Identification of Differentially Expressed Genes in Human Colorectal Cancer Using RNASeq Data Validated on the Molecular Level with Real-Time PCR.

Colorectal cancer (CRC) is a prevalent cancer with high morbidity and mortality rates worldwide. Late diagnosis is a significant contributor to low survival rates in a minority of cases. The study aimed to perform a robust pipeline using integrated bioinformatics tools that will enable us to identify potential diagnostic and prognostic biomarkers for early detection of CRC by exploring differentially expressed genes (DEGs). In addition to, testing the capability of replacing chemotherapy with plant extract in CRC treatment by validating it using real-time PCR. RNA-seq data from cancerous and adjacent normal tissues were pre-processed and analyzed using various tools such as FastQC, Kallisto, DESeq@ R package, g:Profiler, GNEMANIA-CytoScape and CytoHubba, resulting in the identification of 1641 DEGs enriched in various signaling routes. MMP7, TCF21, and VEGFD were found to be promising diagnostic biomarkers for CRC. An in vitro experiment was conducted to examine the potential anticancer properties of 5-fluorouracile, Withania somnifera extract, and their combination. The extract was found to exhibit a positive trend in gene expression and potential therapeutic value by targeting the three genes; however, further trials are required to regulate the methylation promoter. Molecular docking tests supported the findings by revealing a stable ligand-receptor complex. In conclusion, the study's analysis workflow is precise and robust in identifying DEGs in CRC that may serve as biomarkers for diagnosis and treatment. Additionally, the identified DEGs can be used in future research with larger sample sizes to analyze CRC survival.

Telmisartan versus metformin in downregulating myostatin gene expression and enhancing insulin sensitivity in the skeletal muscles of type 2 diabetic rat model.

Objective: Telmisartan is an angiotensin receptor blocker (ARB) that specifically blocks angiotensin II type-1 receptors (AT1R). Telmisartan has been proven to have antidiabetic effects via a variety of mechanisms, and it can be utilized in some diabetic patients due to its dual benefit for hypertensive patients with type 2 DM (T2DM) and when the other oral antidiabetic medications are intolerable or contraindicated. However, its precise underlying hypoglycemic mechanism is still obscure. Aim of work: We sought to establish a link between telmisartan administration and myostatin expression in skeletal muscles of T2DM rat model as a potential hypoglycemic mechanism of telmisartan. Materials and Methods: 32 male albino rats were included in the study; 8 rats served as controls (group I). T2DM was inducted in the other 24 rats, which were then randomly subdivided into 3 groups (8 in each): (group II) the Diabetic group and (groups III and IV) which were treated with either telmisartan (8 mg/kg/day) or metformin (250 mg/kg/day) respectively via oral gavage for a 4-week period. Results: Telmisartan administration resulted in a significant improvement in OGTT, HOMA-IR, glucose uptake, and muscle mass/body ratios in Telmisartan group as compared to Diabetic group (p < 0.05). Additionally, telmisartan induced a significant boost in adiponectin and IL-10 serum levels with a substantial drop in TNF-α and IL-6 levels in Telmisartan group compared to diabetic rats (p < 0.05). Moreover, telmisartan significantly boosted SOD and GSH, and decreased MDA levels in the skeletal muscles of telmisartan group. Furthermore, a significant downregulation of myostatin and upregulation of insulin receptor, IRS-1, and IRS-3 genes in the skeletal muscles of Telmisartan group were also detected. Histologically, telmisartan attenuated the morphological damage in the skeletal muscle fibers compared to diabetic rats, as evidenced by a considerable decrease in the collagen deposition area percentage and a reduction in NF-kB expression in the muscle tissues of group III. Conclusion: Telmisartan administration dramatically reduced myostatin and NF-kB expressions in skeletal muscles, which improved insulin resistance and glucose uptake in these muscles, highlighting a novel antidiabetic mechanism of telmisartan in treating T2DM.

Long non-coding RNA maternally expressed gene 3, miR-125a-5p, CXCL13, and NF-kB in patients with immune thrombocytopenia.

The main aim of this study was to assess the expression level of circulating long non-coding RNA maternally expressed gene 3 (lncRNA-MEG3), microRNA (miR-125a-5P), the chemokine C-X-C motif ligand13 (CXCL13), and the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) in immune thrombocytopenia (ITP) cases and to study its relation to the disease severity and treatment response. This case-control study included 45 patients newly diagnosed as ITP and 45 healthy subjects. We assessed complete blood count, antinuclear antibodies, hepatitis B and C virus serology, lncRNA-MEG3, miR-125a-5P, and CXCL13 expression in serum by real-time PCR and NF-kb protein by ELISA. In ITP patients compared to control, lncRNA-MEG3 was significantly increased, and miRNA-125a-5P was decreased, and this was associated with higher CXCL13 and NF-kB levels (P < 0.001, for all).There was a significant negative correlation between platelet count and lncRNA-MEG3, CXCL13, and NF-kb, while a positive correlation with miR-125a-5p in ITP patients. Patients who responded to steroids had significantly higher miR-125a-5p (P = 0.016) and significantly lower lncRNA-MEG3 (P < 0.001), CXCL13 (P = 0.005), and NF-kb (p = 0.002). Based on the ROC curves, lncRNA-MEG3 displayed the highest area under the curve (AUC) in the identification of organ bleeding (AUC = 0.805), the response to steroids (AUC = 0.853), and the need for splenectomy (AUC = 0.75).

