The delayed effect of mustard gas on housekeeping gene expression in lung biopsy of chemical injuries

ObjectiveSulfur mustard (SM) was used as a chemical weapon in Iraq-Iran war. Exposed people have major complications in important organs such as pulmonary system. Some studies have shown that SM could affect the expression of endogenous genes and non-housekeeping genes, time dependently. To understand the accurate molecular mechanism of the delayed effect of SM, the identification of the gene expression pattern in these patients is essential. Hence, we have evaluated mRNA expression of four common housekeeping genes (ACTIN, PGK1, β2m, GAPDH) in SM-exposed and non-exposed (control) formalin-fixed, paraffin-embedded (FFPE) human lung tissues.MethodParaffin block of lung biopsy of SM-exposed people (11 cases) and people without exposure to SM as control group (9 cases) have been selected. The mRNA expression of four endogenous control genes has been evaluated by qRT-PCR. The stability value of each gene was calculated by different methods.ResultIt was found that ACTIN mRNA has the highest expression (30.26±2.87) and PGK1 has the lowest standard deviation (SD) (30.885±2.215) between pooled groups. The best correlation was between ACTIN and PGK1 expressions. The M value has shown that ACTIN and then PGK1 are the most stable housekeeping genes among. The results obtained from the GeNorm and NormFinder have indicated that the pair ACTIN- PGK1 is the most suitable choice for endogenous control genes.ConclusionACTIN and PGK1 genes are stable in studied lung tissues and are the better than two other housekeeping genes. In addition, mustard gas does not affect their expression in long term.     

Effect of bone marrow–derived mesenchymal stromal cells on hepatoma

Background aimsThe aim of the study was to evaluate the effect of mesenchymal stromal cells (MSCs) on tumor cell growth in vitro and in vivo and to elucidate the apoptotic and anti-proliferative mechanisms of MSCs on a hepatocellular carcinoma (HCC) murine model.MethodsThe growth-inhibitory effect of MSCs on the Hepa 1–6 cell line was tested by means of methyl thiazolyl diphenyl-tetrazolium assay. Eighty female mice were randomized into four groups: group 1 consisted of 20 mice that received MSCs only by intrahepatic injection; group 2 consisted of 20 HCC mice induced by inoculation of Hepa 1–6 cells into livers without MSC treatment; group 3 consisted of 20 mice that received MSCs after induction of liver cancer; group 4 consisted of 20 mice that received MSCs after induction of liver cancer on top of induced biliary cirrhosis.ResultsMSCs exhibited a growth-inhibitory effect on Hepa 1–6 murine cell line in vitro. Concerning in vivo study, decreases of serum alanine transaminase, aspartate transaminase and albumin levels after MSC transplantation in groups 2 and 3 were found. Gene expression of α-fetoprotein was significantly downregulated after MSC injection in the HCC groups. We found that gene expression of caspase 3, P21 and P53 was significantly upregulated, whereas gene expression of Bcl-2 and survivin was downregulated in the HCC groups after MSC injection. Liver specimens of the HCC groups confirmed the presence of dysplasia. The histopathological picture was improved after administration of MSCs to groups 2 and 3.ConclusionsMSCs upregulated genes that help apoptosis and downregulated genes that reduce apoptosis. Therefore, MSCs could inhibit cell division of HCC and potentiate their death.     

The p53-signaling pathway and colorectal cancer: Interactions between downstream p53 target genes and miRNAs

IntroductionWe examined expression of genes in the p53-signaling pathway. We determine if genes that have significantly different expression in carcinoma tissue compared to normal mucosa also have significantly differentially expressed miRNAs. We utilize a sample of 217 CRC cases.MethodsWe focused on fold change (FC) > 1.50 or <0.67 for genes and miRNAs, that were statistically significant after adjustment for multiple comparisons. We evaluated the linear association between the differential expression of miRNA and mRNA. miRNA:mRNA seed-region matches also were determined.ResultsEleven dysregulated genes were associated with 37 dysregulated miRNAs; all were down-stream from the TP53 gene. MiR-150-5p (HR = 0.82) and miR-196b-5p (HR 0.73) significantly reduced the likelihood of dying from CRC when miRNA expression increased in rectal tumors.ConclusionsOur data suggest that activation of p53 from cellular stress, could target downstream genes that in turn could influence cell cycle arrest, apoptosis, and angiogenesis through mRNA:miRNA interactions.     

