CRISPR/Cas9 Ablated BCL11A Unveils the Genes with Possible Role of Globin Switching

Purpose

Fetal hemoglobin (HbF) upregulation is a mitigating factor in β-hemoglobinopathies therapy like β-thalassemia and sickle cell diseases. Finding molecular mechanisms and the key regulators responsible for globin switching could be helpful to develop effective ways to HbF upregulation. In our prior in silico report, we identified a few factors that are likely to be responsible for globin switching. The goal of this study is to experimentally validate the factors.

Methods

We established K562 cell line with BCL11A knock down leading to increase in HBG1/2 using CRISPR/Cas9 system. Then, using quantitative polymerase chain reaction (qPCR), we determined the expression level of the factors which were previously identified in our prior in silico study.

Results

our analysis showed that BCL11A was substantially knocked down, resulting in the upregulation of HBG1/2 in the BCL11A-ablated K562 cells using CRISPR/Cas9 system. Additionally, the experimental data acquired in this study validated our prior bioinformatics findings about three potentially responsible genes for globin switching, namely HIST1H2Bl, TRIM58, and Al133243.2.

Conclusion

BCL11A is a promising candidate for the treatment of β-hemoglobinopathies, with high HbF reactivation. In addition, HIST1H2BL, TRIM58 and Al133243.2 are likely to be involved in the mechanism of hemoglobin switching. To further validate the selected genes, more experimental in vivo and in vitro studies are required.

Identification of Potential Key Genes Linked to Gender Differences in Bladder Cancer Based on Gene Expression Omnibus (GEO) Database

Background

Growing evidence strongly indicates pivotal roles of gender differences in the occurrence and survival rate of patients with bladder cancer, with a higher incidence in males and poorer prognosis in females. Nevertheless, the molecular basis underlying gender-specific differences in bladder cancer remains unknown. The current study has tried to detect key genes contributing to gender differences in bladder cancer patients.

Materials and Methods

The gene expression profile of GSE13507 was firstly obtained from the Gene Expression Omnibus (GEO) database. Further, differentially expressed genes (DEGs) were screened between males and females using R software. Protein-protein interactive (PPI) network analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Kaplan-Meier survival analyses were also performed.

Results

We detected six hub genes contributing to gender differences in bladder cancer patients, containing IGF2, CCL5, ASPM, CDC20, BUB1B, and CCNB1. Our analyses demonstrated that CCNB1 and BUB1B were upregulated in tumor tissues of female subjects with bladder cancer. Other genes, such as IGF2 and CCL5, were associated with a poor outcome in male patients with bladder cancer. Additionally, three signaling pathways (focal adhesion, rheumatoid arthritis, and human T-cell leukemia virus infection) were identified to be differentially downregulated in bladder cancer versus normal samples in both genders.

Conclusion

Our findings suggested that gender differences may modulate the expression of key genes that contributed to bladder cancer occurrence and prognosis.

Roles of non-coding RNAs in cell death pathways involved in the treatment of resistance and recurrence of cancer

Considering the burden of cancer, a number of methods have been applied to control or stop it. However, because of drug resistance or cancer recurrence, these treatments usually face failure. Combination of modulation of expression of non-coding RNAs (ncRNAs) with other treatments can increase treatment-sensitivity of tumors but these approaches still face some challenges. Gathering information in this field is a prerequisite to find more efficient cures for cancer. Cancer cells use ncRNAs to enhance uncontrolled proliferation originated from inactivation of cell death routs. In this review article, the main routes of cell death and involved ncRNAs in these routes are discussed. Moreover, extant information in the role of different ncRNAs on cell death pathways involved in the treatment resistance and cancer recurrence is summarized.

Using chitosan-stabilized, hyaluronic acid-modified selenium nanoparticles to deliver CD44-targeted PLK1 siRNAs for treating bladder cancer

Aims: Achieving an effective biocompatible system for siRNAs delivery to the tumor site remains a significant challenge. Materials & methods: Selenium nanoparticles (SeNPs) modified by chitosan (CS) and hyaluronic acid (HA) were fabricated for PLK1 siRNAs (siPLK1) delivery to the bladder cancer cells. The HA-CS-SeNP@siPLK1 efficacy was evaluated using in vitro and in vivo models. Results: HA-CS-SeNP@siPLK1 was selectively internalized into T24 cells through clathrin-mediated endocytosis. Treatment with HA-CS-SeNP@siPLK1 successfully silenced the PLK1 gene, inhibited cell proliferation and induced cell cycle arrest in vitro. HA-CS-SeNP@siPLK1 could also inhibit tumor growth in vivo without causing systemic toxicity. Conclusion: Our results suggest that HA-CS-SeNPs may provide a good vehicle for delivering siPLK1 to the bladder tumor site.

Promoter Methylation of Two HOXA9 and NISCH Genes in Opium Users

BACKGROUND

Opiate abuse has been critically increased in the world, especially in Iran. Owing to the association of opiate use with multiple human cancers and neurological disorders, seeking for genetic and epigenetic effects of opium can pave the way for early diagnosis of major health defects in addicted users. Accordingly, the present study aimed to determine the methylation status of the promoter of two genes, which are actively involved in neurodevelopment and cancer evolution.

METHODS

DNA was isolated from peripheral blood of 28 opium abusers and 19 healthy controls and then subjected to sonication. Sonicated DNAs undergone methylated DNA immunoprecipitation-real time polymerase chain reaction (MeDIP-Real Time PCR) using specific primer pairs designed for HOXA9 and NISCH genes. Obtained data were analyzed using SPSS software.

FINDINGS

HOXA9 and NISCH genes were found to be significantly methylated in addicted users compared to controls (P<0.001) which was significantly associated with the mean of the age regarding HOXA9 gene (P=0.002). Neither opium amount nor duration or route of using was associated with the methylation status of HOXA9 or NISCH genes.

CONCLUSION

Hypermethylation of HOXA9 and NISCH genes as tumor suppressor in opium-addicted individuals can be considered as confirmatory evidence for carcinogenesis of opium. Further studies are required to figure out the role of epigenetic alterations in cancer evolution among opium users.

Identification of TSGA10 and GGNBP2 splicing variants in 5' untranslated region with distinct expression profiles in brain tumor samples

Introduction

Brain tumors (BTs) are perceived as one of the most common malignancies among children. The specific regulation of each gene can play a critical role in cancer progression. The present study aimed to determine the transcripts of the TSGA10 and GGNBP2 genes, considering the alternative 5'UTR region, and investigating the expression of these different transcripts in BTs.

Material and methods

Public data on brain tumor microarray datasets in GEO were analyzed with R software to evaluate the expression levels of TSGA10 and GGNBP2 genes (the Pheatmap package in R was also used to plot DEGs in a heat map). In addition, to validate our in-silico data analysis, RT-PCR was performed to determine the splicing variants of TSGA10 and GGNBP2 genes in testis and brain tumor samples. The expression levels of splice variants of these genes were analyzed in 30 brain tumor samples and two testicular tissue samples as a positive control.

Results

In silico results show that the differential expression levels of TSGA10 and GGNBP2 were significant in the GEO datasets of BTs compared to normal samples (with adjusted p-value<0.05 and log fold change > 1). This study's experimental results showed that the TSGA10 gene produces four different transcripts with two distinct promoter regions and splicing exon 4. The relative mRNA expression of transcripts without exon 4 was higher than transcripts with exon 4 in BT samples (p-value<001). In GGNBP2, exon 2 in the 5'UTR region and exon 6 in the coding sequence were spliced. The expression analysis results showed that the relative mRNA expression of transcript variants without exon 2 was higher than other transcript variants with exon 2 in BT samples (p-value<001).

Conclusion

The decreased expression levels of transcripts with longer 5'UTR in BT samples than in testicular or low-grade brain tumor samples may decrease their translation efficiency. Therefore, decreased amounts of TSGA10 and GGNBP2 as potential tumor suppressor proteins, especially in high-grade brain tumors, may cause cancer development by angiogenesis and metastasis.

