基于转录组的肝豆状核变性调控网络的构建和分析

本研究旨在利用生物信息学方法构建经铜诱导的ATP7B基因敲除HepG2细胞系的转录调控网络。探讨关键转录因子在肝豆状核变性发生、发展中的潜在作用机制。收集公共基因表达数据库(gene expression omnibus, GEO)中包含野生型、ATP7B基因敲除型、铜诱导的野生型和铜诱导的ATP7B基因敲除型HepG2细胞系数据。筛选由铜诱导产生的差异表达基因(differentially expressed genes,DEGs)后进行基因本体论(gene ontology,GO)、京都基因和基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)富集分析。基于蛋白相互作用网络,识别疾病关键基因和功能模块,并对关键功能模块中的基因进行富集分析。最后,构建转录调控网络,筛选核心转录因子。共筛选出1 034个差异表达基因,其中上调525个,下调509个。上、下调关键功能模块分别包括了3785个和3931个基因。关键功能模块中的基因主要定位于细胞-基质连接、染色体、剪接复合体、核糖体等区域,共同参与了mRNA加工、组蛋白修饰、RNA剪切...     

Recombinant protein subunit vaccine booster following two-dose inactivated vaccines dramatically enhanced anti-RBD responses and neutralizing titers against SARS-CoV-2 and Variants of Concern

Dear Editor, As of October,2021,SARS-CoV-2 has infected more than 230 million people;promoting roll-out vaccinations could help build herd immunity for the pand...     

Intraspecific trait variation of woody species reduced in a savanna community,southwest China

Plants deploy various ecological strategies in response to environmental heterogeneity. In many forest ecosystems, plants have been reported to have notable inter- and intra-specific trait variation, as well as clear phylogenetic signals, indicating that these species possess a degree of phenotypic plasticity to cope with habitat variation in the community. Savanna communities, however, grow in an open canopy structure and exhibit little species diversification, likely as a result of strong environmental stress. In this study, we hypothesized that the phylogenetic signals of savanna species would be weak, the intraspecific trait variation (ITV) would be low, and the contribution of intraspecific variation to total trait variance would be reduced, owing to low species richness, multiple stresses and relatively homogenous community structure. To test these hypotheses, we sampled dominant woody species in a dry-hot savanna in southwestern China, focusing on leaf traits related to adaptability of plants to harsh conditions (year-round intense radiation, low soil fertility and seasonal droughts). We found weak phylogenetic signals in leaf traits and low ITV (at both individual and canopy-layer levels). Intraspecific variation (including leaf-, layer- and individual-scales) contributed little to the total trait variance, whereas interspecific variation and variation in leaf phenology explained substantial variance. Our study suggests that intraspecific trait variation is reduced in savanna community. Furthermore, our findings indicate that classifying species by leaf phenology may help better understand how species coexist under similar habitats with strong stresses.     

EGFR/MET promotes hepatocellular carcinoma metastasis by stabilizing tumor cells and resisting to RTKs inhibitors in circulating tumor microemboli

The receptor tyrosine kinases (RTKs) family is well-recognized as vital targets for the treatment of hepatocarcinoma cancer (HCC) clinically, whereas the survival benefit of target therapy sorafenib is not satisfactory for liver cancer patients due to metastasis. EGFR and MET are two molecules of the RTK family that were related to the survival time of liver cancer patients and resistance to targeted therapy in clinical reports. However, the mechanism and clinical therapeutic value of EGFR/MET in HCC metastasis are still not completely clarified. The study confirmed that EGFR/MET was highly expressed in HCC cells and tissues and the phosphorylation was stable after metastasis. The expression of EGFR/MET was up-regulated in circulating tumor microemboli (CTM) to accelerate IL-8 production and resistance to the lethal effect of leukocytes. Meanwhile, highly expressed EGFR/MET effectively regulated the Ras/MAPK pathway and stabilized suspended HCC cells by facilitating proliferation and inhibiting apoptosis. Moreover, EGFR/MET promoted phosphorylation of hetero-RTKs, which was dependent on high-energy phosphoric acid compounds rather than their direct interactions. In conclusion, highly expressed EGFR/MET could be used in CTM identification and suitable for preventing metastasis of HCC in clinical practice.Subject terms: Liver cancer, Metastasis     

High glucose represses the proliferation of tendon fibroblasts by inhibiting autophagy activation in tendon injury

Diabetic foot ulcer (DFU) is a kind of common and disabling complication of Diabetes Mellitus (DM). Emerging studies have demonstrated that tendon fibroblasts play a crucial role in remodeling phase of wound healing. However, little is known about the mechanism underlying high glucose (HG)-induced decrease in tendon fibroblasts viability. In the present study, the rat models of DFU were established, and collagen deposition, autophagy activation and cell apoptosis in tendon tissues were assessed using Hematoxylin–Eosin (HE) staining, immunohistochemistry (IHC), and TdT-mediated dUTP Nick-End Labeling (TUNEL) assay, respectively. Tendon fibroblasts were isolated from Achilles tendon of the both limbs, and the effect of HG on autophagy activation in tendon fibroblasts was assessed using Western blot analysis, Cell Counting Kit-8 (CCK-8) assay, and flow cytometry. We found that cell apoptosis was increased significantly and autophagy activation was decreased in foot tendon tissues of DFU rats compared with normal tissues. The role of HG in regulating tendon fibroblasts viability was then investigated in vitro, and data showed that HG repressed cell viability and increased cell apoptosis. Furthermore, HG treatment reduced LC3-II expression and increased p62 expression, indicating that HG repressed autophagy activation of tendon fibroblasts. The autophagy activator rapamycin reversed the effect. More importantly, rapamycin alleviated the suppressive role of HG in tendon fibroblasts viability. Taken together, our data demonstrate that HG represses tendon fibroblasts proliferation by inhibiting autophagy activation in tendon injury.     

幽门螺杆菌感染胃组织基因芯片生物信息学分析

为探讨幽门螺杆菌感染胃组织后差异基因变化,深入分析参与疾病发生、发展的分子机制。从GEO(Gene Expression Omnibus)数据库下载幽门螺杆菌感染胃组织基因芯片数据(GSE5081),根据胃粘膜组织是否受损分组,分别比较幽门螺杆菌感染者与阴性对照组,获得差异基因并进行功能分析包括GO分析、信号通路分析,基因相互作用及基因共表达,得到重要核心基因,并通过实时定量PCR方法进行验证。结果表明:得到参与幽门螺杆菌感染后上调的44个主要基因,主要涉及的GO分析及信号通路包括免疫反应、炎症反应、抗原提呈、细胞因子通路、因子受体关联,细胞粘附分子等。研究发现核心基因CXCR4,CCL20,JAK3,TNFAIP2,PLEK,HLA-DMA,PTPRC,CXCL13,BCL2A1,并通过实时定量PCR的方法进行部分验证,CXCR4,CXCL5,CXCL2在幽门螺杆菌感染后的胃黏膜组织表达高于对照组。幽门螺杆菌感染后胃粘膜组织引起免疫反应,炎症反应,抗原提呈,因子受体关联,细胞粘附分子通路的激活。同时发现一些主要的趋化因子相关基因CXCR4,CXCL5,CXCL2,CCL20,CXCL1等,涉及增殖,炎症,免疫,凋亡基因JAK3,TNFAIP2,PLEK,HLA-DMA,PTPRC,BCL2A1等的表达上调,并实时定量PCR验证部分相关基因的表达。这些结果为从分子网络机制层面上认识幽门螺杆菌感染提供分析思路及基础。