Iranian Journal of Biotechnology最新文献

{"title":"The <i>HLA rs9267649</i> and <i>CYP24A1 rs2248359</i> Variants are Associated with Multiple Sclerosis: A Study on Iranian Population.","authors":"Sevil Babashpour,&nbsp;Mitra Ataei,&nbsp;Ferdous Rastgtar Jazii,&nbsp;Shekoofeh Alaie,&nbsp;Mohammad Hossein Sanati","doi":"10.30498/ijb.2022.276921.3012","DOIUrl":"https://doi.org/10.30498/ijb.2022.276921.3012","url":null,"abstract":"<p><strong>Background: </strong>Studies have shown that MS results from synergism between genetic and environmental factors. As a genetic factor, the <i>rs9267649</i> variant through the regulatory effect on the <i>HLA-DRB1</i> expression is involved in the MS development. In addition, vitamin D deficiency through involvement of <i>rs2248359</i> variant of <i>CYP24A1</i> has shown to play important role in the risk of MS.</p><p><strong>Objectives: </strong>The aim of this study was to investigate both the <i>HLA rs9267649</i> and <i>CYP24A1 rs2248359</i> variants with risk of multiple sclerosis (MS) in Iranian population.</p><p><strong>Materials and methods: </strong>The <i>rs9267649</i> and <i>rs2248359</i> variants were genotyped in 82 Iranian Relapsing-Remitting Multiple Sclerosis (RRMS) patients and 100 matched healthy controls, using the PCR-RFLP method. The genotype and allele frequencies were calculated and statistically analyzed.</p><p><strong>Results: </strong>A significant difference was found in the allele distribution for the both <i>rs9267649</i> and <i>rs2248359</i> variants, such that the A allele of <i>rs9267649</i> and the C allele of <i>rs2248359</i> were found to be more frequent in MS patients than in the healthy controls (p-value: 0.009, OR: 2.264, 95% CI: 1.211-4.231 and p-value: 0.028 OR: 1.594, 95% CI: 1.052-2.415), respectively.</p><p><strong>Conclusions: </strong>The present research results provide further evidence on the association of the two variants <i>rs9267649</i> of the <i>HLA</i> and <i>rs2248359</i> of the <i>CYP24A1</i> gene with MS etiology and an increased risk of MS in Iranian RRMS patients. However, further large-scale investigations in various ethnicities and in the functional genomics level are demanded to confirm our findings.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/5b/a2/IJB-20-e3012.PMC9618012.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40704275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Meta-Analysis of EGF-Stimulated Normal and Cancer Cell Lines to Discover EGF-Associated Oncogenic Signaling Pathways and Prognostic Biomarkers.","authors":"Shahrokh Garousi,&nbsp;Sodabeh Jahanbakhsh Godehkahriz,&nbsp;Kasra Esfahani,&nbsp;Tahmineh Lohrasebi,&nbsp;Amir Mousavi,&nbsp;Ali Hatef Salmanian,&nbsp;Mahsa Rezvani,&nbsp;Maryam Moein","doi":"10.30498/ijb.2022.323464.3245","DOIUrl":"https://doi.org/10.30498/ijb.2022.323464.3245","url":null,"abstract":"<p><strong>Background: </strong>Although epidermal growth factor (EGF) controls many crucial processes in the human body, it can increase the risk of developing cancer when overexpresses.</p><p><strong>Objectives: </strong>This study focused on detecting cancer-associated genes that are dysregulated by EGF overexpression.</p><p><strong>Materials and methods: </strong>To identify differentially expressed genes (DEGs), two independent meta-analyses with normal and cancer RNA-Seq samples treated by EGF were conducted. The new DEGs detected only via two meta-analyses were used in all downstream analyses. To reach count data, the tools of FastQC, Trimmomatic, HISAT2, SAMtools, and HTSeq-count were employed. DEGs in each individual RNA-Seq study and the meta-analysis of RNA-Seq studies were identified using DESeq2 and metaSeq R package, respectively. MCODE detected densely interconnected top clusters in the protein-protein interaction (PPI) network of DEGs obtained from normal and cancer datasets. The DEGs were then introduced to Enrichr and ClueGO/CluePedia, and terms, pathways, and hub genes enriched in Gene Ontology (GO) and KEGG and Reactome were detected.