Comprehensive interrogation of gene lists from genome-scale cancer screens with oncoEnrichR

Genome-scale screening experiments in cancer produce long lists of candidate genes that require extensive interpretation for biological insight and prioritization for follow-up studies. Interrogation of gene lists frequently represents a significant and time-consuming undertaking, in which experimental biologists typically combine results from a variety of bioinformatics resources in an attempt to portray and understand cancer relevance. As a means to simplify and strengthen the support for this endeavor, we have developed oncoEnrichR, a flexible bioinformatics tool that allows cancer researchers to comprehensively interrogate a given gene list along multiple facets of cancer relevance. oncoEnrichR differs from general gene set analysis frameworks through the integration of an extensive set of prior knowledge specifically relevant for cancer, including ranked gene-tumor type associations, literature-supported proto-oncogene and tumor suppressor gene annotations, target druggability data, regulatory interactions, synthetic lethality predictions, as well as prognostic associations, gene aberrations and co-expression patterns across tumor types. The software produces a structured and user-friendly analysis report as its main output, where versions of all underlying data resources are explicitly logged, the latter being a critical component for reproducible science. We demonstrate the usefulness of oncoEnrichR through interrogation of two candidate lists from proteomic and CRISPR screens. oncoEnrichR is freely available as a web-based service hosted by the Galaxy platform ( https://oncotools.elixir.no ), and can also be accessed as a stand-alone R package ( https://github.com/sigven/oncoEnrichR ).     

Prostate cancer incidence in men with prostate-specific antigen below 3 ng/mL: The Finnish Randomized Study of Screening for Prostate Cancer

Prostate-specific antigen (PSA)-based screening for prostate cancer (PCa) can reduce PCa mortality, but also involves overdetection of low-risk disease with potential adverse effects. We evaluated PCa incidence among men with PSA below 3 ng/mL and no PCa diagnosis at the first screening round of the Finnish Randomized Study of Screening for PCa. Follow-up started at the first screening attendance and ended at PCa diagnosis, emigration, death or the common closing date (December 2016), whichever came first. Cox regression analysis was used to estimate hazard ratios and their confidence intervals (CI). Among men with PSA <3 ng/mL, cumulative PCa incidence was 9.1% after 17.6 years median follow-up. Cumulative incidence was 3.6% among men with baseline PSA 0 to 0.99 ng/mL, 11.5% in those with PSA 1.0 to 1.99 ng/mL and 25.7% among men with PSA 2 to 2.99 ng/mL (hazard ratio 9.0, 95% CI: 7.9-10.2 for the latter). The differences by PSA level were most striking for low-risk disease based on Gleason score and EAU risk group. PSA values <1 ng/mL indicate a very low 20-year risk, while at PSA 2 to 2.99 ng/mL risks are materially higher, with 4- to 5-fold risk for aggressive disease. Using risk-stratification and appropriate rescreening intervals will reduce screening intensity and overdetection. Using cumulative incidence of clinically significant PCa (csPCa) as the criterion, rescreening intervals could range from approximately 3 years for men with initial PSA 2 to 2.99 ng/mL, 6 years for men with PSA 1 to 1.99 ng/mL to 10 years for men with PSA <1 ng/mL.     

Trends in cancer incidence by socioeconomic deprivation in Germany in 2007 to 2018: An ecological registry-based study

