基于TCGA和GEO数据库的胃癌lncRNA筛选与ceRNA网络构建

胃癌(gastric cancer,GC)是我国最常见的恶性肿瘤之一,严重危害人类健康。胃癌发病机制复杂,缺乏特异性预后生物标志物。长链非编码RNA (long non-coding RNA,lncRNA)可作为竞争性内源RNA (competing endogenous RNA,ceRNA),影响microRNA (miRNA)与mRNA的结合,从而影响胃癌的发生、发展。基于TCGA和GEO数据库的转录组数据,筛选GC 中差异表达的 lncRNAs,并构建基于 6 条 lncRNAs(HAGLROS、TMEM92-AS1、LINC01745、HOXC-AS3、SEMA3B-AS1、FEZF1-AS 1)的lncRNA-miRNA-mRNA网络。网络核心基因的KEGG/GO富集和蛋白质互作分析结果显示,lncRNA可能通过miRNA海绵吸附作用,调控胃癌的发生、发展与转移。AC011352.1、AC087636.1、AC093627.1、GAS1RR与胃癌患者的预后相关性具有统计学意义(P<0.05),并可能成为胃癌患者潜在的预后生物标志物。     

PAMM不影响人脂肪干细胞的成脂分化能力

目的 PAMM（peroxiredoxin-like 2 activated in M-CSF stimulated monocytes）是近年来发现的一种在脂肪组织中高表达的分泌因子,但其生物学功能尚不完全清楚。为了给PAMM功能研究提供新线索,本文探讨了PAMM在白色脂肪生成中的可能作用及PAMM调节的下游基因。方法 利用成脂分化液或“成脂分化液+IL-1α”建立人脂肪干细胞（adipose-derived stem cells,ADSCs）的成脂分化和成脂抑制模型。用siRNA干扰和过表达质粒转染的方法抑制或上调PAMM表达水平。采用基因芯片、mRNA测序及定量RT-PCR检测基因的mRNA表达水平,采用蛋白质印迹法评价蛋白质表达水平,用油红O染色检测脂滴沉积。结果 随着ADSCs向白色脂肪分化,PAMM表达水平明显上升,而随着成脂抑制,PAMM表达明显下降。在ADSCs中沉默或过表达PAMM后,再进行成脂分化。结果发现,上调或下调PAMM对脂滴形成及成脂相关基因的表达均无明显影响。类似地,在高度分化的脂肪细胞中敲低PAMM表达,对细胞形态及脂滴含量亦无明显影响。本文进一步利用siRNA干扰、mRNA测序及qRT-PCR,筛选和验证了一批受PAMM调节的下游基因及功能性基因集,包括SULF1、A2M基因及调节P53稳定性的基因集等。结论 PAMM可作为白色成脂分化的标志基因,但其自身对白色脂肪细胞生成无明显影响,本研究筛选出来的PAMM下游基因及基因集,可为进一步研究PAMM的功能提供新线索。     

Uric Acid Promotes Osteogenic Differentiation and Inhibits Adipogenic Differentiation of Human Bone Mesenchymal Stem Cells

To investigate the effect of uric acid on the osteogenic and adipogenic differentiation of human bone mesenchymal stem cells (hBMSCs). The hBMSCs were isolated from bone marrow of six healthy donors. Cell morphology was observed by microscopy and cell surface markers (CD44 and CD34) of hBMSCs were analyzed by immunofluorescence. Cell morphology and immunofluorescence analysis showed that hBMSCs were successfully isolated from bone marrow. The number of hBMSCs in uric acid groups was higher than that in the control group on day 3, 4, and 5. Alizarin red staining showed that number of calcium nodules in uric acid groups was more than that of the control group. Oil red‐O staining showed that the number of red fat vacuoles decreased with the increased concentration of uric acid. In summary, uric acid could promote the proliferation and osteogenic differentiation of hBMSCs while inhibit adipogenic differentiation of hBMSCs.     

Suppressive Role of Boron on Adipogenic Differentiation and Fat Deposition in Human Mesenchymal Stem Cells

Biological Trace Element Research - Over the past years, adipose tissue has become an invaluable source of mesenchymal stem cells (MSCs) due to development of improved isolation methodologies. In a...     

