卵巢浆液性囊腺癌及囊腺瘤的差异蛋白质组学分析

目的探讨卵巢浆液性囊腺癌与卵巢浆液性囊腺瘤的差异表达蛋白质谱,从而寻找特异性诊断标志物。方法采用二维液质联用分析技术。结果卵巢浆液性囊腺癌与卵巢浆液性囊腺瘤两组间差异蛋白数共计128个。其中116个蛋白在卵巢浆液性囊腺癌中表达上调,12个蛋白表达下调。结论纤维结合蛋白1,基膜聚糖,核心蛋白多糖,骨诱导因子,微管蛋白A、B,肌动蛋白,肌动蛋白素,角蛋白8,结蛋白,膜联蛋白A1、A2,YWHAZ,踝蛋白1,转酮醇酶1,组织蛋白酶D,X线交错互补修复基因6,谷胱甘肽转移酶,核仁蛋白,抑制素,抗原提呈蛋白1,补体4A等22个差异蛋白在卵巢浆液性囊腺癌中的表达异常为首次报道。这些蛋白将有利于卵巢浆液性囊腺癌及卵巢浆液性囊腺瘤的鉴别诊断。与肿瘤物质和能量代谢异常相关的蛋白质可以用于卵巢癌诊断的代谢组学识别模式的建立。     

应用磁珠联合MALDI-TOF MS技术建立前列腺癌血清差异蛋白诊断模型

  目的  应用蛋白组学技术对前列腺癌血清差异蛋白进行筛选, 并建立前列腺癌诊断模型。  方法  2010年3月至5月间于北京协和医院泌尿外科病房采集12例前列腺癌患者及11例非前列腺癌对照者血清样本, 应用弱阳离子磁珠联合基质辅助激光解吸电离飞行时间质谱(matrix-assisted laser desorption/ionization time of flight mass spectrometry, MALDI-TOF MS)技术对前列腺癌患者和对照者血清进行差异蛋白研究, 筛选出多个前列腺癌血清差异蛋白, 并应用ClinProTools 2.2软件通过遗传算法建立诊断模型。  结果  共筛选出前列腺癌与对照组之间差异蛋白峰126个, 具有较明显差异的蛋白峰24个(P=0.178)。通过遗传算法优化选择, 筛选出符合条件的15个差异蛋白峰建立诊断模型, 交叉验证准确性为81.82%, 识别能力为100%。  结论  应用磁珠联合MALDI-TOF MS技术及遗传算法成功建立前列腺癌血清差异蛋白的诊断模型, 该模型识别能力高, 有助于减少前列腺癌的漏诊率。     

构建腰椎间盘突出症血瘀证的血清蛋白指纹图谱模型

背景：腰椎间盘突出症血瘀证与非血瘀证的相互关系尚不明确。〈br〉 目的：构建腰椎间盘突出症血瘀证的血清蛋白指纹图谱模型。〈br〉 方法：按照病例对照研究方法,遵循组间民族、性别及年龄等相匹配原则筛选180例研究对象,其中120例分为腰椎间盘突出症血瘀证组及腰椎间盘突出症非血瘀证组,每组60例;健康对照组60例。抽取受试者外周血的血清样本,应用表面增强激光解吸/电离飞行时间质谱及蛋白质芯片技术检测并绘制蛋白质质谱图,随后用Biomarker Wizard软件识别蛋白峰信息,建立腰椎间盘突出症血瘀证的血清诊断模型,并通过双盲验证法对模型进行验证及通过ExPASy数据库对相关差异蛋白进行蛋白检索。结果与结论：在腰椎间盘突出症血瘀证、腰椎间盘突出症非血瘀证及健康者各组之间找到11个蛋白质峰有统计学意义（P＜0.05）,其中2个蛋白质呈高表达、9个蛋白质呈低表达;用Biomarker Patterns Software构建腰椎间盘突出症血瘀证血清学诊断模型并验证,其敏感性为86.667%,特异性为94.167%,阳性预测值为88.136%。表明腰椎间盘突出症血瘀证患者的血清中存在多种异常表达的蛋白质;由11个差异蛋白组成的血清蛋白质指纹图谱模型可作为腰椎间盘突出症血瘀证的血清标志物诊断模型。     

