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Drug Metabolism and Personalized Therapy Mar 2018The carboxylesterase 1 gene (CES1) encodes a hydrolase that metabolizes commonly used drugs. The CES1-related pseudogene, carboxylesterase 1 pseudogene 1 (CES1P1), has... (Review)
Review
The carboxylesterase 1 gene (CES1) encodes a hydrolase that metabolizes commonly used drugs. The CES1-related pseudogene, carboxylesterase 1 pseudogene 1 (CES1P1), has been implicated in gene exchange with CES1 and in the formation of hybrid genes including the carboxylesterase 1A2 gene (CES1A2). Hence, the CES1 region is complex. Using in silico PCR and alignment, we assessed the specificity of PCR-assisted procedures for genotyping CES1, CES1A2 and CES1P1 in studies identified in PubMed. We identified 33 such studies and excluded those that were not the first to use a procedure or lacked sequence information. After this 17 studies remained. Ten of these used haplotype-specific amplification, restriction enzyme treatment or amplicon sequencing, and included five that were predicted to lack specificity. All procedures for genotyping of single nucleotide polymorphisms in eight studies lacked specificity. One of these studies also used amplicon sequencing, thus being present in the group above. Some primers and their intended targets were mismatched. We provide experimental evidence that one of the procedures lacked specificity. Additionally, a complex pattern of segmental duplications in the CES1 region was revealed. In conclusion, many procedures for CES1, CES1A2 and CES1P1 genotyping appear to lack specificity. Knowledge about the segmental duplications may improve the typing of these genes.
Topics: Carboxylic Ester Hydrolases; Genotyping Techniques; Humans; Polymorphism, Single Nucleotide; Sensitivity and Specificity
PubMed: 29427553
DOI: 10.1515/dmpt-2017-0023 -
Pathogens and Global Health Feb 2021Several studies have evaluated the association between killer-cell immunoglobulin-like receptors (KIR) genes and susceptibility risk to tuberculosis (TB) infection.... (Meta-Analysis)
Meta-Analysis
Several studies have evaluated the association between killer-cell immunoglobulin-like receptors (KIR) genes and susceptibility risk to tuberculosis (TB) infection. Nonetheless, their outcomes have not been conclusive and consistent. Here we implemented a systematic review and meta-analysis of KIR genes association to susceptibility risk of pulmonary TB (PTB) infection to attain a clear understanding of the involvement of these genes in susceptibility to PTB infection. A systematic search was conducted in the MEDLINE/PubMed and Scopus databases to find case-control studies published before November 2020. Pooled odds ratio (OR) and 95% confidence interval (95% CI) were calculated to determine the association between KIR genes and risk of PTB infection. After comprehensive searching and implementing the inclusion and exclusion criteria, 10 case-control studies were included in the meta-analysis. Four KIR genes were found to have significant positive association with PTB susceptibility risk of infection, including (OR = 1.454, 95% CI = 1.157-1.827; = 0.001), (OR = 1.481, 95% CI = 1.334-1.837; < 0.001), (OR = 1.782, 95% CI = 1.273-2.495; = 0.001) and (OR = 1.726, 95% CI = 1.277-2.333; < 0.001). However, the results showed that the remaining KIR genes () and two pseudogenes ( and ) did not have significant associations with risk of PTB infection. This meta-analysis provides reliable evidence that the KIR genes , and may be associated with an increased risk of PTB infection.
Topics: Genetic Predisposition to Disease; Genotype; Humans; Receptors, KIR; Tuberculosis, Pulmonary
PubMed: 33258733
DOI: 10.1080/20477724.2020.1848271 -
Gene Mar 2018Colorectal cancer is one of the most common malignant tumours. Competitive endogenous RNA (ceRNA) networks have been hypothesized, in which various RNAs regulate each... (Review)
Review
Colorectal cancer is one of the most common malignant tumours. Competitive endogenous RNA (ceRNA) networks have been hypothesized, in which various RNAs regulate each other's expression using microRNA response elements (MREs). Recent evidence has highlighted the crucial regulatory roles of ceRNA networks in colorectal cancer. In this review, we summarize the present research methods as well as the currently known ceRNA competitors and targets in colorectal cancer. In addition, we discuss the significance of ceRNA and shortcomings of current studies of colorectal cancer.
