MTHFR-Ala222Val and male infertility: a study in Iranian men, an updated meta-analysis and an in silico-analysis

AbstractCanine and human bladder cancer present several similar anatomical, morphological and molecular characteristics and dogs can be considered a model for human bladder cancer. However, the veterinary literature lacks information regarding cross validation analysis between human and canine large-scale data. Therefore, this research aimed to perform a meta-analysis of the previous canine literature on bladder cancer, identifying genes and protein previously evaluated in these studies. Besides that, we also performed a cross validation of the canine transcriptome data and the human data from The Cancer Genome Atlas (TCGA) to identify potential markers for both species. It was performed a meta-analysis using the following indexing terms “bladder” AND “carcinoma” AND “dog” in different international databases and 385 manuscripts were identified in our initial search. Then, several inclusion criteria were applied and only 25 studies met these criteria. Among these studies, five presented transcriptome data and 20 evaluated only isolated genes or proteins.Regarding the studies involving isolated protein analysis, HER-2 protein was the most studied (3/20), followed by TAG-72 (2/20), COX-2 (2/2), Survivin (2/2) and CK7 (2/2). Regarding the cross-validation analysis of human and canine transcriptome data, we identified 35 deregulated genes, including ERBB2, TP53, EGFR and E2F2. Our results demonstrated that the previous canine literature on bladder cancer was focused on the evaluation of isolated markers with no association with patient’s survival. Besides that, the lack of information regarding tumor muscle-invasion can be considered an important limitation when comparing human and canine bladder tumors. Our in-silico analysis involving canine and human transcriptome data provided several genes with potential to be markers for both human and canine bladder tumors and these genes should be considered for future studies on canine bladder cancer.

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A Comparative Meta-Analysis and in silico Analysis of Differentially Expressed Genes and Proteins in Canine and Human Bladder Cancer

Frontiers in Veterinary Science ◽

10.3389/fvets.2020.558978 ◽

2020 ◽

Vol 7 ◽

Author(s):

Victoria Vitti Gambim ◽

Renee Laufer-Amorim ◽

Ricardo Henrique Fonseca Alves ◽

Valeria Grieco ◽

Carlos Eduardo Fonseca-Alves

Keyword(s):

Bladder Cancer ◽

Differentially Expressed Genes ◽

In Silico ◽

Meta Analysis ◽

In Silico Analysis ◽

Differentially Expressed ◽

Human Bladder Cancer ◽

Human Bladder ◽

Silico Analysis

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The associations between Toll-like receptor 4 gene polymorphisms and hepatitis C virus infection: a systematic review and meta-analysis

Bioscience Reports ◽

10.1042/bsr20182470 ◽

2019 ◽

Vol 39 (2) ◽

Cited By ~ 3

Author(s):

Narttaya Chaiwiang ◽

Teera Poyomtip

Keyword(s):

Hepatocellular Carcinoma ◽

Systematic Review ◽

Hepatitis C Virus ◽

Hepatitis C ◽

In Silico ◽

Meta Analysis ◽

In Silico Analysis ◽

Hcv Infection ◽

Toll Like Receptor ◽

Silico Analysis

Abstract Background and objective: The hepatitis C virus (HCV) is able to cause a life-threatening disease relating to lethal hepatocellular carcinoma. Previous, Toll-like receptor polymorphisms were proposed as promising biomarker for HCV-related hepatocellular carcinoma and disease progression. This study aimed to summarize the association of TLR4 polymorphisms and HCV infection through meta-analysis. Methods: We applied a systematic review and meta-analysis performed by using PubMed, EMBASE and Web of Science searches. The Modified Newcastle-Ottawa scale was used for quality assessment. The odd-ratio (OR) and 95% confidence interval (CI) were calculated to assess the association. In silico analysis was applied for proposing the function as microRNA (miRNA) of non-coding polymorphism. Finally, the miRNA target was predicted and annotated to suggest the possible relationship between polymorphism and HCV infection. Results: Our meta-analysis incorporated seven studies involving rs4986791, rs4986790 and rs2149356. No association exists between rs4986791 and HCV infection. However, the heterozygous model (AG vs GG) of rs4986790 significantly associates with HCV infection (OR = 0.33, 95% CI = 0.21–0.49, P<0.0001). Moreover, the rs2149356 TG genotype also associates with HCV infection in the over-dominant model (TG vs TT+TG: OR = 0.54, 95% CI = 0.40–0.75). In silico analysis of rs2149356G allele showed that this mutation is siRNA, which targets the set of genes, especially in the autophagy pathway. Conclusion: We demonstrated that rs4986790 and rs2149356 are associated with HCV infection.

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In silico analysis of candidate proteins sharing homology with Streptococcus agalactiae proteins and their role in male infertility

Systems Biology in Reproductive Medicine ◽

10.1080/19396368.2016.1243741 ◽

2016 ◽

Vol 63 (1) ◽

pp. 15-28 ◽

Cited By ~ 4

Author(s):

Rajeshwari Parida ◽

Luna Samanta

Keyword(s):

Male Infertility ◽

Streptococcus Agalactiae ◽

In Silico ◽

In Silico Analysis ◽

Silico Analysis

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TP73 G4C14-A4T14 polymorphism and cancer susceptibility: evidence from 36 case–control studies

Bioscience Reports ◽

10.1042/bsr20181452 ◽

2018 ◽

Vol 38 (6) ◽

Cited By ~ 4

Author(s):

Jialin Meng ◽

Shuo Wang ◽

Meng Zhang ◽

Song Fan ◽

Li Zhang ◽

...

Keyword(s):

Colorectal Cancer ◽

Cervical Cancer ◽

In Silico ◽

Cancer Susceptibility ◽

Meta Analysis ◽

In Silico Analysis ◽

Case Control ◽

Genetic Models ◽

Case Control Studies ◽

Silico Analysis

G4C14-A4T14 polymorphism of TP73 gene has been reported with a potential association in cancer risks through affected cell homeostasis; however the results were not consistent. We performed a comprehensive meta-analysis to explore the associations between G4C14-A4T14 polymorphism and cancer susceptibility. Extensive retrieve was performed in PubMed, EMBASE, Google Scholar, Web of Science, Wanfang database and CNKI database up to May 20, 2018. Odds ratios (ORs) and 95% confidence intervals (CIs) were conducted to evaluate the overall strength of the associations in five genetic models, as well as in subgroup analyses. Q-test, false-positive report probability analysis and trial sequential analysis, Egger’s test and Begg’s funnel plot were applied to evaluate the robustness of the results. In silico analysis was managed to demonstrate the relationship of TP73 expression correlated with cancer tissues. Finally, 36 case–control studies with a total of 9493 cancer cases and 13,157 healthy controls were enrolled into the meta-analysis. The pooled results present a significantly higher risk of G4C14-A4T14 polymorphism in all the five genetic models, as well as in the subgroups of Caucasian, cervical cancer, colorectal cancer, H-B subgroup and comfort to Hardy–Weinberg equilibrium subgroup. In silico analysis revealed that the expression of TP73 in cervical cancer tissue is higher than it in corresponding normal tissue, as well as in cervical cancer. All in all, TP73 G4C14-A4T14 polymorphism causes an upgrade cancer risk, especially in Caucasian population. G4C14-A4T14 polymorphism might be a potential biomarker for judging the tumorigenesis of cervical cancer and colorectal cancer.

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