Covalent vs. Non‐Covalent Inhibition: Tackling Drug Resistance in EGFR – A Thorough Dynamic Perspective

A persistent challenge in the treatment of non‐small cell lung cancer (NSCLC) with EGFR is the emergence of drug‐resistant caused by somatic mutations. The EGFR L858R/T790 M double mutant (EGFR^DM) was found to be the most alarming variant. Despite the development of a wide range of inhibitors, none of them could inhibit EGFR^DM effectively. Recently, 11h and 45a , have been found to be potent inhibitors against EGFR^DM through two distinctive mechanisms, non‐covalent and covalent binding, respectively. However, the structural and dynamic implications of the two modes of inhibitions remain unexplored. Herein, two molecular dynamics simulation protocols, coupled with free‐energy calculations, were applied to gain insight into the atomistic nature of each binding mode. The comparative analysis confirmed that there is a significant difference in the binding free energy between 11h and 45a (ΔΔG_bind=?21.17 kcal/mol). The main binding force that governs the binding of both inhibitors is vdW, with a higher contribution for 45a . Two residues ARG841 and THR854 were found to have curtailed role in the binding of 45a to EGFR^DM by stabilizing its flexible alcohol chain. The 45a binding to EGFR^DM induces structural rearrangement in the active site to allow easier accessibility of 45a to target residue CYS797. The findings of this work can substantially shed light on new strategies for developing novel classes of covalent and non‐covalent inhibitors with increased specificity and potency.     

Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis

DNA methylation status is closely associated with diverse diseases, and is generally more stable than gene expression, thus abnormal DNA methylation could be important biomarkers for tumor diagnosis, treatment and prognosis. However, the signatures regarding DNA methylation changes for pan-cancer diagnosis and prognosis are less explored. Here we systematically analyzed the genome-wide DNA methylation patterns in diverse TCGA cancers with machine learning. We identified seven CpG sites that could effectively discriminate tumor samples from adjacent normal tissue samples for 12 main cancers of TCGA (1216 samples, AUC > 0.99). Those seven potential diagnostic biomarkers were further validated in the other 9 different TCGA cancers and 4 independent datasets (AUC > 0.92). Three out of the seven CpG sites were correlated with cell division, DNA replication and cell cycle. We also identified 12 CpG sites that can effectively distinguish 26 different cancers (7605 samples), and the result was repeatable in independent datasets as well as two disparate tumors with metastases (micro-average AUC > 0.89). Furthermore, a series of potential signatures that could significantly predict the prognosis of tumor patients for 7 different cancer were identified via survival analysis (p-value < 1e-4). Collectively, DNA methylation patterns vary greatly between tumor and adjacent normal tissues, as well as among different types of cancers. Our identified signatures may aid the decision of clinical diagnosis and prognosis for pan-cancer and the potential cancer-specific biomarkers could be used to predict the primary site of metastatic breast and prostate cancers.     

Systematic Dissection of the Metabolic-Apoptotic Interface in AML Reveals Heme Biosynthesis to Be a Regulator of Drug Sensitivity

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Functional profiling of nucleotide Excision repair in breast cancer

Homologous recombination deficiency conferred by alterations in BRCA1 or BRCA2 are common in breast tumors and can drive sensitivity to platinum chemotherapy and PARP inhibitors. Alterations in nucleotide excision repair (NER) activity can also impact sensitivity to DNA damaging agents, but NER activity in breast cancer has been poorly characterized. Here, we apply a novel immunofluorescence-based cellular NER assay to screen a large panel of breast epithelial and cancer cell lines. Although the majority of breast cancer models are NER proficient, we identify an example of a breast cancer cell line with profound NER deficiency. We show that NER deficiency in this model is driven by epigenetic silencing of the ERCC4 gene, leading to lack of expression of the NER nuclease XPF, and that ERCC4 methylation is also strongly correlated with ERCC4 mRNA and XPF protein expression in primary breast tumors. Re-expression of XPF in the ERCC4-deficient breast cancer rescues NER deficiency and cisplatin sensitivity, but does not impact PARP inhibitor sensitivity. These findings demonstrate the potential to use functional assays to identify novel mechanisms of DNA repair deficiency and nominate NER deficiency as a platinum sensitivity biomarker in breast cancer.     

Downregulation of CENPF Remodels Prostate Cancer Cells and Alters Cellular Metabolism

Metabolic alterations in prostate cancer (PC) are associated with progression and aggressiveness. However, the underlying mechanisms behind PC metabolic functions are unknown. The authors’ group recently reported on the important role of centromere protein F (CENPF), a protein associated with the centromere–kinetochore complex and chromosomal segregation during mitosis, in PC MRI visibility. This study focuses on discerning the role of CENPF in metabolic perturbation in human PC3 cells. A series of bioinformatics analyses shows that CENPF is one gene that is strongly associated with aggressive PC and that its expression is positively correlated with metastasis. By identifying and reconstructing the CENPF network, additional associations with lipid regulation are found. Further untargeted metabolomics analysis using gas chromatography‐time‐of‐flight‐mass spectrometry reveals that silencing of CENPF alters the global metabolic profiles of PC cells and inhibits cell proliferation, which suggests that CENPF may be a critical regulator of PC metabolism. These findings provide useful scientific insights that can be applied in future studies investigating potential targets for PC treatment.     

