Differential expression of STAT3 gene and its regulatory long non-coding RNAs, namely lnc-DC and THRIL, in two eastern Iranian ethnicities with multiple sclerosis.

OBJECTIVE: Genome-wide association studies (GWASs) revealed that variants of STAT3 are associated with multiple sclerosis (MS) risk. There are several studies showing the effect of ethnicity and genetic background on the characteristics of MS. Here, we aimed to investigate STAT3 gene expression status along with its two regulatory long non-coding RNAs, lnc-DC and THRIL, in order to compare the expression of these target genes among two different ethnicities in the east of Iran. METHODS: A case-control study was performed between two groups of MS populations in east of Iran. We recruited individuals with Kurdish ethnicity from North Khorasan and Sistani ethnicity from southeast of Iran. The peripheral blood mononuclear cells were obtained from all participants, and total RNA was extracted. The gene expression of the selected genes was evaluated by qPCR. RESULTS: The expression of THRIL in North Khorasan MS patients was significantly higher than controls (P = 0.03). The results of simultaneous analysis of expression of the target genes (STAT3, THRIL, and lnc-DC) in both ethnic groups failed to show any significant difference between the MS patients and controls (P > 0.05). In addition, the expression of STAT3 and THRIL genes in Sistani MS patients was statistically meaningful lower than healthy controls (P < 0.05). CONCLUSION: To our knowledge, this is the first study that compared the expression of the STAT3 gene and its regulatory molecules between two ethnic groups of Iranian MS patients. We suggested that STAT3 and its associated molecules might be differentially expressed and regulated in MS patients with different genetic background.

HOTAIR but not ANRIL long non-coding RNA contributes to the pathogenesis of multiple sclerosis.

Studies have revealed that dysregulation in gene expression is one of the main aspects of multiple sclerosis (MS) pathogenesis. Although the molecular pathways underlying the immunomodulatory role of vitamin D (VD) in MS is not completely elucidated, VD has more recently become a topic of interest in immune regulation and is widely administered to patients with MS as an immunomodulatory supplement. Long non-coding RNAs (lncRNAs) are known to play important roles in regulation of gene expression via different mechanisms. Given that VD-related genes are regulated by epigenetic mechanisms, here we aimed to evaluate the role of VD in combination with HOTAIR and ANRIL lncRNAs using in vivo, in vitro and in silico experiments in MS pathogenesis. Our data revealed that HOTAIR but not ANRIL lncRNA is probably involved in the pathogenesis of MS and experimental autoimmune encephalomyelitis through an unclear mechanism and it seems that by affecting the expression, inflammation and VD can influence HOTAIR-related mechanisms, which require further study.

Sistani population: a different spectrum of ß-thalassemia mutations from other ethnic groups of Iran.

This study aimed to characterize the molecular spectrum of ß-thalassemia (ß-thal) mutations and evaluate the services available for prenatal diagnosis (PND) among the Sistani population of Iran. Mutations were analyzed with amplification refractory mutation system (ARMS), gap-polymerase chain reaction (gap-PCR), multiplex ligation-dependent probe amplification (MLPA) analysis and direct sequencing. Fetal diagnosis was also confirmed by linkage analysis. Over a 9-year period (2002-2011), 405 at-risk Sistani couples were referred for mutation analysis and/or PND. Of the referred couples, 18.5% had one to three affected children with ß-thal major (ß-TM) and the remainder had no children or were not married. Most of the couples (73.3%) lived in urban areas and the rate of consanguineous marriage was 76.8%. Twenty-one mutations were identified, of which the most frequent ones were IVS-I-5 (G>C) with a frequency of 74.1%, followed by codon 15 G>A (5.0%), codon -88 (C>T) (3.8%), IVS-II-1 (G>A) (3.4%), codons 8/9 (+G) (2.9%) and IVS-I-1 (G>T) (2.7%), which accounted for about 91.9% of the total ß-thal mutations for this region. Furthermore, fetal DNA was obtained from chorionic villus sampling (CVS) for 266 pregnant women and 68 (25.5%) fetuses were diagnosed as affected. In summary, ß-thal mutations are very heterogeneous and significantly different from those found in other parts of Iran and are similar to those of Pakistani and Indian populations. These results could greatly facilitate timely and accurate PND.