Inhibition of non-muscle myosin II leads to G0/G1 arrest of Wharton's jelly-derived mesenchymal stromal cells

Background aimsMesenchymal stromal cells (MSCs) have remarkable clinical potential for cell-based therapy. Wharton's jelly-derived mesenchymal stromal cells (WJ-MSCs) from umbilical cord share unique properties with both embryonic and adult stem cells. MSCs are found at low frequency in vivo, and their successful therapeutic application depends on rapid and efficient large-scale expansion in vitro. Non-muscle myosin II (NMII) has pivotal roles in different cellular activities, such as cell division, migration and differentiation. We performed this study to understand the role of NMII in proliferation and cell cycle progression in WJ-MSCs.MethodsWJ-MSCs were cultured in the presence of blebbistatin, and cell cycle analysis was performed using flow cytometry, proliferation kinetics, senescence assay and gene expression profile using polymerase chain reaction array.ResultsWhen cultured in the presence of blebbistatin, an inhibitor of NMII adenosine triphosphatase activity, WJ-MSCs exhibited dose-dependent reduction in proliferative potential along with increase in cell size and induction of early senescence. Inhibition of NMII activity also affected cell cycle progression in WJ-MSCs and led to an increase in the percentage of cells in G₀/G₁ phase with a corresponding reduction in the percentage of cells in G₂/M phase. Blebbistatin-induced G₀/G₁ arrest of WJ-MSCs was further associated with up-regulation of cell cycle inhibitory genes CDKN1A, CDKN2A and CDKN2B and down-regulation of numerous genes related to progression through S and M phases of the cell cycle.ConclusionsOur study demonstrates that inhibition of NMII activity in WJ-MSCs leads to G₀/G₁ arrest and alteration in the expression levels of certain key cell cycle-related genes.     

microRNA-151-5p在肾血管性高血压大鼠血管内皮细胞中的表达及意义

目的:研究microRNA-151-5p(miR-151-5p)在两肾一夹(2K1C)肾血管性高血压大鼠中的表达,并为miR-151-5p参与调节血管内皮细胞功能提供理论依据。方法:建立2K1C大鼠模型,获得胸主动脉血管内皮,采用荧光定量PCR技术检测血管内皮细胞中miR-151-5p的表达,通过数据库及生物信息学软件预测miR-151-5p的靶基因,并对靶基因进行GO富集和KEGG pathway分析。结果:与假手术组大鼠相比较,实验组大鼠胸主动脉血管内皮细胞miR-151-5p的表达量显著升高(P0.05)。GO分析显示miR-151-5p的靶基因参与蛋白加工水解、Notch受体加工等多种生物学功能(P0.01);KEGG pathway分析显示miR-151-5p的靶基因参与Notch信号通路、血管平滑肌收缩、代谢途径、细菌感染和RNA转运等信号通路。结论:2K1C大鼠血管内皮细胞中miR-151-5p表达升高,可能通过对其靶基因APH1A的调控参与血管内皮细胞功能调节。     

Noncoding RNAs within the HOX gene network in tumor pathogenesis and progression

HOX genes are involved with normal development, cell identity, cell differentiation, cell metabolism, apoptosis, autophagy as well as with diseases such as tumor pathogenesis and progression. In particular, the genes belonging to HOX paralogous 13 seem to carry out a relevant role in both tumor development and disease progression. In recent years, several noncoding RNAs (ncRNA) sequences have been identified in HOX loci, including long noncoding RNA (lncRNA) and microRNA (miRNA), highly conserved during evolution. Many studies have shown that specific intergenic ncRNAs in HOX loci could directly modulate HOX genes expression in normal and pathological conditions. In the present review we attempt to describe the role of these ncRNAs, through the regulation of the HOX gene network, in normal cell biology, and, with particular emphasis, in diseases such as in cancer pathogenesis and progression.     