Oncogenic and Non‐Malignant Pancreatic Exosome Cargo Reveal Distinct Expression of Oncogenic and Prognostic Factors Involved in Tumor Invasion and Metastasis

Exosomes are small extracellular membrane vesicles important in intercellular communication, with their oncogenic cargo attributed to tumor progression and pre‐metastatic niche formation. To gain an insight into key differences in oncogenic composition of exosomes, human non‐malignant epithelial and pancreatic cancer cell models and purified and characterized resultant exosome populations are utilized. Proteomic analysis reveals the selective enrichment of known exosome markers and signaling proteins in comparison to parental cells. Importantly, valuable insights into oncogenic exosomes (362 unique proteins in comparison to non‐malignant exosomes) of key metastatic regulatory factors and signaling molecules fundamental to pancreatic cancer progression (KRAS, CD44, EGFR) are provided. It is reported that oncogenic exosomes contain factors known to regulate the pre‐metastatic niche (S100A4, F3, ITGβ5, ANXA1), clinically‐relevant proteins which correlate with poor prognosis (CLDN1, MUC1) as well as protein networks involved in various cancer hallmarks including proliferation (CLU, CAV1), invasion (PODXL, ITGA3), metastasis (LAMP1, ST14) and immune surveillance escape (B2M). The presence of these factors in oncogenic exosomes offers an understanding of select differences in exosome composition during tumorigenesis, potential components as prognostic and diagnostic biomarkers in pancreatic cancer, and highlights the role of exosomes in mediating crosstalk between tumor and stromal cells.     

5例前列腺癌T细胞受体β链CDR3的多样性分析

T淋巴细胞受体(TCRs)在抗原识别免疫应答中作用重要,其多样性与宿主免疫反应及肿瘤预后判断密切相关。目的:采用高通量测序技术研究前列腺癌组织和癌旁组织中T细胞受体(TCR)克隆多样性及其克隆序列。方法:收集5例PC患者的癌组织和癌旁组织,提取DNA后经多重PCR技术对TCRβ链CDR3区进行扩增。用Illumina MiSeq进行测序,经过数据处理和比对分析,比较前列腺癌组织TCR CDR3组库的组成特征。结果:前列腺癌组织具有更高程度的克隆百分比和较高的高度扩增克隆比HEC(HEC:频率样本总读数的0. 5%的TCR克隆),并获得了24对在癌组织样本中差异表达的V-J基因组合、16对在癌旁组织样本中差异表达的V-J基因组合。结论:前列腺癌组织与癌旁组织均存在差异性的V-J基因组合以及高克隆表达的HEC,其中癌组织样品具有更高的HEC。PC发生发展对免疫学研究提供了新的数据,对PC免疫监视、T细胞受体变异标志等研究提供了参考,对以后继续研究打下了基础。     

加速康复外科理念在根治性子宫切除术患者中的应用研究

目的:探讨加速康复外科理念对行根治性子宫切除术的宫颈癌患者的围手术期应用价值。方法:选取2013年1月至2018年7月在我院行因宫颈癌行根治性子宫切除术的66例患者作为研究对象。将入院患者随机分为观察组及对照组,观察组接受加速康复外科理念治疗(30例),对照组为常规治疗组(36例)。比较两组患者的肠鸣音恢复时间、肛门排气时间、下床行走时间、术后住院时间以及术后并发症的发生情况。结果:观察组与对照组肠鸣音恢复时间分别为(35.9±3.4)h及(39.6±3.0)h,术后首次排气时间分别为(50.7±2.7)h及(54.8±3.2)h,下床行走时间分别为(49.9±2.6)h及(53.6±3.2)h。术后住院时间分别为(7.6±1.7)d及(9.2±1.8)d,观察组以上指标均显著短于对照组(P0.01)。观察组与对照组的术后并发症总发生率分别为10.11%及23.44%,观察组显著低于对照组(P0.05)。两组拔除尿管后尿潴留的发生情况比较差异无统计学意义(P0.05)。结论:加速康复外科理念用于宫颈癌根治术患者的围手术期可有效加速患者的康复,且安全性较高。     

环氧合酶-2/5-脂氧合酶抑制剂对酒精相关性口腔癌的抑制作用

目的:分析和比较选择性环氧合酶-2 (Cox-2)抑制剂塞来昔布、5-脂氧合酶(5-Lox)抑制剂齐留通及Cox/5-Lox双酶抑制剂利克飞龙对酒精相关性口腔癌的抑制作用。方法:选择66只C57BL/6小鼠,分为阴性对照组、模型组(4NQO组)、阳性对照组、齐留通干预组、塞来昔布干预组和利克飞龙干预组。阴性对照组不做任何处理,其余各组饮用50μg/m L四硝基喹啉-1-氧化物(4NQO)溶液16周后,阳性对照组及各干预组以8%酒精溶液代替饮用水喂养8周,同时开始分别用三蒸水和同等药量的齐留通、塞来昔布、利克飞龙(100 mg·kg-1·d-1)灌胃8周;于24周处死动物,取舌行组织病理学观察、BrdU免疫组化染色、蛋白质印迹法(Western-blot)检测舌组织中5-Lox、Cox-2蛋白的表达。结果:饮用酒精后,口腔癌发生率从16.7%增加到58.3%,5-Lox、Cox-2蛋白表达显著增加癌组织中BrdU阳性率显著升高。齐留通干预后,口腔癌发生率(41.7%)显著降低,5-Lox表达显著减少,Cox-2表达显著增加,Brd U阳性率显著降低;塞来昔布干预后,口腔癌发生率(50.0%)显著降低,Cox-2表达显著减少,5-Lox表达显著增加,BrdU阳性率显著降低;利克飞龙干预后,口腔癌发生率(25%),Brd U阳性率与阳性对照组、齐留通干预组和塞来昔布干预组相比均显著降低,5-Lox、Cox-2蛋白表达比阳性对照组显著减少(P0.05)。结论:酒精促进口腔癌变的过程可能与5-Lox和Cox-2的表达上调关系密切;齐留通和塞来昔布可以分别抑制5-Lox和Cox-2活性,使口腔癌的发生率显著降低;利克飞龙对口腔癌的抑制作用优于齐留通和塞来昔布。