Group testing in mediation analysis

We consider the scenario where there is an exposure, multiple biologically defined sets of biomarkers, and an outcome. We propose a new two-step procedure that tests if any of the sets of biomarkers mediate the exposure/outcome relationship, while maintaining a prespecified familywise error rate. The first step of the proposed procedure is a screening step that removes all groups that are unlikely to be strongly associated with both the exposure and the outcome. The second step adapts recent advances in postselection inference to test if there are true mediators in each of the remaining candidate sets. We use simulation to show that this simple two-step procedure has higher statistical power to detect true mediating sets when compared with existing procedures. We then use our two-step procedure to identify a set of Lysine-related metabolites that potentially mediate the known relationship between increased body mass index and the increased risk of estrogen-receptor positive breast cancer in postmenopausal women.     

Emerging from their burrow: Hedgehog pathway inhibitors for cancer

Introduction: Cancer treatment is moving away from conventional cytotoxic drugs and towards agents that target specific proteins and mechanisms important to cancer development or survival. The Hedgehog Pathway (HhP) is a signal transduction pathway and its constitutive activation is tumorigenic in basal cell carcinoma (BCC). The HhP enables phenotypic flexibility, and channels tumor-stroma interactions. As a result, it is over-expressed in numerous cancers as well as in the tumor microenvironment and may represent a promising therapeutic target.

Areas covered: In this article, we review the rationale for targeting HhP and its role as an oncogenic driver, in tumor epithelial-to-mesenchymal transition (EMT), and in the tumor microenvironment and describe the results of preclinical and clinical studies involving HhP inhibitors.

Expert opinion: HhP activation plays an important role in both the tumor microenvironment and tumor EMT which can lead to treatment resistance for a number of different malignancies. In addition to standard use in BCC, several HhP inhibitors are in preclinical, early, and mid-stage clinical development for other solid and hematologic malignancies.     

Immunohistochemical and molecular analysis of PI3K/AKT/mTOR pathway in esophageal carcinoma

Among the numerous signaling pathways involved in tumorigenesis, PI3K‐AKT‐mTOR is a key one that regulates diverse cellular functions. However, its prognostic value in esophageal carcinoma remains unclear. In our study, we examined the immunohistochemical expression of phosphorylated (p‐) AKT, mTOR, p70S6K and 4E‐BP1 along with the mutational status of PIK3CA and AKT1 genes by High Resolution Melting Analysis and Pyrosequencing in 44 esophageal carcinomas. The results were correlated with the clinicopathological characteristics of the patients in an effort to define their possible prognostic significance. Total p‐mTOR cytoplasmic expression, assessed in 10 random areas, was positively correlated with tumor stage (Kruskal–Wallis ANOVA, I/II vs III/IV, p = 0.0500). Μoreover, maximum p‐mTOR cytoplasmic immunoexpression, estimated in hot spot areas, was positively associated with tumor grade (Mann–Whitney U test, I/II vs III, p = 0.0565). Interestingly, p‐4E‐BP1 immunoreactivity was negatively correlated with tumor histological grade (Mann–Whitney U test, I/II vs III, p = 0.0427). No mutation was observed in exons 9 and 20 of PIK3CA gene and in exon 4 of AKT1 gene. In conclusion, our findings depict the presence of activated PI3K/AKT/mTOR pathway in esophageal cancer bringing forward p‐mTOR and p‐4E‐BP1 for their potential role in esophageal carcinogenesis. Additional studies are warranted to validate our findings.     

