دکتر مریم مقدم متین

Colorectal cancer is one of the deadliest cancers worldwide, which can be prevented and even cured by early diagnosis and more efficient treatment modalities. Comprehensive transcriptional analysis has highlighted the importance of lncRNAs in CRC tumorigenesis. In this study, we identified co-expressed lncRNA networks based on public RNA sequencing data for biomarker prediction in CRC and then verified the best candidate experimentally. 

Publicly available RNA-sequencing data (BioProject PRJEB27536) of CRC samples and normal adjacent tissues were reanalyzed using the DESeq2 package in R to find differentially expressed lncRNAs. Pathway enrichment and gene network analysis were accomplished using GSEA and WGCNA to identify potential functions of lncRNAs with possible roles in tumorigenesis pathways. Subsequently, the expression of RP11-109D20.2 (lnc-Duox2-1:1) was assessed in fresh/frozen tissues obtained from 46 CRC patients by quantitative RT-PCR. 

A total of 17939 DElncRNAs were identified between CRC and normal tissues via bioinformatics analyses. A significant up-regulation of RP11-109D20.2 (48%) was observed in CRC samples. Functional enrichment analysis showed that RP11-109D20.2 was mainly related to pathways like phosphoric ester hydrolase, oxidoreductase, phosphoric diester hydrolase, and cyclic-nucleotide phosphodiester activities. Moreover, elevated expression of DUOX2 in tumors with high levels of RP11-109D20.2 suggests a link between these genes.

Our data revealed that RP11-109D20.2 may have a considerable role in CRC progression. However, further functional analyses are essential to evaluate the probable role of RP11-109D20.2 as a potential diagnostic marker and its potential role in the dysregulation of cyclic nucleotide phosphodiesterase genes in CRC.

Transplantation of mesenchymal stem cells (MSCs) is a promising strategy in regenerative medicine. These cells can differentiate into chondrocytes, fibroblasts, or osteoblasts, essential components in bone healing. Dysregulated inflammation, resulting from a decreased or augmented immune response, can suppress bone healing. To overcome this problem, different strategies have been applied to improve the anti-inflammatory and immunomodulatory potencies of MSCs. Several studies have explored the potential of using small molecules to enhance the process of bone formation and regeneration. In addition to the proven safety and efficacy of lithium in managing bipolar disorder over many years, it has been reported in several studies that it could potentially contribute to an increase in bone mass. Some have focused on the role of lithium chloride (LiCl) in activating the WNT/β-Catenin pathway, which is involved in the differentiation of MSCs into osteoblasts. In this study, we evaluated the ability of adipose-derived mesenchymal stem cells (Ad-MSCs) treated with LiCl to differentiate into bone cells. To assess osteogenesis, mineralization was evaluated in cells cultured in an osteogenic induction medium. In addition to checking the expression of genes related to bone formation, we also investigated the expression of several genes related to immunomodulation at the mRNA level. We observed that LiCl enhanced the osteogenesis of Ad-MSCs, as evidenced by an increase in mineralization and the enhanced expression of osteogenic markers. Moreover, the expression of cytokines, which promote the anti-inflammatory behavior of these cells, was augmented. These findings could potentially be clinically relevant to improving conditions associated with bone loss, such as osteopenia and osteoporosis.

