食管鳞癌的蛋白质组学

大部分食管鳞癌（esophageal squamous cell carcinoma, ESCC）确诊时已发展至中晚期,临床治疗效果差,是导致我国华北地区ESCC死亡率居高不下的主要原因之一.因此,亟需筛查ESCC特异性、敏感性的生物标志物,以期用于ESCC早期诊断、个体化分子靶向治疗和预后评价. 与相对稳定、携带遗传信息的基因组不同,蛋白质组具有时空变化特性,由此构成生命活动复杂性的物质基础.在病理情况下,蛋白质组能够精确反映患病组织器官的功能状态,因此为疾病的监测提供了窗口.本文总结了ESCC蛋白质组研究现状及差异表达的蛋白质谱,并探讨了ESCC候选分子标志物的潜在临床应用价值.     

基于多组学数据的早期宫颈鳞状细胞癌分类

从分子层面对泛癌进行研究已经得到了很大的进展,但是对宫颈鳞状细胞癌的分子分类研究仍然需要更多的探索.为了找到宫颈鳞状细胞癌潜在的子类,本文提出了一个基于多维组学数据的癌症亚型分类分析流程.通过统计学方法对癌症基因组图谱(The Cancer Genome Atlas,TCGA)宫颈鳞状细胞癌的mRNA表达数据、小分子核糖核酸(microRNA,miRNA)表达数据、DNA甲基化数据以及拷贝数变异数据4个维度包含的分子进行筛选,然后对筛选后的分类特征进行整合聚类,进一步筛选能够区分不同子类的关键分类特征,并使用这些关键分类特征建立宫颈鳞状细胞癌分类模型.本研究为宫颈鳞状细胞癌分子层面子类的识别提供了分析流程,得到了两个临床生存水平具有显著性差异的宫颈鳞状细胞癌子类,并确定了8个宫颈鳞状细胞癌的关键分类特征.本研究中识别的宫颈鳞状细胞癌子类和关键分类特征为宫颈鳞状细胞癌早期分类及分类标志物的鉴定提供了重要参考.     

食管鳞癌与腺癌差异基因表达的对比分析

目的：研究食管鳞癌（esophageal squamous cell carcinoma,ESCC）与食管腺癌（esophageal adenocarcinoma,EAC）的基因差异表达,探讨ESCC与EAC发生发展的基因学基础。方法：选取8例ESCC和8例EAC组织抽提mRNA,应用cDNA芯片技术通过芯片杂交、生物信息学处理,找出两者间差异表达基因。结果：采用BioStarH-40芯片发现差异表达基因541条,差异表达基因占13．8％,其中表达增强309条（显著增强73条）,表达降低232条（显著降低61条）。结论：ESCC与EAC基因表达比较,差异有统计学意义,这些差异可能在两类肿瘤不同的生物学行为中起重要作用。     

食管鳞癌与腺癌差异基因表达的对比分析

目的:研究食管鳞癌(esophageal squamous cell carcinoma,ESCC)与食管腺癌(esophageal adenocarcinoma,EAC)的基因差异表达,探讨ESCC与EAC发生发展的基因学基础。方法:选取8例ESCC和8例EAC组织抽提mRNA,应用cDNA芯片技术通过芯片杂交、生物信息学处理,找出两者间差异表达基因。结果:采用BioStarH-40芯片发现差异表达基因541条,差异表达基因占13.8%,其中表达增强309条(显著增强73条),表达降低232条(显著降低61条)。结论:ESCC与EAC基因表达比较,差异有统计学意义,这些差异可能在两类肿瘤不同的生物学行为中起重要作用。     

肺鳞状细胞癌癌症发展模式识别分类模型及特征基因识别

本文利用先进的生物信息学方法,首次从全基因组水平综合基因表达、甲基化水平和拷贝数变异三类数据,寻找与肺鳞状细胞癌(LUSC)发生和发展密切相关的特征基因,为进一步解释其内在机理、开发新的靶向药物和治疗手段提供更加深入的理论依据.为克服全基因组数据超高维高噪声小样本特性对机器学习算法性能的影响,防止信息饱和现象的干扰,本文创新性地组合应用4种特征基因筛选方法,分别从特异性、相关性、生物学功能和对肿瘤分类模型的贡献等多个方面,通过迭代降维技术递归筛选真正的特征基因.研究中,我们以TCGA(The Cancer Genome Atlas project)数据库中的LUSCⅠ~Ⅲ期病人样本为例,对其基因表达数据(GE)、基因甲基化数据(ME)以及拷贝数变异数据(CNV)进行分析.结果筛选出67个GE特征基因,对3类样本分类的平均准确率达到86.29%,70个ME特征基因,相应的分类准确率为90.92%,31个CNV特征基因,相应的分类准确率为69.16%.KEGG(Kyoto Encyclopedia of Genes and Genomes)和IPA(Ingenuity Pathway Analysis)对上述3类特征基因集在代谢通路水平和基因调控网络水平上的分析,证明了其在调控水平上的密切关系.同时也表明,识别的特征基因与LUSC肿瘤进展之间有着重要的直接关系,这对了解肿瘤机理以及新靶向治疗的发展非常重要.     