左金丸抗幽门螺杆菌感染的分子网络调控机制研究

目的基于网络药理学和生物信息学方法探究左金丸抗幽门螺杆菌(Hp)感染的分子网络调控机制。方法通过中药系统药理学数据库和分析平台(TCMSP)检索左金丸化学成分,筛选并预测其入血活性成分和作用靶点,检索疾病数据库中与Hp感染相关的作用靶点,构建左金丸成分靶点与疾病靶点的交互网络,获得左金丸抗Hp的特征性基因;通过DAVID6.8数据库对上述特征性基因进行GO功能富集和KEGG通路富集分析;利用Cytohubba筛选出左金丸抗Hp感染的关键靶点。结果通过TCMSP筛选、预测得到左金丸32个入血活性成分和197个作用靶点。GO分析共得到199条富集结果,其中生物过程包含炎症反应、RNA信号转录、信号传导等152条,细胞组分包含细胞核、细胞外基质、蛋白复合物等19条,分子功能包含细胞因子活性、DNA结合、ATP结合等28条。KEGG分析结果显示,Jak-STAT信号通路、T细胞受体信号通路、细胞周期信号通路、Wnt信号通路等65条通路与左金丸抗Hp感染密切相关。经Cytohubba筛选得到CXCL8、IL10、IL4、VEGFA、MMP9等10个关键基因。结论左金丸抗Hp感染具有多成分、多靶点、多通路协同作用的特点,可为其活性成分研究和抗Hp药效及机制研究提供依据。     

基于TCGA数据初步探查肝内胆管癌预后相关基因

目的 分析tCGA数据库中肝内胆管癌（ICC）高通量测序数据，寻找其预后相关基因，构建风险模型，并研究其在ICC组织中表达及作用通路。方法 下载tCGA数据库中33例ICC组织和8例癌旁组织中的RNA-seq表达矩阵数据和患者临床资料信息，利用edgeR软件包进行基因差异表达分析，通过单因素Cox回归分析筛选出预后相关差异基因，对差异基因绘制生存曲线，筛选出具有临床意义的基因，经多因素Cox回归分析并构建风险模型，通过京都基因与基因组百科全书（KEGG）通路富集分析了解预后相关基因的作用通路。结果 通过edgeR分析后得到6 617个差异基因（筛选标准为|log2 Fold Change|＞1，P＜0.05），其中高表达组4 094个，低表达组2 523个。通过功能富集发现，这些基因主要集中在化学物致癌作用、药物代谢-细胞色素P450系统、细胞色素P450对异生物质的代谢影响以及视黄醇代谢通路。经单因素Cox回归、R软件“survival”包生存曲线分析显示，UCN2、CST1、PROS1、SLC35E4、PEMT五个基因对ICC患者预后存在显著性影响。通过多因素Cox回归分析，CST1、PEMT、PROS1构建的风险模型对ICC患者预后具有判断作用。结论 UCN2、CST1、PROS1、SLC35E4、PEMT基因可能成为ICC预后判断指标，为后续临床试验提供数据支持。     

△LuxS的表型分析及其在GBS毒力调控机制研究中的应用

目的采用LuxS缺失突变株模型对B型链球菌中数量感应相关分子LuxS的功能及与其相关的自诱导因子-2数量感应通路进行研究，以探索其毒力调控机制。方法采用RT-PCR法、菌落印迹分析、生长曲线测定、cAMP因子测定等方法对该缺失突变菌株的表型特性进行了研究。最后应用哈氏弧菌作为报告菌株，通过生物发光测定法分析了突变株对B型链球菌诱导报告菌株中的生物发光活性的影响。结果发现此缺失突变可导致B型链球菌中scpB基因表达的上调；与野生株相比，突变株的生物发光诱导活性比野生株降低了大约两倍。结论本研究结果证实了LuxS在GBS中AI-2数量感应通路中的重要性，并为GBS中毒力调控机制的进一步研究提供了新的线索。     

Growth cones and axon trajectories of a sensory pathway in the amphibian spinal cord