Inter-strain expression of sequence-diverse HET domain genes severely inhibits growth of Aspergillus oryzae

ABSTRACT

In the Pezizomycotina (filamentous ascomycete) species, genes that encode proteins with an HET domain (Pfam: PF06985) are reportedly involved in heterokaryon incompatibility (HI) in which cell death or growth defects are induced after fusion of cells that are genetically incompatible owing to diversities in their nucleotide sequence. HET domain genes are commonly found in Pezizomycotina genomes and are functionally characterized in only a few species. Here, we compared 44 HET domain genes between an incompatible strain pair of Aspergillus oryzae RIB40 and RIB128 and performed inter-strain expression of 37 sequence-diverse genes for mimicking HI. Four HET domain genes were identified to cause severe growth inhibition in a strain- or sequence-specific manner. Furthermore, SNPs responsible for the inhibition of cell growth were identified. This study provides an important insight into the physiological significance of sequence diversity of HET domain genes and their potential functions in HI of A. oryzae.     

Bacillus sp.ZJS3基因组测序及砷胁迫下相关基因表达分析

【背景】环境中高毒性As³⁺的微生物氧化在砷的生物地球化学循环中起重要作用,具有潜在的应用价值。【目的】Bacillus sp.ZJS3菌株是本实验室前期分离鉴定的一株As³⁺耐受菌株,而且对多种重金属具有耐受性,期望进一步明确该菌株在As³⁺胁迫下菌体形态变化及应对砷胁迫的遗传基础,为As³⁺耐受细菌的研究提供基础数据。【方法】使用单分子实时测序（single-molecule real-time sequencing,SMRT）及Illumina测序技术对Bacillus sp.ZJS3菌株进行全基因组测序,对其基因进行功能注释和生物信息学分析,并结合绝对定量PCR技术对砷抗性及砷代谢相关基因进行分析。【结果】Bacillus sp.ZJS3菌株基因组大小为5.82 Mb,GC含量为35.9%,包含染色体1个、质粒3个、CDS数量为5 981个、tRNA 104个、sRNA 136个、rRNA 42个、串联重复序列173个、基因岛13个、转运蛋白1 023个、跨膜蛋白1 717个和双组分调控基因160个。NR、Swiss-Prot、Pfam、COG、GO和KEGG数据库分别可注释Bacillus sp.ZJS3菌株基因组中97.66%、69.30%、78.52%、65.49%、67.65%和43.87%的基因。绝对定量PCR结果表明,arsC基因在砷处理条件下显著高于对照组,而arsB基因在砷处理条件下显著低于对照组。【结论】Bacillus sp.ZJS3菌株在As³⁺胁迫下可能导致细胞分裂无法正常进行,进而影响细胞形态。基因组中aqpZ、arsA、arsB、arsC等基因的存在表明该菌株具有As³⁺外排和还原As⁵⁺的能力,phoUpstBACS的存在表明菌株可以吸收As⁵⁺,但菌株受到外界环境As³⁺胁迫时arsB表达水平降低。     

Yeast RAS2 affects cell viability,mitotic division and transient gene expression in Nicotiana species

Overexpression of the budding yeast RAS2 gene in Nicotiana plumbaginifolia cells revealed that RAS2 acted as a suicide gene in freshly isolated protoplasts from leaves and blocked cell proliferation in cell suspension-derived protoplasts. Among a series of genes tested (such as npt II, CDC35, PDE2), RAS2 was the only one to block the expression of the cat gene, as measured in a transient gene expression assay. Another ras gene, v-Ha-ras, had similar effects. Furthermore, the RAS2 effect was species-specific and depended on the modulation of hormonal metabolism in the transfected cells, while no differences were noticed between the normal and the activated val19 gene. Transfected plant cells are shown to synthesize a RAS2 protein of the same electrophoretic mobility as the yeast RAS2 product. The results are discussed in the broader context of the evolutionarily conserved ras genes involved in vital cellular functions.     

