林州居民食管癌p53基因突变谱分析与不同地区食管癌和其他类型肿瘤的比较

目的：分析河南省林州市与其他地区食管癌前病变和鳞状细胞癌p53突变谱,探讨食管癌变的发病因素。方法：采用生物信息学和Monte Carlo方法,依据IARC p53突变数据库、Curic研究院p53突变数据库和郑州大学医学院癌症研究所实验室的资料,用FileMark Pro3.0软件系统建立局部资料库进行分析。结果：林州食管癌高发区食管鳞癌碱基替换的发生率低于其他地区食管鳞癌的发生率（32.8 vs 39.8%),但CpG位点G：C→A：T的发生率高于其他地区食管癌（29.6% vs 16.4%)。林州食管癌突变位点具有明显的特征,主要发生在273（占所有错义突变的11.3%)、175（9.7%)、159（6.5%)和282（6.5%)位密码子的CpG位点上。林州地区食管鳞癌p53突变与其他地区食管鳞癌以及头颈部鳞癌p53突变相比,差异有显著性（P=0.02)。结论：林州食管癌p53突变具有内、外源致癌原所致突变的特征,提示慢性炎症、饮食习惯和接触致癌原,可能是林州居民发生食管鳞癌的主要危险因素。     

人程序化死亡分子5(PDCD5)核酸和蛋白质序列的数据发掘

目的：以程序化死亡分子5(PDCD5)为靶分子,对其核酸与蛋白质序列进行生物信息学分析,为PDCD5功能的实验研究提供基础,同时也为人类功能基因的生物信息学分析提供新的技术路线。方法：利用数据库相似性搜索、同源物结构比较、表达谱分析和查询基因“邻居”等技术进行数据发掘和数据综合分析。结果：发现人PDCD5在12号和5号染色体上分别存在返座假基因(retropseudogene),小鼠1号染色体也存在小鼠PDCD5 cDNA的返座假基因。热自养甲烷杆菌的PDCD5同源物、泛素及核糖体蛋白S13具有与人PDCD5相似的折叠方式。线虫的PDCD5同源物、泛素及正IAP(inhibitor of apoptosis proteins)分子等在表达谱拓扑图上属于同一基因簇成员,该基因簇与生物合成和蛋白质合成相关。PDCD5同源物在多个基因组中与多种核糖体蛋白相邻。结论：PDCD5存在2个拷贝的假基因。PDCD5除参与细胞凋亡外,预测还与泛素有功能相关性,并可能参与蛋白质的翻译调控。     

Identification of a vaccine against schistosomiasis using bioinformatics and molecular modeling tools

Schistosomiasis is a serious public health problem in Brazil and worldwide. Although the drugs used to treatment schistosomiasis are effective, the disease continues to expand in all endemic countries due to constant reinfection, poor sanitation, and the lack of effective programs for disease control. However, advances generated through genome projects have provided important information that has improved the understanding of the biology of this parasite. These advances, associated with the advent of bioinformatic analysis, are becoming an important tool in reverse vaccinology.Through database access to the DNA and protein sequences of Schistosoma mansoni and the use of bioinformatics programs, fourteen epitopes were identified. Five epitopes were obtained from proteins whose immunogenic potential had already been assessed in other studies (KP), and nine whose immunogenic potential is unknown (UP). To improve stimulation of the host immune system, the selected epitopes were modeled with a sugar moiety. After this addition, all of the epitopes showed structures similar to those observed in the native proteins, but only eleven of the peptides presented thermodynamically stable structures. Prediction analysis and molecular modeling showed that the glycopeptides presented here are important targets in the search for a vaccine against schistosomiasis. Additionally, they suggest that these molecules may be used in immunological assays to evaluate the level of protection, the effect on pathology reduction and the profile of cytokines and antibodies induced by them.     

Supporting retrieval of diverse biomedical data using evidence-aware queries

Though there have been many advances in providing access to linked and integrated biomedical data across repositories, developing methods which allow users to specify ambiguous and exploratory queries over disparate sources remains a challenge to extracting well-curated or diversely-supported biological information. In the following work, we discuss the concepts of data coverage and evidence in the context of integrated sources. We address diverse information retrieval via a simple framework for representing coverage and evidence that operates in parallel with an arbitrary schema, and a language upon which queries on the schema and framework may be executed. We show that this approach is capable of answering questions that require ranged levels of evidence or triangulation, and demonstrate that appropriately-formed queries can significantly improve the level of precision when retrieving well-supported biomedical data.     

AhR-mediated gene expression in the developing mouse telencephalon

We hypothesize that TCDD-induced developmental neurotoxicity is modulated through an AhR-dependent interaction with key regulatory neuronal differentiation pathways during telencephalon development. To test this hypothesis we examined global gene expression in both dorsal and ventral telencephalon tissues in E13.5 AhR−/− and wildtype mice exposed to TCDD or vehicle. Consistent with previous biochemical, pathological and behavioral studies, our results suggest TCDD initiated changes in gene expression in the developing telencephalon are primarily AhR-dependent, as no statistically significant gene expression changes are evident after TCDD exposure in AhR−/− mice. Based on a gene regulatory network for neuronal specification in the developing telencephalon, the present analysis suggests differentiation of GABAergic neurons in the ventral telencephalon is compromised in TCDD exposed and AhR−/− mice. In addition, our analysis suggests Sox11 may be directly regulated by AhR based on gene expression and comparative genomics analyses. In conclusion, this analysis supports the hypothesis that AhR has a specific role in the normal development of the telencephalon and provides a mechanistic framework for neurodevelopmental toxicity of chemicals that perturb AhR signaling.     