</p><p><strong>Results: </strong>The meta-analysis of normal and cancer datasets revealed 990 and 541 new DEGs, all upregulated. A number of DEGs were enriched in protein K48-linked deubiquitination, ncRNA processing, ribosomal large subunit binding, and protein processing in endoplasmic reticulum. Hub genes overexpression (DHX33, INTS8, NMD3, OTUD4, P4HB, RPS3A, SEC13, SKP1, USP34, USP9X, and YOD1) in tumor samples were validated by TCGA and GTEx databases. Overall survival and disease-free survival analysis also confirmed worse survival in patients with hub genes overexpression.</p><p><strong>Conclusions: </strong>The detected hub genes could be used as cancer biomarkers when EGF overexpresses.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b6/f6/IJB-20-e3245.PMC9618017.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40687228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Growth of <i>Spirulina Maxima</i> in an Optimized Concentric Internal Tube Photobioreactor.","authors":"Alfredo de Jesús,&nbsp;Martínez Roldán,&nbsp;Brenda Paloma,&nbsp;Gómez Lozano","doi":"10.30498/ijb.2022.273070.2985","DOIUrl":"https://doi.org/10.30498/ijb.2022.273070.2985","url":null,"abstract":"<p><strong>Background: </strong>Microalgae have the potential to generate high-value products. The design of photobioreactors (PBRs), in which microalgae are cultured, is crucial because alterations in their configuration and operational conditions can affect the biomass production and productivity.</p><p><strong>Objective: </strong>The objective of this study was to optimize the diameter of the internal tube of an airlift PBR and to characterize the growth of <i>Spirulina maxima</i> in an optimized design.</p><p><strong>Material and methods: </strong><i>S. maxima</i> was cultured in a mineral medium without an organic carbon source. The PBR consisted of an acrylic cylinder with an operational volume of 7 L. Daily determinations of biomass (by filtration), chlorophyll, N-NO₃ and P-PO₄ (spectrophotometrically) were carried out.</p><p><strong>Results: </strong>The use of a concentric tube with a diameter of 3 inches led to an increased biomass concentration of 1.14 ± 0.136 g.L_-1, allowing a global biomass productivity of 153 mg.L_-1.d_-1. The culture reached a volumetric consumption velocity of 27.34 ± 1.596 and 2.29 ± 0.353 mg.L_-1.d_-1 for N and P, respectively.</p><p><strong>Conclusions: </strong>It was concluded that operational conditions must be specifically selected for each cultivated strain and that this configuration of airlift PBR can produce <i>Spirulina</i> biomass under laboratory conditions with a high biomass productivity.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/26/0e/IJB-20-e2985.PMC9618013.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40704271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Survey of Gasoline Ameliorator, Methyl-Tert-Butyl Ether (MTBE) on Bovine Serum Albumin: A Spectroscopy and Molecular Dynamic Simulation Study.","authors":"Ebrahim Shahmansoorian,&nbsp;Seyed-Mohammad Atyabi,&nbsp;Parichehreh Yaghmaei,&nbsp;Faramarz Mehrnejad","doi":"10.30498/ijb.2022.297646.3111","DOIUrl":"https://doi.org/10.30498/ijb.2022.297646.3111","url":null,"abstract":"<p><strong>Background: </strong>Methyl-Tert-Butyl Ether (MTBE) as a gasoline modifier is frequently added to fuels and used in plenty of worldwide applications. MTBE biodegradation in groundwater occurs slowly and produces water miscibility; therefore, it causes diverse environmental and human health concerns.</p><p><strong>Objectives: </strong>The interaction of MTBE with bovine serum albumin (BSA) as a model protein at physiological conditions is investigated to illustrate the possible interactions of MTBE with the body's proteins.</p><p><strong>Materials and methods: </strong>Uv-visible, fluorescence, circular dichroism (CD) spectroscopy methods, and molecular modeling were used to analyze the MTBE's effect on BSA structure and dynamics. The constant protein concentration and various MTBE contents were used for possible interactions.