Reference genes for quantitative RT-PCR data in gastric tissues and cell lines

Wisnieski, Fernanda

doi:10.3748/wjg.v19.i41.7121

Cited by 42 publications

(27 citation statements)

References 29 publications

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“…The boundary value suggested by geNorm was 0.15, however, rather than a stringent standard consideration, which provided guidance to determine the optimal number of reference genes. Regarding the standardized principle of RT-qPCR, previous studies have recommended selecting a minimum of 3 internal control genes to perform relative quantitative investigations (24). The present study also recommended that a combination of 3 reference genes was sufficient for normalizing relative quantitative investigations.…”

Section: Discussionmentioning

confidence: 78%

Validation of reference genes for the normalization of RT-qPCR expression studies in human tongue carcinoma cell lines and tissue

Liu

Ren

et al. 2017

Oncology Letters

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Abstract. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) has become a frequently used strategy in gene expression studies. The relative quantification method is an important and commonly used method for the evaluation of RT-qPCR data. The key aim of this method is to identify an applicable internal reference gene. However, there are currently no data concerning the expression of reference genes for gene analysis in human tongue carcinoma cell lines and tissues. In the present study, screening was performed using 12 common reference genes, which were selected in order to provide an experimental basis for the investigation of gene expression in human tongue carcinoma. Tca-8113 and CAL-27 cell lines and a total of 8 tongue carcinoma tissue samples were investigated. The gene expression stability and the applicability of the 12 reference gene candidates were determined using the geNorm, NormFinder and BestKeeper software programs. The results from the three software programs were demonstrated to be variable following comparison. The recommended combinations were 5'-aminolevulinate synthase 1 + glucuronidase β + ribosomal protein L29 (RPL29) for the cell line + tissue group, β-2-microglobulin + RPL29 for the cell line group and peptidylprolyl isomerase A + hydroxymethylbilane synthase + RPL29 for the tissue group. These recommended internal reference genes may improve the accuracy of relative quantitation analysis of target gene expression performed by the RT-qPCR method in further gene expression research on human tongue carcinoma.

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Section: Discussionmentioning

confidence: 78%

Validation of reference genes for the normalization of RT-qPCR expression studies in human tongue carcinoma cell lines and tissue

Liu

Ren

et al. 2017

Oncology Letters

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“…In the present study, the analysis was focused on non-neoplastic tissues; however, ACTB intergroup variation was observed to be higher in the samples with intestinal metaplasia, which is considered a precancerous lesion (55), thus affecting the gene stability value. The study by Wisnieski et al (25) analyzing normal and adenocarcinoma samples of gastric tissue and cell lines, determined that ACTB was the most appropriate reference gene for all tissues; however, SDHA was not included in their analysis.…”

Section: Discussionmentioning

confidence: 99%

“…In the IM group, 62.5% (n=5) of patients received previous HP treatment, 25.0% (n=2) were HP + , while 12.5% of this group (n=1) had no prior report of H. pylori infection. The groups classified as normal and ICG were diagnosed as HP -.…”

Section: Classification According To Histological Analysismentioning

confidence: 99%

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Effect of Helicobacter pylori on NFKB1, p38α and TNF-α mRNA expression levels in human gastric mucosa

Oliveira

Biolchi

Medeiros

et al. 2016

Experimental and Therapeutic Medicine

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Abstract.Helicobacter pylori infects ~50% of the world population, causing chronic gastritis and other forms of cellular damage. The present study assessed the influence of H. pylori on the mRNA expression levels of nuclear factor-κB1 (NFKB1), p38α and tumor necrosis factor-α (TNF-α) in human gastric mucosa in a southern Brazilian population. Human gastric tissue was collected by upper endoscopy and H. pylori diagnosis was performed using a rapid urease test and histological analysis. Total RNA was extracted and purified for subsequent cDNA synthesis and analysis by quantitative polymerase chain reaction (qPCR). The gastric tissue samples were divided into four groups as follows: Normal, inactive chronic gastritis, active chronic gastritis and intestinal metaplasia. The SDHA gene was classified as the most stable when compared with ACTB, GAPDH, B2M and HPRT1 genes, and was therefore selected as the reference gene for qPCR data normalization. TNF-α mRNA expression was significantly higher in samples that were positive for H. pylori and with active chronic gastritis. However, no difference was detected in the mRNA expression levels of NFKB1 and p38α between the groups. The present study concluded that the presence of H. pylori is associated with TNF-α upregulation in human gastric mucosa, but had no effect on NFKB1 and p38α mRNA expression levels.

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“…A common shortcoming of many previous attempts is that tissue specificity of the genes was reported [102][103][104][105][106][107][108][109][110][111][112], or avoided [113][114][115]. However, no attempts were made to actually use such data for quality control or evaluation of the expression data, or if they were, it was for cancer analysis within one tissue [116][117][118] or to study the expression of synonymous codons in plants [119].…”

Section: Existing Expression Data Quality Control Methods and Their Amentioning

confidence: 99%

Quality Control of Expression Profiling Data

Soloviev¹,

Milnthorpe²

2015

J Proteomics Bioinform

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Reference genes for quantitative RT-PCR data in gastric tissues and cell lines

Abstract: GAPDH + B2M or ACTB + B2M is the best combination of reference gene for all the gastric tissues, and ACTB + B2M is the best combination for the cell lines tested.

Cited by 42 publications

References 29 publications

Validation of reference genes for the normalization of RT-qPCR expression studies in human tongue carcinoma cell lines and tissue

Validation of reference genes for the normalization of RT-qPCR expression studies in human tongue carcinoma cell lines and tissue

Effect of Helicobacter pylori on NFKB1, p38α and TNF-α mRNA expression levels in human gastric mucosa

Quality Control of Expression Profiling Data

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