Epsin3在结直肠癌中的差异表达及生物信息学分析

目的 探讨介导内吞作用的衔接蛋白epsin 3（EPN3）在结直肠癌中的表达及意义,为深入研究EPN3的调控模式提供实验依据。 方法 分别运用GEPIA和GEDS数据库分析EPN3在结直肠癌组织和细胞中的表达情况,并通过SMART和cBioPortal数据库分析EPN3基因甲基化和拷贝数变异与其表达水平的关系;利用Metascape数据库对EPN3相关的共表达基因集进行GO富集和通路分析;运用BioPlex蛋白互作数据库分析EPN3在HCT116细胞中的蛋白作用网络。为了对EPN3进一步验证,我们收集13对结直肠癌癌旁组织和癌组织标本,用Real-time PCR检测EPN3 mRNA表达;并通过敲减EPN3观察其对肿瘤细胞增殖、集落形成和迁移能力的影响。 结果 GEPIA、GEDS、SMART和cBioPortal等数据库分析显示,EPN3在结直肠肿瘤组织中高表达(P<0.01)。其表达水平与甲基化和拷贝数变异相关。EPN3相关基因的富集结果显示主要与细胞黏附相关。EPN3与UBB、CCDC130、TNFAIP1、PHGDH、EPN2等构成的蛋白相对作用网络与蛋白泛素化有关。Real-time PCR结果显示,EPN3在癌组织中高表达(P<0.05)。通过沉默EPN3可以抑制HCT116和HT29细胞的增殖、集落形成和迁移能力。 结论 EPN3在结直肠癌组织中高表达,且与细胞黏附和蛋白泛素化等生物学过程有关,敲低EPN3可抑制结直肠癌细胞系HCT116和HT29的增殖、集落形成和迁移等过程。     

基于网络药理学探讨大黄牡丹汤治疗溃疡性结肠炎的作用机制

目的：分析大黄牡丹汤的有效化学成分及作用靶点,研究其治疗溃疡性结肠炎（Ulcerative Colitis,UC）的作用机制。方法：运用中药系统药理学数据库与分析平台(TCMSP)检索大黄牡丹汤的活性成分及靶点蛋白;应用基因组注释数据库平台（Genecards）预测疾病的作用靶点,再将药物-靶点-疾病关系制作成网络图形式。通过String数据库平台构建蛋白质-蛋白质相互作用（PPI）网络,寻找PPI核心基因,再进行基因本体（GO）富集分析和京都基因和基因组百科全书（KEGG）富集分析,找出所涉及的信号通路,构建靶点-通路网络图。结果：通过筛选,搜索出大黄牡丹汤治疗UC的关键化学成分18个,共同靶点28个,得到15个PPI核心基因,分别为MYC、JUN、CASP3、ESR1、PTGS2、HSP90AA1、CASP8、CASP9、IL1B、CCNB1、CDKN1A、CHEK1、PPARG、BAX、KDR。GO富集分析发现紫外线应答、膜筏、半胱氨酸型内肽酶活性参与凋亡过程等;KEGG富集通路分析发现P53信号通路、小细胞肺癌信号通路、乙型肝炎信号通路、大肠癌信号通路等。结论：大黄牡丹汤可通过调节PTGS2、PTGS1、HSP90AA1、BAX、CASP3、ESR1、ESR2、FASN、JUN、NOS2等靶点,调控P53信号通路等来抑制炎症反应、调节免疫功能对UC起到治疗作用。     

Bioinformatics-based SARS-CoV-2 epitopes design and the impact of spike protein mutants on epitope humoral immunities

BackgroundEpitope selection is the key to peptide vaccines development. Bioinformatics tools can efficiently improve the screening of antigenic epitopes and help to choose the right ones.ObjectiveTo predict, synthesize and testify peptide epitopes at spike protein, assess the effect of mutations on epitope humoral immunity, thus provide clues for the design and development of epitope peptide vaccines against SARS-CoV-2.MethodsBioinformatics servers and immunological tools were used to identify the helper T lymphocyte, cytotoxic T lymphocyte, and linear B lymphocyte epitopes on the S protein of SARS-CoV-2. Physicochemical properties of candidate epitopes were analyzed using IEDB, VaxiJen, and AllerTOP online software. Three candidate epitopes were synthesized and their antigenic responses were evaluated by binding antibody detection.ResultsA total of 20 antigenic, non-toxic and non-allergenic candidate epitopes were identified from 1502 epitopes, including 6 helper T-cell epitopes, 13 cytotoxic T-cell epitopes, and 1 linear B cell epitope. After immunization with antigen containing candidate epitopes S_206-221, S_403-425, and S_1157-1170 in rabbits, the binding titers of serum antibody to the corresponding peptide, S protein, receptor-binding domain protein were (415044, 2582, 209.3), (852819, 45238, 457767) and (357897, 10528, 13.79), respectively. The binding titers to Omicron S protein were 642, 12,878 and 7750, respectively, showing that N211L, DEL212 and K417N mutations cause the reduction of the antibody binding activity.ConclusionsBioinformatic methods are effective in peptide epitopes design. Certain mutations of the Omicron would lead to the loss of antibody affinity to Omicron S protein.