代谢组学在胃肠肿瘤诊断中的应用

代谢组学是继基因组学、转录组学和蛋白质组学之后发展起来的一门新的组学方法,因其独特的优势,已广泛应用到肿瘤诊断生物标志物的筛选之中.目前利用代谢组学方法在胃肠肿瘤患者组织、血液、尿液、粪便中已发现了一些诊断相关生物标志物,有助于胃肠恶性肿瘤的早期诊断及个体化治疗.     

微小RNA与肿瘤

 相关研究发现在肿瘤患者的血液或尿液中,存在着相对特异的微小RNA（miRNA）表达谱,血液、尿液中的miRNA稳定性强、重复性好,可将其作为肿瘤早期诊断、个性化治疗、预后监测或跟踪随访的非创伤性生物标志物。     

蛋白质组学在恶性胸腔积液研究中的应用现状及进展

蛋白质组学的研究对象是生命活动的执行者——蛋白质,而恶性胸腔积液中富含蛋白质,尤其是组织特异性、肿瘤相关性的蛋白,所以通过蛋白质组学研究恶性胸腔积液对于认识其蛋白谱、找出疾病相关的生物标志物、发现病因有重要意义。本文主要从组成蛋白质组学及比较蛋白质组学两方面,对近年来蛋白质组学在恶性胸腔积液中的研究进行综述。     

蛋白质组学法检测膀胱移行细胞癌患者尿液中特异性肿瘤标志物

 目的:检测膀胱移行细胞癌患者尿液中差异表达蛋白质,筛选新的肿瘤标志物,进而探讨其与TCC发病机制的相关性,以及蛋白质组学法在膀胱移行细胞癌早期无创诊断方面的研究应用价值。 方法:选取青岛大学医学院附属医院泌尿外科TCC住院病人尿液标本24例,另外选取12例TCC术后病人、12例健康志愿者的尿液标本作为对照。采用蛋白质芯片技术结合表面增强激光解析/离子化-飞行时间-质谱技术检测各组尿液标本的差异表达蛋白质,然后到蛋白数据库中鉴定筛选肿瘤标志物。 结果:TCC组与对照组尿液标本的蛋白质存在差异表达,IMAC-Cu-3蛋白质芯片共发现6个蛋白及2个蛋白簇表达水平发生变化。联合检测3438Da及8002Da蛋白可使诊断TCC的敏感度达83.3%,特异性达75.0%。3438Da蛋白已被鉴定为α-defensin蛋白;搜索SWISS-PRO蛋白数据库,4310Da~5150Da蛋白簇为gp40蛋白。 结论:SELDI-TOF-MS蛋白质芯片技术是一种快速、简便易行、用量少和高通量分析方法,能直接筛选出膀胱移行细胞癌患者尿液中特异的肿瘤标志物,为蛋白组学方法在膀胱移行细胞癌早期无创诊断、判断预后及探讨发病机制方面的研究应用开拓了广阔前景。     

基于质谱的高通量蛋白质组学技术探索肿瘤蛋白标志物的研究进展

蛋白质组学研究虽已开展20余年，早期研究基于Western blot技术，后来采用质谱技术鉴定蛋白质。但最初质谱技术的测序深度和鉴定蛋白质数量有限，使蛋白质组学研究遇到瓶颈。近年来，随着质谱技术的飞速发展，实现了高通量的蛋白质组学鉴定，从此蛋白质组学研究进入新时代。目前，高通量蛋白质组学技术在肿瘤领域的应用主要包括揭示肿瘤发生发展机制、寻找特异性生物标志物、阐明耐药性产生机制和发现新治疗靶点等。肿瘤的早期发现和诊断有助于及时地进行医疗干预，从而大幅提高患者的生存率及生存质量。国内外研究已发现了很多候选肿瘤生物标志物，但仅极少数应用于临床。因此，仅针对探索肿瘤特异性生物标志物，本文选取并分析高通量蛋白质组学技术应用较为广泛深入、且发病率/死亡率较高的肺癌、乳腺癌、结直肠癌和肝癌4种肿瘤类型。在不同肿瘤类型中筛选发表期刊影响因子较高、经扩大样本量验证或功能验证、证据较强的研究。介绍基于质谱的高通量蛋白质组学技术和常用标本类型，重点综述在上述4种高发癌症中，基于该技术发现的可能用于早期诊断、预测预后、靶向治疗的蛋白质标志物，旨在为实现肿瘤精准诊疗提供新的理论依据。      