Genetic and epigenetic effects on couple adjustment in context of romantic relationship: A scoping systematic review

Introduction: Couples' relationships defined by a complex interaction between the two partners and their intrapersonal traits. Romantic; relationships and love are associated with marital satisfaction and stability, as well as couples' happiness and health. Personality traits influence romantic relationships and, personality influenced by genetical and non-genetically factors. The roles of non-genetically factors such as socioeconomic position and external appearance have revealed in determining the quality of romantic relationships. Methods: We; performed a scoping systematic review to assess the association between genetics and epigenetic factors and romantic relationship. Relevant articles were identified by PubMed, EMBASE, Web of Science, Scopus, and the APA PsycInfo searching between inception and 4 June 2022. Results: Different studies evaluated the associated polymorphisms in 15 different genes or chromosomal regions. In the first step; we classified them into four groups: (1) Oxytocin-related signaling pathway (OXTR, CD38, and AVPR1A); (2) Serotonin-related signaling pathway (SLC6A4, HTR1A, and HTR2A); (3) Dopamine and catecholamine-related signaling pathway (DRD1, DRD2, DRD4, ANKK1, and COMT); and (4) other genes (HLA, GABRA2, OPRM1, and Y-DNA haplogroup D-M55). Then, we evaluated and extracted significant polymorphisms that affect couple adjustment and romantic relationships. Discussion: Overall, the findings suggest that genetic and epigenetics variants play a key role in marital adjustment and romantic relationships over time.

Evaluation of IGF2, KRT14, and KRT20 as Urinary Biomarkers in Patients with Bladder Cancer

Background

Many researchers have tried to identify bladder cancer biomarkers to reduce the need for cystoscopy. The aim of this study was to identify and measure appropriate transcripts in patient urine to develop a non-invasive screening test.

Methods

From February 2020 to May 2022, 49 samples were obtained from Velayat Hospital, Qazvin University of Medical Sciences, Qazvin, Iran. Twenty-two samples were obtained from bladder cancer patients and 27 from bladder cancer-free subjects. RNA was extracted from participant samples, quantitative RT-PCR was performed, and TNP plots were used to assess IGF2 (NCBI Gene ID: 3481), KRT14 (NCBI Gene ID: 3861) and KRT20 (NCBI Gene ID: 54474) expression. For UCSC Xena analysis, Dataset ID: TCGA-BLCA was used to compare transitional cell carcinoma (TCC) and normal samples for survival rates.

Results

IGF and KRT14 were more greatly expressed in patient urine samples than in those of the normal group. However, KRT20 expression did not significantly differ between the two groups. IGF2 had 45.45 and 88.89% sensitivity and specificity, respectively, for detecting TCC in urine samples while KRT14 had 59 and 88.89% sensitivity and specificity, respectively. Also, these results infer that overexpression of IGF would be prognosticators of poor TCC outcomes.

Conclusion

Our study showed that IGF2 and KRT14 are overexpressed in bladder cancer patient urine, and IGF2 could be a potential biomarker for poor prognoses in TCC.

Antioxidant and anti-apoptotic effects of selenium nanoparticles and Lactobacillus casei on mice testis after X-ray

Radiation can lead to various damages in the process of spermatogenesis that lead to a decrease in the number of sperm, an increase in spermatogenesis disorders, and defective sperm function. Radioprotectors are considered a good approach to reducing the damage caused by radiation. The goal of this work was to study how X-ray radiation affects testicular tissue and the process of spermatogenesis, as well as the radioprotective effects of selenium nanoparticles (SeNPs) and Lactobacillus casei (L. casei) as probiotic compounds, given alone or together. This study included 64 adult Syrian male mice weighing approximately 20 ± 5 g and aged 10 ± 1 weeks. Animals were randomly divided into eight groups: control group, SeNPs, probiotic, SeNPs and probiotic, X-ray radiation, SeNPs (X-ray), probiotic (X-ray), and SeNPs and probiotic (X-ray). Histology parameters and levels of oxidative stress biomarkers such as catalase, malondialdehyde, superoxide dismutase, and glutathione peroxidase were examined. In addition, the level of apoptosis was measured in testicular cells that had been treated with SeNPs and L. casei as a probiotic. The results showed that the administration of SeNPs or probiotic diminished the effects of X-ray radiation. These compounds induced a significant decreased in malondialdehyde, caspase 3, and caspase 9 gene levels and a remarkable increased in catalase, superoxide dismutase, and Catsper gene expression. SeNPs and probiotic exhibited a potent antioxidant effect and elevated the mean number of spermatogonia cells, sperm cell count, spermatogenesis percentage, and sperm motility percentage. The prescribed compound exhibited an ideal radioprotective effect with the ability to reduce the side effects of ionizing radiation and to protect normal tissues. SeNPs and probiotic inhibit testicular injury and improve the antioxidant state in male mice.

CRISPR-Based Fluorescent Reporter (CBFR) Assay for Sensitive, Specific, Inexpensive, and Visual Detection of a Specific EGFR Exon 19 Deletion in NSCLC

Epidermal growth factor receptor (EGFR) is a transmembrane glycoprotein receptor with intracellular tyrosine kinase activity. Mutations in the EGFR gene, including deletions in exon 19 and the mutation L858R, induce responsiveness of non-small cell lung cancer (NSCLC) to a group of drugs known as tyrosine kinase inhibitors. Here, we report the development of the CRISPR-based fluorescent reporter (CBFR) assay including a two-step strategy combining PCR amplification and Cas12a-driven cleavage to detect the delE746_A750 subtype of EGFR exon 19 deletions. Sensitivity and specificity of the CBFR assay were analyzed with different concentrations of fluorescence reporter and different amounts of PCR product. The results demonstrated that increasing the fluorescent reporter to 4 μM and the PCR product to 5 μl enhanced sensitivity. The CBFR assay could detect EGFR exon 19 deletion even with a frequency of 1% in samples. In clinical NSCLC samples, optimized CBFR assay enabled visual detection of the delE746_A750 subtype in less than 1 h. The CBFR assay provides a sensitive, specific, and simple strategy designed based on a straightforward and inexpensive process. We suggest that the CBFR assay could serve as a diagnostic approach to detect mutations, deletions, and pathogens in underequipped laboratories and promote personalized therapeutic approaches.

Cellular Immunity in Mice Vaccinated with Recombinant Phospholipase D Toxoid of Hemiscorpius lepturus Scorpion

Background

Hemiscorpius lepturus is one of the most dangerous scorpions in Iran and the world. Numerous studies have been conducted on phospholipases, especially phospholipase D, in this scorpion's venom, and the results have shown this protein to be the main cause of death. Therefore, one of the most effective ways of preventing fatalities is to produce a toxoid vaccine from the deadly toxin of the venom. The present study was conducted to assess the non-toxicity of this toxoid and the safety of the vaccine candidate in BALB/c mice.

Methods

The production of interferon-gamma and interleukin-4 cytokines in the spleen cells of the mice was measured using ELISpot assay 28 days following immunization with rPLD toxoid.

Results

The unpaired t-test results showed a significant increase in the concentration of IFN-γ cytokine in the vaccinated mice (P= 0.001), indicating that the immune system is directed toward the Th1 pattern, while no significant difference was observed in the levels of IL-4 (P= 0.16) despite an increase in this cytokine. The in-vivo tests showed that the mice immunized with interval doses of 80µg of toxoid were completely protected against 10 × the LD₁₀₀ of the venom. Moreover, the toxoid had no dermonecrotic effects and caused no necrotic and inflammatory complications in the rabbit skin.

Conclusion

As a vaccine, the toxoid has the potential to increase the Th1 cytokine response and, subsequently, increase acquired cellular immunity. Thus, this toxoid appears to be able to provide an effective vaccine against the venom of Hemiscorpius lepturus.

Antiproliferative effects of AAV-delivered CRISPR/Cas9-based degradation of the HPV18-E6 gene in HeLa cells

Human papillomavirus infections are associated with most cervical cancers, which are the fourth most common cancer in women. HPV-E6 protein binds to protein p53 and inhibits its function, leading to the switching of normal cells toward cancer cells. Here, we disrupted the HPV-E6 gene and investigated its effects on the proliferation and apoptosis of HeLa cells. The HPV18-E6 gene was targeted with two designed sgRNAs cloned into an AAV-CRISPR-based plasmid. The AAV-E6-CRISPR/Cas9 virions were prepared and titrated in HEK293t cells. The cleavage created in the HPV-E6 gene was detected using the T7E1 assay. Cell cycle profiling, MTT assay, and annexin V/PI staining were performed. Also, the p53 protein level was measured by Western blotting. Our data showed that disruption of the HPV-E6 gene led to increased cell apoptosis and decreased cell proliferation. A significant accumulation of infected cells in sub-G1 phase was observed in the cell profiling assay. Also, HPV-E6 gene disruption resulted in a significant increase in the level of P53 protein. Our findings indicated that AAV-mediated delivery of CRISPR/Cas9 can effectively target the HPV-E6 gene in HeLa cells, and its antiproliferative effects may provide therapeutic benefits of local administration of this gene-editing system for HPV-related cervical cancers.