脂肪基质细胞脂向分化过程中MicroRNA-21的表达变化

目的:了解脂肪基质细胞(ADSCs)在脂向分化过程中MicroRNA-21(miRNA-21)表达变化情况.方法:从8只出生30 d雄性体健SD幼鼠体内取出脂肪,采用密度梯度离心结合贴壁培养法获得了纯度高的脂肪基质细胞,采用脂向诱导液对第3代的脂肪基质细胞进行诱导培养,并以未诱导的细胞为对照.成脂诱导培养液[DMEM培养液中加入地塞米松(1 μmol·L-1)、3-异丁基-1甲基黄嘌呤(0.5 mmol.L-1)、胰岛素(10 mg·L-1)].应用microRNA芯片技术检测脂肪基质细胞脂向诱导后7 d和未诱导microRNA-21的表达差异.采用实时定量PCR检测microRNA-21在脂肪基质细胞脂向分化前后表达量变化.结果:经显微镜下观察、油红O染色及PPARγ免疫细胞化学染色检测证实脂肪基质细胞已经脂向分化,miRNA芯片及实时定量PCR结果均表明miRNA-21在脂肪基质细胞体外脂向分化过程中表达显著下调.结论:miRNA-21在脂肪基质细胞脂向分化后的表达有显著降低,可能参与调控ADSCs的脂向分化过程.     

Construction of lncRNA-associated ceRNA networks to identify prognostic lncRNA biomarkers for glioblastoma

Long noncoding RNAs (lncRNAs) serve as competitive endogenous RNAs (ceRNAs) that play significant regulatory roles in the pathogenesis of tumors. However, the role of lncRNAs, especially the lncRNA-related ceRNA regulatory network, in glioblastoma (GBM) has not been fully elucidated. The goal of the current study was to construct lncRNA-microRNA-mRNA-related ceRNA networks for further investigation of their mechanism of action in GBM. We downloaded data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases and identified differential lncRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) associated with GBM. A ceRNA network was constructed and analyzed to examine the relationship between lncRNAs and patients’ overall survival. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGGs) were used to analyze the related mRNAs to indirectly explain the mechanism of action of lncRNAs. The potential effective drugs for the treatment of GBM were identified using the connectivity map (CMap). After integrated analysis, we obtained a total of 210 differentially expressed lncRNAs, 90 differentially expressed miRNAs, and 2508 differentially expressed mRNAs (DEmRNAs) from the TCGA and GEO databases. Using these differential genes, we constructed a lncRNA-associated ceRNA network. Six lncRNAs in the ceRNA network were associated with the overall survival of patients with GBM. Through KEGG analysis, it was found that the DEmRNAs involved in the network are related to cancer-associated pathways, for instance, mitogen-activated protein kinase and Ras signaling pathways. CMap analysis revealed four small-molecule compounds that could be used as drugs for the treatment of GBM. In this study, a multi-database joint analysis was used to construct a lncRNA-related ceRNA network to help identify the regulatory functions of lncRNAs in the pathogenesis of GBM.     

Zfp423 Promotes Adipogenic Differentiation of Bovine Stromal Vascular Cells

Intramuscular fat or marbling is critical for the palatability of beef. In mice, very recent studies show that adipocytes and fibroblasts share a common pool of progenitor cells, with Zinc finger protein 423 (Zfp423) as a key initiator of adipogenic differentiation. To evaluate the role of Zfp423 in intramuscular adipogenesis and marbling in beef cattle, we sampled beef muscle for separation of stromal vascular cells. These cells were immortalized with pCI neo-hEST2 and individual clones were selected by G418. A total of 288 clones (3×96 well plates) were isolated and induced to adipogenesis. The presence of adipocytes was assessed by Oil-Red-O staining. Three clones with high and low adipogenic potential respectively were selected for further analyses. In addition, fibro/adipogenic progenitor cells were selected using a surface marker, platelet derived growth factor receptor (PDGFR) α. The expression of Zfp423 was much higher (307.4±61.9%, P<0.05) in high adipogenic cells, while transforming growth factor (TGF)-β was higher (156.1±48.7%, P<0.05) in low adipogenic cells. Following adipogenic differentiation, the expression of peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer binding protein α (C/EBPα) were much higher (239.4±84.1% and 310.7±138.4%, respectively, P<0.05) in high adipogenic cells. Over-expression of Zfp423 in stromal vascular cells and cloned low adipogenic cells dramatically increased their adipogenic differentiation, accompanied with the inhibition of TGF-β expression. Zfp423 knockdown by shRNA in high adipogenic cells largely prevented their adipogenic differentiation. The differential regulation of Zfp423 and TGF-β between low and high adipogenic cells is associated with the DNA methylation in their promoters. In conclusion, data show that Zfp423 is a critical regulator of adipogenesis in stromal vascular cells of bovine muscle, and Zfp423 may provide a molecular target for enhancing intramuscular adipogenesis and marbling in beef cattle.     