突触蛋白质组学分析中双向电泳技术的优化

背景：双向电泳是突触蛋白质组学分析中最流行最通用的蛋白质分离方法之一.但文献中突触蛋白双向电泳对线性固相pH梯度（immobilized pH gradients,IPG）胶条和十二烷基磺酸钠聚丙烯酰胺凝胶电泳（sodium dodecyl sulfate-polyacrylamide gel electroph-oresis,SDS-PAGE）浓度的选择很多,尚未见统一标准.目的：对突触蛋白双向电泳的IPG胶条和SDS-PAGE凝胶浓度进行优化,以获得高质量的突触蛋白双向电泳图谱.方法：以大鼠海马突触蛋白为试材,比较pH 5.0-8.0与pH 3.0-10.0线性IPG胶条,线性与非线性pH 3.0-10.0IPG胶条,以及单一浓度10％与12％ SDS-PAGE对双向电泳的影响.此外,还使用计算机检索了1989至2013年中国知网及PubMed数据库中关于突触蛋白双向电泳的文献,对文献中选择的IPG胶条、SDS-PAGE凝胶浓度进行了统计和评价,并总结了突触蛋白在不同pH值IPG胶条和不同浓度SDS-PAGE凝胶的双向电泳图谱上的分布特征.结果与结论：结果表明,使用pH 3.0-10.0的非线性胶条及单一浓度10％ SDS-PAGE凝胶进行突触蛋白双向电泳较为适宜,电泳图谱质量好,实验操作便利;同时还推荐合并使用pH 4.0-7.0和pH 6.0-11.0的IPG胶条,以及线性梯度浓度9％-16％ SDS-PAGE凝胶,也适用于突触蛋白双向电泳分析.     

蛋白质组学技术分析小鼠中脑能量代谢蛋白

目的：采用蛋白质组学技术鉴定小鼠中脑部位与能量代谢相关的蛋白,探讨这些蛋白与神经性疾病的关系。方法提取小鼠中脑蛋白质,采用双向电泳分离,切取蛋白点进行基质辅助激光解吸/电离飞行时间质谱(MALDI-TOF MS)鉴定。结果双向电泳技术结合 MALDI-TOF MS 成功鉴定出24个与能量代谢相关蛋白。结论建立了小鼠中脑部位蛋白质的鉴定方法,为探讨这类蛋白质在神经系统疾病中的作用奠定了基础。     

Mass spectrometry-based membrane proteomics in cancer biomarker discovery

Membrane proteins are involved in central processes such as cell signaling, cell–cell interactions and communication, ion and metabolite transport and in general play a crucial role in cell homeostasis. Cancer and cancer metastasis have been correlated to protein expression levels and dysfunction, with membrane proteins playing an important role, and are thus used as drug targets and potential biomarkers for prognostic or diagnostic purposes. Despite the critical biological significance of membrane proteins, proteomic analysis has been a challenging task due to their hydrophobicity. In this review, recent advances in the proteomic analysis of membrane proteins are presented, focusing on membrane fraction enrichment techniques combined with labeled or label-free shotgun proteomics approaches for the identification of potential cancer biomarkers.     

Identification of differentially expressed proteins in human stage I lung adenocarcinoma and tumor-adjacent tissues with two-dimension gel electrophoresis profiling

Objective： The aim of this study was to establish reproducible two-dimensional electrophoretic assay used for profiling and identification of differentially expressed proteins in human stage I lung adenocarcinoma and paired normal tumor-adjacent tissue. Methods： The proteins from 12 human stage I lung adenocarcinoma tissues and normal tumor-adjacent tissues were separated using isoelectric focusing electrophoresis （the first dimension） and the subsequent homogeneous SDS-polyacrylamide gel electrophoresis （SDS-PAGE） （the second dimension）. The differentially expressed proteins were determined with PDQuest image analysis software, and identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry （MALDI-TOF-MS） and database searching. Results： The well-reproducible 2-DE gel patterns of human stage I lung adenocarcinoma and normal tumor-adjacent tissues were profiled and 26 differentially expressed proteins uncovered. Nine of these 26 protein spots were cut out from the preparation gels and determined with MALDI-TOF-MS. Searching against the protein database, four candidate proteins were identified. They were 60S acidic ribosomal protein P2, Cathepsin B1, Apolipoprotein A-I precursor, and La 4.1 protein. Conclusion： In this study, high reproducible 2-DE gel protein images of human stage I lung adenocarcinoma and paired normal tumor-adjacent tissues were achieved successfully, and 4 differentially expressed proteins were revealed. These data will be helpful for screen of early biomarker and study of molecular mechanisms of human lung adenocarcinoma.     