</p><p><strong>Results: </strong>The protein structural analysis shows that MTBE binds to BSA via positive enthalpy and entropy via hydrophobic interactions. Molecular docking shows the participation of several amino acids in the MTBE-BSA interaction. The CD spectroscopy results show that the BSA structure was not changed in the MTBE concentrations utilized in the study. Molecular dynamics (MD) simulation results suggest that MTBE can slightly change protein structure in the last 50ns.</p><p><strong>Conclusion: </strong>Comparing experimental and MD simulation results demonstrated that the BSA secondary structure was maintained in the low concentration of the MTBE. The entropy and enthalpy parameters asserted the hydrophobic interaction was the major force in the interaction between the BSA and MTBE.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a3/b8/IJB-20-e3111.PMC9618015.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40687229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acceleration of Yeast Autolysis by Addition of Fatty Acids, Ethanol and Alkaline Protease.","authors":"Zeinab Takalloo,&nbsp;Robabeh Nemati,&nbsp;Marjan Kazemi,&nbsp;Hadi Ghafari,&nbsp;Reza HasanSajedi","doi":"10.30498/ijb.2022.282895.3036","DOIUrl":"https://doi.org/10.30498/ijb.2022.282895.3036","url":null,"abstract":"<p><strong>Background: </strong>Autolysate products from yeast origin are very interesting for food, feed, cosmetic, pharmaceutical, and fermentation industries. The lysis process greatly influences the quality and efficiency of the final autolysates.</p><p><strong>Objectives: </strong>Here, we have compared four lysis methods based on autolysis, plasmolysis (with ethanol 1.5% (v/v) and coconut fatty acids 1% (w/w)) and hydrolysis (with alkaline protease 0.4 % (v/w)) on degrading the baker's yeast <i>Saccharomyces cerevisiae</i>.</p><p><strong>Materials and methods: </strong>The efficiency of processes was evaluated according to the recovered solid and protein contents, release of intracellular materials, cell viability, microscopy imaging, degree of hydrolysis and electrophoresis studies.</p><p><strong>Results: </strong>Results showed that the increased recovered solids and proteins, as well as a higher degree of hydrolysis (DH) were obtained for the enzymatic hydrolyzed cells using alkaline protease. SDS-PAGE analysis also confirmed the results. Further, functionality of the final products by agglutination test showed that the hydrolyzed cells could effectively bind pathogenic bacteria compared to the other cell lysates.</p><p><strong>Conclusions: </strong>In conclusion, this work provides adequate evidence for efficiency of alkaline protease for producing the nutritional cell lysates from baker's <i>S. cerevisiae</i> used in food, feed, cosmetic, and pharmaceutical applications. Moreover, this was the first report on using coconut fatty acids and alkaline protease in lysis of baker's yeast.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/16/3e/IJB-20-3036.PMC9618019.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40704274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fabrication and Characterization of pcDNA3.1(+) Location within Chitosan/Nanoparticles Complexes for Enhanced Gene Delivery.","authors":"Tohid Piri-Gharaghie,&nbsp;Abbas Doosti,&nbsp;Seyed Abbas Mirzaei","doi":"10.30498/ijb.2022.297534.3110","DOIUrl":"https://doi.org/10.30498/ijb.2022.297534.3110","url":null,"abstract":"<p><strong>Background: </strong>Chitosan nanoparticles (CSNP) are becoming a popular alternative for delivering nucleic acids to tissues for gene transfer (gene therapy). The size and morphology of these biodegradable nano-carriers are adjustable, and their positive charge allows them to interact strongly with negatively charged nucleic acids.</p><p><strong>Objective: </strong>This study aimed to fabricate and characterize pcDNA3.1 (+) plasmid (pDNA) and CSNP complexes and determine the plasmid location in these vehicles.