Asiatic Acid Inhibits Adipogenic Differentiation of Bone Marrow Stromal Cells

Bone marrow mesenchymal stromal cells (BMSCs) are the common precursors for both osteoblasts and adipocytes. With aging, BMSC osteoblast differentiation decreases whereas BMSC differentiation into adipocytes increases, resulting in increased adipogenesis and bone loss. In the present study, we investigated the effect of asiatic acid (AA) on adipocytic differentiation of BMSCs. AA inhibited the adipogenic induction of lipid accumulation, activity of glycerol-3-phosphate dehydrogenase, and expression of marker genes in adipogenesis: peroxisome proliferation-activated receptor (PPAR)γ, adipocyte fatty acid-binding protein (ap) 2, and adipsin. Further, we found that AA did not alter clonal expansion rate and expression of C/EBPβ, upstream key regulator of PPARγ, and binding activity of C/EBPβ to PPARγ promoter was not affected by AA as well. These findings suggest that AA may modulate differentiation of BMSCs to cause a lineage shift away from the adipocytes, and inhibition of PPARγ by AA is through C/EBPβ-independent mechanisms. Thus, AA could be a potential candidate for a novel drug against osteoporosis.     

基于人类信号网络和表达谱数据挖掘动脉粥样硬化相关模块

目的:动脉粥样硬化是一种高致死率的慢性炎症疾病,其发生和发展的机制尚不明确。本文基于人类信号网络和基因表达谱数据对动脉粥样硬化相关模块进行挖掘,以探究其在疾病发生发展中的作用机制。方法:结合人类信号网络和基因表达谱数据,设计显著差异模块筛选策略,通过功能分析,挖掘动脉粥样硬化相关模块,对动脉粥样硬化的致病机制进行研究。结果:基于网络模块的平均表达值改变量,采用两种随机方法,进行显著差异模块筛选,最终获得8个动脉粥样硬化相关的显著差异模块。结论:应用本文提出的整合筛选策略,能识别与动脉粥样硬化相关的模块,获得潜在的致病基因,并从外周血的基因表达改变来探究动脉粥样硬化致病机制,这对动脉粥样硬化的诊断、治疗以及发生发展机制的研究具有重要意义。     

MiRNA Expression Profile of Human Subcutaneous Adipose and during Adipocyte Differentiation

Background

Potential regulators of adipogenesis include microRNAs (miRNAs), small non-coding RNAs that have been recently shown related to adiposity and differentially expressed in fat depots. However, to date no study is available, to our knowledge, regarding miRNAs expression profile during human adipogenesis. Thereby, the aim of this study was to investigate whether miRNA pattern in human fat cells and subcutaneous adipose tissue is associated to obesity and co-morbidities and whether miRNA expression profile in adipocytes is linked to adipogenesis.

Methodology/Principal Findings

We performed a global miRNA expression microarray of 723 human and 76 viral mature miRNAs in human adipocytes during differentiation and in subcutaneous fat samples from non-obese (n = 6) and obese with (n = 9) and without (n = 13) Type-2 Diabetes Mellitus (DM-2) women. Changes in adipogenesis-related miRNAs were then validated by RT-PCR. Fifty of 799 miRNAs (6.2%) significantly differed between fat cells from lean and obese subjects. Seventy miRNAs (8.8%) were highly and significantly up or down-regulated in mature adipocytes as compared to pre-adipocytes. Otherwise, 17 of these 799 miRNAs (2.1%) were correlated with anthropometrical (BMI) and/or metabolic (fasting glucose and/or triglycerides) parameters. We identified 11 miRNAs (1.4%) significantly deregulated in subcutaneous fat from obese subjects with and without DM-2. Interestingly, most of these changes were associated with miRNAs also significantly deregulated during adipocyte differentiation.

Conclusions/Significance

The remarkable inverse miRNA profile revealed for human pre-adipocytes and mature adipocytes hints at a closely crosstalk between miRNAs and adipogenesis. Such candidates may represent biomarkers and therapeutic targets for obesity and obesity-related complications.     

