriages.