Unraveling the link between PTBP1 and severe asthma through machine learning and association rule mining method.

Severe asthma is a chronic inflammatory airway disease with great therapeutic challenges. Understanding the genetic and molecular mechanisms of severe asthma may help identify therapeutic strategies for this complex condition. RNA expression data were analyzed using a combination of artificial intelligence methods to identify novel genes related to severe asthma. Through the ANOVA feature selection approach, 100 candidate genes were selected among 54,715 mRNAs in blood samples of patients with severe asthmatic and healthy groups. A deep learning model was used to validate the significance of the candidate genes. The accuracy, F1-score, AUC-ROC, and precision of the 100 genes were 83%, 0.86, 0.89, and 0.9, respectively. To discover hidden associations among selected genes, association rule mining was applied. The top 20 genes including the PTBP1, RAB11FIP3, APH1A, and MYD88 were recognized as the most frequent items among severe asthma association rules. The PTBP1 was found to be the most frequent gene associated with severe asthma among those 20 genes. PTBP1 was the gene most frequently associated with severe asthma among candidate genes. Identification of master genes involved in the initiation and development of asthma can offer novel targets for its diagnosis, prognosis, and targeted-signaling therapy.

Investigation and confirmation of differentially expressed miRNAs, as well as target gene prediction in papillary thyroid cancer, with a special emphasis on the autophagy signaling pathway.

Papillary thyroid carcinoma (PTC) is the most common endocrine cancer. However, the role of biomechanics in the development and progression of PTC is obscure. The microarray dataset GSE104005 was examined to identify important microRNAs (miRNAs or miRs) and their probable roles in the carcinogenesis of PTC. The gene expression omnibus (GEO) database was used to obtain the data. R was used to access the differentially expressed miRNAs (DEMs) and genes (DEGs). The multiMiR software was used to predict DEM targets. To validate the top DEMs and DEGs, thirty tissue samples were obtained from PTC patients who had their thyroids removed and compared with 30 normal samples. The total RNA content of the tumor and corresponding non-tumoral adjacent samples were purified and converted to cDNA. Expression levels of top dysregulated miRNAs and their target and predicted DEG were evaluated using the RT-qPCR method. miR-182 and miR-183 were top upregulated miRs and miR-30d was the most downregulated miR among DEMs. Furthermore, FOXO1 which was shown to be targeted by aforementioned miRNAs, was the most downregulated genes among other DEGs. 10 hub nodes were detected by PPI construction. PTEN was the hub node with highest score. The in vitro gene expression analysis was also showed the same expression pattern in tissues. Significant increase in miR-182-5p and miR-183-5p expressions, as well as a significant decrease in FOXO1 and miR-30d-5p expressions, suggest that PTC cells may tend to preserve their autophagy capability.

Upregulation of miR-142 in papillary thyroid carcinoma tissues: a report based on in silico and in vitro analysis.

Papillary thyroid carcinoma (PTC) accounts for approximately 80% of all human thyroid malignancies. Recently, there has been a dramatic rise in the prevalence of thyroid cancer all over the globe. Through analysis of the GEO database, GSE104005, the authors of the current research were able to determine the differential expression of microRNAs (DEMs) as well as their target genes. Real-time PCR was used on a total of 40 samples, 40 of which were from PTC samples and 40 from normal tissues, in order to validate the discovered DEMs and the genes. Gene Ontology (GO) categories were identified, and KEGG was used to conduct pathway enrichment analysis. The multiMiR R package was used to predict target genes of DEMs. Mir-142 was found to be overexpressed in PTC samples, as compared to normal tissues, and this was validated by the identification and validation. In addition, metal ion binding and the cellular response to metal ions were identified as essential pathways in the carcinogenesis of PTC. This demonstrates their significance in the development of this malignancy. The results of our research will serve as the foundation for further research in the area of miRNA-based cancer treatment.

Terminalia Catappa Extract (TCE) Reduces Proliferation of Lung and Breast Cancer Cell by Modulating miR-21 and miR-34a Expressions.

BACKGROUND: After cardiovascular illness, cancer is the one of the main and second cause of death in the worldwide. Despite significant advances in this field, low survival, drug resistance, and side effects of chemotherapy remain an unsolved problem. Due to the high mortality rate among cancer patients, finding the new substance to treatment with low side effects is important. Previous studies have been informed that positive effects of herbal medicines on cancer patients, which are very efficient in the treatment of cancer. METHODS: In this study, the antitumor effect of ethanolic Terminalia catappa leaf extract (TCE) on MCF-7, MDA-231, and A549 cell lines was examined. For this reason, the effects of TCE on cell migration, gene expression, and growth were investigated by scratch, test, real-time PCR (qPCR) qPCR, and MTT tests respectively. RESULTS: As a reported by the MTT outcomes, TCE significantly decreased the viability of A549, MCF-7, and MDA-231 cells (P < 0.05).  Moreover, genes expression patterns that are related to proliferation (miR-21, miR-34a), migration (MMP-13, Vimentin), and apoptosis (Cas-3, Cas-8, Cas-9, Bcl-2, Bax) also have changed significantly after treatment with TCE. Also, in the A549 cell line, Bax (p value: 0.029), Cas-9 (p value: 0.00023), miR-34a (p value: 0.031), Bcl-2 (p value: 0.0076), MMP-13 (p value: 0.041), Cas-3 (p value: 0.00051) and in MCF-7 cell line Bax (p value: 0.0004), Cas-3 (p value: 0.0003), Cas-9(p value: 0.037), miR-34a (p value: 0.005), Bcl-2(pvalue:0.0007), mir-21(p value:0.016), MMP-13(p value: 0.011) and in MDA-231 cell line Bax(p value<0.0001), Cas-3(p value: 0.003), Cas-9(p value: 0.0004). mir-34a (p value:0.0019), Bcl-2(p value:0.0023), MMP-13(p value: 0.032) have significantly changed compare to control group. CONCLUSION: The outcomes of this research determined that T. Catappa might be a potential source of antitumor compounds and could be a candidate for further research.
.

CpG Islands Methylation Analysis of CDH11, EphA5, and HS3ST2 Genes in Gastric Adenocarcinoma Patients.

PURPOSE: Gastric cancer is an aggressive disease which is the fourth prevalent malignancy in the world. Beside the genetic factors, epigenetic alterations such as promoter CpG island hyper methylation are involved in the emergence of gastric cancer. Herein, we investigated the methylation status of CDH11, EphA5, and HS3ST2 genes in patients with and without gastric adenocarcinoma for the first time. METHODS: In the study 40 paraffin-embedded tissue sections from gastric adenocarcinoma patients and 40 specimens from patients with functional dyspepsia were taken. DNA extraction was performed using a modified salting out method. Epizen DNA methylation kit was used to the bisulfite DNA conversion. The methylation status of CDH11, EphA5, and HS3ST2 genes were analyzed by methylation-specific PCR (MSP) technique. RESULTS: Among the 80 specimens, 71 DNA samples were achieved (34 gastric adenocarcinoma patients and 37 control patients). The results showed that CDH11, EphA5, and HS3ST2 genes are methylated in 28 (82.45%), 19 (55.88%), and 26 (76.47%) of 34 DNA samples from gastric adenocarcinoma patients, respectively, whereas, these genes are methylated in 7 (18.91%), 9 (24.32%) and 7 (18.91%) of 37 samples from noncancerous patients, respectively. Statistical analyses using a chi-squared test showed that there is a statistically significant difference in methylation level of CDH11, EphA5, and HS3ST2 genes between gastric cancer and uncancerous patients (p < 0.05). CONCLUSION: To the best of our knowledge, this is the first report on methylation of CDH11, EphA5, and HS3ST2 promoters' in gastric adenocarcinoma patients using MSP. Identification of novel cancer-related molecular mechanisms can be useful in detection of new treatment strategies.

Evaluating pre- and post-operation plasma miRNAs of papillary thyroid carcinoma (PTC) patients in comparison to benign nodules.

BACKGROUND: Thyroid cancer is the most common endocrinology cancer that its incidence has increased in recent decades. miRNAs are new biomarkers in recent studies in the diagnosis and follow-up of these patients. METHODS: Blood and thyroid tissue samples were obtained from two groups of included patients (PTC and benign nodules), pre- and post-operation. miRNAs were extracted from these plasma samples and were measured quantitatively. After cDNA synthesis, qPCR was carried out. Then tissue samples were investigated, and their relation to miR expression was studied. These results were analyzed by paired- and independent samples t-test, and non-parametric tests. RESULTS: miR-222 and miR-181a declined in PTC patients before and after surgery, significantly (P < 0.001 for both groups), with no significant difference in control group before and after surgery (P = 0.61 for miR-222 and P = 0.06 for miR-181a). The difference between the two groups, pre-and post-operation, was statistically significant (P = 0.01 for miR-222 and P < 0.001 for miR-181a). Comparing case and control groups, pre- and post-operatively, yielded no significant difference, in miR-155-5p levels (P = 0.61 and P = 0.53, respectively). Comparing PTC and control groups before surgery showed a significant difference (P = 0.01), while no significant difference was observed comparing them after surgery, in miR146-a (P = 0.27). Our results depicted a higher miR-155-5p and miR-146a expression before surgery than after it (P < 0.001 in both groups, for both miRs). We found a significant relationship between miR-222 and BRAFV600E mutation and significantly higher levels of miR-181a with increasing tumor size in PTC patients. CONCLUSION: miR-222 showed overexpression in all PTC cases, which is indicative of a relation between miRNA and PTC. Also, comparing miR-181 and miR-146a showed a significant difference between cancerous and benign cases. miR-155-5p as an inflammatory factor, showed no significant changes, comparing two groups.

Different expression of Micro RNA-126, 133a and 145 in aorta and saphenous vein samples of patients undergoing coronary artery bypass graft surgery.

Introduction: microRNAs (miRNAs) are highly conserved, noncoding RNA molecules that regulate gene expression on the post-transcriptional level. Some evidence indicates that microRNAs dysfunction plays a crucial role in human disease development. The role of microRNAs in cardiac growth, hypertrophy, heart failure, cardiovascular complications in diabetes and many other hearth conditions are demonstrated. In this study we aimed to evaluate the expression of six microRNAs (mir-100, mir-126, mir-127, mir-133a, mir-133b and mir-145) that have been shown to overexpress in aortic and carotid plaques. Methods: Thirty Coronary Artery Disease patients who underwent elective coronary artery bypass graft surgery were enrolled in the study. The expression patterns of six miRNAs (mir-100, mir-126, mir-127, mir-133a, mir-133b, and mir-145) were examined in 30 patients of whom we obtained aorta and saphenous vein samples. Results: In three miRNAs, mir-100, mir-127 and mir-133b, we did not obtain expression data from real-time experiments. We found that the expression level of mir-126, mir-133a and mir145 were lower in aorta in comparison with saphenous vein. Mir-126 was highly expressed in saphenous vein samples (13.8±1.1) when compared with aorta samples (20.2±1.1), although mir133a was highly expressed in saphenous vein samples (16.1±0.5) when compared with the aorta (17.9±1.5). Expression of mir-145 saphenous vein samples was also dramatically higher than aorta (7.2±0.5 versus 10.8±0.6) that was statistically significant (P<0.05). Conclusion: Understanding the role of miRNAs in cardiovascular physiology and diseases might suggest miRNA- based therapeutic methods in the management of coronary artery disease.

Reduced Levels of miR-28 and miR-200a Act as Predictor Biomarkers of Aggressive Clinicopathological Characteristics in Gastric Cancer Patients.