Alfalfa (Medicago sativa L.) is an important source of phytoestrogens. The abundance of alkaloids, phenols, flavonoids, and isoflavonoids has made this plant a rich source of these plant estrogens. Cultivation of alfalfa as a rich source of phytoestrogens for medicinal purposes has provided opportunities for alternative use of this forage. The study was carried out as a hydroponic culture in a perlite-cocopeat compacted bed with three replications. Roots and shoots of alfalfa plants were sampled separately in two stages (the 30th and 60th days after sowing). Plant samples were extracted with methanol solvent, and total phenols, flavonoids, and isoflavonoids contents were measured by spectrophotometric colorimetric method. The data analysis showed a significant effect of plant organ and harvest time on the contents of total phenols, flavonoids, and isoflavonoids (P≤0.05). The maximum accumulation of these compounds was in the plant shoots, and with the increase of the harvest time, the content of these phytoestrogens increased. Spearman's correlation analysis showed the different effects of the plant organ on the correlation level of the mentioned metabolites, so the flavonoids of the roots and shoots showed the most positive correlation, while isoflavonoids did not show a significant correlation (P≤0.05). The presence of the maximum contents of total phenols, flavonoids, and isoflavonoids in the shoots of alfalfa can be concluded that the distribution of secondary metabolites in plants, the same as the primary metabolites, is mainly dependent on the plant organ and tissue. Furthermore, the maximum content of these metabolites in the vegetative stage of alfalfa is due to the transition from the vegetative stage to the reproductive stage in these plants. Therefore, the late vegetative stage is the best phenological stage and the most suitable harvest time for medicinal applications.

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Although for a long time, it was thought that intervening sequences (introns) were junk DNA without any function, their critical roles and the underlying molecular mechanisms in genome regulation have only recently come to light. Introns not only carry information for splicing, but they also play many supportive roles in gene regulation at different levels. They are supposed to function as useful tools in various biological processes, particularly in the diagnosis and treatment of diseases. Introns can contribute to numerous biological processes, including gene silencing, gene imprinting, transcription, mRNA metabolism, mRNA nuclear export, mRNA localization, mRNA surveillance, RNA editing, NMD, translation, protein stability, ribosome biogenesis, cell growth, embryonic development, apoptosis, molecular evolution, genome expansion, and proteome diversity through various mechanisms.

Evidence Acquisition: 

In order to fulfill the objectives of this study, the following databases were searched: Medline, Scopus, Web of Science, EBSCO, Open Access Journals, and Google Scholar. Only articles published in English were included.

The intervening sequences of eukaryotic genes have critical functions in genome regulation, as well as in molecular evolution. Here, we summarize recent advances in our understanding of how introns influence genome regulation, as well as their effects on molecular evolution. Moreover, therapeutic strategies based on intron sequences are discussed. According to the obtained results, a thorough understanding of intron functional mechanisms could lead to new opportunities in disease diagnosis and therapies, as well as in biotechnology applications.

Esophageal cancer is one of the most aggressive gastrointestinal malignancies, and esophageal squamous cell carcinoma (ESCC) is the most prevalent esophagus neoplastic disease with high mortality rates in some Asian countries. Nonetheless, the etiology of ESCC continues to be vaguely comprehended, and the role of long noncoding RNAs in different clinical stages of this type of malignancy remains to be clarified. Here, we aimed to investigate the crucial genes corresponding to various clinical stages of ESCC, determine the hub lncRNAs in these stages, and predict patients’ overall survival time. In the current study, the cancer genome atlas (TCGA) RNA-seq public data was analyzed in order to discover novel biomarkers or therapeutic targets implicated in the progression of ESCC. Stage-related genes were analyzed, the protein-protein interaction network for any stage was constructed and the top 5 genes with the most Maximal Clique Centrality score in each network were selected as the hub mRNAs. LncRNAs interacting with each stage hub mRNA were also determined as stage-related hub lncRNAs. Gene set enrichment analysis on stage-associated modules was also carried out. Finally, Cox regression analysis was performed to assess the prognostic significance of identified hub lncRNAs in the survival of patients with ESCC. Finally, hub mRNAs and hub lncRNAs associated with ESCC progression were identified, which may have implications as biomarkers and targets for therapeutic interventions. Six lncRNAs, including AC013391.2, AC104088.1, AC026341.3, AL139023.1, AL583808.1, and LINC01707 were also identified to be significantly correlated with ESCC patients’ overall survival time, which could be potential predictors for the survival rate of patients, however, more research is required in order to confirm the results experimentally.