Antimicrobial and anti-biofilm potencies of dermcidin-derived peptide DCD-1L against Acinetobacter baumannii: an in vivo wound healing model

BACKGROUND

The global emergence of Acinetobacter baumannii resistance to most conventional antibiotics presents a major therapeutic challenge and necessitates the discovery of new antibacterial agents. The purpose of this study was to investigate in vitro and in vivo anti-biofilm potency of dermcidin-1L (DCD-1L) against extensively drug-resistant (XDR)-, pandrug-resistant (PDR)-, and ATCC19606-A. baumannii.

METHODS

After determination of minimum inhibitory concentration (MIC) of DCD-1L, in vitro anti-adhesive and anti-biofilm activities of DCD-1L were evaluated. Cytotoxicity, hemolytic activity, and the effect of DCD-1L treatment on the expression of various biofilm-associated genes were determined. The inhibitory effect of DCD-1L on biofilm formation in the model of catheter-associated infection, as well as, histopathological examination of the burn wound sites of mice treated with DCD-1L were assessed.

RESULTS

The bacterial adhesion and biofilm formation in all A. baumannii isolates were inhibited at 2 × , 4 × , and 8 × MIC of DCD-1L, while only 8 × MIC of DCD-1L was able to destroy the pre-formed biofilm in vitro. Also, reduce the expression of genes involved in biofilm formation was observed following DCD-1L treatment. DCD-1L without cytotoxic and hemolytic activities significantly reduced the biofilm formation in the model of catheter-associated infection. In vivo results showed that the count of A. baumannii in infected wounds was significantly decreased and the promotion in wound healing by the acceleration of skin re-epithelialization in mice was observed following treatment with 8 × MIC of DCD-1L.

CONCLUSIONS

Results of this study demonstrated that DCD-1L can inhibit bacterial attachment and biofilm formation and prevent the onset of infection. Taking these properties together, DCD-1L appears as a promising candidate for antimicrobial and anti-biofilm drug development.

A Computational Framework to Infer Prostate Cancer-Associated Long Noncoding RNAs and Analyses for Identifying a Competing Endogenous RNA Network

Background: Prostate cancer (PC) is the second leading cause of cancer death after lung cancer in men. Current biomarkers are ineffective for the treatment and management of the disease. Long noncoding RNAs (lncRNAs) are a heterogeneous group of transcripts that are involved in complex gene expression regulatory networks. Although lncRNAs have been suggested to be promising as future biomarkers, the connection between the majority of lncRNAs and human disease remains to be elucidated. One approach to elucidate the roles of lncRNAs in disease is through the development of computational models. For example, a novel computational model termed HyperGeometric distribution for LncRNA-Disease Association (HGLDA) has been developed. Such models need to be developed on a tumor-specific basis to better suit the particular problem. Methods: In this study, we constructed a potential pipeline through two models, HGLDA and pathway-based using data from several databases. To validate the obtained data, the expression levels of selected lncRNAs were investigated quantitatively in the DU-145, LNCaP, and PC3 PC cell lines using quantitative real-time PCR. Results: We obtained a number of lncRNAs from both models, many of which were filtered through several databases that ultimately resulted in identification of six high-value lncRNA targets. Their expression was correlated with one important component of the PI3K pathway, known to be related to PC. Conclusion: Through the assembly of a lncRNA-miRNAs-mRNA competing endogenous RNA network, we successfully predicted lncRNAs interfering with miRNAs and coding genes related to PC.

JPX and LINC00641 ncRNAs expression in prostate tissue: a case-control study

Background and purpose

Prostate cancer (PC) is the second most prevalent cancer in men. Prostate-specific antigen (PSA) is the main biomarker for screening PC. An increase in PSA could lead to false-positive results. Thus, more appropriate markers should be investigated. In the present study, JPX and LINC00641 expression levels were measured in tumoral prostate tissue compared with the non-tumor tissue.

Experimental approach

43 pairs of prostate tumoral and non-tumor tissue were prepared. The expression levels of JPX and LINC00641 were investigated by RT-qPCR.

Findings/Results

Significant upregulation of LINC00641 (2.47 ± 0.5 vs 1.41 ± 0.2) and downregulation of JPX (1.42 ± 0.6 vs 2.83 ± 1.0) were observed in PC tissues compared with the normal tissues (their adjacent non-tumoral tissues).

Conclusion and implications

Dysregulation of JPX and LINC00641 in PC patients could be used in the future as a prognostic biomarker in PC.

New evidence on tumor suppressor activity of PTEN and KLLN in papillary thyroid carcinoma

This study aimed to address the hypothesis that the expression of PTEN and KLLN tumor suppressor genes could diminish in papillary thyroid cancer (PTC) compared to paired normal tissue (PNT) and multinodular goiter (MNG). PTEN and KLLN expressions were assessed at both mRNA and protein levels in 82 tissue samples, including 30 PTC, 30 PNT, and 26 MNG using SYBR-Green Real-Time PCR and enzyme-linked immunosorbent assay (ELISA), respectively. Bioinformatics studies were performed to evaluate the genomic location and the genes promoter region. The mRNA expression of PTEN and KLLN in PTC was significantly lower than PNT (PTEN, P = 0.0033; KLLN, P = 0.0005). A significant decrease in the mRNA level of KLLN was also observed in PTC than MNG (P = 0.0304). Decreased level of PTEN mRNA (odds ratio=0.391; P = 0.013) or KLLN mRNA (odds ratio=0.023; P = 0.025) was associated with an increased risk of PTC tumorigenesis. Areas under the ROC curve for PTEN and KLLN were 0.69 and 0.78, respectively. PTEN and KLLN protein expressions in PTC compared to PNT or MNG were not significantly different. The bioinformatics studies revealed the sequence near the promoter region is lowly conserved across species. Four GC boxes were found upstream of the PTEN transcription start site (TSS), and one TATA box and one GC box were found upstream of KLLN TSS. The results suggest PTEN and KLLN are the two tumor suppressor genes that decreasing or loss of both of them occurs in sporadic PTC tumorigenesis. It appears they could have a promising application in both diagnostic and therapeutic areas.

The Effect of Lactobacillus casei Consumption in Improvement of Obsessive-Compulsive Disorder: an Animal Study

Obsessive-compulsive disorder (OCD) is an important neuropsychiatric disorder worldwide. Common treatments of OCD include serotonergic antidepressants, which can cause potentially serious side effects. We assessed the effects of Lactobacillus casei (L. casei) Shirota consumption in an animal model of OCD. OCD-like symptoms were induced in rats by the chronic injection of the D2/D3 dopamine agonist quinpirole hydrochloride. Rats were classified into five groups of 6 rats. Four groups were injected chronically with quinpirole (0.5 mg/kg, twice weekly for 5 weeks). They were fed with L. casei Shirota (10⁹ CF/g, daily for 4 weeks) (group 1), fluoxetine (10 mg/kg, daily for 4 weeks) (group 2), combination of L. casei Shirota and fluoxetine (group 3), and normal saline (positive control group). The last group did not receive dopamine agonist and was only injected with saline (negative control group). Expression levels of brain-derived neurotrophic factor (Bdnf), solute carrier family 6 member 4 (Slc6a4), and 5-hydroxytryptamine receptor type 2A (Htr2a) were assessed in orbitofrontal cortex tissues of all rats. Behavioral tests showed improvement of OCD signs in rats treated with L. casei Shirota, fluoxetine, and a combination of drugs. Quantitative PCR analysis showed a remarkable decrease in the expression of Bdnf and an increase in the expression of Htr2a in quinpirole-treated rats. After treatment with L. casei Shirota and fluoxetine, the expression level of Bdnf was increased remarkably, whereas Htr2a expression was decreased. The current study showed the effectiveness of L. casei Shirota in the treatment of OCD in a rat model. The beneficial effects of this probiotic are possibly exerted through the modulation of serotonin-related genes expression.

Bioinformatics Evaluation of SPATA19 Gene Expression in Different Parts of Brain

Background: Determining the expression pattern of testis genes in the brain is essential for understanding tissue functions and correlation or inter-correlation between testis and the brain. In this study, we examined spermatogenesis-associated 19 (SPATA19 gene) expression in 10 parts of the brain with bioinformatics analysis. Materials and Methods: The public dataset GSE46706, including 1231 samples originated from 134 Caucasian individuals, was downloaded from NCBI Gene Expression Omnibus (GEO). SPATA19 gene expression in the cerebellar cortex, frontal cortex, hippocampus, medulla, occipital cortex, putamen, substantia nigra, temporal cortex, thalamus, and white matter was examined against each other using R software and the t-test. Results: Out of 10 brain parts examined, the cerebellar cortex and white matter showed the highest expression, and the temporal cortex showed the lowest expression of the gene. So the cerebellar cortex had a 5.6% and 6.2% increase in gene expression relative to the putamen and temporal cortex with P values of 6.04e-13 and 2.15e-17, respectively. Also, the white matter had a 4% increase in gene expression over the temporal cortex with a P value of 1.89e-13. Conclusion: SPATA19 had more expression in the cerebellar cortex and white matter than other brain parts. These two parts make up the cerebellum.