蛋白质组学在肿瘤早期检测中的应用

肿瘤是严重危害人类健康的疾病之一,其发病率和死亡率都较高。通过筛查,早期检测出肿瘤,及时治疗,可以降低死亡率。理想的筛查方法应具有特异性高、敏感性高、成本低且受试者依从性好等特点。肿瘤标志物尤其是体液中的肿瘤标志物有可能成为理想的筛查工具。肿瘤标志物的研究需要多门学科多种技术的参与。蛋白质组学是一门新兴的学科,能够从整体上研究疾病的发生机制,寻找与疾病相关的标志蛋白。近年来,运用蛋白质组学技术已经发现和鉴定了许多肿瘤标志物。尽管这些技术目前还存在一些缺点,但它处于不断地完善和改进之中,将在肿瘤早期检测中发挥重要作用。     

蛋白质组学在实体瘤肿瘤标志物研究中的应用

在后基因组时代,生物学的中心任务是认识基因组的功能。由于基因功能主要是通过其表达蛋白质来实现的,要了解基因的全部信息,必须深入研究不同基因编码的蛋白质,因此蛋白质组学在生命科学研究中已具有重要的地位。肿瘤细胞或组织蛋白质样本通常经过双向电泳等技术可以按不同大小、等电点或类型得以分离(profiling),然后通过质谱技术和蛋白质数据库比较,进一步将特殊的感兴趣的蛋白质鉴定出来。肿瘤蛋白质组学是整个蛋白质组学研究中的一项重要内容,通过蛋白质组分析技术将能够从细胞整体水平上认识在肿瘤的发生、发展过程中蛋白表达谱的变化,为寻找特异的肿瘤标志物这一研究领域带来了新的希望。近几年来,使用蛋白质组学和激光捕获显微切割技术(laser capture microdissection,LCM)已在多种肿瘤中发现了许多有研究前景的肿瘤标志物侯选蛋白,尽管目前被肯定的肿瘤特异性标志物尚为数不多,但和以往相比已经有了十分显著的进步,本文对此做了简要综述。     

血清蛋白质组技术在肿瘤标志物筛查中的应用

蛋白质组学研究可以动态、整体、定量的检测肿瘤发生、发展过程中蛋白质种类、数量的改变,有助于寻找与鉴定肿瘤诊断和预后的特异标志物及药物治疗靶点,目前已广泛应用于生物学各研究领域.近年来,出现了将蛋白质组技术与血清学相结合的新方法,为在血清中筛选、鉴定肿瘤标志物提供了技术平台,运用这些技术有可能在多种肿瘤中发现更多有研究前景的肿瘤标志物候选蛋白.     

血清蛋白质组技术在肿瘤标志物筛查中的应用

蛋白质组学研究可以动态、整体、定量的检测肿瘤发生、发展过程中蛋白质种类、数量的改变，有助于寻找与鉴定肿瘤诊断和预后的特异标志物及药物治疗靶点，目前已广泛应用于生物学各研究领域。近年来，出现了将蛋白质组技术与血清学相结合的新方法，为在血清中筛选、鉴定肿瘤标志物提供了技术平台，运用这些技术有可能在多种肿瘤中发现更多有研究前景的肿瘤标志物候选蛋白。     

蛋白质芯片质谱仪在肿瘤标志物研究中的应用

表面加强激光解析电离飞行时间质谱(SELDI-TOF MS)是一种新的蛋白质检测技术.与传统的蛋白质组学方法相比,该技术具有快速、灵敏、高通量等特点.利用该技术制成的蛋白质芯片质谱仪已成为蛋白质组学研究中的重要工具.现综述该技术在肿瘤标志物研究中的应用.     

