Up-regulation of FOXC2 and FOXQ1 is associated with the progression of gastric-type adenocarcinoma

Objective: Forkhead box [FOX] proteins are important regulators of the epithelial-to-mesenchymal transition [EMT], which is the main mechanism of cancer metastasis. Different studies have shown their potential involvement in progression of cancer in different tissues such as breast, ovary and colorectum. In this study, we aimed to analyze the expression of genes encoding two FOX proteins in gastric adenocarcinoma

Materials and Methods: In this experimental case-control study, the expression of FOXC2 and FOXQ1 was examined in 31 gastric adenocarcinoma tumors and 31 normal adjacent gastric tissues by reverse transcription polymerase chain reaction [PCR]

Results: The expression of both genes was significantly up-regulated in gastric adenocarcinoma tumors compared with the normal tissues [P<0.05]. The differential expression of these two genes was also correlated with the grade of tumors [P<0.01]

Conclusion: We show that up-regulation of FOXC2 and FOXQ1 are likely to be involved in the progression of gastric adenocarcinoma

Differential expression of OCT4 pseudogenes in pluripotent and tumor cell lines

Objective: The human OCT4 gene, the most important pluripotency marker, can generate at least three different transcripts [OCT4A, OCT4B, and OCT4B1] by alternative splicing. OCT4A is the main isoform responsible for the stemness property of embryonic stem [ES] cells. There also exist eight processed OCT4 pseudogenes in the human genome with high homology to the OCT4A, some of which are transcribed in various cancers. Recent conflicting reports on OCT4 expression in tumor cells and tissues emphasize the need to discriminate the expression of OCT4A from other variants as well as OCT4 pseudogenes

Materials and Methods: In this experimental study, DNA sequencing confirmed the authenticity of transcripts of OCT4 pseudogenes and their expression patterns were investigated in a panel of different human cell lines by reverse transcription-polymerase chain reaction [RT-PCR]

Results: Differential expression of OCT4 pseudogenes in various human cancer and pluripotent cell lines was observed. Moreover, the expression pattern of OCT4-pseudogene 3 [OCT4-pg3] followed that of OCT4A during neural differentiation of the pluripotent cell line of NTERA-2 [NT2]. Although OCT4-pg3 was highly expressed in undifferentiated NT2 cells, its expression was rapidly down-regulated upon induction of neural differentiation

Analysis of protein expression of OCT4A, OCT4-pg1, OCT4-pg3, and OCT4-pg4 by Western blotting indicated that OCT4 pseudogenes cannot produce stable proteins. Consistent with a newly proposed competitive role of pseudogene microRNA docking sites, we detected miR-145 binding sites on all transcripts of OCT4 and OCT4 pseudogenes

Conclusion: Our study suggests a potential coding-independent function for OCT4 pseudogenes during differentiation or tumorigenesis

6-Methoxy Podophyllotoxin induces Apoptosis via inhibition of TUBB3 and TOPIIA Gene expressions in 5637 and K562 Cancer cell lines

Objective: Podophyllotoxin [PTOX], a natural compound in numerous plants, contains remarkable biological properties that include anti-tumor, anti-viral such as anti-human im-munodeficiency virus [HIV] activities. In order to avoid its adverse effects, various compounds have been derived from PTOX. 6-methoxy PTOX [MPTOX] is one of the natural PTOX derivatives with an extra methoxy group. MPTOX is mostly isolated from the Linum species. This study has sought to determine the biological effects of MPTOX on cancer cell lines, 5637 and K562

Materials and Methods: In this experimental study, we treated the 5637 and K562 cancer cell lines with MPTOX in a dose- and time-dependent manner. Apoptosis was examined by flow cytometry and viability rate was analyzed by the MTT assay. Expressions of the tubulin [TUBB3] and topoisomerase II [TOPIIA] genes were determined by real-time polymerase chain reaction [PCR]

Results: Treatment with MPTOX led to significant induction of apoptosis in cancer cells compared to control cells. Gene expression analysis showed reduced levels of TUBB3 and TOPIIA mRNA following MPTOX treatment

Conclusion: MPTOX inhibited TUBB3 and TOPIIA gene expression and subsequently induced cell death through apoptosis. These results suggested that MPTOX could be considered a potential anti-tumor agent

[Identification and discovery of novel microRNAs in the human genome]

Although more than 98% of the human genome is transcribed, most of these transcripts are not translated into proteins. Rather, they are considered as non-coding RNAs. MicroRNAs [miRNAs] are very short non-coding RNAs approximately 22 nucleotides in length which regulate many key processes of cells such as growth, proliferation, differentiation, cell cycle, apoptosis [programmed cell death] and metabolism. On the other hand, it is known that these small regulatory molecules are involved in many human diseases such as different cancers and cardiovascular disorders. Therefore, discovery and functional characterization of novel miRNAs is a prominent achievement. Low abundance and spatiotemporal expression of these mediator molecules make their discovery difficult by conventional methods. Therefore, bioinformatics software have been designed for the prediction of stem-loop structures capable of producing miRNA precursors in the human genome. On the other hand, there are several bioinformatics tools for prediction of miRNA target genes. Prediction of miRNA target genes helps to characterize the function of a miRNA. In this paper, we have reviewed some of the common efficient bioinformatics tools and experimental approaches used for prediction and identification of the miRNA genes and their target genes

[Decrease of inosine triphosphatase gene expression in human gastric adenocarcinoma tumors]