COVID-19 Death Rates in Iran and Iraq: Possible Relations Between Iraq's Pre-COVID-19 Mass Gatherings and Its Low Death Rate.

In recent years, COVD-19 has made millions of death worldwide. When reviewing the death rate, we encountered a very notable difference in death rate of Iran and Iraq, which are two neighboring countries. Investigating the COVID-19 risk factors, parameters, such as ethnicity and vaccination, do not appear not to be affecting our observation. We also could not find important differences in mortality rate being under-reported in the two countries. In this letter, we tried to discuss the possible effect of Iraq pre-COVID-19 mass gatherings on the death rate. The authors would like to highlight the effect of immune system on COVID-19.

Web-based tools for miRNA studies analysis.

In recent years, thousands of microRNAs (miRNA) have been found in numerous species. The huge data resulting from miRNA researches are ordered in several levels including miRNA discovery, the sequence of mature and precursor miRNAs, role in diseases, pathway interaction, target validation, and prediction, etc. To prepare a simple approach to this information, numerous databases for miRNA records have been established. The selection of the correct database can be laborious and prolonged, especially for scientists who do not have experience in this field. To facilitate access to these resources, we have classified the available databases into seven categories and have described each one. The different categories of miRNA databanks contain miRNA sequence, target validation, target prediction, expression, function, role in pathways and networks, and their roles in diseases. Moreover, examples are included to describe the prototype databases for the most common applications. Hence, this review introduces available miRNA databases and presents a convenient overview of these databases that will enable researchers with different backgrounds to find suitable miRNA-related bioinformatics web tools and relevant microRNA information rapidly.

Structure-specific recognition of Friedreich's ataxia (GAA)n repeats by benzoquinoquinoxaline derivatives.

Expansion of GAA triplet repeats in intron 1 of the FXN gene reduces frataxin expression and causes Friedreich's ataxia. (GAA)n repeats form non-B-DNA structures, including triple helix H-DNA and higher-order structures (sticky DNA). In the proposed mechanisms of frataxin gene silencing, central unanswered questions involve the characterization of non-B-DNA structure(s) that are strongly suggested to play a role in frataxin expression. Here we examined (GAA)n binding by triplex-stabilizing benzoquinoquinoxaline (BQQ) and the corresponding triplex-DNA-cleaving BQQ-1,10-phenanthroline (BQQ-OP) compounds. We also examined the ability of these compounds to act as structural probes for H-DNA formation within higher-order structures at pathological frataxin sequences in plasmids. DNA-complex-formation analyses with a gel-mobility-shift assay and sequence-specific probing of H-DNA-forming (GAA)n sequences by single-strand oligonucleotides and triplex-directed cleavage demonstrated that a parallel pyrimidine (rather than purine) triplex is the more stable motif formed at (GAA)n repeats under physiologically relevant conditions.

Competitive inhibition of natural antisense Sok-RNA interactions activates Hok-mediated cell killing in Escherichia coli.

Short regulatory RNAs are widespread in bacteria, and many function through antisense recognition of mRNA. Among the best studied antisense transcripts are RNA antitoxins that repress toxin mRNA translation. The hok/sok locus of plasmid R1 from Escherichia coli is an established model for RNA antitoxin action. Base-pairing between hok mRNA and Sok-antisense-RNA increases plasmid maintenance through post-segregational-killing of plasmid-free progeny cells. To test the model and the idea that sequestration of Sok-RNA activity could provide a novel antimicrobial strategy, we designed anti Sok peptide nucleic acid (PNA) oligomers that, according to the model, would act as competitive inhibitors of hok mRNA::Sok-RNA interactions. In hok/sok-carrying cells, anti Sok PNAs were more bactericidal than rifampicin. Also, anti Sok PNAs induced ghost cell morphology and an accumulation of mature hok mRNA, consistent with cell killing through synthesis of Hok protein. The results support the sense/antisense model for hok mRNA repression by Sok-RNA and demonstrate that antisense agents can be used to out-compete RNA::RNA interactions in bacteria. Finally, BLAST analyses of approximately 200 prokaryotic genomes revealed that many enteric bacteria have multiple hok/sok homologous and analogous RNA-regulated toxin-antitoxin loci. Therefore, it is possible to activate suicide in bacteria by targeting antitoxins.