</p><p><strong>Materials and methods: </strong>The characteristics of the pDNA/CSNP complex after production were investigated by SEM, XRD, DLS, TGA, and FTIR. The capacity of CSNP to form complexes with pDNA was investigated by labeling free plasmids with the fluorescent intercalating dye OliGreen. The stability of pDNA/CSNP in the presence of chitosanase was evaluated. Surface-Enhanced Raman Spectroscopy (SERS) for pDNA localization was performed, and absorption rate in BALB/c mice was assessed by real-time PCR.</p><p><strong>Results: </strong>The optimum pDNA/CSNP ratio for plasmid complex formation was established to be 1:2 (w.w) by measuring spectroscopy. At these optimum complex formation ratios, spectroscopy, and gel digest experiments, SERS indicated that a part of the pDNA was present on the complex outer surface. The findings of plasmid absorption in mouse thigh tissue by real-time PCR revealed that the rate of gene uptake was significantly greater at a dose of 1:2 (w.w) of pDNA/CSNP than in other groups (P< 0.001).</p><p><strong>Conclusions: </strong>The findings of this study reveal exactly pDNA fits into polymer nanostructured delivery systems, allowing the formulation to be adjusted for selective distribution. This understanding will aid future research into the system's functioning in vitro and in vivo.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/60/1d/IJB-20-e3110.PMC9618014.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40704270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ectopic expression of OCT4B1 Decreases Fertility Rate and Changes Sperm Parameters in Transgenic Mice.","authors":"Marzieh Naseri,&nbsp;Ehsan Ranaei Pirmardan,&nbsp;Seyed Javad Mowla,&nbsp;Mehdi Shamsara,&nbsp;Mansoreh Movahedin,&nbsp;Saeideh Nouri,&nbsp;Karim Nayernia,&nbsp;Maryam Kabir Salmani,&nbsp;Maryam Shahali","doi":"10.30498/ijb.2022.278266.3019","DOIUrl":"https://doi.org/10.30498/ijb.2022.278266.3019","url":null,"abstract":"<p><strong>Background: </strong>The octamer-binding transcription factor-4 (OCT4) is known as an established important regulator of pluripotency, as well as a genetic \"master switch\" in the self-renewal of embryonic stem and germ cells. <i>OCT4B1</i>, one of the three spliced variants of human OCT4, plays crucial roles in the regulation of pluripotency and stemness.</p><p><strong>Objectives: </strong>The present study developed a transgenic mouse model containing an <i>OCT4B1</i>-expressing construct under the transcriptional direction of mouse mammary tumor virus promoter (pMMTV) to evaluate the role of OCT4B1 in the function of male germ cells in terms of fertility potential. Additionally, the effect of ectopic OCT4B1 overexpression on endogenous OCT4 expression was examined in mouse embryonic stem cells (mESCs).</p><p><strong>Material and methods: </strong>The <i>pMMTV-OCT4B1cDNA</i> construct was injected into the pronuclei of 0.5-day NMRI embryos. Transgenic mice were identified based on the PCR analysis of tail DNA. Further, Diff-Quik staining was applied to assess sperm morphology, while the other sperm parameters were analyzed through a conventional light microscopic evaluation according to World Health Organization (WHO) criteria. The fertility rate was scored by using in vitro frtilization (IVF) method. Furthermore, mESCs was electroporated with the <i>OCT4B1cDNA</i>-containing constructs, followed by analyzing through employing semi-quantitative RT-PCR and western blotting.</p><p><strong>Results: </strong>The results demonstrated the changes in sperm morphology, as well as a statistically significant decrease in the other sperm parameters (count, viability, and motility) and fertility rate (p<0.05) in the transgenic mice compared with the control group. The assessment of the cause of the embryonic stem cell (ESC) death following transfection revealed a significant reduction in the endogenous OCT4 expression at both mRNA and protein levels in the transfected mESCs compared to the control ones.</p><p><strong>Conclusion: </strong>In general, the <i>in vivo</i> results suggested a potential role of OCT4B1 in the spermatogenesis process. These results represented that the overexpression of OCT4B1 may induce its role in spermatogenesis and fertility rate by interfering endogenous OCT4 expression. However, further studies are required to clarify the mechanisms underlying OCT4B1 function.