Bi-functionalized aminoguanidine-PEGylated periodic mesoporous organosilica nanoparticles: a promising nanocarrier for delivery of Cas9-sgRNA ribonucleoproteine

BACKGROUND

There is a great interest in the efficient intracellular delivery of Cas9-sgRNA ribonucleoprotein complex (RNP) and its possible applications for in vivo CRISPR-based gene editing. In this study, a nanoporous mediated gene-editing approach has been successfully performed using a bi-functionalized aminoguanidine-PEGylated periodic mesoporous organosilica (PMO) nanoparticles (RNP@AGu@PEG1500-PMO) as a potent and biocompatible nanocarrier for RNP delivery.

RESULTS

The bi-functionalized MSN-based nanomaterials have been fully characterized using electron microscopy (TEM and SEM), nitrogen adsorption measurements, thermogravimetric analysis (TGA), X-ray powder diffraction (XRD), Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy (ATR-FTIR), and dynamic light scattering (DLS). The results confirm that AGu@PEG1500-PMO can be applied for gene-editing with an efficiency of about 40% as measured by GFP gene knockdown of HT1080-GFP cells with no notable change in the morphology of the cells.

CONCLUSIONS

Due to the high stability and biocompatibility, simple synthesis, and cost-effectiveness, the developed bi-functionalized PMO-based nano-network introduces a tailored nanocarrier that has remarkable potential as a promising trajectory for biomedical and RNP delivery applications.

Association of OLR1 gene polymorphisms with the risk of coronary artery disease: A systematic review and meta-analysis

BACKGROUND

Oxidized LDL receptor 1 (OLR1) encodes LOX-1, LOXIN, and OLR1D4 transcript variants. Up-regulation of LOX-1 and down-regulation of LOXIN have an essential role in causing coronary artery disease (CAD). Discovery of risk single nucleotide polymorphisms (SNPs) in OLR1 gene is clinically important as these polymorphisms could be candidate biomarkers of CAD.

OBJECTIVES

The purpose of this study is quantitative evidence synthesis on how OLR1 polymorphisms in the haplotype block impact the risk of CAD.

METHODS

First, a systematic keyword-based search in PubMed, Web of Science, and Scopus was conducted. After data extraction, pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated for OLR1 polymorphisms and CAD. Twelve case-control studies, including 6,238 cases and 15,773 controls, were concluded in the meta-analysis.

RESULTS

Our findings demonstrate significant association of OLR1 polymorphisms in the haplotype block with CAD risk in all genetic models (allelic model: OR = 1.19, 95%CI = 1.06-1.34; additive model: OR = 1.54, 95%CI = 1.16-2.05; recessive model: OR = 1.26, 95%CI = 1.04-1.53; dominant model: OR = 1.28, 95%CI = 1.09-1.51). Subgroup analysis based on the type of polymorphism revealed that rs1050283 (3'UTR*188 C > T) and rs3736235 (IVS4-14 A > G) are more significantly associated with the risk of CAD compared to other polymorphisms in the haplotype block.

CONCLUSIONS

We found a significant association between OLR1 polymorphisms in the haplotype block, especially rs1050283 and rs3736235, with CAD. We also suggest that precise determination of disease association with polymorphisms in a haplotype requires investigation of all SNPs rather than a single SNP in that specific haplotype.

Spata19 Inactivation as a Cause of Oligospermia

Background: Spermatogenesis associated 19 (Spata19) was introduced as a testis-specific gene that was probably involved in spermatogenesis cell apoptosis. Therefore, this study aimed to investigate the effect of Spata19 inactivation on sperm count. Materials and Methods: We generated global Spata19 knockout mice by CRISPR/Cas9 nickase technology. Disability was validated in three levels of DNA, RNA, and protein using PCR, RT-PCR, and immunohistochemistry. Histological studies were performed for testis. Sperm characteristics were also assessed with CASA software. Results: Spata19 knockout mice had a 43 nucleotides deletion in exon 4 of this gene. The presence and absence of Spata19 were confirmed in normal and knockout mice, respectively. The presence of Spata19 in normal NMRI mice was detected in the brain, heart, and thymus by semi-nested RT-PCR and in Leydig cells by immunohistochemistry. Histological studies revealed a decrease in sperm count in knockout mice. Also, CASA parameters were significantly reduced (P<0.05). Conclusion: These data indicate that Spata19 inactivation is a cause of oligospermia, and its role could be beyond an adhesive molecule.

Whole-Exome Sequencing Uncovers Novel Causative Variants and Additional Findings in Three Patients Affected by Glycogen Storage Disease Type VI and Fanconi-Bickel Syndrome

Glycogen storage diseases (GSDs) are the heterogeneous group of disorders caused by mutations in at least 30 different genes. Different types of GSDs, especially liver GSDs, take overlapping symptoms and can be clinically indistinguishable. This survey evaluated the use of whole-exome sequencing (WES) for the genetic analysis of the liver GSD-suspected patients in three unrelated families. An in-house filtering pipeline was used to assess rare pathogenic variants in GSD-associated genes, autosomal recessive/mendelian disorder genes (carrier status for genetic counseling subjects), and the ACMG's list of 59 actionable genes. For the interpretation of the causative variants and the incidental/secondary findings, ACMG guidelines were applied. Additionally, we have explored PharmGKB class IA/IB pharmacogenetic variants. The segregation analysis was performed using Sanger sequencing for the novel causative variants. Bioinformatics analysis of the exome data in three individuals revealed three novel homozygous causative variants in the GSD-associated genes. The first variant, c.298_307delATGATCAACC in PYGL gene has related to HERS disease (GSD VI). Both variants of c.1043dupT and c.613-1G > C in SLC2A2 gene have been associated with Fanconi-Bickel syndrome (GSDXI). Eight pathogenic/likely pathogenic medical actionable findings in Mendelian disease genes and 10 pharmacogenetic variants with underlying drug response phenotypes have been identified. No known/expected pathogenic variants were detected in the ACMG's list of 59 actionable genes. The logical filtering steps can help in finding other medical actionable secondary/incidental findings as well as effectively identifying the causative variants in heterogeneous conditions such as GSDs. Three novel variants related to GSD genes recognized in liver GSD-suspected patients with early infantile and childhood-age onset.

FSH regulates RA signaling to commit spermatogonia into differentiation pathway and meiosis

BACKGROUND

Spermatogenesis is a complex process that is controlled by interactions between germ cells and somatic cells. The commitment of undifferentiated spermatogonia to differentiating spermatogonia and normal spermatogenesis requires the action of gonadotropins. Additionally, numerous studies revealed the role of retinoic acid signaling in induction of germ cell differentiation and meiosis entry.

MAIN TEXT

Recent studies have shown that expression of several RA signaling molecules including Rdh10, Aldh1a2, Crabp1/2 are influenced by changes in gonadotropin levels. Components of signaling pathways that are regulated by FSH signaling such as GDNF, Sohlh1/2, c-Kit, DMRT, BMP4 and NRGs along with transcription factors that are important for proliferation and differentiation of spermatogonia are also affected by retinoic acid signaling.

CONCLUSION

According to all studies that demonstrate the interface between FSH and RA signaling, we suggest that RA may trigger spermatogonia differentiation and initiation of meiosis through regulation by FSH signaling in testis. Therefore, to the best of our knowledge, this is the first time that the correlation between FSH and RA signaling in spermatogenesis is highlighted.

Depression Is Associated with Downregulation of IPS-1 in Chronic HBV-Infected Patients in a Sex-Dependent Manner

BACKGROUND

Depression and anxiety can modulate immune-related molecule expressions. The chronic HBV-infected (CHB) patients suffer from inappropriate immune responses. Additionally, psychological disorders are prevalent among the patients. Thus, depression and anxiety may alter immune-related molecule expression. This study aimed to examine IPS-1 and RIP1 mRNA levels in CHB patients suffering from various degrees of anxiety and depression.

METHODS

Sixty patients with CHB participated in this research and completed standard questionnaires to evaluate depression and anxiety. The expression levels of IPS-1 and RIP1 were examined using real-time PCR techniques.

RESULTS

The result revealed that although the expression of IPS-1 and RIP1 did not change in the CHB patients with various ranges of depression and anxiety, IPS-1 was significantly decreased in the male CHB patients who suffered from mild, moderate, and severe depression when compared to the patients with no depression.

CONCLUSION

So, it was hypothesized that depression may be associated with alteration in the expression of IPS-1 in a sex-dependent manner. In other words, it appears that the male CHB patients are at risk of depression-related alteration in immune-related gene expression.