Landscape of surfaceome and endocytome in human glioma is divergent and depends on cellular spatial organization

Therapeutic strategies directed at the tumor surfaceome (TS), including checkpoint inhibitor blocking antibodies, antibody drug conjugates (ADCs), and chimeric antigen receptor T (CAR-T) cells, provide a new armament to fight cancer. However, a remaining bottleneck is the lack of strategies to comprehensively interrogate patient tumors for potential TS targets. Here, we have developed a platform (tumor surfaceome mapping [TS-MAP]) integrated with a newly curated TS classifier (SURFME) that allows profiling of primary 3D cultures and intact patient glioma tumors with preserved tissue architecture. Moreover, TS-MAP specifically identifies proteins capable of endocytosis as tractable targets for ADCs and other modalities requiring toxic payload internalization. In high-grade gliomas that remain among the most aggressive forms of cancer, we show that cellular spatial organization (2D vs. 3D) fundamentally transforms the surfaceome and endocytome (e.g., integrins, proteoglycans, semaphorins, and cancer stem cell markers) with general implications for target screening approaches, as exemplified by an ADC targeting EGFR. The TS-MAP platform was further applied to profile the surfaceome and endocytome landscape in a cohort of freshly resected gliomas. We found a highly diverse TS repertoire between patient tumors, not directly associated with grade and histology, which highlights the need for individualized approaches. Our data provide additional layers of understanding fundamental to the future development of immunotherapy strategies, as well as procedures for proteomics-based target identification and selection. The TS-MAP platform should be widely applicable in efforts aiming at a better understanding of how to harness the TS for personalized immunotherapy.

Cell-surface proteins have a key role in drug development, and approximately two-thirds of approved human drugs target a cell-surface protein (1). Recently, tumor cell–surface proteins integrated with the plasma membrane (tumor surfaceome [TS]) have attracted considerable attention as targets for immunotherapies in cancer. Immune checkpoint-blocking antibodies (e.g., ipilimumab and nivolumab), antibody drug conjugates (ADCs, e.g., trastuzumab emtansin), radioimmunotherapy (RIT, e.g., ⁹⁰Y ibritumomab tiuxetan), and chimeric antigen receptor T (CAR-T) cells are all directed at the TS and currently revolutionize cancer treatment (2–6). With the impressive development of creative methods for antibody and T cell engineering, a remaining challenge is the lack of strategies to comprehensively map potential TS target antigens for the design of more rational, individualized treatments (7). Although advancements in DNA and RNA sequencing provide high throughput data for prediction algorithms, e.g., personalized peptide vaccine trials (8, 9), the predicted proteome derived from these platforms is not necessarily expressed and available for targeting. Moreover, proteomics-based strategies involve analysis of the bulk from disintegrated tumor tissue, resulting in loss of spatial information and limited coverage of the less abundant and hydrophobic TS proteins (10, 11). Of particular relevance, ADC, RIT, and other intracellular drug delivery strategies rely on TS targets that functionally engage in endocytic internalization (12). Clearly, despite its great targeting potential in cancer immunotherapy, the TS remains an elusive treasure for further discovery.Procedures for unbiased mapping of the TS and target identification should include specific labeling of the TS in freshly resected patient tumors with preserved tissue architecture. Enrichment of TS proteins and reduction of noise from intracellular proteins as well as abundant extracellular matrix collagens and glycoproteins would greatly improve downstream mass spectrometry analysis. Moreover, the approach should allow functional and dynamic profiling of TS internalization in an intact tissue environment. With the aim to address these challenges and to provide insight into the complexity of the TS, we have developed a versatile technology for TS mapping (TS-MAP). As proof of concept, we focused on primary brain tumors that remain among the most aggressive forms of cancer and for which attempts to conquer the most common variant, glioblastoma (GBM) (World Health Organization [WHO] grade IV) have failed so far (13). TS-MAP is compatible with spheroids from primary human stem cell–like GBM cultures, as well as mouse and patient brain tumors, and separately profiles surface resident and internalized TS proteins. Moreover, a TS classifier (SURFME) was curated for filtering and categorization of bona fide membrane proteins exposed to the extracellular space. We find significant differences in the TS between the 2D and 3D spheroid format, which underlines the importance of cellular spatial organization. In strong support of the need of individualized approaches, our findings suggest substantial intertumoral heterogeneity in the relative abundance of TS proteins in a cohort of freshly resected patient gliomas.     