BACKGROUND: MicroRNAs (miRNAs) play critical roles in different pathological processes including cancer development and progression. To find novel molecular diagnostic and prognostic markers and promising therapeutic tools for gastric cancer (GC), we aimed to investigate the relationship of the expression levels of miR-28-5p or miR-200a-3p with the clinicopathological criteria and to explore their impacts on the progression of human GC. MATERIALS AND METHODS: Quantitative RT-PCR was performed to analyze miR-28 and miR-200a expression in 60 GC and 60 non-GC tissue samples. RESULT: Our results revealed that the expressions of miR-200a and miR-28 were significantly downregulated in GC in comparison with non- GC tissues. Tumors with low miR-28 expression had larger tumor size, more advanced histological grade, and a higher incidence of lymph node and distal metastasis than the tumors with high miR-28 expressions. Furthermore, receiver operating characteristic (ROC) analyses demonstrate that the expression of miR-28 is a predictive biomarker allows predicting the histological grade, tumor size, and occurrence of nodal and distal metastases. We also found a significant inverse association between miR-200a expression and the rate of lymph node metastasis (p = 0.010, r = -0.334). CONCLUSION: Our findings suggest that the miR-28 and miR-200a have tumor-suppressor functions and may be considered as potential biomarkers for gastric cancer diagnosis and prognosis.

A new insight on reciprocal relationship between microRNA expression and epigenetic modifications in human lung cancer.

Lung cancer stands among the leading causes of cancer-related death in the world. Although the molecular network implicated in lung cancer development is extensively revealed, the mortality rate is only slightly improved. MicroRNAs are small, endogenous single-stranded evolutionary conserved non-coding RNAs which involve in a wide variety of biological processes including cell growth, proliferation, metabolism, and differentiation. MicroRNAs, as novel biomarkers, have multiple functions in normal lung tissue development, and aberrant expression profiles of certain microRNAs could induce lung tumorigenesis. Similar to that of protein-coding genes, microRNA expression and function are regulated by multiple factors as well as the epigenetic network including DNA methylation and histone modification mechanisms. Furthermore, microRNAs can themselves regulate key enzymes which drive epigenetic modifications and have a pivotal effect on the cell biology. In this review, we will look into the regulatory loop linkage between microRNA expression and epigenetic modifications, and then, we will discuss the effects of epigenetics on the miRNome, as well as the role of epi-microRNAs in controlling the epigenome in human lung cancer. Better knowledge of reciprocal connection between microRNAs and epigenome will help to develop novel microRNA-orientated diagnostic, prognostic and therapeutic strategies related to human lung cancer in future.

Effect of Alpha-Hederin, the active constituent of Nigella sativa, on miRNA-126, IL-13 mRNA levels and inflammation of lungs in ovalbumin-sensitized male rats.

OBJECTIVE: In previous studies the therapeutic effects of Nigella sativa have been demonstrated on asthmatic animals. In the present study, the preventive effect of single dose of alpha-hederin, its active constituent, has been evaluated on lung inflammation and some inflammatory mediators in lungs of ovalbumin sensitized rat in order to elicit its mechanism. MATERIALS AND METHODS: Forty rats were randomly grouped in 4 groups; control (C), sensitized (S), sensitized pretreated groups with thymoquinone (3 mg/kg i.p., S+TQ) and alpha-hederin (0.02 mg/kg i.p., S+AH). Levels of IL-13 mRNA and miRNA-126 in lung tissue and its pathological changes in each group were assessed. RESULTS: Elevated levels of miRNA-126, IL-13 mRNA and pathological changes were observed in the sensitized group compared to the control group (p<0.001 to p<0.05). All of these factors were significantly reduced in S+TQ and S+AH groups in comparison to S group (p<0.001 to p<0.05). Although alpha-hederin decreased the levels of miRNA-126, IL-13 mRNA and pathological changes in comparison with thymoquinone, the results were statistically not significant. CONCLUSION: The results suggested that alpha-hederin had preventive effect on sensitized rats like thymoquinone. It may intervene in miRNA-126 expression, which consequently could interfere with IL-13 secretion pathway leading to a reduction in inflammatory responses.

Alteration in Inflammation-related miR-146a Expression in NF-KB Signaling Pathway in Diabetic Rat Hippocampus.