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/45/2a/IJB-20-e3019.PMC9618016.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40704269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhanced Acetate Tolerance and Recombinant Protein Accumulation in <i>Escherichia coli</i> by Transgenic Expression of a Heat Shock Protein from Carrot (<i>Daucus carota</i> L.).","authors":"Minhye Kim,&nbsp;Eunju Im,&nbsp;Yeh Jin Ahn","doi":"10.30498/ijb.2022.309657.3177","DOIUrl":"https://doi.org/10.30498/ijb.2022.309657.3177","url":null,"abstract":"<p><strong>Background: </strong>In <i>Escherichia coli</i> (<i>E. coli</i>) culture, acetate accumulates as an undesirable by-product of aerobic fermentation on glucose and inhibits cell growth and recombinant protein production.</p><p><strong>Objectives: </strong>We examined whether the heterologous expression of a eukaryotic heat shock protein (Hsp) can confer tolerance to acetate in <i>E. coli</i>.</p><p><strong>Materials and methods: </strong>Transgenic cell lines (TCLs) heterologously expressing a small heat shock protein (sHsp) from carrot (<i>Daucus carota</i> L.), DcHsp17.7, were exposed to heat, sodium acetate, and alkaline conditions. The cell growth and cell viability were examined by measuring O.D.₆₀₀ and colony-forming units (CFU), respectively. The His-tagged recombinant alcohol dehydrogenase (ADH) gene cloned in a pET11a expression vector was introduced into TCL1 and expressed by isopropyl β-D-1-thiogalactopyranoside treatment. After purifying using Ni-NTA affinity chromatography, its accumulation levels were examined using SDS-PAGE in the presence of acetate.</p><p><strong>Results: </strong>TCLs constitutively expressing DcHsp17.7 showed improved growth, cell density, and cell viability under the stress conditions of heat, acetate, and alkaline compared to an empty vector control line. In acetate stress conditions, TCL1 accumulated more cellular proteins (approximately 130%) than the control. The recombinant ADH accumulated to a higher level in TCL1 (2.2-fold at 16 °C) than the control. The addition of acetate reduced the recombinant ADH level by 70% in the control when compared with the absence of acetate. In contrast, recombinant ADH accumulation was not affected by acetate in TCL1. In the presence of acetate, TCL1 accumulated 6.4-fold more recombinant ADH than did the control. Furthermore, recombinant ADH produced in TCL1 showed 1.5-fold higher enzyme activity than that produced in the control in the presence or absence of acetate.</p><p><strong>Conclusion: </strong>Our study showed that heterologously expressed DcHsp17.7 from carrot can alleviate the negative effects of acetate on <i>E. coli</i>.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d5/d5/IJB-20-e3177.PMC9618011.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40704272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Potential Prognostic Markers and Key Therapeutic Targets in Hepatocellular Carcinoma Using Weighted Gene Co-Expression Network Analysis: A Systems Biology Approach.","authors":"Hengameh Sharifi,&nbsp;Hossein Safarpour,&nbsp;Maryam Moossavi,&nbsp;Mohsen Khorashadizadeh","doi":"10.30498/ijb.2022.269817.2968","DOIUrl":"https://doi.org/10.30498/ijb.2022.269817.2968","url":null,"abstract":"<p><strong>Background: </strong>As the most prevalent form of liver cancer, hepatocellular carcinoma (HCC) ranks the fifth highest cause of cancer-related death worldwide. Despite recent advancements in diagnostic and therapeutic techniques, the prognosis for HCC is still unknown.</p><p><strong>Objectives: </strong>This study aimed to identify potential genes contributing to HCC pathogenicity.</p><p><strong>Materials and methods: </strong>To this end, we examined the GSE39791 microarray dataset, which included 72 HCC samples and 72 normal samples. An investigation of co-expression networks using WGCNA found a highly conserved blue module with 665 genes that were strongly linked to HCC.