Objective: A pure nucleotide pool is essential for correct DNA replication in addition to the prevention of mutagenesis and abnormalities in a living cell. Inosine triphosphatase [ITPase] is a critical enzyme for the removal of deaminated rough purine nucleotides such as inosine from the nucleotide pool. It has been shown that abnormal function and expression of the ITPA gene is followed by an increased substitution mutation rate in the genome. This study compares the ITPA gene expression level between human adenocarcinoma tumors and their normal marginal tissues

Method: We examined ITPA gene expression in 24 pairs of gastric adenocarcinoma tumors and their normal adjacent tissues by quantitative real-time PCR

Result: There was reduced ITPA gene expression in tumor tissues compared with the adjacent normal tissues. The decline in ITPA gene expression was more significant in the higher grade samples

Conclusion: ITPA is involved in omitting deaminated purines from the nucleotide pool. Therefore its abnormal function increases the frequency of mutations and causes higher genomic instability. Our data suggest that lower expression of ITPA can be considered a risk factor for the development and progression of gastric cancer

[Hsa-miR-133b expression profile during cardiac progenitor cell differentiation and its inhibitory effect on SRF expression]

Cardiac cell differentiation with the help of miRNAs has recently opened a promising window for the restoration of myocardial infarction. Independent miR-1-2/133a-1 and miR-206/133b clusters are known to be expressed in cardiac and skeletal muscles, respectively. miR-133b differs from miR-133a by only one nucleotide. The sequence similarity of these two miRNAs suggests that they target the same pathways and similar mRNA targets. The present study seeks to determine if miR-133b is expressed during the cardiac cell differentiation and if its expression is in reverse correlation with the SRF and CCND2 [as potential target genes] expression patterns. Human cardiac progenitor cells were prepared from Royan Stem Cell Bank [RSCB] and differentiated into cardiomyocytes. To initiate differentiation, cells were treated with 5-azacytidine as a demethylation factor. Then, ascorbic acid and TGFB1 were added every other day and twice per week, respectively. Differentiation into cardiomyocytes was confirmed by immunocytochemistry [ICC], flow cytometry and realtime PCR for some of the cardiac marker genes. The expression profiles of hsa-miR-133b and two of its potential target genes were also analyzed during the cardiac differentiation. Three weeks after the first differentiation induction, expression level of hsa-miR-133b was approximately five times higher than early stage expression [p<0.05]. During this process, the expression profile of SRF target gene was inversely correlated with hsamiR-133b expression. It is known that SRF is critically involved in the cell cycle. Considering increased miR-133b and decreased SRF expression levels during the late stages of heart cell differentiation, here we speculate that elevated expression of miR-133b blocks SRF expression and decreases cardiomyocytes proliferation in order to induce differentiation with direct targeting of SRF. Taken together, our data suggest that miR-133b along with miR-133a may be involved in cardiomyocytes differentiation.

Analysis of the effect of chronic morphine treatment on miRNA profile and introduction of the MAPK pathway as the target of differentially expressed miRNAS

Different signaling pathways have been identified that are involved in the cellular response to opiates. The mitogen-activated protein kinase pathway is one of the most important signaling pathways underlying the neuronal response to opiates. MicroRNAs [miRNAs] are considered to be post-transcriptional regulators of gene expression with paramount significance, which plays key roles in modulating cellular processes such as neuronal plasticity and synaptic consolidation. The purpose of this study is to identify miRNAs that are differentially expressed in response to chronic morphine treatment, and predict those genes that have a possible role in this process. Because the MAPK pathway in involved in morphine dependence and participates in hypersensitivity to pain, determining miRNAs that modulate this pathway could be insightful in morphine dependence treatment and pain control. In this study, the BE[2]-C neuroblastoma cell line was chronically treated with morphine sulphate and the changes in expression of 750 miRNAs were analyzed by real time PCR. Two up- and down- regulated groups of miRNAs were determined to be differentially expressed in response to morphine: i] has-mir-193a-3p, -212, -181c, -362-3p, -639, -646 and ii] has-mir-412, -937, -558, -552, -943, -628-5p, -593, -555, -636, -643, 566, -571, -642, -653, -611, -31, let7-g. The analysis of differentially expressed miRNAs showed that the MAPK signaling pathway could be regarded as a signaling pathway with utmost significance in chronic morphine response. Due to the role played by MAPK pathway in cellular response to morphine exposure, we can propose that protein phosphorylation has a presumable part in this response

Independence of color intensity variation in red flesh apples from the number of repeat units in promoter region of the MdMYB10 gene as an allele to MdMYB1 and MdMYBA

MdMYB10 gene expression results in accumulation of anthocyanin in many tissues including flesh of apple fruit. The MdMYB1 and MdMYBA genes are close homologues to MdMYB10 gene and both are responsible for red color phenotype in apple fruit skin. In the current study, an apple genome sequence draft analysis indicated that these three genes are located in a unique contig. Further analysis suggested that these homologues are alleles of a single locus and they differ in a repeated sequence of the promoter region. This repeated sequence ensures high expression level of MdMYB10 in most of the plant tissues while MdMYB1 and MdMYBA alleles lack such a repeated sequence in their promoters and their expression is confined to the fruit skin. Also, we suggest a tissueand genome-specific expression pattern for these three alleles considering our data and other recent publications. No variation was detected in the sequence or in the number of repeats of MdMYB10 promoter in Iranian red flesh apple geo-variants, pointing that the number of repeat is not related to flesh color intensity or variation, and the repeat elements have occurred once during the evolution