Variable coordination of cotranscribed genes in Escherichia coli following antisense repression.

BACKGROUND: A majority of bacterial genes belong to tight clusters and operons, which complicates gene functional studies using conventional knock-out methods. Antisense agents can down-regulate the expression of genes without disrupting the genome because they bind mRNA and block its expression. However, it is unclear how antisense inhibition affects expression from genes that are cotranscribed with the target. RESULTS: To examine the effects of antisense inhibition on cotranscribed genes, we constructed a plasmid expressing the two reporter genes gfp and DsRed as one transcriptional unit. Incubation with antisense peptide nucleic acid (PNA) targeted to the mRNA start codon region of either the upstream gfp or the downstream DsRed gene resulted in a complete expression discoordination from this artificial construct. The same approach was applied to the three cotranscribed genes in the endogenously expressed lac-operon (lacZ, Y and A) and partial downstream expression coordination was seen when the lacZ start codon was targeted with antisense PNA. Targeting the lacY mRNA start codon region showed no effect on the upstream lacZ gene expression whereas expression from the downstream lacA gene was affected as strongly as the lacY gene. Determination of lacZ and lacY mRNA levels revealed a pattern of reduction that was similar to the Lac-proteins, indicating a relation between translation inhibition and mRNA degradation as a response to antisense PNA treatment. CONCLUSION: The results show that antisense mediated repression of genes within operons affect cotranscribed genes to a variable degree. Target transcript stability appears to be closely related to inhibition of translation and presumably depends on translating ribosomes protecting the mRNA from intrinsic decay mechanisms. Therefore, for genes within operons and clusters it is likely that the nature of the target transcript will determine the inhibitory effects on cotranscribed genes. Consequently, no simple and specific methods for expression control of a single gene within polycistronic operons are available, and a thorough understanding of mRNA regulation and stability is required to understand the results from both knock-down and knock-out methods used in bacteria.

Association study of four polymorphisms in the interleukin-7 receptor alpha gene with multiple sclerosis in Eastern Iran.

OBJECTIVES: Multiple sclerosis (MS) is an autoimmune demyelinating disease of the central nervous system (CNS) with unknown etiology. Various genetics and environmental factors contribute to the pathogenesis of the disease. The interleukin-7 receptor alpha chain (IL-7Ra) was identified as the first non-major histocompatibility complex (non-MHC) MS susceptibility locus. In this study we are trying to find the association of IL-7Ra gene polymorphisms with MS susceptibility in Eastern Iran. MATERIALS AND METHODS: A case-control study was performed in two provinces Sistan & Baluchistan and Khorasan with 219 patients and 258 unrelated matched healthy controls, using PCR-RFLP method for four single nucleotide polymorphisms (SNPs) rs7718919, rs11567685, rs11567686 and rs6897932 of IL-7Ra gene. RESULTS: We found a tendency toward association with genotyping analyses in SNP rs7718919 (P=0.048, OR=4.344, and 95% CI=0.892-21.146); also genotype and allele frequency in gender and MS subtype stratification were shown to have significant association with MS. Analysis of two provinces separately showed a significant difference in results of the allele and genotype frequencies. Moreover, haplotyping analysis showed that (GTGC) has an association only in the male secondary-progressive multiple sclerosis (SPMS) patients in comparison to the healthy controls (P=0.043, OR=0.413, and 95% CI=0.179-0.955). CONCLUSION: IL7-Ra could be a susceptible gene to MS within the Eastern Iran population especially after MS and gender stratification.

Expression of suppressor of cytokine signaling 1 (SOCS1) gene dramatically increases in relapsing-remitting multiple sclerosis.