Prognostic significance of the genetic variant of lymphotoxin alpha (p.Thr60Asn) in egyptian patients with advanced hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide in terms of mortality, and susceptibility is attributed to genetic, lifestyle, and environmental factors. Lymphotoxin alpha (LTA) has a crucial role in communicating the lymphocytes with stromal cells and provoking cytotoxic effects on the cancer cells. There are no reports on the contribution of the LTA (c.179 C>A; p.Thr60Asn; rs1041981) gene polymorphism to HCC susceptibility. The main aim of this study is to investigate the association of LTA (c.179 C>A; p.Thr60Asn; rs1041981) variant with the HCC risk in the Egyptian population. METHODS: This case-control study included 317 participants (111 HCC patients, and 206 healthy controls). The LTA (c.179 C>A; p.Thr60Asn; rs1041981) polymorphism was assessed by tetra-primer amplification refractory mutation system polymerase chain reaction (T-ARMS-PCR) technique. RESULTS: The frequencies of the dominant and recessive models (CA + AA; AA) of the LTA (c.179 C>A; p.Thr60Asn; rs1041981) variant were statistically significant among HCC patients in comparison to controls (p = 0.01; p = 0.007; respectively). The A-allele of LTA (c.179 C>A; p.Thr60Asn; rs1041981) variant was statistically significant in HCC patients in comparison to controls (p ˂ 0.001). CONCLUSION: The LTA (c.179 C>A; p.Thr60Asn; rs1041981) polymorphism was independently associated with an increased risk for hepatocellular carcinoma in the Egyptian population.

Comparative study on effect of mesenchymal stem cells and endothelial progenitor cells on treatment of experimental CCL4-induced liver fibrosis.

BACKGROUND: We speculated impacts of BM-MSCs and UC-EPCs on reversal of hepatic injury induced by carbon tetrachloride (CCl4). Fifty adult rats were divided into five groups: control group, CCl4A group, CCl4B group, CCl4/BM-MSCs group and CCl4/UC-EPCs group. Blood samples were driven to measure concentration of albumin and ALT. Quantitative expression of HGF, TGF-ß, MMP-2, and VEGF were assessed by PCR. Histological and immunohistochemistry examination of the liver tissue were performed. RESULTS: There was elevating albumin (p < .05) and reducing ALT (p < .05) concentrations in groups treated with BM-MSCs and UC-EPCs compared to untreated CCL4A&B groups. UC-EPCs treated group have significantly higher MMP-2 and VEGF (p < .01) genes expression than BM-MSCs treated group. Furthermore, UC-EPCs were more valuable than BMMSCs in increasing gene expression of HGF (p < .05) and immunohistochemistry of α-SMA and Ki-67 (p < .01). BM-MSCs have significantly lower TGF-ß (p < .00) compared to UC-EPCs. CONCLUSION: This study highlighted on liver regeneration role of both UC-EPCs and BM-MSCs in liver fibrosis.

Association between long noncoding RNA taurine-upregulated gene 1 and microRNA-377 in vitiligo.

BACKGROUND: Taurine-upregulated gene 1 (TUG1) is one of the long noncoding RNAs (lncRNAs) that plays a role in melanogenesis. MicroRNA-377 (miRNA-377) is a conserved noncoding RNA that regulates angiogenesis and promotes oxidative stress. Peroxisome proliferator-activated receptors (PPARs) are components of the nuclear hormone receptor superfamily. PPAR-γ activators stimulate melanogenesis. Interleukin (IL)-17 has been implicated in the pathogenesis of several immunological diseases. This work aimed at detecting the expression levels of lncRNA TUG1, miRNA-377, PPAR-γ, and IL-17 among vitiligo subjects and to investigate their possible role in the pathogenesis of vitiligo. METHODS: This study was conducted on 30 healthy controls and 30 vitiligo patients. LncRNA TUG1 and miRNA-377 were detected in serum by real-time polymerase chain reaction (PCR). Also, expressions of PPAR-γ and IL-17 were assessed in tissue by real-time PCR. RESULTS: LncRNA TUG1 and PPAR-γ levels were significantly downregulated in the vitiligo group compared with the control group. On the other hand, miRNA-377 and IL-17 were significantly upregulated in the vitiligo group compared with the control group. CONCLUSION: This study demonstrated the dysregulated expressions of lncRNA TUG1 and miRNA-377 in patients with vitiligo suggesting that both contributed to the pathogenesis of vitiligo that might be through PPAR-γ downregulation and IL-17 upregulation.