胃癌细胞多药耐药相关蛋白质筛选鉴定的蛋白质组学研究

目的 在胃癌细胞株SGC7901及稳定的耐药细胞株SGC7901/VCR中寻找与胃癌多药耐药(MDR)直接相关的蛋白质,观察其功能.方法 胃癌细胞株SGC7901和稳定的耐药细胞株SGC7901/VCR培养后提取总蛋白,采用蛋白质组学技术(双向凝胶电泳和基质辅助激光解吸电离-飞行时间质谱鉴定)筛选并鉴定差异表达的蛋白质,并应用蛋白印迹试验法对鉴定出的部分蛋白质在胃癌细胞株中的表达进行验证.结果 在两种细胞株中找到表达差异明显的蛋白质点9个,经质谱分析,7种蛋白质得到鉴定,为S60核糖体蛋白L23、电压依赖性阴离子选择性通道蛋白1、锌指蛋白394、角蛋白Ⅰ型细胞骨架9、核糖核酸3'-端磷酸化酶1、matrin型锌指蛋白2、Sideroflexin-1.这些蛋白质与胃癌MDR直接相关.蛋白印迹试验法检测部分蛋白质在胃癌细胞株中的表达,与蛋白质组学所得结果一致.结论 胃癌细胞SGC7901和SGC7901/VCR蛋白质表达存在差异.

Abstract：

Objective To investigate multidrug resistance related proteins in human gastric carci noma cell lines SGC7901 and SGC7901/VCR by comparative proteomics.Methods After culture,the holoproteins of human gastric carcinoma cell lines SGC7901 and GC7901/VCR were extracted,and then measured by two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization time-offlight mass spectrometry (MALDI-TOF-MS).Some proteins obtained through proteomics were tested by Western blotting in the cell lines.Results There were different proteins in these 2 human gastric carcinoma cell lines.Nine different protein spots were found in these 2 gastric carcinoma cell lines,and 7 spots were identified by MALDI-TOF-MS,and these proteins were 60S ribosomal protein L23 ( RL23),voltagedependent anion-selective channel protein-1 (VDAC1),zinc finger protein (ZNF) 394,keratin,type Ⅰcytoskeletal 9 ( KIC9),RNA 3' -terminal phosphate cyclase 1 ( RTC1 ),zinc finger matrin-type protein 2,Sideroflexin-1.These proteins had a direct relationship with multidrug resistance in gastric carcinoma.Results of Western blotting about protein expression were in consonance with those of proteomics.Conclusion Different proteins were found in human gastric carcinoma cell lines SGC7901 and SGC7901/VCR.     

尿道下裂仔鼠阴茎蛋白质组学分析及膜联蛋白A3的表达变化研究

目的:探讨邻苯二甲酸二丁酯(DBP)胚胎期暴露对仔鼠阴茎组织蛋白表达谱的影响,分离并鉴定差异表达蛋白质。验证膜联蛋白A3在仔鼠阴茎中的表达变化,初步探讨其在尿道下裂发生中的作用。方法:SPF级SD孕鼠20只,妊娠14～18d(GD14～GD18),随机均分为2组,实验组给予DBP按800mg/kg染毒孕鼠,对照组按大豆油5ml/kg,2组孕鼠均每天灌胃1次连续5d。出生后3d取出实验组尿道下裂雄性仔鼠阴茎和对照组正常雄性仔鼠阴茎,提取总蛋白,进行二维凝胶电泳分离和图像分析,筛选出的差异蛋白质点利用质谱技术进行鉴定,并运用Western印迹和免疫组化法分析膜联蛋白A3在仔鼠阴茎中的表达变化。结果:共筛选出31个差异表达蛋白,其中17个通过质谱分析和SwissProt蛋白数据库检索得到鉴定,包括丙酮酸激酶M2、α烯醇化酶、膜联蛋白A3等。膜联蛋白A3相对表达量在尿道下裂组为1.851±0.014(n=10),正常对照组为2.603±0.012(n=10),两组的差异具有显著性(P<0.05)。膜联蛋白A3主要定位于仔鼠尿道上皮细胞。结论:运用蛋白质组学方法,建立了DBP孕期暴露致尿道下裂雄性仔鼠与正常仔鼠阴茎蛋白质差异表达谱系。膜联蛋白A3的表达变化可能在尿道下裂尿道沟融合障碍过程中发挥重要作用。