Expression profiling revealed up-regulation of three lncRNAs in breast cancer samples

Long non-coding RNAs (lncRNAs) have been vastly investigated for their critical roles in the pathogenesis of breast cancer. Yet, the expression pattern and clinical significance of three lncRNAs namely CTBP1AS2, LINC-ROR and SPRY4-IT1 in breast cancer are not completely clarified. In the present investigation, we assessed expression of these lncRNAs in breast cancer tissues and paired non-cancerous specimens from the same patients using quantitative real time PCR. Notably, expression of CTBP1AS2, LINC-ROR and SPRY4-IT1 were upregulated in breast cancer tissues compared with non-cancerous tissues (ER = 17.62, P value<0.000; ER = 4.62, P value = 0.001 and ER = 3.47, P value = 0.005, respectively). Relative expression of LINC-ROR in tumoral tissues compared with non-tumoral tissues was associated with a history of hormone replacement therapy (P = 0.04). Expression levels of CTBP1AS2, LINC-ROR and SPRY4-IT1 were significantly correlated with each other in both tumoral and non-tumoral tissues. The strongest correlations were detected between CTBP1AS2/ LINC-ROR and CTBP1AS2/ SPRY4-IT1 pairs in non-tumoral tissues. CTBP1AS2 and SPRY4-IT1 had the best sensitivity (80%) and specificity (64%) values, respectively. Based on AUC values, the best diagnostic power belonged to CTBP1AS2. The current study potentiates CTBP1AS2, LINC-ROR and SPRY4-IT1 as putative contributors in the pathogenesis of breast cancer and suggests these lncRNAs as candidates for functional analysis in this kind of cancer.

Anti-angiogenic effects of testis-specific gene antigen 10 on primary endothelial cells

Growing evidence indicates the antitumor and antiangiogenesis activities of testis-specific gene antigen 10 (TSGA10). However, the underlying mechanisms and precise role of TSGA10 in angiogenesis are still elusive. In this study, we isolated human umbilical cord vein endothelial cells (HUVECs) and stably transfected with pcDNA3.1 carrying TSGA10 coding sequence. We demonstrated that TSGA10 over-expression significantly decreases HUVEC tubulogenesis and interconnected capillary network formation. HUVECs over-expressing TSGA10 exhibited a significant decrease in migration and proliferation rates. TSGA10 over-expression markedly decreased expression of angiogenesis-related genes, including VEGF-A, VEGFR-2, Ang-1, Ang-2, and Tie-2. Our ELISA results showed the decrease in VEGF-A mRNA expression level is associated with a significant decrease in its protein secretion. Additionally, over-expressing TSGA10 decreased expression levels of marker genes of cell migration (MMP-2, MMP-9, and SDF-1a) and proliferation (PCNA and Ki-67. Furthermore, ERK-1 and AKT phosphorylation significantly reduced in HUVECs over-expressing TSGA10. Our findings suggest a potent anti-angiogenesis activity of TSGA10 in HUVECs through down-regulation of ERK and AKT signalling pathways, and may provide therapeutic benefits for the management of different pathological angiogenesis.

Stimulatory effects of Lactobacillus casei derived extracellular vesicles on toll-like receptor 9 gene expression and cytokine profile in human intestinal epithelial cells

Background

A complex community of microorganisms in the gastrointestinal (GI) tract, known as the gut microbiota, exerts major effects on gene expression and cytokine profile. Extracellular vesicles (EVs) which are produced by bacteria could be sensed by Toll like receptors (TLRs). The interaction between gut microbiota and TLRs affects homeostasis and immune responses. In this study, we evaluated TLR9 gene expression and cytokines level in Caco-2 cell line treated with Lactobacillus casei as one of the gut microbiota and its EVs.

Methods

In the present study, L. casei derived EVs was extracted via ultracentrifugation. The quality control assessment included the evaluation of physicochemical characteristics of EVs. For the treatment of Caco-2 cell line, L. casei and its EVs (100 and 150 μg/mL) were used. In addition, qRT-PCR assay was carried out to evaluate the mRNA expression of TLR9 gene. ELISA assay was also performed to determine the levels of IFN_γ, TNF-α, GM-CSF, IL-1α, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-12, IL-17A, and IL-10 cytokines.

Results

The results showed that L. casei slightly increased TLR9 gene expression in the Caco-2 cell line. It was also found that EVs at concentrations of 100 and 150 μg/mL could significantly decrease TLR9 gene expression. Furthermore, L. casei significantly increased IL-10 and IFN_γ levels. Based on the findings, the level of IL-17A, as a proinflammatory cytokine, decreased by L. casei. Both concentrations of EVs decreased the level of IFN_γ, while increasing the concentrations of IL-4 and IL-10. EVs from L. casei could modulate immune responses in the Caco-2 cell line. Both EVs and L. casei activated the expression and secretion of several cytokines.

Conclusions

L. casei and its EVs have pivotal role in the cross talk between gut microbiota and the host especially in the modulation of the immune system. This study shows for the first time the increasing level of anti-inflammatory cytokines by EVs released by L. casei. Based on the last studies on immunomodulatory effect of EVs on immune cells and our results in cell line level, we postulate that L. casei derived EVs could be possible candidates for the reduction of immune responses.

Investigation of promoter methylation of MCPH1 gene in circulating cell-free DNA of brain tumor patients

INTRODUCTION

Despite advanced diagnostic and therapeutic techniques, many brain tumors are still diagnosed at high grades and, therefore finding novel molecular markers may assist in early detection and reducing brain tumors-related mortality rate. Owing to the previous reports on the importance of MCPH1 gene in tumorigenesis, the present study was aimed to study the promoter methylation of MCPH1 gene in paired circulating cell-free DNA (cfDNA) and tumor tissues of brain tumor patients.

MATERIALS AND METHODS

Fourteen fresh paired serum and tumor tissue samples in addition to 18 isolated serum samples were collected from patients affected by different grades of brain tumor. Genomic DNA and cfDNA was isolated from tissue and serum samples using QIAamp DNA Mini Kit Norgen Bioteck Kit, respectively. Methylation DNA immunoprecipitation Real-time polymerization chain reaction (MeDIP-Real-time PCR) was performed on isolated DNA samples using EpiQuik MeDIP Ultra Kit and specific primer pairs. cfDNA quantity was determined through Real-time PCR analysis using specific primer pairs designed for GAPDH gene.

RESULTS

MCPH1 was methylated in 54% of cfDNA samples which was significantly associated with tumor grade, as well (P-value = 0.02). The methylation rate of MCPH1 was found as 78% in the tissue samples which was meaningfully associated with tumor grade (P-value = 0.03). Moreover, methylation of the MCPH1 gene was consistent in 57% of the same cfDNA and tissue samples. Methylation of MCPH1 gene in neither tumor tissues nor cfDNA was not correlated with age and sex of the patients.

DISCUSSION AND CONCLUSION

Due to the conformity of methylation of MCPH1 gene in cfDNA and tissue samples in more than half of the enrolled patients, especially in higher grades of tumors, it seems that MCPH1 promoter methylation could be a potential epimarker in not only detection of brain tumors but also in response to chemo- and radiotherapy which warranted further assessment.

Efficacy of co-immunization with the DNA and peptide vaccines containing SYCP1 and ACRBP epitopes in a murine triple-negative breast cancer model

Multiepitope cancer vaccines have gained lots of attention for prophylactic and therapeutic purposes in cancer patients. In our previous study, multiepitope DNA and peptide cancer vaccines consisted of the most immunodominant epitopes of ACRBP and SYCP1 antigens were designed by bioinformatic tools. In this study, the effect of prophylactic co-immunization with these DNA and peptide cancer vaccines in the 4T1 breast cancer animal model was assessed. Serum levels of the peptide-specific IgG total, IgG2a and IgG1 were measured by enzyme-linked immunosorbent assay (ELISA). Also, the efficacy of the immunized mice splenocytes' for producing interleukin-4 (IL-4) and interferon-γ (IFN-γ) was evaluated. The co-immunization caused a significant (P < .05) increase in the serum levels of IgG1 and IgG2a. The co-immunized mice splenocytes exhibited significantly enhanced IL-4 (6.6-fold) and IFN-γ (19-fold) production. Also, their lymphocytes exhibited higher proliferation rate (3-fold) and granzyme B production (6.5-fold) in comparison with the control. The prophylactic co-immunization significantly decreased the breast tumors' volume (78%) and increased the tumor-bearing mice survival time (37.5%) in comparison with the control. Taking together, prophylactic co-immunization with these multiepitope DNA and peptide cancer vaccines can activate the immune system against breast cancer. However, further experiments are needed to evaluate their efficacy from different angles.