喜树碱-氟尿苷纳米颗粒对口腔鳞癌细胞Tca-8113增殖与迁移的影响

目的:探究喜树碱-氟尿苷(CPT-FUDR)纳米颗粒对口腔鳞癌Tca-8113细胞增殖与迁移的影响。方法:制备喜树碱-氟尿苷纳米颗粒,通过丁达尔现象证明已组装完毕。将制备好的纳米颗粒组和喜树碱(CPT)单药组、氟尿苷(FUDR)单药组以及两种单药混合组(CPT/FUDR)作对比,采用MTT实验检测药物对口腔鳞癌细胞Tca-8113增殖的抑制作用,通过划痕实验探究CPT-FUDR纳米颗粒和CPT/FUDR混合药物对细胞迁移能力的影响。结果:MTT结果显示:在药物浓度大于0.1μM时,随着浓度的增加,四组细胞存活率均明显下降(P0.05),而CPT-FUDR纳米颗粒组Tca-8113细胞的存活率明显低于单药CPT、FUDR和CPT/FUDR混合物组(P0.05)。在划痕实验中,培养48 h后,CPT/FUDR混合物组和CPT-FUDR纳米颗粒组均显著低于空白组(P0.05),且CPT-FUDR纳米颗粒组显著低于CPT/FUDR混合物组(P0.05)。结论:在体外,CPT-FUDR纳米颗粒对口腔鳞癌Tca-8113细胞的增殖与迁移有较好的抑制作用,且抑制效果优于CPT/FUDR两种单药混合。     

Approaching MALDI molecular imaging for clinical proteomic research: current state and fields of application

MALDI imaging mass spectrometry (‘MALDI imaging’) is an increasingly recognized technique for biomarker research. After years of method development in the scientific community, the technique is now increasingly applied in clinical research. In this article, we discuss the use of MALDI imaging in clinical proteomics and put it in context with classical proteomics techniques. We also highlight a number of upcoming challenges for personalized medicine, development of targeted therapies and diagnostic molecular pathology where MALDI imaging could help.     

High-dimensional Cytometry (ExCYT) and Mass Spectrometry of Myeloid Infiltrate in Clinically Localized Clear Cell Renal Cell Carcinoma Identifies Novel Potential Myeloid Targets for Immunotherapy

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Highlights

• •Using ExCYT, genomics, and Mass Spectrometry, we were able to uncover immune cell marker alterations that provide new insight into the biology of early stage ccRCC.
• •Among the CD45⁺ population, we observed a high level of myeloid cell infiltration in treatment-naïve ccRCC tissues.

     

The Use of Salivary Levels of Matrix Metalloproteinases as an Adjuvant Method in the Early Diagnosis of Oral Squamous Cell Carcinoma: A Narrative Literature Review

Oral squamous cell carcinoma (OSCC) is an aggressive malignancy with increased mortality, in which the early diagnosis is the most important step in increasing patients’ survival rate. Extensive research has evaluated the role of saliva as a source of diagnostic biomarkers, among which matrix metalloproteinases (MMPs) have shown a valuable potential for detecting even early stages of OSCC. The aim of this review was to present recent clinical data regarding the significance of salivary MMPs in the detection of early malignant transformation of the oral mucosa. A narrative review was conducted on articles published in PubMed, Cochrane Library, Web of Science, EBSCO and SciELO databases, using specific terms. Our search revealed that MMP-1, MMP-2, MMP-3, MMP-8, MMP-9, MMP-10, MMP-12 and MMP-13 had significantly higher levels in saliva from patients with OSCC compared to controls. However, the strength of evidence is limited, as most information regarding their use as adjuvant diagnostic tools for OSCC comes from studies with a low number of participants, variable methodologies for saliva sampling and diagnostic assays, and insufficient adjustment for all covariates. MMP-1, MMP-3 and MMP-9 were considered the most promising candidates for salivary diagnosis of OSCC, but larger studies are needed in order to validate their clinical application.     

Phosphotyrosine-based Phosphoproteomics for Target Identification and Drug Response Prediction in AML Cell Lines

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Highlights

• •pY phosphoproteomes and dedicated ranking analyses for 16 AML cell lines.
• •RTK drivers, 6 mutant cell lines confirmed, identification for 4 more cell lines.
• •MAPK1/3 phosphorylation for cell lines without TK driver, indicating RAS mutation.
• •Drug target space phosphorylation correlates with drug IC50s in specific cell lines.