巴斯德毕赤酵母不同生长阶段内参基因的筛选与验证

【背景】巴斯德毕赤酵母(Komagataella phaffii)是一种甲基营养型酵母,近年来作为生产重组蛋白和构建生物合成途径的细胞工厂受到广泛关注。实时荧光定量PCR (real-time quantitative PCR,RT-qPCR)是巴斯德毕赤酵母表达系统研究中一种快速、高效的基因表达水平检测技术,但需要进行归一化处理才能保证所得结果的可靠性。【目的】筛选并验证巴斯德毕赤酵母在不同生长阶段最稳定的内参基因用于精准归一化RT-qPCR的结果。【方法】通过转录组数据分析初步筛选出16个候选内参基因(rps8b、rpl35a、rpl10、eif5a、rpl19a、por1、rpl23b、0887、tif1、ole1、rpl14b、gs、sun、sdh2、trx1和ccp1)。通过RT-qPCR技术得到候选内参基因的C_t值,利用qBASE软件中的geNorm程序综合NormFinder算法评估内参基因的表达稳定性。【结果】通过geNorm分析得出精准归一化所需的最佳内参基因个数为2,最稳定的基因是rpl19a和tif1,NormFinder分析得到稳定性最高的内参基因为tif1。此外,利用甲酸脱氢酶编码基因fdh和乙醇脱氢酶甲醛脱氢酶双功能酶的编码基因afdh对候选内参基因进行验证。【结论】巴斯德毕赤酵母不同生长阶段的RT-qPCR进行精准归一化需要tif1和rpl19a这2个内参基因,为相关功能基因的表达定量提供了可靠的分析依据,补充了RT-qPCR分析中的内参基因,为巴斯德毕赤酵母不同生长阶段的基因表达调控及其应用研究提供了新的参考。     

Affymetrix基因表达谱芯片在新疆维吾尔族与汉族胰腺癌组织样本间差异表达基因筛选中的运用

目的:运用基因表达谱芯片筛选并分析新疆维吾尔族与汉族胰腺癌组织样本间的差异表达基因。方法:收集我院2014年1月至2016年6月间行手术切除的维吾尔族与汉族胰腺导管细胞癌组织并提取总RNA,选取经Nanodrop 2000与Agilent 2100仪器质检合格的样本总RNA采用Affymetrix基因表达谱芯片筛选出差异表达基因并绘制统计图,运用基因本体(GO)分析及信号通路(Pathway)分析对这些差异表达基因的生物信息进行汇总分析。结果:通过基因表达谱芯片分析,新疆维吾尔族与汉族胰腺癌组织样本间共检测到1063个基因存在差异表达,在维吾尔族胰腺癌标本中显著上调表达的基因共281个,差异表达倍数最高的为IGLV1-44基因(差异倍数:9.99)下调表达的基因共782个,差异表达倍数最高的为CPB1基因(差异倍数:33.76);在Gene Ontology数据库中共检索到815个上述差异表达基因具有明确的GO分类,差异表达倍数最高的为CPB1基因(差异倍数:33.76);Pathway分析中共检测到30条信号通路包含有上述差异表达基因,共涉及196个基因,其中以FAK信号通路差异表达基因富集程度最高,差异表达倍数最高的基因为COL11A1基因(差异倍数:5.02)。结论:基因表达谱芯片分析结果显示,在新疆维吾尔族与汉族胰腺癌组织样本间存在大量的差异表达基因,这些基因与胰腺癌的增殖分化、侵袭转移及多药耐药等特性密切相关,且参与了多条生物体内重要信号转导通路的调控。     