Suppressor of cytokine signaling 1 (SOCS1) is a key regulator of cytokines signaling and plays the most important role in the regulation of the autoimmune responses. The absence of SOCS1 leads to aberrant thymocyte development and systemic inflammation. This study was conducted to evaluate the expression level of SOCS1 mRNA in peripheral blood mononuclear cells (PBMCs) of relapsing-remitting (RR)-multiple sclerosis (MS) patients. In addition, the association of rs243324 SNP with MS and the assessment of this SNP role on the expression level of SOCS1 were aimed to be evaluated. Our results revealed that, SOCS1 mRNA overexpressed (24.5 times) in MS patients versus healthy controls. The rs243324 SNP showed no association with MS susceptibility and this SNP was not in Hardy-Weinberg equilibrium in MS patients. Moreover, there was a significant correlation between SOCS1 expression levels with age of female control group (r=-0.43, P=0.03). Thus, we have probably shown some new evidences for the complex role of SOCS1 gene in the pathogenesis of MS.

Overexpression of enhancer of zeste human homolog 2 (EZH2) gene in human cytomegalovirus positive glioblastoma multiforme tissues.

Glioblastoma multiforme (GBM) is considered to be one of the most invasive human cancers, characterized by a high mortality rate and an average survival is <1 year. These tumors are highly aggressive and insensitive to conventional radio and chemotherapy. An interesting aspect of glioblastoma is the association of active human cytomegalovirus (HCMV) infection, which is evident by the presence of viral DNA, mRNA and protein level in most glioblastoma tissues. Although the presence of the HCMV infection in glioblastoma is well established, but the oncomodulatory role of HCMV is not defined yet. Enhancer of zeste human homolog 2 (EZH2) is a key protein of the polycomb repressive complex 2, epigenetic gene silencers. There have been several reports that EZH2 activity is essential in GBM pathogenesis. In our previous research, we have found a high rate of HCMV infection in a cohort of Iranian glioblastoma patients. In this study, we investigated the expression of EZH2 in HCMV-negative versus HCMV-positive GBM tissues in comparison to non-tumor tissues. The level of expression was determined by real time PCR and the differences were calculated using the Livac or 2(-ΔΔCt) and analysis of variance (ANOVA). Relative expression of EZH2 in HCMV-negative glioblastoma tissues were increased 6.053-fold compared to non-neoplastic brain tissues, while EZH2 gene expression was increased 41.098-fold in HCMV-positive glioblastoma tissues. ANOVA test showed that there is a significant difference in EZH2 expression between normal brain tissue, HCMV-negative and HCMV-positive glioblastoma tumors (p value = 0.0001). Our data indicate that EZH2 expression can be considered a risk factor in glioblastoma and EZH2 inhibitors may serve as potential new treatment in glioblastoma. This would be an interesting new field to investigate in more detail.

Expression of insulin-like growth factor binding protein-2 (IGFBP-2) gene in negative and positive human cytomegalovirus glioblastoma multiforme tissues.

Glioblastoma multiforme (GBM), a WHO grade IV malignant glioma, is the most common and lethal primary brain tumor in adults and has but few treatments. The median survival of glioblastoma patients is 12 months. The (possible) relationship between human cytomegalovirus (HCMV) infection and cancer has been investigated for decades. Detection of viral DNA, mRNA and/or antigens in tumor tissues suggests that HCMV infection has a role to play in the etiology of several human malignancies. HCMV gene products can promote the various signaling pathways critical to tumor growth, including platelet derived growth factor receptor, phosphatidyl inositol 3-kinases (PI3K/AKT), signal transducer and activator of transcription 3 and glycogen synthase kinase 3 beta that are involved in apoptosis, angiogenesis, invasion and immune evasion. Insulin-like growth factor binding protein 2 (IGFBP2) is a biomarker of the PI3K/AKT pathway so we decided to evaluate the expression of this gene in 3 groups: HCMV-negative GBM tissues, HCMV-positive GBM tissues and non-tumor tissues. The presence of HCMV was assessed according to our previous article. HCMV was present in %75 of glioblastoma tissues. Then RNA was extracted, cDNA was synthesized, and real-time PCR was performed. Then, the rate of increased expression was calculated using the Livac or 2(-ΔΔCt). ΔCt of samples in the three groups were compared using analysis of variance (ANOVA). The expression of IGFBP2 gene relative to GAPDH gene in HCMV-negative glioblastoma tissues and HCMV-positive glioblastoma tissues, respectively, was increased 5.486 and 15.032 times compared to non-neoplastic brain tissues. ANOVA tests showed that the difference of mean ΔCt for IGFBP2 gene between healthy subjects and patients with HCMV-positive and HCMV-negative glioblastoma tumors statistically significant.