Age-standardized cancer incidence has decreased over the last years for many cancer sites in developed countries. Whether these trends led to narrowing or widening socioeconomic inequalities in cancer incidence is unknown. Using cancer registry data covering 48 million inhabitants in Germany, the ecological association between age-standardized total and site specific (colorectal, lung, prostate and breast) cancer incidence in 2007 to 2018 and a deprivation index on district level (aggregated to quintiles) was investigated. Incidence in the most and least deprived districts were compared using Poisson models. Average annual percentage changes (AAPCs) and differences in AAPCs between deprivation quintiles were assessed using Joinpoint regression analyses. Age-standardized incidence decreased strongly between 2007 and 2018 for total cancer and all cancer sites (except female lung cancer), irrespective of the level of deprivation. However, differences in the magnitude of trends across deprivation quintiles resulted in increasing inequalities over time for total cancer, colorectal and lung cancer. For total cancer, the incidence rate ratio between the most and least deprived quintile increased from 1.07 (95% confidence interval: 1.01-1.12) to 1.23 (1.12-1.32) in men and from 1.07 (1.01-1.13) to 1.20 (1.14-1.26) in women. Largest inequalities were observed for lung cancer with 82% (men) and 88% (women) higher incidence in the most vs the least deprived regions in 2018. The observed increase in inequalities in cancer incidence is in alignment with trends in inequalities in risk factor prevalence and partly utilization of screening. Intervention programs targeted at socioeconomically deprived and urban regions are highly needed.     

Redox active or thiol reactive? Optimization of rapid screens to identify less evident nuisance compounds

Compounds that exhibit assay interference or undesirable mechanisms of bioactivity are routinely encountered in assays at various stages of drug discovery. We observed that assays for the investigation of thiol-reactive and redox-active compounds have not been collected in a comprehensive review. Here, we review these assays and subject them to experimental optimization to improve their reliability. We demonstrate the usefulness of our assay cascade by assaying a library of bioactive compounds, chemical probes, and a set of approved drugs. These high-throughput assays should complement the array of wet-lab and in silico assays during the initial stages of hit discovery campaigns to pursue only hit compounds with tractable mechanisms of action.     

大黄附子汤对重症急性胰腺炎小鼠肠道微皱褶细胞变化的影响

目的研究大黄附子汤对重症急性胰腺炎(SAP)小鼠肠道微皱褶细胞(M细胞)变化的影响，为大黄附子汤临床防治SAP提供理论基础。 方法选取40只健康SPF级C57BL/6J雄性小鼠，随机分为4组(每组10只)：空白对照组、大黄附子汤对照组、SAP组、大黄附子汤治疗组，其中SAP组和大黄附子汤治疗组分别以3.5 g/kg剂量腹腔注射20% L-精氨酸，空白对照组和大黄附子汤对照组注射等剂量的等渗盐水；于造模后12、24、36 h，空白对照组和SAP组给予等渗盐水0.2 mL，大黄附子汤对照组和治疗组给予大黄附子汤0.2 mL灌肠，均于造模完成48 h后处死取材，使用ELISA检测血清淀粉酶、内毒素、IL-1β及TNF-α含量，取回肠及胰腺组织行HE染色、评分，免疫组化染色检测M细胞特异性蛋白GP2并评分。 结果(1)一般情况：对照组腹腔注射后小鼠一般情况好，精神状态良好，能正常进水，四肢活动自如，行动未受影响；SAP组小鼠腹腔注射后一般情况差，精神萎靡，反应迟钝，行动迟缓，呼吸急促，拱背收腹，饮水减少。(2)SAP组淀粉酶、内毒素、IL-1β及TNF-α水平较对照组明显升高(P<0.05)；与SAP组进行对比，大黄附子汤治疗组血清淀粉酶、内毒素、IL-1β及TNF-α水平出现显著下降(P<0.05)。(3)HE染色：SAP组胰腺及回肠组织坏死严重，可见大量白细胞浸润。大黄附子汤治疗组胰腺及回肠组织轻度坏死，可见少量中性粒细胞等白细胞浸润。(4)免疫组化染色：SAP组与对照组相比GP2表达降低(P<0.05)；相较于SAP组，大黄附子汤治疗组GP2的表达水平升高(P<0.05)。 结论大黄附子汤治疗可改善作为肠道免疫应答起始的M细胞数量与功能，增强肠道免疫应答，减轻肠免疫屏障损伤，减少内毒素入血，改善SAP症状。     

Effects of the Cerebral Aneurysm Treatment Method on Coil Packing Density and Its Relationship with the Ostium Area