Urinary biomarkers predict brain tumor presence and response to therapy.

PURPOSE: A major difficulty in treating brain tumors is the lack of effective methods of identifying novel or recurrent disease. In this study, we have evaluated the efficacy of urinary matrix metalloproteinases (MMP) as diagnostic biomarkers for brain tumors. EXPERIMENTAL DESIGN: Urine, cerebrospinal fluid, and tissue specimens were collected from patients with brain tumors. Zymography, ELISA, and immunohistochemistry were used to characterize the presence of MMP-2, MMP-9, MMP-9/neutrophil gelatinase-associated lipocalin (NGAL), and vascular endothelial growth factor (VEGF). Results were compared between age- and sex-matched controls and subjected to univariate and multivariate statistical analyses. RESULTS: Evaluation of a specific panel of urinary biomarkers by ELISA showed significant elevations of MMP-2, MMP-9, MMP-9/NGAL, and VEGF (all P < 0.001) in samples from brain tumor patients compared with controls. Multiplexing MMP-2 and VEGF provided superior accuracy compared with any other combination or individual biomarker. Receiver-operating characteristics curves for MMP-2 and VEGF showed excellent discrimination. Immunohistochemistry identified these same proteins in the source tumor tissue. A subset of patients with longitudinal follow-up revealed subsequent clearing of biomarkers after tumor resection. CONCLUSION: We report, for the first time, the identification of a panel of urinary biomarkers that predicts the presence of brain tumors. These biomarkers correlate with presence of disease, decrease with treatment, and can be tracked from source tissue to urine. These data support the hypothesis that urinary MMPs and associated proteins are useful predictors of the presence of brain tumors and may provide a basis for a novel, noninvasive method to identify new brain tumors and monitor known tumors after treatment.     

Discovery of Potential Bladder Cancer Biomarkers by Comparative Urine Proteomics and Analysis

ObjectiveWe searched for bladder tumor markers by analyzing urine samples from patients with bladder cancer and from normal controls.MethodsProteins in urine samples of patients with bladder cancer and with normal controls were systematically examined by 2-dimensional electrophoresis combined with matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The expression of the protein apolipoprotein A-I (apoA-I) was confirmed by Western blot analysis and further evaluated.ResultsWe successfully obtained the 2-dimensional electrophoresis gel maps of urinary proteins in patients with bladder cancer and in normal controls. Thirty differentially expressed protein spots were successfully matched by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Combined with the SWISS-PROT database, only 14 proteins (beta-2-microglobulin, fatty acid–binding protein adipocyte, gelsolin, isoform 1 of gelsolin, myoglobin, isoform 2 of fibrinogen alpha chain, apoA-I, prostaglandin D₂ synthase 21 kDa [brain], protein AMBP, transthyretin, keratin type II cytoskeletal 1, type II cytoskeletal 8, putative uncharacterized protein ALB, putative uncharacterized protein MASP2 [fragment]) were identified, including 2 putative proteins. Furthermore, apoA-I was confirmed by Western blot analysis, and the high level of apoA-I was found in urine samples from patients with bladder tumors compared with normal controls.ConclusionsAnalysis of urinary proteome may be a feasible, noninvasive, and efficient strategy for searching for potential bladder tumor biomarkers. A significant relationship of expressed apoA-I was established between bladder cancer and normal controls. We concluded that 14 differential spots included the apoA-I and would be potential urinary biomarkers for the diagnosis and surveillance of bladder cancer.     

Collection, processing, and storage of biological samples in epidemiologic studies: sex hormones, carotenoids, inflammatory markers, and proteomics as examples.