Evaluation of the Epigenetic Demethylation of NRF2, a Master Transcription Factor for Antioxidant Enzymes, in Colorectal Cancer

Background

Epigenetic changes in CpG islands of the promoter regions of homeostasis-related genes, including nuclear factor erythroid 2-related factor 2 (NRF2), have been shown to hold a significant role in the development of colorectal cancer. Therefore, we aimed to examine the DNA demethylation pattern of the NRF2 promoter region in cancerous lesions from patients with colorectal cancer and the association of methylation status with clinicopathological features in the Iranian population.

Methods

In this cross-sectional study, 114 colorectal tissue samples were collected. These samples included: 34 tumour tissue samples, 60 precancerous polyps, and 20 normal tissue samples. The promoter methylation status of the NRF2 gene was examined using methylation-specific PCR. Additionally, the relationship between the methylation status and the clinicopathological features was investigated.

Results

The frequency of NRF2 demethylation in the tumour samples was significantly higher compared to the polyp tissues (p= 0.003) and normal tissue (p= 0.009), indicating that cancerous colorectal tissues exhibit increased demethylation of the NRF2 promoter. After examining the demethylation status of tissue samples, the clinicopathological features were compared to the demethylation results. No significant association was found between NRF2 promoter demethylation and the clinicopathological features of patient samples.

Conclusion

Our findings suggest that the epigenetic modifications leading to NRF2 demethylation found in colorectal tumour samples may contribute to cancer progression from precancerous polyps to cancerous lesions.

Influence of Follicular Fluid and Seminal Plasma on The Expression of Endometrial Receptivity Genes in Endometrial Cells

Objective

Endometrial receptivity plays a key role in pregnancy success in assisted reproduction cycles. Recent evidence suggests that seminal plasma (SP) and follicular fluid (FF) influence the uterine endometrium to improve implantation of the embryo and the establishment of pregnancy. In this study, we attempt to assess the influence of FF and SP on the expression levels of main endometrial receptivity genes (HOXA10, HOXA11, ITGAV, ITGB3 and LIF) in endometrial stromal cells.

Materials and Methods

In this experimental study, SP and FF were collected from 15 healthy fertile men and 15 healthy fertile women, respectively. Tissue specimens of the endometrium were obtained from 12 women undergoing hysterectomy for benign conditions. After endometrial stromal cell isolation and culture, dose- and time-dependent cytotoxic effects of pooled FF and SP on 3D-cultured endometrial cells were evaluated. A second independent set of 12 endometrium samples was treated under determined optimum conditions and evaluated for gene expression analysis using quantitative real-time polymerase chain reaction (qRT-PCR).

Results

The results of this study indicated that exposure of endometrial stromal cells to FF resulted in the elevated expression of HOXA10 (fold change=2.6, P=0.02), HOXA11 (fold change=3.3, P=0.002), LIF (fold change=4.6, P=0.0003), ITGB3 (fold change=3.5, P=0.012), and ITGAV (fold change=2.8, P=0.001) compared to untreated cells. In addition, we found that SP-treated endometrial cells showed increased mRNA levels of only the LIF gene (fold change=2.5, P=0.008) compared to untreated cells.

Conclusion

Human SP and FF may modulate the endometrial receptivity and improve the implantation rate in assisted reproduction cycles through the up-regulation of endometrial receptivity genes.

Expression analysis of vimentin and the related lncRNA network in breast cancer

Vimentin (VIM) is a mesenchymal marker which is expressed in some cancer types including breast cancer. A long non-coding RNA (lncRNA) has been identified to be transcribed from VIM gene locus and positively regulate expression of VIM. This lncRNA has been named as VIM-antisense 1 (VIM-AS1). Expression of VIM is also regulated by another lncRNA namely AGAP2-antisense RNA 1 (AGAP2-AS1). In the current study, we aimed at identification of the expression pattern of VIM, VIM-AS1, AGAP2 and AGAP2-AS1 in 78 breast cancer samples and their paired adjacent non-cancerous tissues (ANCTs) by means of real time PCR. All mentioned genes were significantly down-regulated in tumoral tissues compared with ANCTs (P values less than 0.000). Relative expression of VIM-AS1 in tumoral tissues versus ANCTs was associated with menopause age (P = .02) in a way that this gene was down-regulated in most of patients whose menopause age was between 40 and 50 years. Moreover, AGAP2-AS1 relative expression was associated with patients' body mass index (P = .03). There were trends toward association between VIM relative expression and tumor size (P = .07) and association between VIM-AS1 relative expression and obesity (P = .06). Expression of VIM was significantly higher in tumoral tissues of patients who had history of hormone replacement therapy compared with those without such history (P = .03). Moreover, expression levels of both VIM and AGAP2-AS1 were lower in patients whose menarche age was between 10 and 12 years old compared with those whose menarche age was between 13 and 15 years old (P values = .01 and 0.04, respectively). Transcript quantities of VIM, VIM-AS1, AGAP2 and AGAP2-AS1 were correlated with each other both in tumoral tissues and in ANCTs. Among four assessed genes, AGAP2 had the best diagnostic power for discrimination of tumoral tissues from ANCTs (AUC value = 0.87). Combination of four genes led to enhancement of AUC value to 0.94. The current study shows the importance of VIM and its associated lncRNAs in breast cancer and potentiates these genes as biomarkers for this malignancy. Moreover, these lncRNAs might be regarded as therapeutic targets in breast cancer.

Evaluation of lactic acid bacteria isolated from poultry feces as potential probiotic and its in vitro competitive activity against Salmonella typhimurium

The efficacy of probiotics as alternatives to antibiotics has been defined as one of the potential strategies to prevent Salmonella spp. infection in poultry. The purpose of this study was to isolate probiotic native Lactic acid bacteria (LAB) with high compatibility to intestinal tract and prevention of Salmonella typhimurium from broiler chicken feces. Thirty-seven samples of chicken feces were collected from seven broiler chicken farms in Northern Iran. The isolates identification was carried out with morphological and biochemical tests. Agar diffusion methods were used to evaluate the antimicrobial activities against Escherichia coli and S. typhimurium. The primary probiotic characteristics such as resistance to acid and bile and adhesion to Caco-2 cells were studied. Indeed, the ability of LAB isolates to inhibit adhesion of S. typhimurium to Caco-2 cells was evaluated by exclusion, competition and displacement assays. Among 42 isolates, S08, S01 and S06 isolates which showed appropriate probiotics characteristics were selected. Isolates S08 and S01 showed to be able to adhere strongly and also S06 was adhered moderately. In the exclusion assay, the isolates S08, S01 and S06 significantly hampered adhesion of S. typhimurium cell, in the competition assay, the isolates S08, S01 showed significant level of competition activity against S. typhimurium adherence to Caco-2 cells and isolate S08 showed the greatest displacement activity. The 16S rDNA sequence revealed that S08, S01, and S06 isolates were 99.00% similar to Lactobacillus salivarius, Lactobacillus johnsonii, and Pediococcus acidilactici, respectively. The result of this study suggested that LAB isolated from broiler chicken feces could be a remarkable reservoir for identification of probiotic to inhibit the pathogenic bacteria growth.

Heat shock factor 5 is essential for spermatogenesis in mice: Detected by a new monoclonal antibody

OBJECTIVES

Here, we examined the function of our produced monoclonal antibody (mAb10C3) to recognize one of the most important members of the HEAT shock factor family, Hsf5, in embryonic development and in spermatogenic cells of adult mouse testis.

MATERIALS AND METHODS

The targeting effects of mAb10C3 were investigated by immunohistochemistry analysis in the different phases of the embryo and in the adult testis tissue sections.

RESULTS

The results of immunohistochemistry staining on the mouse embryos by the supernatant of hybridoma clone that produced mAb10C3, in the early and late phases (E7.5 and E14.5) of embryonic development, indicated that mAb10C3 could only detect Hsf5 in E7.5 and it did not have any targeting activity in the late phase of development. Therefore, we showed that the hsf5 gene has expressed in early mouse embryonic development. On the other hand, mAb10C3 could detect Hsf5 in spermatogonia and spermatocytes of adult testis in comparison with a known anti-Hsf5 antibody (ab98939) and an anti-PCNA antibody as a marker of spermatogonia cells.

CONCLUSION

Taken together, these data indicated that generated anti-testis mAb10C3 was generated against anti-testis proteins, specifically to target Hsf5, and can be useful as a scientific tool to investigate the critical genes in the development and spermatogenesis.