Salmonella is a gram-negative bacillus that lives in the intestinal tract of human and animals and causes diarrhea. Salmonella could be found in undercooked products of poultry with no impact on the taste, smell, or appearance. Since poultry eggs and meat might be sources of Salmonella and pose a hazard to public health, it is important to accurately detect Salmonella infection. In this regard, the present study aimed to develop a rapid and sensitive method for the diagnosis of Salmonella spp. in samples from the poultry industry. To do so, the sensitivity of S. enterica serotype Enteritidis detection was assessed with ten-fold serial dilutions in peptone water to give suspensions containing 100 to 105 CFU/mL. For artificial inoculation, skin samples were sequentially inoculated with the serial dilutions, while a control sample was included to ensure that the skin was not naturally contaminated with Salmonella. 53 commercial chicken skin samples were obtained from different local shops. Then, DNA was extracted from all samples, and the quality of extracted DNAs was checked by spectrophotometry and confirmed by agarose gel electrophoresis. For PCR, a pair of oligonucleotide primers, INVA, was designed to amplify the invA gene. Results revealed a band of 796 bp in samples artificially contaminated with S. Enteritidis. Likewise, the 796 bp band was detected in 38 samples (71%) with deferent intensities, which presented different amounts of contamination. Accordingly, the present study provided a valuable method for the detection and control of Salmonella infection in the poultry industry, since results would be available in less time than with the conventional cultural method.

Some Staphylococcus species are believed to be the main cause of bacterial infections and foodborne outbreaks. Several reports have discussed the enterotoxigenic properties of some Staphylococcus species, but due to the shortage of efficient diagnostic techniques, most studies have focused only on Staphylococcus aureus. Thus, developing a culture-independent, selective, and rapid detection method for Staphylococcus species in food products is of great importance. In this study, PCR-amplified tuf gene sequences were assessed by temporal temperature gradient gel electrophoresis (TTGE) in order to detect and differentiate between different Staphylococcus species in Iranian food samples. The PCR sensitivity and specificity were evaluated against DNA samples extracted from six Staphylococcus species, including S. aureus, S. epidermidis, S. saprophyticus, S. intermedius, S. chromogenes, and S. hominis, using a commercially available kit and a cost-effective, rapid, non-commercial boiling method. Using the boiling method, the sensitivity of the tuf PCR was 9 × 101 CFU/mL for the salami samples spiked with S. aureus, ten times less sensitive than the commercial kit. After optimizing the TTGE conditions, a species-specific TTGE pattern was obtained based on the differences between the amplified sequences from various species. This TTGE pattern was applied to detect Staphylococcus species in food samples from the market. The presence of Staphylococcus species was confirmed in 6 out of 10 tested salami products. The results demonstrate that the PCR-TTGE method is an alternative method that may be specific and sensitive enough to assess the presence of possible Staphylococcus contamination in meat processed food samples. More studies using different food samples should be considered for an in-depth analysis of bacterial contamination.

The aim of this study was to acquire an effective method for preparation of rat decellularized kidney scaffolds capable of supporting proliferation and differentiation of human adipose tissue derived mesenchymal stem cells (AD-MSCs) into kidney cells. We compared two detergents, the sodium dodecyl sulfate (SDS) and triton X-100 for decellularization. The efficiency of these methods was assessed by Hematoxylin and Eosin (H&E), 4', 6 diamidino-2-phenylindole and immunohistochemistry (IHC) staining. In the next step, AD-MSCs were seeded into the SDS-treated scaffolds and assessed after three weeks of culture. Proliferation and differentiation of AD-MSCs into kidney-specific cell types were then analyzed by H&E and IHC staining. The histological examinations revealed that SDS was more efficient in removing kidney cells at all-time points compared to triton X-100. Also, in the SDS-treated sections the native extracellular matrix was more preserved than the triton-treated samples. Laminin was completely preserved during decellularization procedure using SDS. Cell attachment in the renal scaffold was observed after recellularization. Furthermore, differentiation of AD-MSCs into epithelial and endothelial cells was confirmed by expression of Na-K ATPase and vascular endothelial growth factor receptor 2 (VEGFR-2) in seeded rat renal scaffolds, respectively. Our findings illustrated that SDS was more effective for decellularization of rat kidney compared to triton X-100. We presented an optimized method for decellularization and recellularization of rat kidneys to create functional renal natural scaffolds. These natural scaffolds supported the growth of AD-MSCs and could also induce differentiation of these cells into epithelial and endothelial cells.