PURPOSE: The purpose of the present study is to evaluate the expression of miR-146a gene, its adaptor genes (TRAF6, NF-KB, and IRAK1), and possible changes in the cellular signaling pathway in diabetic hippocampus tissue. METHODS: Male Sprague-Dawley rats are randomly selected and divided into control and diabetic (n=6) groups. Diabetes induced by the single-dose injection of nicotinamide [110 mg/kg, (i.p.)], 15 min before streptozotocin (50 mg/kg; i.p.) in 12-h fasted rats. The rats are kept at the laboratory for two months. After anaesthetization, hippocampus of the rats was removed in order to measure the expression of miR-146a, NFK-B, IRAK1, and TRAF6 genes using real-time PCR and activity of NF-KB as well as amount of apoptosis rate using ELISA. RESULTS: The results indicated a reduction in expression of miR-146a and an increase in expression of IRAK1, NF-KB, and TRAF6 genes in the hippocampus of diabetic rats compared to control. Also it reveals an increase in the activity of NF-KB and apoptosis rate in the hippocampus of diabetic rats. CONCLUSION: Our results report the probability that reduction of miR-146a expression in the negative feedback loop between miR-146a and NF-KB increases NF-kB expression and thus intensifies inflammation and apoptosis in hippocampus.

Effect of α-Hederin on IL-2 and IL-17 mRNA and miRNA-133a Levels in Lungs of Ovalbumin-Sensitized Male Rats.

α-hederin, a saponin that is a major constituent of English Ivy (Hedera helix) is effective in the treatment of asthma. In the present study, the effect of α-hederin on lung tissue pathology and the levels of the inflammatory mediators; IL-2 mRNA, IL-17 mRNA, and MicroRNAs (miRNA)-133a was evaluated in a rat ovalbumin (OVA)-sensitized model of asthma. Rats were divided randomly into control (C), OVA-sensitized (S), OVA-sensitized pretreated with the antioxidant, thymoquinone (3 mg/kg, S + TQ) or OVA-sensitized pretreated with α-hederin (0.02 mg/kg, S + AH) groups. Levels of IL-2 and IL-17 mRNA were higher in the OVA-sensitized group than controls while the level of miRNA-133a gene expression was lower. IL-2 mRNA and miRNA-133a gene expression in the S + TQ group was higher than in the control and OVA-sensitized groups while the level of IL-17 mRNA in the S + TQ group was lower than in the OVA-sensitized group. Pretreatment with α-hederin decreased IL-17 mRNA levels and increased miRNA-133a gene expression compared with OVA-sensitized animals. All pathological changes in pretreated groups were lower than the OVA-sensitized group. These results showed a beneficial effect of α-hederin in OVA-sensitized rats, suggesting that α-hederin affects the IL-2 and IL-17 secretion pathways, altering miRNA-133a expression.

A signature of microRNA-155 in the pathogenesis of diabetic complications

The current study was designed to explore the potential involvement of miR-155 in the pathogenesis of diabetes complications. Male rats were divided into control and diabetic groups (n = 6). Type 2 diabetes was induced by a single-dose injection of nicotinamide (110 mg/kg; intraperitoneal (i.p.)), 15 min before injection of streptozotocin (STZ; 50 mg/kg; i.p.) in 12-h fasted rats. Two months after induction of diabetes, the rats were sacrificed for subsequent measurements. The nuclear factor kappa B (NF-κB) activity was higher in diabetic peripheral blood mononuclear cells (PBMCs), aorta, heart, kidney, liver, and sciatic nerve, than the control counterparts. Also, apoptosis rate was increased in these tissues, except the aorta. NF-κB messenger RNA (mRNA) expression level was higher in the kidney, heart, PBMCs, and sciatic nerve of diabetic rats than their control counterparts. Except the liver, the miR-155 expression level was significantly decreased in diabetic kidney, heart, aorta, PBMCs, and sciatic nerve versus the controls. Moreover, the expression of miR-155 was negatively correlated with NF-κB activity and apoptosis rate. These results suggest that changes in the expression of miR-155 may participate in the pathogenesis of diabetes-related complications, but causal relationship between miR-155 dysregulation and diabetic complications is unknown

A signature of microRNA-155 in the pathogenesis of diabetic complications.