</p><p><strong>Results: </strong><i>APOF</i>, <i>NAT2</i>, <i>LCAT</i>, <i>TTC36</i>, <i>IGFALS</i>, <i>ASPDH</i>, and <i>VIPR1</i> were the blue module's top 7 hub genes. According to the results of hub gene enrichment, the most related issues in the biological process and KEGG were peroxisome organization and metabolic pathways, respectively. In addition, using the drug-target network, we discovered 19 FDA-approved medication candidates for different reasons that might potentially be employed to treat HCC patients through the modulation of 3 hub genes of the co-expression network (<i>LCAT</i>, <i>NAT2</i>, and <i>VIPR1</i>). Our findings also demonstrated that the 3 scientifically validated miRNAs regulated the co-expression network by the <i>VIPR1</i> hub gene.</p><p><strong>Conclusion: </strong>We found co-expressed gene modules and hub genes linked with HCC advancement, offering insights into the mechanisms underlying HCC progression as well as some potential HCC treatments.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b8/ff/IJB-20-e2968.PMC9618018.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40704273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid Isolation of Gastric Adenocarcinoma Cancer Stem Cells as a Target for Autologous Dendritic Cell-Based Immunotherapy.","authors":"Vahid Bagheri,&nbsp;Seyed-Alireza Esmaeili,&nbsp;Mehran Gholamin,&nbsp;Mohammad Reza Abbaszadegan","doi":"10.30498/ijb.2021.284841.3045","DOIUrl":"https://doi.org/10.30498/ijb.2021.284841.3045","url":null,"abstract":"<p><strong>Background: </strong>Gastric cancer (GC) is a malignancy cause associated with a high death rate in the world. Cancer stem cells (CSCs) are a rare immortal subpopulation of cells within tumors with characteristics of the ability to self-renew, initiate tumor, and differentiate into defined progenies as well as and high resistance to conventional therapies.</p><p><strong>Objectives: </strong>Despite the use of surgery and chemotherapy for GC therapy, there are no efficient therapeutic protocols for it to date. Therefore, rapid isolation of CSCs in order to therapeutic targets, especially immunotherapy is very important.</p><p><strong>Materials and methods: </strong>Cancerous cell suspension isolated from patients with GC was cultured in the serum-free medium containing EGF, bFGF, LIF, and heparin under non-adherent culture conditions to generate spheres. Expression of mRNA level stemness transcription factors (OCT4, SOX2, SALL4, and Cripto-1), CD44 variable isoforms (CD44s, CD44v3, CD44v6, CD44V8-10) of spheroid-forming single cells compared with gastric normal tissue cells using real time PCR and molecules of CD44, CD54, and EpCAM as gastric CSC markers, and stemness factor Oct4 using flow cytometry, as well as tumorgenicity using subcutaneous injection of sphere-forming cells to nude mice were investigated.</p><p><strong>Results: </strong>Few cancerous cells isolated from patients with GC were able to generate three-dimensional spheroid colonies in the serum-free medium containing EGF, bFGF, LIF, and heparin under non-adherent culture conditions, and form xenograft tumors in immunodeficient nude mice after subcutaneous injection. Spheroid-forming single cells upregulated stemness transcription factors OCT4, SOX2, SALL4, and Cripto-1 that are associated with pluripotency and self-renewal and CD44 isoforms (CD44s, CD44v3, CD44v6, CD44V8-10) compared with gastric normal tissue cells. Finally, molecules of CD44, CD54, and EpCAM as gastric CSC markers and stemness factor Oct4 were expressed in sphere-forming cells.</p><p><strong>Conclusion: </strong>We suggested that the sphere formation and tumorigenicity assays are two procedures, leading to the rapid isolation of cancer cells with certain stem-like properties in order to target CSCs using autologous dendritic cell therapy, especially in patients with advanced disease.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/67/bc/IJB-20-e3045.PMC9583826.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40456220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}