Aberrant expression of imprinted genes in post-implantation rat embryos

AimImprinted genes are known regulators of embryo growth. Studies from our laboratory have demonstrated that treatment of adult male rats with tamoxifen increased post-implantation loss at around midgestation. Expression of insulin like growth factor 2 (Igf2), a paternally expressed imprinted gene was down-regulated in the resorbing embryos obtained at embryonic day 13. Hypomethylation of Igf2-H19 imprint control region was observed in the resorbing embryo sires and spermatozoa obtained from tamoxifen-treated rats thereby suggesting that errors in imprint acquisition during spermatogenesis can result in embryo loss. The present study aims at studying the expression of other imprinted genes, besides Igf2 in the embryos sired by tamoxifen-treated males.Main methodsGene expression profiles of resorbing versus normal embryos were assessed by microarrays. Real time quantitative RT-PCR for six imprinted genes and four genes involved in cell cycle was done to validate gene expression data. The affected pathways and functions were identified in the resorbing embryos and effect on cell cycle was confirmed by flow cytometry.Key findingsAberrant expression of a number of imprinted genes was observed in the resorbing embryos when compared to the normal embryos at embryonic days 11 and 13. Down-regulation of Notch signaling, Wnt signaling and cell cycle pathway was observed in the resorbing embryos.SignificanceThe study suggests that exposure of male germ cells to tamoxifen during adulthood results in aberrant expression of imprinted genes and down-regulation of development associated pathways in the F₁ progeny thereby causing embryo loss.     

Expression and regulation of genes associated with cell death during murine preimplantation embryo development

The newly fertilized preimplantation embryo depends entirely on maternal mRNAs and proteins deposited and stored in the oocyte prior to its ovulation. If the oocyte is not sufficiently equipped with maternally stored products, or if zygotic gene expression does not commence at the correct time, the embryo will die. One of the major abnormalities observed during early development is cellular fragmentation. We showed previously that cellular fragmentation in human embryos can be attributed to programmed cell death (PCD). Here, we demonstrate that the PCD that occurs during the 1-cell stage of mouse embryogenesis is likely to be regulated by many cell death genes either maternally inherited or transcribed from the embryonic genome. We have demonstrated for the first time the temporal expression patterns of nine cell death regulatory genes, and our preliminary experiments show that the expression of these genes is altered in embryos undergoing fragmentation. The expression of genes involved in cell death (MA-3, p53, Bad, and Bcl-xS) seems to be elevated, whereas the expression of genes involved in cell survival (Bcl-2) is reduced. We propose that PCD may occur by default in embryos that fail to execute essential developmental events during the first cell cycle. Mol. Reprod. Dev. 51:243–253, 1998. © 1998 Wiley-Liss, Inc.     

The tissue- and developmental stage-specific involvement of autophagy genes in aggrephagy

ABSTRACT

Genetic screens have identified two sets of genes that act at distinct steps of basal autophagy in higher eukaryotes: the pan-eukaryotic ATG genes and the metazoan-specific EPG genes. Very little is known about whether these core macroautophagy/autophagy genes are differentially employed during multicellular organism development. Here we analyzed the function of core autophagy genes in autophagic removal of SQST-1/SQSTM1 during C. elegans development. We found that loss of function of genes acting at distinct steps in the autophagy pathway causes different patterns of SQST-1 accumulation in different tissues and developmental stages. We also identified that the calpain protease clp-2 acts in a cell context-specific manner in SQST-1 degradation. clp-2 is required for degradation of SQST-1 in the hypodermis and neurons, but is dispensable in the body wall muscle and intestine. Our results indicate that autophagy genes are differentially employed in a tissue- and stage-specific manner during the development of multicellular organisms.

Abbreviations: ATG: autophagy related; CLP: calpain family; EPG: ectopic PGL granules; ER: endoplasmic reticulum; ESCRT: endosomal sorting complex required for transport; GFP: green fluorescent protein; LGG-1/LC3: LC3, GABARAP and GATE-16 family; MIT: microtubule interacting and transport; PGL: P granule abnormality protein; SQST-1: sequestosome-related; UPS: ubiquitin-proteasome system     