Topics: Colorectal Neoplasms; Gene Expression Regulation, Neoplastic; Gene Regulatory Networks; Humans; MicroRNAs; Pseudogenes; RNA; RNA, Circular; RNA, Long Noncoding; Response Elements
PubMed: 29273554
DOI: 10.1016/j.gene.2017.12.036 -
Critical Reviews in Eukaryotic Gene... 2021The junk DNA "pseudogenes," known as genomic fossils, are characterized by their ubiquitousness and abundance within the genomic structure. These genomics sets are...
The junk DNA "pseudogenes," known as genomic fossils, are characterized by their ubiquitousness and abundance within the genomic structure. These genomics sets are recognized by the potential activity of meta-regulating the parent genes; these are transcribed into interfering RNA, consequently acting on miRNA concentration, thereby shedding light on the crosstalk of the pseudogenes' miRNA, siRNA, lncRNA/tumor therapy co-relationship. Moreover, an upcoming visualization regarding pseudogenes is under investigation, which describes the potentiality of pseudogenes as a fundamental component of cancerous evolutionary processing tools. Accordingly, here is a systematic review covering pseudobirth, pseudosignatures, and functional properties of pseudogenes, concluding that these pseudogenes are hypothetically predictive tumor therapies.
Topics: Biological Evolution; Genetic Therapy; Genomics; Humans; Neoplasms; Pseudogenes; RNA Interference; RNA, Small Interfering
PubMed: 34591392
DOI: 10.1615/CritRevEukaryotGeneExpr.2021039540 -
Stem Cell Reviews and Reports Aug 2013Mesenchymal stem cells (MSC) from fetal-placental tissues have translational advantages over their adult counterparts, and have variably been reported to express... (Meta-Analysis)
Meta-Analysis Review
Mesenchymal stem cells (MSC) from fetal-placental tissues have translational advantages over their adult counterparts, and have variably been reported to express pluripotency markers. OCT-4 expression in fetal-placental MSC has been documented in some studies, paradoxically without tumourogenicity in vivo. It is possible that OCT-4 expression is insufficient to induce true "stemness", but this issue is important for the translational safety of fetal-derived MSC. To clarify this, we undertook a systematic literature review on OCT-4 in fetal or adnexal MSC to show that most studies report OCT-4 message or protein expression, but no study provides definitive evidence of true OCT-4A expression. Discrepant findings were attributable not to different culture conditions, tissue sources, or gestational ages but instead to techniques used. In assessing OCT-4 as a pluripotency marker, we highlight the challenges in detecting the correct OCT-4 isoform (OCT-4A) associated with pluripotency. Although specific detection of OCT-4A mRNA is achievable, it appears unlikely that any antibody can reliably distinguish between OCT-4A and the pseudogene OCT-4B. Finally, using five robust techniques we demonstrate that fetal derived-MSC do not express OCT-4A (or by default OCT-4B). Reports suggesting OCT-4 expression in fetal-derived MSC warrant reassessment, paying attention to gene and protein isoforms, pseudogenes, and antibody choice as well as primer design. Critical examination of the OCT-4 literature leads us to suggest that OCT-4 expression in fetal MSC may be a case of "The Emperor's New Clothes" with early reports of (false) positive expression amplified in subsequent studies without critical attention to emerging refinements in knowledge and methodology.
Topics: Animals; Female; Fetus; Gene Expression Regulation, Developmental; Humans; Mesenchymal Stem Cells; Octamer Transcription Factor-3; Placenta; Pluripotent Stem Cells; Pregnancy
PubMed: 22161644
DOI: 10.1007/s12015-011-9336-5