Wnt Antagonist Secreted Frizzled-Related Protein 4 Upregulates Adipogenic Differentiation in Human Adipose Tissue-Derived Mesenchymal Stem Cells

With more than 1.4 billion overweight or obese adults worldwide, obesity and progression of the metabolic syndrome are major health and economic challenges. To address mechanisms of obesity, adipose tissue-derived mesenchymal stem cells (ADSCs) are being studied to detail the molecular mechanisms involved in adipogenic differentiation. Activation of the Wnt signalling pathway has inhibited adipogenesis from precursor cells. In our study, we examined this anti-adipogenic effect in further detail stimulating Wnt with lithium chloride (LiCl) and 6-bromo indirubin 3’oxime (BIO). We also examined the effect of Wnt inhibition using secreted frizzled-related protein 4 (sFRP4), which we have previously shown to be pro-apoptotic, anti-angiogenic, and anti-tumorigenic. Wnt stimulation in LiCl and BIO-treated ADSCs resulted in a significant reduction (2.7-fold and 12-fold respectively) in lipid accumulation as measured by Oil red O staining while Wnt inhibition with sFRP4 induced a 1.5-fold increase in lipid accumulation. Furthermore, there was significant 1.2-fold increase in peroxisome proliferator-activated receptor gamma (PPARγ) and CCAAT/enhancer binding protein alpha (C/EBPα), and 1.3-fold increase in acetyl CoA carboxylase protein levels. In contrast, the expression of adipogenic proteins (PPARγ, C/EBPα, and acetyl CoA carboxylase) were decreased significantly with LiCl (by 1.6, 2.6, and 1.9-fold respectively) and BIO (by 7, 17, and 5.6-fold respectively) treatments. These investigations demonstrate interplay between Wnt antagonism and Wnt activation during adipogenesis and indicate pathways for therapeutic intervention to control this process.     

Mechanism of Butyrate Stimulation of Triglyceride Storage and Adipokine Expression during Adipogenic Differentiation of Porcine Stromovascular Cells

Short chain fatty acids (SCFA), products of microbial fermentation of dietary fiber, exert multiple metabolic effects in cells. Previously, we had demonstrated that soluble fiber influenced fat mass accumulation, gut microbial community structure and SCFA production in pigs. The current study was designed to identify effects of SCFA treatment during adipogenic differentiation of porcine stromovascular cells on lipid metabolism and adipokine expression. Differentiating cells were treated with varying concentrations of butyrate. Results show that butyrate treatment enhanced adipogenesis and lipid accumulation, perhaps through upregulation of glucose uptake and de novo lipogenesis and other mechanisms that include induction of SREBP-1c, C/EBPα/β, GLUT4, LPL, PPARγ, GPAT4, DGAT1 and DGAT2 expression. In addition, butyrate induced adiponectin expression, resulting in activation of downstream target genes, such as AMPK and AKT. Activation of AMPK by butyrate led to phosphorylation of ACC. Although increased ACO gene expression was seen with butyrate treatment, experiments with the peroxisomal fatty acid inhibitor, thioridazine, suggest that butyrate may have an inhibitory effect on peroxisomal fatty acid oxidation. Our studies also provide evidence that butyrate may inhibit lipolysis, perhaps in an FFAR3-dependent manner. Therefore, this study presents a novel paradigm for butyrate action in adipocytes and shows that adipocytes are capable of utilizing butyrate, leading to increased expression of adiponectin for enhanced glucose uptake and improved insulin sensitivity.     

Angiogenic Expression Profile of Normal and Neurofibromin-Deficient Human Schwann Cells

Peripheral nerve sheath tumors from individuals with Neurofibromatosis Type 1 (NF1) are highly vascular and contain Schwann cells which are deficient in neurofibromin. This study examines the angiogenic expression profile of neurofibromin-deficient human Schwann cells relative to normal human Schwann cells, characterizing both pro-angiogenic and anti-angiogenic factors. Conditioned media from neurofibromin-deficient Schwann cell lines was pro-angiogenic as evidenced by its ability to stimulate endothelial cell proliferation and migration. Using gene array and protein array analysis, we found increased expression of pro-angiogenic factors and decreased expression of anti-angiogenic factors in neurofibromin-deficient Schwann cells relative to normal human Schwann cells. Neurofibromin-deficient Schwann cells also showed increased expression of several growth factor receptors and decreased expression of an integrin. We conclude that neurofibromin-deficient Schwann cells have dysregulated expression of pro-angiogenic factors, anti-angiogenic factors, growth factor receptors, and an integrin. These dysregulated molecules may contribute to the growth and progression of NF1 peripheral nerve sheath tumors.     