The measurement of biomarkers in blood specimens has become an integral component of many epidemiologic studies and introduces several decision points about specimen collection, processing, and storage for the investigator. We briefly discuss the current state of knowledge for four commonly assessed biomarkers: estrogens and other sex hormones, ascorbic acid and carotenoids, cytokines involved in the inflammatory response, and proteomics. Sex hormones are relatively robust to type of sample collected, delayed processing (if chilled), and long-term storage at <-70 degrees C. Ascorbic acid and carotenoids also are relatively robust to sample type and delayed processing (if chilled); however, the blood sample should not be exposed to sunlight and must be stored at <-70 degrees C to prevent substantial degradation. If ascorbic acid is of primary interest, an acid stabilizer should be added during processing. Less is known for cytokines and proteomics, although initial research suggests that these assays are sensitive to varying collection, processing, and storage methods. Overall, we recommend conducting pilot studies if any nonstandard collection, processing, or storage procedure is used. Finally, decisions about these issues depend primarily on the scientific questions of most interest, cost, flexibility, and resources.     

Research Progress in Applying Proteomics Technology to Explore Early Diagnosis Biomarkers of Breast Cancer,Lung Cancer and Ovarian Cancer

According to the China tumor registry 2013 annual report , breast cancer, lung cancer, and ovarian cancer arethree common cancers in China nowadays, with high mortality due to the absence of early diagnosis technology.However, proteomics has been widespreadly implanted into every field of life science and medicine as an importantpart of post-genomics era research. The development of theory and technology in proteomics has provided newideas and research fields for cancer research. Proteomics can be used not only for elucidating the mechanismsof carcinogenesis focussing on whole proteins of the tissue or cell, but also seeking the biomarkers for diagnosisand therapy of cancer. In this review, we introduce proteomics principles, covering current technology used inexploring early diagnosis biomarkers of breast cancer, lung cancer and ovarian cancer     

Contribution of oncoproteomics to cancer biomarker discovery

Oncoproteomics is the study of proteins and their interactions in a cancer cell by proteomic technologies. Proteomic research first came to the fore with the introduction of two-dimensional gel electrophoresis. At the turn of the century, proteomics has been increasingly applied to cancer research with the wide-spread introduction of mass spectrometry and proteinchip. There is an intense interest in applying proteomics to foster an improved understanding of cancer pathogenesis, develop new tumor biomarkers for diagnosis, and early detection using proteomic portrait of samples. Oncoproteomics has the potential to revolutionize clinical practice, including cancer diagnosis and screening based on proteomic platforms as a complement to histopathology, individualized selection of therapeutic combinations that target the entire cancer-specific protein network, real-time assessment of therapeutic efficacy and toxicity, and rational modulation of therapy based on changes in the cancer protein network associated with prognosis and drug resistance. Besides, oncoproteomics is also applied to the discovery of new therapeutic targets and to the study of drug effects. In pace with the successful completion of the Human Genome Project, the wave of proteomics has raised the curtain on the postgenome era. The study of oncoproteomics provides mankind with a better understanding of neoplasia. In this article, the discovery of cancer biomarkers in recent years is reviewed. The challenges ahead and perspectives of oncoproteomics for biomarkers development are also addressed. With a wealth of information that can be applied to a broad spectrum of biomarker research projects, this review serves as a reference for biomarker researchers, scientists working in proteomics and bioinformatics, oncologists, pharmaceutical scientists, biochemists, biologists, and chemists.     