PurposeTo test the following hypotheses: (a) balloon or stent assistance increases coil packing density (CPD) in the endovascular treatment of intracranial aneurysms, and (b) CPD correlates to ostium area (OA) and aneurysm volume (AV).Materials and MethodsThis retrospective study included 60 aneurysms (54 ruptured and 6 unruptured) treated with simple coiling (SC) (n = 18), balloon-assisted coiling (BAC) (n = 7), or stent-assisted coiling (SAC) (n = 35) at the authors’ institution between August 2017 and December 2019. AV and OA measurements were obtained from 3-dimensional digital subtraction angiography images using commercial software. Coil sizes were retrieved from patient files, and coil volume (CV) measurements were obtained from https://www.angiocalc.com/. Analysis of covariance, multivariate covariance analysis, and Pearson correlation analyses were performed.ResultsThe median value for AV, CV, CPD, and OA was 63.4 mm³ (range, 5.5–1,771.4 mm³), 23.13 mm³ (range, 2.03–296.95 mm³), 33.29% (range, 13.41%–81.02%), and 10.7 mm² (range, 2.7–49.9 mm²), respectively. Multivariate analysis showed that the CPD values were not significantly different among the treatment groups, although OA significantly differed between the SC and SAC groups (P < .05). Pearson correlations showed that similar to AV, OA was negatively correlated with CPD (r = ?0.321, P < .05).ConclusionsThe CPD value in cerebral aneurysms treated with BAC or SAC did not differ from that in aneurysms treated with SC.     

lncRNA CYTOR靶向调控miR-503/CCNE1信号轴促进上皮性卵巢癌细胞增殖北大核心

目的:探讨细胞骨架调节剂(lncRNA cytoskeleton regulator,CYTOR)是否通过靶向调控miR-503来促进细胞周期蛋白E1(cyclin E1,CCNE1)影响上皮性卵巢癌增殖。方法:实时定量聚合酶链反应(RT-qPCR)检测CYTOR在不同临床分期、病理分级和有无淋巴结转移患者人上皮性卵巢癌组织、癌旁组织和正常组织以及不同卵巢癌细胞中的表达;starBase数据库(网址:http://starbase.sysu.edu.cn/)预测分析CYTOR和miR-503以及miR-503与CCNE1之间的关系,同时荧光素酶实验进行验证;RT-qPCR和免疫荧光分别检测miR-503与CCNE1在人上皮性卵巢癌组织、癌旁组织和正常组织以及不同卵巢癌细胞中的表达;RNA转染技术在A2780中细胞分别沉默CYTOR、过表达miR-503和沉默CCNE1表达,CCK-8检测各组细胞增殖能力变化;RT-qPCR和免疫荧光检测沉默CYTOR后miR-503和CCNE1的表达以及过表达miR-503后CCNE1的表达。结果:CYTOR和CCNE1在上皮性卵巢癌组织中表达增加,同时在临床分期III-IV期、病理分级G_(3)级、淋巴结转移阳性患者肿瘤组织中表达同样显著增加且导致卵巢癌患者术后预后较差;通过数据库分析CYTOR可直接靶向抑制miR-503,而miR-503可直接靶向抑制CCNE1表达,双荧光素酶实验结果与之相同;CYTOR和CCNE1促进上皮性卵巢癌增殖,而miR-503抑制上皮性卵巢癌增殖作用。结论:lncRNA CYTOR通过调控miR-503/CCNE1轴促进上皮性卵巢癌的增殖。     

Current guidelines in the surgical management of hereditary colorectal cancers

Incidence of colorectal cancer (CRC) is on rise. While approximately 70% of all CRC cases are sporadic in nature, 20%-25% have familial aggregation and only < 5% is hereditary in origin. Identification of individuals with hereditary predilection for CRC is critical, as it has an impact on their overall surgical management including surgical timing, approach & technique and determines the role of prophylactic surgery and outcome. This review highlights the concept of hereditary CRC, provides insight into its molecular basis, possibility of its application into clinical practice and emphasizes the current treatment strategies with surgical management, based on the available international guidelines.