The current study was designed to explore the potential involvement of miR-155 in the pathogenesis of diabetes complications. Male rats were divided into control and diabetic groups (n = 6). Type 2 diabetes was induced by a single-dose injection of nicotinamide (110 mg/kg; intraperitoneal (i.p.)), 15 min before injection of streptozotocin (STZ; 50 mg/kg; i.p.) in 12-h fasted rats. Two months after induction of diabetes, the rats were sacrificed for subsequent measurements. The nuclear factor kappa B (NF-κB) activity was higher in diabetic peripheral blood mononuclear cells (PBMCs), aorta, heart, kidney, liver, and sciatic nerve, than the control counterparts. Also, apoptosis rate was increased in these tissues, except the aorta. NF-κB messenger RNA (mRNA) expression level was higher in the kidney, heart, PBMCs, and sciatic nerve of diabetic rats than their control counterparts. Except the liver, the miR-155 expression level was significantly decreased in diabetic kidney, heart, aorta, PBMCs, and sciatic nerve versus the controls. Moreover, the expression of miR-155 was negatively correlated with NF-κB activity and apoptosis rate. These results suggest that changes in the expression of miR-155 may participate in the pathogenesis of diabetes-related complications, but causal relationship between miR-155 dysregulation and diabetic complications is unknown.

The Effect of Regular Moderate Exercise on miRNA-192 Expression Changes in Kidney of Streptozotocin-Induced Diabetic Male Rats.

PURPOSE: The purpose of this study was to investigate the regular moderate exercise effect on the miR-192 expression changes in kidney of Streptozotocin- induced diabetic rats. METHODS: Forty adult male Wistar rats were divided into four groups of 10, including Sedentary Control group, Healthy 60 days Exercise group, diabetic group and Diabetic 60 days Exercise. Diabetes was induced by injection of 60 mg/kg Streptozotocin and after 48 hour blood glucose levels higher than 250 mg/dl were included to diabetic rats. After 48 hour of induction diabetes, exercise protocol was begun. Animals performed 5 days of consecutive treadmill exercise (60 min/day) with 22 m/min speeds for 60 days. Kidney of the rats has removed and MicroRNA was extracted from kidney using miRCURY(TM) RNA isolation kit. RESULTS: Exercise upregulated miR-192 expression level significantly in the kidney of diabetic rats in comparison to healthy group. There is not any significant change in miR-192 expression in diabetic 60 days exercise compared to control group. CONCLUSION: These results may indicate that exercise can help to prevent the progression of diabetic nephropathy.

Upregulation of microRNA-146a was not accompanied by downregulation of pro-inflammatory markers in diabetic kidney.

The present study was designed to evaluate whether microRNA-146a and its adapter proteins (TRAF6 and IRAK1) are involved in the pathogenesis of diabetes-induced kidney damage. Male Sprague-Dawley rats were divided into control and diabetic groups (n = 6 in each). Diabetes was induced by injection of streptozotocin (55 mg/kg; i.p.) in 12 h fasted rats. Diabetic kidney damage was diagnosed by renal hypertrophy, thickened glomerular basement membrane, widened filtration slits, mesangial expansion, as well as by elevated levels of blood urea and creatinine in diabetic rats 2 months after induction of diabetes. While the expression of NF-κB mRNA and miR-146a were increased in diabetic kidney compared to the sham controls (p < 0.01 for both comparisons), the mRNA levels of IRAK1 and TRAF6 did not statistically reduce. The NF-κB activity and the concentrations of TNF-α, IL-6 and IL-1ß in the kidney of diabetic rats were higher than the kidney of controls (p < 0.05 for TNF-α and NF-κB; p < 0.01 for IL-6 and IL-1ß). Our results indicate that the upregulation of miR-146a was not accompanied by downregulation of inflammatory mediators in diabetic kidney. It is possible that a defect in the miR-146a-mediated negative loop provides a situation for sustained activation of NF-κB and its targets to promote cells toward abnormalities.