三棱内酯B调控人冠状动脉内皮细胞基因表达谱的生物信息学分析

目的:分析三棱内酯B在人冠状动脉内皮细胞中的表达谱数据集,寻找三棱内酯B调控血管内皮功能的关键作用靶点。方法:基于GEO公共数据库,下载原始表达谱数据集(GSE44598),经过差异基因筛选,功能注释,通路富集,信号通路网络以及基因互作网络分析,找出三棱内酯B对人冠状动脉内皮细胞基因表达谱产生影响的关键基因和信号通路。结果:同对照组相比,三棱内酯B给药组共有5224个基因有显著性差异,包括2628个上调基因和2596个下调基因。基因功能注释和信号通路富集分析表明,差异基因主要参与了细胞周期过程。网络分析显示,MAPK信号通路、细胞周期通路以及PLCG2,PRKACA和ADCY4等为关键信号通路和基因。结论:三棱内酯B通过影响PLCG2,PRKACA,ADCY4等基因的表达,参与MAPK和细胞周期等信号通路,从而调节人冠状内皮细胞的功能。这些关键基因和信号通路是三棱内酯B在心血管疾病治疗应用中潜在的作用靶点。     

基于CRISPR/Cas9技术构建CELF6基因敲除细胞系并探讨CELF6与p53基因的关系

目的:构建CELF6基因敲除细胞系并探讨CELF6与p53基因之间的关系。方法:CRISPR/Cas9双载体慢病毒系统通过两个慢病毒载体分别向细胞中导入Cas9蛋白和sg RNA序列表达框,从而实现对CELF6基因的敲除。通过Surveyor(错配酶法)检测sg RNA活性并利用Western blot(蛋白质免疫印迹)检测CELF6的敲除效率。进一步利用CCK-8试剂盒检测敲除CELF6和过表达CELF6对细胞增殖的影响。利用公开可用的癌症基因组图谱(TCGA)数据库分析CELF6在多种肿瘤组织中的表达情况。结果:CELF6基因敲除的HCT116细胞系成功构建。Western blot检测发现CELF6基因敲除的细胞系中p53、p-RB蛋白的表达水平显著下调,而CELF6过表达的细胞中p53、p-RB蛋白的表达水平明显上调。CCK-8实验结果显示敲除CELF6基因后,细胞增殖活性显著增强;而过表达CELF6后,细胞的增殖活性受到明显抑制。生物信息学分析发现CELF6在结肠癌、胶质母细胞瘤、子宫内膜癌、肾嫌色细胞癌、乳腺癌、甲状腺癌等肿瘤组织中显著低表达。结论:推测CELF6是一种新的潜在肿瘤抑制基因,其可能在肿瘤的发生、发展过程中发挥重要作用。     

Differential Gene Expression Profiling of Dystrophic Dog Muscle after MuStem Cell Transplantation

BackgroundSeveral adult stem cell populations exhibit myogenic regenerative potential, thus representing attractive candidates for therapeutic approaches of neuromuscular diseases such as Duchenne Muscular Dystrophy (DMD). We have recently shown that systemic delivery of MuStem cells, skeletal muscle-resident stem cells isolated in healthy dog, generates the remodelling of muscle tissue and gives rise to striking clinical benefits in Golden Retriever Muscular Dystrophy (GRMD) dog. This global effect, which is observed in the clinically relevant DMD animal model, leads us to question here the molecular pathways that are impacted by MuStem cell transplantation. To address this issue, we compare the global gene expression profile between healthy, GRMD and MuStem cell treated GRMD dog muscle, four months after allogenic MuStem cell transplantation.ResultsIn the dystrophic context of the GRMD dog, disease-related deregulation is observed in the case of 282 genes related to various processes such as inflammatory response, regeneration, calcium ion binding, extracellular matrix organization, metabolism and apoptosis regulation. Importantly, we reveal the impact of MuStem cell transplantation on several molecular and cellular pathways based on a selection of 31 genes displaying signals specifically modulated by the treatment. Concomitant with a diffuse dystrophin expression, a histological remodelling and a stabilization of GRMD dog clinical status, we show that cell delivery is associated with an up-regulation of genes reflecting a sustained enhancement of muscle regeneration. We also identify a decreased mRNA expression of a set of genes having metabolic functions associated with lipid homeostasis and energy. Interestingly, ubiquitin-mediated protein degradation is highly enhanced in GRMD dog muscle after systemic delivery of MuStem cells.ConclusionsOverall, our results provide the first high-throughput characterization of GRMD dog muscle and throw new light on the complex molecular/cellular effects associated with muscle repair and the clinical efficacy of MuStem cell-based therapy.