Bioinformatics analysis reveals disturbance mechanism of MAPK signaling pathway and cell cycle in Glioblastoma multiforme

Background & objectives

To analyze the reversal gene pairs and identify featured reversal genes related to mitogen-activated protein kinases (MAPK) signaling pathway and cell cycle in Glioblastoma multiforme (GBM) to reveal its pathogenetic mechanism.

Methods

We downloaded the gene expression profile GSE4290 from the Gene Expression Omnibus database, including 81 gene chips of GBM and 23 gene chips of controls. The t test was used to analyze the DEGs (differentially expressed genes) between 23 normal and 81 GBM samples. Then some perturbing metabolic pathways, including MAPK (mitogen-activated protein kinases) and cell cycle signaling pathway, were extracted from KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database. Cancer genes were obtained from the database of Cancer Gene Census. The reversal gene pairs between DEGs and cancer genes were further analyzed in MAPK and cell cycle signaling pathway.

Results

A total 8523 DEGs were obtained including 4090 up-regulated and 4433 down-regulated genes. Among them, ras-related protein rab-13(RAB13), neuroblastoma breakpoint family member 10 (NBPF10) and disks large homologue 4 (DLG4) were found to be involved in GBM for the first time. We obtained MAPK and cell cycle signaling pathways from KEGG database. By analyzing perturbing mechanism in these two pathways, we identified several reversal gene pairs, including NRAS (neuroblastoma RAS) and CDK2 (cyclin-dependent kinase 2), CCND1 (cyclin D1) and FGFR (fibroblast growth factor receptor). Further analysis showed that NRAS and CDK2 were positively related with GBM. However, FGFR2 and CCND1 were negatively related with GBM.

Interpretation & conclusions

These findings suggest that newly identified DEGs and featured reversal gene pairs participated in MAPK and cell cycle signaling pathway may provide a new therapeutic line of approach to GBM.     

成年小鼠血液系统对亚磁场的响应

目的:研究亚磁场对成年小鼠血液系统的影响。方法:将成年雄性C57BL/6小鼠(4-6周,20±2g,n20,每笼4只)随机分组,分别饲养在模拟亚磁场环境(500nT)和对照地磁场环境(~50μT)。每周定时监测动物体重变化和饮食消耗两次。一个月后,采集亚磁处理小鼠和地磁对照小鼠全血和血清样品,分别进行血常规监测和血清微量元素分析。同时检测血清中过氧化氢(H2O2)的含量,以及超氧化物歧酶(SOD)和过氧化氢酶(CAT)的活力。结果:亚磁场处理过程中,动物体重和饮食消耗与地磁对照没有显著差异,但是体重增量在2周后(14天-24天)比对照组有显著降低(P0.05)。一个月亚磁场处理后,红细胞,血小板和总白细胞处于正常水平,没有发生显著变化,但是中性粒细胞水平显著上升(P0.05)。血清中微量元素水平和氧化应激指标没有显著变化。结论:成年小鼠在亚磁场中经历了一定程度的适应反应。经过一个月连续亚磁场处理,血液系统能够维持健康水平,但是嗜中性粒细胞对亚磁场存在明显响应。     

长期亚磁场处理降低成年雄性小鼠肌肉组织的线粒体功能和运动能力*

亚磁场是深空载人航天任务中的一个关键风险因素。研究表明,亚磁场影响动物多种运动相关行为,但长期亚磁场处理对成年个体运动能力的影响还需要进一步的研究,以评估深空飞行任务中亚磁场的潜在风险。本研究利用三轴亥姆霍兹线圈系统模拟的亚磁环境,长期（一个月）曝露处理成年雄性C57BL/6小鼠,并从行为,组织,细胞,分子水平研究其对小鼠运动能力的影响。相比于地磁组对照,亚磁组小鼠的耐力显著下降。并且,其骨骼肌中柠檬酸水平和肌膜下线粒体数量的下降,以及骨骼肌线粒体形态的变化,表明亚磁场诱导了肌肉线粒体功能抑制,并可能导致其与耐力密切相关的能量代谢的下降。我们的研究结果为线粒体直接响应亚磁场提供了体内证据,并且提示线粒体相关指标可能用于亚磁场效应的风险评估和干预药物的开发。     

Comprehensive gene expression analysis reveals multiple signal pathways associated with prostate cancer

Prostate cancer (PC) depends on androgenic signaling for growth and survival. To data, the exact molecular mechanism of hormone controlling proliferation and tumorigenesis in the PC remains unclear. Therefore, in this study, we explored the differentially expressed genes (DEGs) and identified featured genes related to hormone stimulus from PC. Two sets of gene expression data, including PC and normal control sample, were downloaded from Gene Expression Omnibus (GEO) database. The t-test was used to identify DEGs between PC and controls. Gene ontology (GO) functional annotation was applied to analyze the function of DEGs and screen hormone-related DEGs. Then these hormone-related DEGs were further analyzed in constructed cancer network and Human Protein Reference Database to screen important signaling pathways they participated in. A total of 912 DEGs were obtained which included 326 up-regulated genes and 586 down-regulated genes. GO functional enrichment analysis identified 50 hormone-related DEGs associated with PC. After pathway and PPI network analysis, we found these hormone-related DEGs participated in several important signaling pathways including TGF-β (TGFB2, TGFB3 and TGFBR2), MAPK (TGFB2, TGFB3 and TGFBR2), insulin (PIK3R3, SHC1 and EIF4EBP1), and p53 signaling pathways (CCND2 and CDKN1A). In addition, a total of five hormone-related DEGs (SHC1, CAV1, RXRA, CDKN1A and SRF) were located in the center of PPI network and 12 hormone-related DEGs formed six protein modules. These important signal pathways and hormone-related DEGs may provide potential therapeutic targets for PC.     

Knockdown of CTRP6 reduces the deposition of intramuscular and subcutaneous fat in pigs via different signaling pathways

The regulation of porcine subcutaneous (SC) and intramuscular (IM) fat deposition significantly affects pork quality and the lean meat percentage of the carcass, respectively. The adipokine C1q/tumor necrosis factor-related protein 6 (CTRP6), plays a significant role in regulating animal fat deposition. The purpose of this study was to understand the effects of CTRP6 gene knockdown in IM and SC adipocytes by RNA-seq analysis. A total of 1830 and 2936 differentially expressed genes (DEGs) were identified in SC and IM adipocytes, respectively. 844 were down- and 2092 were upregulated in SC adipocytes, while 648 were down- and 1182 were upregulated in IM adipocytes. Furthermore, 1778 DEGs were detected only in SC adipocytes, 672 DEGs only in IM adipocytes, and 1158 DEGs in both types of adipocytes. GO analysis indicated that DEGs involved in adipocyte differentiation were significantly enriched in both SC and IM adipocytes following treatment with CTRP6-siRNA. Moreover, KEGG pathway enrichment analysis revealed differences of metabolic regulation between IM and SC adipocytes. With CTRP6-silencing, the signaling pathways related to Ras and arachidonic acid metabolism were significantly enriched in IM adipocytes, while four other signaling pathways, encompassing the TNF, MAPK, p53 and adipokine pathway were specifically enriched in SC adipocytes. Interestingly, the effect of CTRP6-siRNA treatment was attenuated by the specific Ras activator ML-097 in IM adipocytes, while the specific p53 activator SJ-172550 had the corresponding effect in SC adipocytes. Altogether, we suggest that CTRP6 may be a differential regulator of the development and metabolism of IM and SC adipose tissues.