Genotype-phenotype correlation and description of two novel mutations in Iranian patients with glycogen storage disease 1b (GSD1b)

Background

Glycogen storage disease (GSD) is a rare inborn error of the synthesis or degradation of glycogen metabolism. GSD1, the most common type of GSD, is categorized into GSD1a and GSD1b which caused by the deficiency of glucose-6-phosphatase (G6PC) and glucose-6-phosphate transporter (SLC37A4), respectively. The high rates of consanguineous marriages in Iran provide a desirable context to facilitate finding the homozygous pathogenic mutations. This study designates to evaluate the clinical and genetic characteristics of patients with GSD1b to assess the possible genotype-phenotype correlation.

Results

Autozygosity mapping was performed on nineteen GSD suspected families to suggest the causative loci. The mapping was done using two panels of short tandem repeat (STR) markers linked to the corresponding genes. The patients with autozygous haplotype block for the markers flanking the genes were selected for direct sequencing. Six patients showed autozygosity in the candidate markers for SLC37A4. Three causative variants were detected. The recurrent mutation of c.1042_1043delCT (p.Leu348Valfs*53) and a novel missense mutation of c.365G > A (p.G122E) in the homozygous state were identified in the SLC37A4. In silico analysis was performed to predict the pathogenicity of the variants. A novel whole SLC37A4 gene deletion using long-range PCR and sequencing was confirmed as well. Severe and moderate neutropenia was observed in patients with frameshift and missense variants, respectively. The sibling with the whole gene deletion has shown both severe neutropenia and leukopenia.

Conclusions

The results showed that the hematological findings may have an appropriate correlation with the genotype findings. However, for a definite genotype-phenotype correlation, specifically for the clinical and biochemical phenotype, further studies with larger sample sizes are needed.

Optimized protocol for soluble prokaryotic expression, purification and refolding of the human inhibin α subunit, a cysteine rich peptide chain

BACKGROUND

Inhibin A, a member of TGF-β superfamily, consists of α and β subunits. These subunits contain several cysteine residues in amino acid sequence that forms inter- and intra-subunits disulfide bonds. Due to the reducing environment of the bacterial cytoplasm, disulfide bonds formation in E.coli cytoplasm is not possible. Therefore, this can cause misfolding, aggregation and inclusion bodies formation during protein expression. As a result, the expression of inhibin subunits in E.coli produces inclusion bodiesOBJECTIVE: We aimed at identification of an optimized protocol for expression and recovery of inhibin α-subunit from inclusion bodies.

METHODS

Two vectors, four different E.coli strains, and six solubilization conditions for were used for the optimization of inhibin α-subunit production. Then, the solubilized proteins were purified through Ni-NTA affinity chromatography, characterized by SDS-PAGE and Western blotting (WB) using anti-his tag antibody, and refolded by dilution.

RESULTS

The results showed that inhibin α-subunits were successfully expressed in both vectors and the pET22b+inhibin α-subunit in ShuffleTM T7 strain had the highest expression; however, most of the expression was in an insoluble form. Among solubilization buffers examined, a buffer containing 2M urea with pH 12 was the best buffer to dissolve the insoluble protein. The high purity of protein was confirmed by SDS-PAGE and WB. Non-reducing SDS-PAGE demonstrating inhibin α-subunit refolded well.

CONCLUSION

The current protocol is an efficient method for protocol for expression and recovery of inhibin α-subunit from inclusion bodies.

Rapamycin Reduces Cervical Cancer Cells Viability in Hypoxic Condition: Investigation of the Role of Autophagy and Apoptosis

BACKGROUND

Rapamycin has been known as an anti-cancer agent that affects different malignancies such as glioblastoma and prostate cancer. However, there are few studies concerning rapamycin effects on the cervical cancer cells. In this study, it was aimed to investigate the possible effect of rapamycin on a cervical cancer cell line and explored the possible mechanism(s) and pathway(s) for this agent.

MATERIALS AND METHODS

To do so, HeLa cells as cervical cancer cell line were used and treated with different concentrations of rapamycin under both normoxic and hypoxic conditions. Then, cell viability assays, Western blot, quantitative real-time polymerase chain reaction (QR-PCR), acridine orange and acridine orange/propidium iodide staining were performed to evaluate rapamycin effect on the mentioned cell line.

RESULTS

The results showed that autophagy and apoptosis-related genes increased significantly in rapamycin-treated HeLa cells compared to controls. Moreover, cervical cancer cell death by rapamycin-induced autophagy in hypoxia was greater than normoxia compared with controls. In this study, it was showed that autophagy induction by rapamycin can mediate programmed cell death of cervical cancer cells, especially in hypoxic condition.

CONCLUSION

These findings provide a new evidence that rapamycin may inhibit hypoxic HeLa cell proliferation through the trigger of programmed cell death, facilitating the development of novel anti-cancer therapy.

Engineered Jurkat Cells for Targeting Prostate-Specific Membrane Antigen on Prostate Cancer Cells by Nanobody-Based Chimeric Antigen Receptor

Background:

Recently, modification of T cells with CAR has been an attractive approach for adoptive immunotherapy of cancers. Typically, CARs contain a scFv. Most often, scfvs are derived from a monoclonal antibody of murine origin and may be a trigger for host immune system that leads to the T-cell clearance. Nanobody is a specific antigen-binding fragment derived from camelid that has great homology to human VH and low immunogenic potential. Therefore, in this study, nanobody was employed instead of scFv in CAR construct.

Methods:

In this study, a CAR was constructed based on a nanobody against PSMA (NBPII-CAR). At first, Jurkat cells were electroporated with NBPII-CAR, and then flow cytometry was performed for NBPII-CAR expression. For functional analysis, CAR T cells were co-cultured with prostate cancer cells and analyzed for IL-2 secretion, CD25 expression, and cell proliferation.

Results:

Flow cytometry results confirmed the expression of NBPII-CAR on the transfected Jurkat cells. Our data showed the specificity of engineered Jurkat cells against prostate cancer cells by not only increasing the IL-2 cytokine (about 370 pg/ml) but also expressing the T-cell activation marker CD25 (about 30%). In addition, proliferation of engineered Jurkat cells increased nearly 60% when co-cultured with LNCaP (PSMA⁺), as compared with DU145 (PSMA^-).

Conclusion:

Here, we describe the ability of nanobody-based CAR to recognize PSMA that leads to the activation of Jurkat cells. This construct might be used as a promising candidate for clinical applications in prostate cancer therapy.

Identification of common vaginal Lactobacilli immunoreactive proteins by immunoproteomic techniques

Lactobacilli are considered as the most important microorganisms in regulating immune system and maintaining vaginal health. The uses and benefits of Lactobacilli as probiotics, particularly the regulation of immune system, are dependent on the strain used and a comprehensive understanding of their effects on the host. Several factors have been identified in Lactobacilli that influence the immune response, such as exopolysaccharides and proteins. The current study was designed to investigate the serum immunoreactivity of healthy women against common vaginal Lactobacilli immunoreactive proteins. Three common vaginal Lactobacillus strains (L. crispatus L1, L. gasseri L9, and L. fermentum L2) were compared for immune response. The ELISA results showed that the levels of total immunoglobulin (Ig-total) antibody for L. crispatus L1, L. fermentum L2, and L. gasseri L9 were 47%, 45% and 29%, respectively. Regarding the lower prevalence of L. fermentum L2 in comparison with the other two strains, the approximately equal levels of Ig-total compared to L. crispatus L1 and more than L. gasseri L9 indicate that L. fermentum L2 has the greater antigenicity ability. Accordingly, the immunoreactive proteins of L. fermentum L2 were identified using MALDI-TOF-MS detected by SDS-PAGE and Western blotting. These proteins included 30s ribosomal protein S4 and 50s ribosomal protein L5. Antigenic epitopes on the 3D structure of these proteins was also predicted using bioinformatics analysis. The presence of antibody in serum of healthy pre-menopausal women indicates that Lactobacilli (normal flora) proteins can stimulate host immune response. Purification and further studies of the proteins may allow their potential use as an adjuvant to improve the efficacy of vaccines.

Clinical Correlation of miR-200c/141 Cluster DNA Methylation and miR-141 Expression with the Clinicopathological Features of Colorectal Primary Lesions/Tumors

BACKGROUND

Abnormal DNA methylation leading to altered transcription of certain genes occurs frequently in colorectal cancer (CRC). As with protein-coding genes, microRNAs (miRNAs) may be targeted for methylation in CRC; however, the methylation state of miRNA genes in CRC, especially in primary lesions, has not yet been completely elucidated. To understand the impact of DNA methylation on the miR-200c/141 cluster promoter, we investigated the methylation and expression of miR-141 in precancerous lesions and colorectal cancer.