     

中国北方汉族人群DNA修复能力的水平与头颈鳞癌发病风险的初步研究

目的:初步探讨北方汉族人DNA修复能力(DNA repair capacity,DRC)的水平与头颈鳞癌发病风险的相关性,为头颈鳞癌的诊断提供新的检测标志物。方法:收集71例头颈鳞癌患者和65例健康对照,均为我国北方地区汉族人。通过宿主细胞再活化(host cell reactivate,HCR)实验检测研究对象外周血淋巴细胞DRC的表达水平。对头颈鳞癌病例组和对照组之间一般特征的差异进行卡方检验,通过t检验及Wilcoxon秩和检验分析两组间DRC水平的差异。通过logistic回归模型计算优势比(OR值)及95%可信区间(95%CI)。此外,我们通过logistic模型计算ROC曲线下面积,进一步评价DRC模型的诊断价值。结果:头颈鳞癌组中DRC的水平在统计学上低于对照组(P=0.007)。在logistic回归模型分析中,矫正完年龄、性别、吸烟状况和饮酒因素后,DRC的水平与头颈鳞癌患病风险关系的ORs,在低水平与其DRC高水平相比为2.35(95%CI,1.11-4.98)。此外,DRC的水平降低与头颈鳞癌风险增加之间也存在剂量反应关系。最后,ROC曲线模型提示DRC模型中曲线下面积有所改善(P=0.068)。结论:北方汉族人中DRC水平的降低与头颈鳞癌发病风险的增加相关。本研究结果需在更大样本的后续研究中进一步验证。     

咖啡酸对食管鳞状细胞癌KYSE450裸鼠移植瘤生长的影响及分子机制研究

摘要 目的：探讨与研究咖啡酸对食管鳞状细胞癌KYSE450裸鼠移植瘤生长的影响及分子机制。方法：将食管鳞状细胞癌移植瘤裸鼠（n=48）随机平分为三组-模型组、5-氟尿嘧啶组与咖啡酸组。三组分别经腹腔注射0.2 mL生理盐水、5-氟尿嘧啶25 g/kg、5-氟尿嘧啶25 g/kg与咖啡酸50 mg/kg,2次/周,持续4周。结果：5-氟尿嘧啶组与咖啡酸组治疗第2周与第4周的体重高于模型组（P<0.05）,咖啡酸组高于5-氟尿嘧啶组（P<0.05）。5-氟尿嘧啶组与咖啡酸组治疗第2周与第4周的肿瘤体积少于模型组（P<0.05）,咖啡酸组高于5-氟尿嘧啶组（P<0.05）。5-氟尿嘧啶组与咖啡酸组治疗第4周的血清TNF-α与IL-6含量低于模型组（P<0.05）,咖啡酸组低于5-氟尿嘧啶组（P<0.05）。5-氟尿嘧啶组与咖啡酸组治疗第4周的移植瘤Bax、Caspase-3蛋白相对表达水平与凋亡指数高于模型组（P<0.05）,咖啡酸组高于5-氟尿嘧啶组（P<0.05）。结论：咖啡酸在食管鳞状细胞癌裸鼠的应用能与5-氟尿嘧啶发挥协同作用,能通过上调Bax、Caspase-3蛋白的表达,促进移植瘤细胞凋亡,抑制炎症因子的表达,减少血管总数,从而抑制移植瘤生长,促进恢复裸鼠体重。     

Functional analysis tools for post‐translational modification: a post‐translational modification database for analysis of proteins and metabolic pathways

Post‐translational modifications (PTMs) are critical regulators of protein function, and nearly 200 different types of PTM have been identified. Advances in high‐resolution mass spectrometry have led to the identification of an unprecedented number of PTM sites in numerous organisms, potentially facilitating a more complete understanding of how PTMs regulate cellular behavior. While databases have been created to house the resulting data, most of these resources focus on individual types of PTM, do not consider quantitative PTM analyses or do not provide tools for the visualization and analysis of PTM data. Here, we describe the Functional Analysis Tools for Post‐Translational Modifications (FAT‐PTM) database ( https://bioinformatics.cse.unr.edu/fat-ptm/ ), which currently supports eight different types of PTM and over 49 000 PTM sites identified in large‐scale proteomic surveys of the model organism Arabidopsis thaliana. The FAT‐PTM database currently supports tools to visualize protein‐centric PTM networks, quantitative phosphorylation site data from over 10 different quantitative phosphoproteomic studies, PTM information displayed in protein‐centric metabolic pathways and groups of proteins that are co‐modified by multiple PTMs. Overall, the FAT‐PTM database provides users with a robust platform to share and visualize experimentally supported PTM data, develop hypotheses related to target proteins or identify emergent patterns in PTM data for signaling and metabolic pathways.     

The hidden potential of glycomarkers: Glycosylation studies in the service of cancer diagnosis and treatment

Changes in the glycosylation process appear early in carcinogenesis and evolve with the growth and spread of cancer. The correlation of the characteristic glycosylation signature with the tumor stage and the appropriate therapy choice is an important issue in translational medicine. Oncologists also pay attention to extracellular vesicles as reservoirs of new cancer glycomarkers that can be potent for cancer diagnosis/prognosis. In this review, we recall glycomarkers used in oncology and show their new glycoforms of improved clinical relevance. We summarize current knowledge on the biological functions of glycoepitopes in cancer-derived extracellular vesicles and their potential use in clinical practice. Is glycomics a future of cancer diagnosis? It may be, but in combination with other omics analyses than alone.