Association of TNF-α -857 Polymorphism with Inflammatory Bowel Disease in a Group of Iranian Azeri Individuals.

BACKGROUND Inflammatory bowel disease (IBD) is a chronic, relapsing, inflammatory disorder of the gastrointestinal tract that includes two entities, Crohn's disease (CD) and ulcerative colitis (UC). As with other complex diseases, both genetic susceptibility and environmental factors play role in the pathogenesis of these diseases. The tumor necrosis factor α (TNF-α) gene is located in the IBD3 region on chromosome 6p21 which is a good functional candidate for involvement in susceptibility to IBD. In addition, the promoter region of TNF-α contains various polymorphisms that have shown a significant association with IBD. METHODS In this case control study we investigated the TNF-α -857 polymorphism in 109 patients (89 UC and 16 CD) who suffered from IBD and 100 healthy age, sex and ethnicity matched adults selected from the same population, as the control group. The polymorphism was checked by amplification refractory system (ARMS) and polymerase chain reaction (PCR). RESULTS Investigation of the association of TNF-α -857 gene promoter polymorphism with both types of IBD showed no significant difference in genotype and allele frequencies of this polymorphism between UC patients and controls. However, a possible association of TNF-α -857 polymorphism (p=0.03) was identified with CD. CONCLUSION TNF-α -857 polymorphism may have a role in the development of CD in the Iranian Azeri Turkish population.

The analysis of correlation between IL-1B gene expression and genotyping in multiple sclerosis patients.

IL-1B is released by monocytes, astrocytes and brain endothelial cells and seems to be involved in inflammatory reactions of the central nervous system (CNS) in multiple sclerosis (MS). This study aims to evaluate the expression level of IL-1B mRNA in peripheral blood mononuclear cells (PBMCs), genotype the rs16944 SNP and find out the role of this SNP on the expression level of IL-1B in MS patients. We found that the expression level of IL-1B in MS patients increased 3.336 times more than controls in PBMCs but the rs16944 SNP in the promoter region of IL-1B did not affect the expression level of this gene and there was not association of this SNP with MS in the examined population. Also, our data did not reveal any correlation between normalized expressions of IL-1B gene with age of participants, age of onset, and disease duration.

Old class but new dimethoxy analogue of benzimidazole: a bacterial topoisomerase I inhibitor.

New antimicrobials are needed to combat drug resistance and have often been equated with the identification and exploitation of novel targets. This study focused on the synthesis of new benzimidazole analogues with improved DNA minor groove-binding affinity and having lower cytotoxicity to mammalian cells as well as selective targeting of bacterial DNA over host DNA. 5-(4-Methylpiperazin-1-yl)-2-[2'-(3,4-dimethoxyphenyl)-5'-benzimidazolyl]benzimidazole (DMA) cleared bacterial infections from mammalian cell culture without apparent cytotoxicity to mammalian cells. Moreover, DMA inhibited microbial topoisomerase over mammalian topoisomerase, with a 50% inhibitory concentration (IC50) value for human topoisomerase I of >54microM compared with an IC50 of <10microM for Escherichia coli topoisomerase I in vitro.

Antisense PNA accumulates in Escherichia coli and mediates a long post-antibiotic effect.

Antisense agents that target growth-essential genes display surprisingly potent bactericidal properties. In particular, peptide nucleic acid (PNA) and phosphorodiamidate morpholino oligomers linked to cationic carrier peptides are effective in time kill assays and as inhibitors of bacterial peritonitis in mice. It is unclear how these relatively large antimicrobials overcome stringent bacterial barriers and mediate killing. Here we determined the transit kinetics of peptide-PNAs and observed an accumulation of cell-associated PNA in Escherichia coli and slow efflux. An inhibitor of drug efflux pumps did not alter peptide-PNA potency, indicating a lack of active efflux from cells. Consistent with cell retention, the post-antibiotic effect (PAE) of the anti-acyl carrier protein (acpP) peptide-PNA was greater than 11 hours. Bacterial cell accumulation and a long PAE are properties of significant interest for antimicrobial development.