METHODS

In this cross-sectional study, 208 colorectal tissue samples, including 34 tumor tissue samples, 60 precancerous lesions with matched normal adjacent tissues, and 20 normal tissue samples, were collected. Promoter methylation of the miR-200c/141 cluster was studied using methylation-specific PCR. MiR-141 expression was examined using quantitative real-time PCR.

RESULTS

Our findings showed that the miR-200c/141 cluster promoter region was most frequently hypermethylated in colorectal tumors and adenomatous polyps, but unmethylated in hyperplastic polyp tissues (P < 0.001). DNA methylation of the miR-200c/141 cluster and the tumor stage were significantly correlated (P = 0.002); however, miR-141 expression difference between the tumor and polyp samples was not significant (p = 0.6).

CONCLUSION

The DNA methylation status of the miR-200c/141 cluster could serve as a progression marker from benign polyps to colorectal cancer.

Physico-chemical and cytotoxic analysis of a novel large molecular weight bacteriocin produced by Lactobacillus casei TA0021

BACKGROUND AND OBJECTIVES

Antimicrobial peptides produced by lactic acid bacteria have gained enormous attention owing to their health benefits. This study aimed to isolate, purify and characterize the antibacterial protein produced by autochthonous Lactobacillus casei TA0021 strain.

MATERIALS AND METHODS

The antagonistic activity of L. casei TA0021 against a number of pathogenic bacteria was tested by agar well diffusion assay. The antimicrobial agent in the neutralized supernatant fluids was subjected to the action of proteolytic enzymes, catalase, lipase and lysozyme, and their tolerance to variable pH and temperature was estimated. The proteinaceous antagonistic compound was precipitated by 60% w/v ammonium sulphate, desalted and subjected to cation exchange and gel filtration chromatography. Approximate molecular weight of Lactocin was determined by SDS-PAGE and non-denaturing gel electrophoresis. Hemoglobin release assay and cytotoxicity effect of Lactocin TA0021 was determined. The results were statistically analyzed.

RESULTS

The antagonistic agent active against Salmonella Typhimurium and Shigella flexneri appeared resistant to catalase and lipase treatments, while sensitive to the tested proteolytic enzymes. Lactocin TA0021 resisted acidic pH values of 3.0, while alkaline pH values of >9 completely destroyed the activity. The antibacterial peptide was approximately 68 KDa and heat labile as lost its activity at 100°C after 5 minutes. The bacteriocin was non-toxic to MRC-5 cell lines and non-hemolytic. Purification method lead to increase in antibacterial activity while, subsequent decrease in recovery and yield was observed with increasing purification fold.

CONCLUSION

The purified antimicrobial protein from L. casei TA0021 might be used for application in medicinal and food products.

Production, purification, and in vivo evaluation of a novel multiepitope peptide vaccine consisted of immunodominant epitopes of SYCP1 and ACRBP antigens as a prophylactic melanoma vaccine

Melanoma cells are significantly resistance to the current treatments. Therefore, the best option for high-risk populations is prevention. Recently, many preventive cancer vaccines have been developed. In our previous study, several bioinformatic tools were employed for selection of the most immunodominant epitopes of acrosin binding protein (ACRBP) and synaptonemal complex protein 1 (SYCP1) antigens to design multiepitope DNA and peptide cancer vaccines. In the current study, the final construct of the multiepitope DNA vaccine was placed into a pcDNA3.1 vector and then, subcloned into a pET-28a (+) expression vector for transfecting BL21 E. coli strain. The recombinant multiepitope peptide vaccine, weighing 6.35 kDa, was purified by Fast protein liquid chromatography technique (FPLC) and detected by western blotting. Subsequently, C57BL/6 mice were immunized by a mixture of the peptide vaccine and incomplete Freund's adjuvant (IFA) (four vaccinations with one-week intervals). Two weeks after the last vaccination, the serum levels of the peptide-specific IgG total, IgG2a, and IgG1 were measured by enzyme-linked immunosorbent assays (ELISA). Also, the immunized mice splenocytes efficacy for producing interleukin-4 (IL-4) and interferon-γ (IFN-γ) after stimulation with the peptide vaccine was evaluated. At last, the prophylactic effect of the peptide vaccine immunization was evaluated in B16-F10 murine melanoma model. The peptide vaccine immunization caused a significant increase in the serum levels of IgG1, IgG2a, and IgG2a. Also, the immunized mice splenocytes exhibited significantly higher ability to produce IL-4 (10-fold) and IFN-γ (16-fold) after stimulation with the peptide vaccine, in comparison with the PBS and IFA groups. The peptide immunized mice exhibited 50.2% and 43% decrease in the mean tumors' volume in comparison with PBS and IFA groups. Also, the mean survival time for the peptide immunized mice was 33 ± 1.3 days which was 5 and 6 days more than the PBS and IFA groups, respectively. The obtained results exhibit high efficacy of the designed multiepitope peptide vaccine for the immune system activation and anti-tumor prophylactic effects in the murine melanoma model.

Development, optimization, and validation of an in-house Dot-ELISA rapid test based on SAG1 and GRA7 proteins for serological detection of Toxoplasma gondii infections

Background

The aim of the present study was to develop a simple, portable, and rapid assay for serodiagnosis of toxoplasmosis based on recombinant Toxoplasma gondii (T. gondii) SAG1 (rSAG1) and GRA7 (rGRA7) proteins.

Methods

The rSAG1 and rGRA7 proteins were expressed in Escherichia coli (E. coli) and purified in a single step by immobilized metal ion affinity chromatography. The immunoreactivity of the recombinant antigens was tested in an in-house IgG and IgM Dot enzyme-linked immunosorbent assay (Dot-ELISA) for potential use in serodiagnosis of T. gondii infection.

Results

Results from the comparison of in-house rSAG1-Dot-ELISA with ELISA for the detection of anti-Toxoplasma IgG and IgM include sensitivity of 83.7% and 81.2%, specificity of 90.2% and 89.3%, positive predictive values of 85.9% and 68.4%, and negative predictive values of 88.6% and 94.3%, respectively. Sensitivity of 66.2%, specificity of 81.2%, positive predictive values of 71.6%, and negative predictive values of 77.1% were concluded from in-house IgG rGRA7-Dot-ELISA. The sensitivity and specificity of IgM rGRA7-Dot-ELISA included 87.5% and 83.9%, respectively. Sensitivity and specificity of in-house Dot-ELISA for a combination of rSAG1 and rGRA7 included 87.5% and 91.1% for IgG and IgM, respectively. Sensitivity and specificity of a combination of rSAG1 and rGRA7 for the detection of IgM in suspected sera to acute toxoplasmosis were higher than those for the detection of IgG in sera with chronic infections (90.6% and 92% instead of 86.2% and 91.6%, respectively).

Conclusion

The highlighted parameters of combined recombinant proteins were more significant than those of single recombinant proteins in in-house Dot-ELISA. These data suggest that the in-house Dot-ELISA based on rSAG1 and rGRA7 combination is a promising diagnostic tool with a similar sensitivity to the native antigens of T. gondii, which can be used for the serodiagnosis of toxoplasmosis in fields as well as less equipped laboratories.

The Impact of Long-term Exposure to Low Levels of Inorganic Arsenic on the Hypomethylation of SEPT9 Promoter in Epithelial-Mesenchymal Transformed Colorectal Cancer Cell Lines

Inorganic arsenicals are worldwide environmental contaminants that affect molecular characteristics in biological systems and lead to genomic and epigenomic instability as well as epithelial mesenchymal transition (EMT). In this study, we aimed to investigate whether low levels of sodium arsenite (iAsIII) can influence EMT and genomic instability through microsatellite analysis. We have also determined epigenomic instability by investigating the methylation status of SEPT9 tumor marker in colorectal cancer (CRC) cell lines, Caco2 and HCT116, which were treated with iAsIII to assess IC50s. Short-term and long-term exposure to low concentrations (1 µM and 0.1 µM) of iAsIII in two separate experiments was implemented to analyze EMT, microsatellite status and the methylation pattern of SEPT9 promoter. As expected, after 20 days of exposure to iAsIII, the expression of CDH1 was significantly decreased while the expression of CDH2, FIB1 and VIM was increased in Caco2 and HCT116, a finding that confirmed EMT induction. However, there was no detectable alteration in the size of microsatellites. As for the methylation pattern, SEPT9 promoter was hypomethylated as a result of long-term exposure to 0.1 µM iAsIII in Caco2. Long-term exposure of HCT116 to both concentrations could induce hypomethylation of SEPT9 promoter. Our findings indicate no linkage between EMT induction and microsatellite status in iAsIII-treated CRC cell lines. For the first time, the current study has shown that the induction of EMT by iAsIII is linked with SEPT9 promoter hypomethylation in Caco2 and HCT116 in a concentration- and time-dependent pattern.