基因组学和蛋白质组学及代谢组学在食管癌筛查与早期诊断应用研究现状

目的食管癌是常见的消化道恶性肿瘤,发病率较高而生存率较低。本文总结基因组学、蛋白质组学及代谢组学在食管癌早期筛查和诊断中的应用,为今后食管癌早期筛查和诊断提供新的平台和科学理论依据。方法以"基因组学、蛋白质组学、代谢组学、食管癌和早期诊断"为关键词检索CNKI期刊全文数据库,以"genomics、proteomics、metabolomics、esophagus cancer、early diagnosis"为关键词检索PubMed,检索建库至2018-12发表的相关文献。纳入标准:(1)基因组学、蛋白质组学和代谢组学相关研究;(2)食管癌早期筛查与诊断。排除标准:(1)综述类文献;(2)研究资料不全;(3)结果重复且相对陈旧的研究。根据纳入和排除标准选择29篇文献进行分析。结果既往研究证实,食管癌患者与健康者在基因、蛋白质表达及代谢表达方面存在差异,且发现TFF1、CCNA1和TFPI2等DNA甲基化,PA28β、AHSG和LRG等差异表达蛋白及蛋白特征组,多个氨基酸的代谢特征及其他物质的代谢失调均可作为食管癌早期筛查及诊断潜在的生物标志物。此外,利用各类组学技术及血液、尿液等生物样本在寻找生物标志物方面均表现出较好的可行性。结论基因组学、蛋白质组学及代谢组学技术有望为食管癌早期筛查及诊断提供新方法。     

维吾尔族妇女宫颈癌相关血浆候选肿瘤标志物的双向荧光差异电泳分析

目的:血清蛋白组学在肿瘤标志物的筛查研究中被广泛应用,本研究采用双向荧光差异电泳联合质谱技术,寻找与维吾尔族妇女宫颈鳞癌相关的血浆蛋白候选肿瘤标志物。方法:收集维吾尔族妇女宫颈病变血浆标本(慢性宫颈炎患者22例,宫颈癌早期患者26例),制备血浆低丰度蛋白质组样品,通过蛋白质双向荧光差异电泳技术分离与鉴别分析,筛选出慢性宫颈炎与宫颈癌早期患者两组间血浆差异表达的蛋白位点,运用质谱和生物信息学技术对其进行鉴定和功能识别分析。结果:确定了宫颈炎和早期宫颈鳞癌患者的血浆低丰度蛋白质组差异荧光电泳图谱,筛选出43个差异表达蛋白位点,通过质谱技术鉴定出16种蛋白质,在宫颈鳞癌早期患者血浆中有7个蛋白上调表达、9个蛋白下调表达。通过生物信息学分析,差异蛋白涉及的通路主要有补体和代谢相关蛋白和酶类。结论:本研究针对新疆维吾尔族妇女宫颈癌及官颈炎患者,展开血浆低丰度蛋白组表达水平的研究,鉴定出多种差异表达蛋白质,为宫颈癌的早期诊断及癌变机制研究提供了依据。     

Protein shedding in urothelial bladder cancer: prognostic implications of soluble urinary EGFR and EpCAM

Background:

Better biomarkers must be found to develop clinically useful urine tests for bladder cancer. Proteomics can be used to identify the proteins released by cancer cell lines and generate candidate markers for developing such tests.

Methods:

We used shotgun proteomics to identify proteins released into culture media by eight bladder cancer cell lines. These data were compared with protein expression data from the Human Protein Atlas. Epidermal growth factor receptor (EGFR) was identified as a candidate biomarker and measured by ELISA in urine from 60 noncancer control subjects and from 436 patients with bladder cancer and long-term clinical follow-up.

Results:

Bladder cancer cell lines shed soluble EGFR ectodomain. Soluble EGFR is also detectable in urine and is highly elevated in some patients with high-grade bladder cancer. Urinary EGFR is an independent indicator of poor bladder cancer-specific survival with a hazard ratio of 2.89 (95% CI 1.81–4.62, P<0.001). In multivariable models including both urinary EGFR and EpCAM, both biomarkers are predictive of bladder cancer-specific survival and have prognostic value over and above that provided by standard clinical observations.

Conclusions:

Measuring urinary EGFR and EpCAM may represent a simple and useful approach for fast-tracking the investigation and treatment of patients with the most aggressive bladder cancers.