Cell-based therapeutic approaches have witnessed significant developments during the last decade especially after approval of MSCs based treatment of graft versus host disease. Several cell-based approaches have shown immunomodulatory behavior during regeneration following the unknown cascade of events but the exact mechanisms are yet to be defined. Clinical applications of cell-based drugs are hampered all over the world because of incomplete understanding of molecular mechanisms requiring the application of mechanistic approaches to solving the mystery. Current work has given us the idea that Nanos2 enhances the cellular pluripotency characteristics while down-regulating the innate immunity genes, simultaneously.

The immunomodulatory behavior of cells was studied against cells carrying the ectopic expression of Nanos2 in comparison with Stella and Oct4 individually and simultaneously using SON vector (Stella, Nanos2 and Oct4).

It was observed that overexpression of Nanos2 leads to down-regulation of Interferon-Stimulated Genes (ISGs)-mRNAs such as Ifitm1, lsg15, Oas2, and Oas12. Nanos2 overexpressing MEF cells have shown restrictive inflammatory effects when cells were treated with inflammatory stimuli such as LPS and Poly (I:C).

From our recent findings in line with many others, it can be concluded that Nanos2 acts as a coin with two sides, regulating pluripotency and immunity together which enhances resistance against inflammatory stimuli. Nanos2 could be a potential candidate as a molecular drug for management of inflammation and immunomodulation but it requires a comprehensive comparative expression analysis of innate immunity genes in vitro and in vivo.

Recent studies have shown that the House Mouse (Mus musculus) has four subspecies in Iran. Although, these four subspecies have been recognized, the house mouse of east Iran showed high heterozygosity in various markers like allozymes, nuclear gene and mitochondrial gene sequences. Also, the taxonomy and diagnostic characters of mice populations in Iran and adjactment regions are poorly understood. In order to define clear characters for the subspecies described and identify the borders of Iranian subspeciese, thirty-one (31) populations were studied using three methods chromosomal morphology, morphology and molecular analysis of the mitochondrial cytochrome b gene. Molecular analysis of the M. musculus samples revealed four clades: 1- clade M. m. isatissus (of Iran) and M. m. castaneus from (of India), 2- clade M. m. bacteriaus from eastern areas with higth intrasubspecies genetic distance, 3- clade M. m. domesticus in the Southern and western regions and 4- M. m. musculus in the northeastern region of Iran. Morphometric characters resulted in three groups that overlapped with each other. The morphological characters could not be separated M. m. isatissus and M. m. bacteriaus, from each other . Analysis of cytogenetic variables showed four clear groups better the molecular clads. In these methods, the central and eastern clades are two distinct groups that are well supported with difference in size of centromeric heterochromatin and their patterns. These results showed that cytogenetic studies are useful and easy methods for identify the diagnostic characters of Iranian subspeciese.

Dental problems are common in human populations. Traditional treatments are focused on managing caries, soft tissue impairments, functional defects, poor aesthetics, digestive disorders and alveolar bone resorption. During the last two decades, basic and clinical researches on adult stem cells have established a potential therapeutic concept in tissue regeneration. Among major cells responsible for tooth development, odontoblasts play a key role in the formation of organic and inorganic constituents of dental tissue. A premier stride in the development of novel stem cell-based strategies for the treatment of reversible and irreversible pulpitis is odontoblast regeneration. Among different candidate cell sources for odontoblastic regeneration, use of dental adult stem cells is a preferred option because of their great ability to differentiate into odontoblasts and also their minimally invasive isolation procedure. This review emphasizes on articles that report successful odontoblast-like differentiation of dental mesenchymal stem cells which in turn provide a background for dentin-pulp complex cell therapies, using genetic or chemical manipulation. The series of experiments both in vitro and in vivo asserted that dental mesenchymal stem cells can efficiently differentiate into functional odontoblast-like cells. However, the review shows there are drawbacks in present methods. Future research should focus on optimizing protocols on odontoblast differentiation of dental stem cells by simultaneously introducing different genes with mutual synergy, combined with chemical or recombinant protein introduction.