基于人类信号网络和表达谱数据研究静脉血栓复发机制

目的:静脉血栓是一种高复发风险和高致死率的疾病,其形成和复发的分子机制尚不明确。基于人类信号网络和基因表达谱数据可针对静脉血栓经华法令抗凝治疗后的复发机制进行研究。方法:结合表达谱数据和人类信号网络,设计差异模块筛选策略,通过功能分析、差异表达分析和已知血栓相关基因及药物靶基因的互作关联研究,获得与静脉血栓复发相关的显著差异模块。结果:最终获得8个与静脉血栓复发密切相关的显著差异模块,评估了华法令治疗静脉血栓的效能,提出了联合用药的3种可能途径。结论:应用本文提出的整合筛选策略,能识别与静脉血栓复发相关的模块,探究静脉血栓复发的分子机制和评估华法令的治疗效能。还提供了潜在的联合用药途径,这对治愈血栓、防治血栓复发及复发机制的研究具有重要意义。     

Membrane Potential Controls Adipogenic and Osteogenic Differentiation of Mesenchymal Stem Cells

Background

Control of stem cell behavior is a crucial aspect of developmental biology and regenerative medicine. While the functional role of electrophysiology in stem cell biology is poorly understood, it has become clear that endogenous ion flows represent a powerful set of signals by means of which cell proliferation, differentiation, and migration can be controlled in regeneration and embryonic morphogenesis.

Methodology/Principal Findings

We examined the membrane potential (V_mem) changes exhibited by human mesenchymal stem cells (hMSCs) undergoing adipogenic (AD) and osteogenic (OS) differentiation, and uncovered a characteristic hyperpolarization of differentiated cells versus undifferentiated cells. Reversal of the progressive polarization via pharmacological modulation of transmembrane potential revealed that depolarization of hMSCs prevents differentiation. In contrast, treatment with hyperpolarizing reagents upregulated osteogenic markers.

Conclusions/Significance

Taken together, these data suggest that the endogenous hyperpolarization is a functional determinant of hMSC differentiation and is a tractable control point for modulating stem cell function.     

Ultraviolet A Regulates Adipogenic Differentiation of Human Adipose Tissue-derived Mesenchymal Stem Cells via Up-regulation of Kruppel-like Factor 2

Adipocyte dysfunction is strongly associated with the development of obesity, which is a major risk factor for many disorders, including diabetes, hypertension, and heart disease. This study shows that ultraviolet A (UVA) inhibits adipogenic differentiation of human adipose tissue-derived mesenchymal stem cells and its action mechanisms. The mRNA levels of peroxidase proliferator-activated receptor (PPAR) γ and CCAAT/enhancer-binding protein α (C/EBPα), but not CCAAT/enhancer-binding protein ((C/EBP) β and δ, were reduced by UVA. Moreover, the mRNA levels of PPAR γ target genes (lipoprotein lipase (LPL), CD36, adipocyte protein (aP2), and liver X receptor α (LXR)) were down-regulated by UVA. Additionally, attempts to elucidate a possible mechanism underlying the UVA-mediated effects revealed that UVA induced migration inhibitory factor (MIF) gene expression, and this was mediated through activation of AP-1 (especially JNK and p42/44 MAPK) and nuclear factor-κB. In addition, reduced adipogenesis by UVA was recovered upon the treatment with anti-MIF antibodies. AMP-activated protein kinase phosphorylation and up-regulation of Kruppel-like factor 2 (KLF2) were induced by UVA. Taken together, these findings suggest that the inhibition of adipogenic differentiation of human adipose tissue-derived mesenchymal stem cells by UVA occurs primarily through the reduced expression of PPAR γ, which is mediated by up-regulation of KLF2 via the activation of MIF-AMP-activated protein kinase signaling.     

Human Serotonin Transporter Expression During Megakaryocytic Differentiation of MEG-01 Cells

The serotonin (5-HT) transporter (SERT) has been found altered in platelets of patients with genetically complex disorders, including mood-anxiety, pain and eating disorders. In this study, we used cell cultures of platelet precursors as models of investigation on mechanisms of SERT regulation: SERT expression was appraised during megakaryocytic differentiation of human megakaryoblastic MEG-01 cells. Cells were cultured for 8 days with 10^?7M 4-β-12-tetradecanoylphorbol-13-acetate (β-TPA) in the presence of 10% fetal bovine serum (FBS) and SERT was assessed by real time PCR, immunofluorescence microscopy, Western blot and [³H]5-HT re-uptake. Results revealed that SERT is present in control-untreated MEG-01 cells. β-TPA-differentiating MEG-01 cells showed a redistribution of SERT fluorescence, diffuse to cell bodies and blebs along with a 3-fold SERT mRNA increase and a moderate raise in SERT protein (1.5/1.4-fold) by immunoblot and re-uptake assays. In summary, we have shown herein that control megakaryoblasts express the SERT protein. SERT is modulated by differentiation events, implying that SERT density in platelets is under the control of megakaryocytopoiesis stages. Differentiation of MEG-01 cells can provide considerable insight into interactions between SERT genetics, transmitter-hormonal/homeostatic mechanisms and signaling pathways.