Central axons of sensory ganglion (SG) neurons of the Xenopus tail enter the spinal cord via the ventral roots and travel dorsally and rostrally following a diagonal course within the lateral marginal zone (LMZ) to reach the dorsolateral fasciculus (DLF) (Nordlander et al.: Brain Res., 440:391-395, 1988). Axons are dispersed as they cross the cord. At the DLF they turn and travel together rostrally, sharing the fascicle with axons of primary sensory neurons (Rohon-Beard cells) already present in the tract. In this paper we analyze the growth patterns of the central projections of SG axons in the tail by using HRP applied to proximal branches of tail spinal nerves. Growth cones of the diagonal route are variable in configuration, often bearing processes that spread within the LMZ. Once the DLF, growth cones change shape, becoming distinctly linear. While growth cones navigating the diagonal part of the route never contact or fasciculate with other diagonal SG axons, SG growth cones and axons of the DLF are more closely associated with their fellows. Measurements of the slopes of SG axons in the diagonal route indicated a limited range with a mean of 23 degrees with respect to the cord axis. On the basis of these observations, we conclude that 1) navigational patterns for growth cones of this pathway differ for the diagonal versus the DLF part of its course, and 2) fasciculation is not a mechanism used by SG axons to reach the DLF, but that instead, each axon is able to find its way independently.     

脑缺血后抑郁大鼠皮层及海马IP3表达及中药的干预作用

目的：从磷脂酰肌醇（PI）信号传导通路上重要调节因子IP3的角度，探讨脑缺血后抑郁模型磷脂酰肌醇（PI）信号传导通路的变化及中药颐脑解郁方的干预作用。方法：在脑缺血后抑郁模型上，采用AlphaScreen受体竞争机制，观察脑缺血后抑郁大鼠前额叶皮层、海马IP3含量的变化及中药颐脑解郁方的干预作用。结果：脑缺血后抑郁模型大鼠皮层及海马IP3含量明显高于正常组，模型组IP3的含量明显高于治疗组。结论：脑缺血后抑郁模型大鼠脑皮层及海马IR含量增加，中药颐脑解郁方能使之明显下调，提示脑缺血后抑郁IPl含量增加，颐脑解郁方的抗抑郁作用可能与调节受体后PI信号通路有关。     

电针对抑郁模型大鼠海马一氧化氮-环磷酸鸟苷信号转导通路的影响

目的:观察电针对抑郁模型大鼠海马一氧化氮-环磷酸鸟苷(NO-cGMP)信号转导通路的影响,探讨电针治疗抑郁症的部分作用机制。方法:SD大鼠随机分为正常组、模型组和电针组,每组10只。用慢性不可预见性轻度刺激结合孤养的方法制造抑郁模型。造模同时针刺治疗电针组动物,选取"百会""印堂"穴,电针20min,每日1次,连续针刺21d。治疗结束后取大鼠海马组织,用免疫组化法检测神经细胞性一氧化氮合酶(nNOS)表达量,用放射免疫法测定cGMP含量。结果:模型组大鼠海马区的nNOS免疫反应阳性颗粒数目减少,电针组nNOS免疫反应阳性颗粒数目较模型组增多。各组测得的nNOS灰度值,模型组明显高于正常组(P<0.01),电针组明显低于模型组(P<0.01)。模型组大鼠海马中cGMP含量与正常组比较有降低的趋势,但差异无统计学意义(P>0.05);电针组大鼠海马中cGMP含量与模型组比较显著升高(P<0.01)。结论:电针"百会""印堂"穴能够提高抑郁模型大鼠海马区nNOS的表达水平,同时提高海马中cGMP的含量,维持NO-cGMP信号转导通路的信息传递功能,从而起到抗抑郁作用。     

胃肠癌化疗患者实施临床路径的可行性探讨

目的 探讨针对肿瘤化学治疗所呈现的周期性规律，探索胃肠癌患者在化疗期间实施临床路径流程的可行性。方法 选择有病理诊断的晚期胃肠癌患者140例，随机分成实验组和对照组各70例，实验组实施临床路径流程，对照组实施传统流程，比较两组住院天数、医疗费用、医疗质量及患者满意度。结果 实验组患者的住院天数明显缩短(P＜0．05)，医疗费用明显降低(P＜0．05)，医疗质量及患者满意度均有较大幅度的提高(P＜0．05)。结论 胃肠癌患者化疗期间实施临床路径流程切实可行。