Despite the importance of CD44 and CD133 in various cancers, the clinicopathological and prognostic values of these biomarkers in esophageal cancer remain debated. Hence, in this study, we did a meta-analysis to explore the correlation between overexpression of these markers and some clinicopathological features and their influence on the survival of esophageal cancer patients. A search in PubMed and Web of Science (among all articles published up to January 16, 2018) was done using the following keywords: esophageal cancer, CD44, CD133, prominin-1, AC133. Suitable studies, that were selected based on the criteria listed in the Materials and Methods section, were chosen and hazard ratios with 95% confidence intervals were estimated if available. Heterogeneity and sensitivity were also analyzed. Furthermore, publication bias was assessed using funnel plots, Egger, and Begg tests. The study included 1346 patients from 13 related studies. The median rates of marker expressions by immunohistochemistry were 35.7% (30%-76.6%) from 9 studies for CD44 and 31.9% (21%–44.2%) from 5 studies for CD133. The accumulative 5-year overall survival rates of CD44-positive and CD133-positive were 1.59% (1.22-2.06) and 1.27% (0.93-1.73), respectively. Meta-analysis showed that CD44 expression had a significant correlation with 5-year overall survival. CD44 overexpression showed a correlation with some clinicopathological features such as lymph node metastasis, vascular invasion, and recurrence of the disease, while it was not the case for coexpression of CD44 and CD133. In conclusion, CD44 overexpression was associated with a 5-year overall survival rate and thus this biomarker can be a suitable prognostic tool in esophageal cancer.

Prostate cancer is one of the leading causes of cancer related deaths in males worldwide. Overexpression of 15-lipoxygenase-1 (15-LOX-1) enzyme and high activity of its metabolic pathway is reported to be a driver for prostate cancer malignancy. Farnesyloxycoumarin derivatives (3f, 4f and 7f) inhibit lipoxygenase enzyme. We hypothesized that farnesyloxycoumarins may exert an anti-cancer effect on prostate cancer cells due to their 15-LOX-1 inhibitory potential.
The enzyme inhibitory activity of 3f, 4f and 7f was initially evaluated on PC-3 and DU145 prostate cancer cell lines. MTT assay was performed on cancer cell lines and HFF3 cell line to assess cytotoxicity of the compounds. The apoptotic morphology of cells after treatments was assessed by DAPI staining and single cell gel electrophoresis. Propidium iodide staining was also performed to detect cell cycle variations after treatment.
7f inhibited 15-LOX-1 at IC50=4.3 µg/mL, while 3f and 4f did not show high inhibitory activity. 7f reduced cell viability in PC-3 cells at IC50=22-31 µg/mL, however, no significant cytotoxicity was revealed on normal cells. DAPI staining and comet assay confirmed apoptosis and DNA damage in PC-3 cells after 7f treatment, while flow cytometry results revealed G1 arrest in PC-3 cells.
The results are indicative of a distinctive cytotoxic mechanism for 7f compared to other coumarins, possibly due to its 15-LOX-1 inhibitory potential. Thus, this compound is valued for further assessments with the aim of developing a promising targeted therapy for prostate cancer patients.

Cancer remains a major cause of death worldwide. Huge research and identification of several markers have resulted in better understanding of its mechanism. Researches focusing on cancer stem cells and their role in metastasis will help the scientific community to propose the therapeutic approaches for treatment of this monstrous disease. Interest of governmental agencies and inter-communications of molecular biologists with clinicians can boost the new ideas in identification and characterizations of cancer stem cells. It will also help to elucidate their roles in tumor progression and hopefully would result in better ways to reduce the mortality related to cancer