Can Micro RNA-24 Affect the Cardiovascular Morbidity in Systemic Lupus Erythematosus by Targeting YKL-40?

Background: Systemic lupus erythematosus (SLE) is an autoimmune disease with inflammatory nature. One of the leading causes of death in SLE patients is cardiovascular (CVS) morbidity. MiRNA-24 is highly expressed in vascular endothelial cells (VECs). This dysregulated expression pattern is associated with dysfunction or even damage of VECs and leads to the occurrence of cardiovascular diseases. YKL- 40 is an inflammatory glycoprotein involved in the pathogenesis of endothelial dysfunction and thereby atherosclerosis. In this work, we aimed at illustrating the possible role of miR-24 and its target YKL-40 in the pathogenesis of the CVS morbidity associated with SLE. Methods: This work was conducted on 40 SLE patients and 40 healthy controls. Quantitative real-time PCR (qPCR) was done to estimate the expression level of miRNA-24 in serum. In addition, we measured the serum level of YKL-40 using ELISA. Results: miR-24-fold change was found to be down-regulated, whereas serum YKL- 40 was up-regulated among SLE patients with observed significant and negative correlation between the two parameters. Conclusion: Our study provided an insight about the role of miR-24 and its target serum YKL-40 protein in the development of SLE-related inflammation and atherosclerosis.

Support for increased cardiovascular risk in non-segmental vitiligo among Egyptians: A hospital-based, case-control study.

BACKGROUND: Data have been accumulating in the past few years that identify vitiligo as a disorder with systemic implications. RESULTS AND METHODS: In this hospital-based, cross-sectional, case-control study, 50 patients with non-segmental vitiligo and 50 age- and sex-matched controls underwent analysis of serum lipid profile, oxidative stress biomarkers and carotid duplex. Hydrogen peroxide (H2 O2 ) and malondialdehyde (MDA) were significantly higher in patients than controls (p-value < .001, <.001, respectively); on the other hand, total antioxidant capacity (TAC) was significantly lower in patients than controls (p-value = .001). A significantly higher percentage of patients had hypercholesterolemia and borderline high, high or very high levels of LDL-C, compared to controls (p-value = .001 and .001, respectively). Atherosclerotic plaques and increased common carotid intima media thickness were significantly detected in patients versus controls. DISCUSSION: Results of the present study suggest that a subset of patients with vitiligo are at a higher risk of developing dyslipidemia and atherosclerosis, which might increase their future risk for the development of cardiovascular disease. Confirmation of these findings would subsequently influence investigative and the treatment strategies in the management plan of vitiligo patients in the near future. SIGNIFICANCE: Vitiligo patients might be at a higher risk of developing dyslipidemia and atherosclerosis, which might increase their risk for the development of cardiovascular disease necessitating prophylactic measures to improve prognosis. Our results might influence the investigative and treatment strategies in the management plan of vitiligo patients in the near future.

miRNA-101-1 and miRNA-221 expressions and their polymorphisms as biomarkers for early diagnosis of hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) is the fifth most common malignant tumor with an increasing incidence. Hepatitis C virus (HCV) is one of the major risk factors that lead to HCC development. MicroRNAs are conserved non-coding RNAs which regulate gene expression at the posttranscriptional level. They have been recently identified as important regulators that affect carcinogenesis. Of these miRNAs, are miR-221 and miR-101-1, which their aberrant expressions have been reported to play an important role in HCC. PATIENTS AND METHODS: In this study, we investigated the association between miR-221 and miR-101-1 polymorphisms and their expressions and the early prediction of HCC in HCV infected patients. Quantitative real-time PCR (qPCR) was done to estimate the expression levels of miRNA-221 and miRNA-101-1 in serum. To detect the genotyping of miR-221 and miR-101-1 related SNPs, DNA was extracted. Then, genotyping was performed using real-time PCR. RESULTS: We found that rs7536540 polymorphism in miR-101-1 is significantly associated with development of HCC. In addition, our results showed no significant association between rs17084733 polymorphism in miR-221 and HCC occurrence. We confirmed the upregulation of miR-221 and the downregulation of miR-101-1 in HCC. As regards HCV patients, miR-221and miR-101-1 were found to be upregulated. CONCLUSION: Both miR-221 and miR-101-1 expression levels may be useful as noninvasive diagnostic biomarkers for early prediction of HCC among HCV patients.