Sayyed Emad Aldin Tayyebi; Mahyar Heydarpour; Hesam Dehghani
Abstract
Colorectal cancer is one of the most common cancers and is one of the leading causes of cancer-related deaths worldwide. The underlying biological mechanisms for the development of colorectal cancer are largely unidentified. Several genes likely involved in the pathogenesis of colorectal cancer have ...
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Colorectal cancer is one of the most common cancers and is one of the leading causes of cancer-related deaths worldwide. The underlying biological mechanisms for the development of colorectal cancer are largely unidentified. Several genes likely involved in the pathogenesis of colorectal cancer have been identified. However, some other genes might have less evident functions. One gene family with prominent functional roles in the normal colon is mucin. Multiple studies have demonstrated the involvement of mucins in the pathogenesis of human malignancies. Therefore, due to the lack of an inclusive investigation of mucins' expression, mechanism of action, and involvement in colon adenocarcinoma's underlying biology, diagnosis, and prognosis, we sought to unearth their potential involvement and related regulatory networks in this disease. In this investigation, a step-wise manner was used, and a plethora of databases and algorithmic tools were applied. Due to a significant upregulation at both mRNA and protein levels and following a thorough evaluation of diagnostic and prognostic values in colon adenocarcinoma, MUC13 was determined to be the most relevant regulatory mucin in colon carcinoma. Altogether, these findings indicate a putative ncRNA-mRNA network, including hsa-mir-136-5p, hsa-mir-27a-3p, NEAT1, and XIST, to be involved in regulating MUC13 in colon cancer. This step-wise investigation implies that MUC13 may have a crucial role in the underlying molecular mechanisms for the initiation or progression of colon cancer. In addition, it provides insights into molecular mechanisms and possible regulatory non-coding RNA networks that might be responsible for regulating MUC13 expression.
Nima Dehdilani; Mohsen Fathi Najafi; Hesam Dehghani
Abstract
To achieve a reliable and persistent expression, the transgene should be precisely integrated into the genome safe harbor (GSH) loci. Little attention has been paid to find the safe harbor loci of the chicken (Gallus gallus domesticus) genome. Identification and characterization of GSH loci that allow ...
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To achieve a reliable and persistent expression, the transgene should be precisely integrated into the genome safe harbor (GSH) loci. Little attention has been paid to find the safe harbor loci of the chicken (Gallus gallus domesticus) genome. Identification and characterization of GSH loci that allow the persistent and reliable expression of knock-in genes could be a major area of interest within the field of transgenic technology and is central to the development of transgenic livestock. Randomly integrated transgenes might encounter position effects and epigenetic silencing, so unstable phenotypes, as well as unreliable and unpredictable expression of the knock-in transgene could occur. In contrast to random gene insertion, site-specific gene targeting provides a superior strategy that exploits homologous recombination to insert a transgene of interest into a pre-determined locus. In this study, based on bioinformatics, gene expression atlas, and Hi-C analyses, the GSH region was predicted in the chicken genome between DRG1 and EIF4ENIF1 genes. To do so, we introduce a fast and easy-to-use pipeline that allows the prediction of orthologue GSH loci in all organisms, especially chickens. In addition, the procedure to design targeting vectors for targeting these predicted GSH regions is described in detail.
Sara Yousefi Taemeh; Jalil Mehrzad; Hesam Dehghani
Abstract
Primordial germ cells (PGCs) are precursors of mature gametes, which transmit genetic information to the next generation. Due to the importance of PGCs in many fields, including developmental biology, genome editing, transgenesis, and conservation of avian genetic resources, various research aspects ...
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Primordial germ cells (PGCs) are precursors of mature gametes, which transmit genetic information to the next generation. Due to the importance of PGCs in many fields, including developmental biology, genome editing, transgenesis, and conservation of avian genetic resources, various research aspects have focused on the cultivation of PGCs. Despite considerable progress in the establishment of specified culture media for the expansion of PGCs, a well-defined PGC culture medium has not yet been developed. This might be due to the complexity of the nutritional requirements of PGCs in the culture. Besides the nutritional needs, including vitamins, amino acids, salts, carbohydrates, and growth factors, a particular source of energy must be provided to sustain growth and viability. Glutamine is a major energy source for cultured cells, commonly added in cell culture media at higher concentrations than other amino acids. However, glutamine is very labile and rapidly degrades in solutions such as culture media. This generates ammonia as a by-product, which is toxic to the cultured cells and can affect cell viability and protein glycosylation. Therefore, the stability of glutamine in culture conditions is another concern for the long-term culture of PGCs. Here, we study the effect of glutamine stability on PGC culture using glutamine and GlutaMax (a commercial stabilized dipeptide form of glutamine). We found that the addition of GlutaMax in the medium promotes PGC proliferation. This effect might be exerted by minimizing production of toxic ammonia that results in maximizing cell performance and media stability.
Hesam Dehghani
Abstract
Pluripotency is a central feature of stem and cancer cells. This feature enables cancer cells to self-renew and trans-differentiate. In this editorial, it is hypothesized that in cancer cells synchronized events rather than segmented procedures may lead to pluripotency.
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Pluripotency is a central feature of stem and cancer cells. This feature enables cancer cells to self-renew and trans-differentiate. In this editorial, it is hypothesized that in cancer cells synchronized events rather than segmented procedures may lead to pluripotency.
Balal Sadeghi; Mohammadreza Nassiri; Ali Masoudi-Nejad; Mojtaba Tahmoorespour; Hesam Dehghani; Hamed Ahmadi
Abstract
MicroRNAs (miRNA) are a class of noncoding and regulatory RNA molecules about 22 nucleotides in
length. MicroRNAs regulate gene expression by an RNA interfering pathway through cleavage or inhibition of
the translation of target mRNA. Many miRNAs have been reported for their important roles in developmental
processes ...
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MicroRNAs (miRNA) are a class of noncoding and regulatory RNA molecules about 22 nucleotides in
length. MicroRNAs regulate gene expression by an RNA interfering pathway through cleavage or inhibition of
the translation of target mRNA. Many miRNAs have been reported for their important roles in developmental
processes in various animals, but there is limited information about cattle and sheep miRNAs. The comparative
genomics approach due to their conserved nature is a good source for the miRNAs discovery. Cattle and sheep
are ideal model organisms for biological and comparative genomics studies. In our study, a computational
method based on expressed sequence tag (EST) analysis was used for detection of cattle and sheep miRNAs. In
cattle, 25 miRNA candidates found by homology searching frequently clustered at certain chromosomes and
28 miRNAs in sheep had been detected. Our results show that the cattle and sheep miRNA database can be
providing useful information for investigating biological functions of miRNAs in cattle and sheep.
Furthermore, the bioinformatics approach is a good manner for studying these functions.
