基于生物质谱和凝集素液相芯片的目标糖蛋白N-糖基化解析
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摘要
本文研究内容涉及化学学科的分析化学、化学生物学,并且还应用到了生物化学相关技术,是属于交叉学科的研究。研究主要通过生物质谱技术、分子生物学相关技术、凝集素芯片技术的应用和创新,高效地、有针对性地揭示了具有重要生物学以及临床诊断意义的目标糖蛋白的糖基化,包括糖基化位点、糖链结构以及正常与疾病状态下的糖基化差异比较。
蛋白质糖基化是最常见的翻译后修饰之一,而糖蛋白则在分化、发育、肿瘤发生与转移、精卵识别、免疫、传染及再生中发挥重要的作用。许多重要的糖蛋白的糖基化变化为肿瘤的早期诊断,进程监测,预后评估提供了重要的信息。因此,我们有必要研究重要目标糖蛋白以揭示其糖基化特征。然而,许多具有重要生理、病理意义的糖蛋白在细胞中的表达量较低,阻碍了糖基化的研究。为了克服这一问题,人们采用重组表达的方式获得足量的糖蛋白。再结合N-糖基化位点突变、凝集素印迹、糖链衍生化等方法,借助生物质谱全面地解析糖蛋白的糖基化位点以及糖链结构。但是仅仅研究目标糖蛋白的糖基化结构对于揭示其如何在疾病中发挥作用是远远不够的。为了研究糖基化的重要生物诊断分子在不同疾病状态下的糖基化变化,人们还发展了一系列芯片技术,如抗体芯片、凝集素芯片以及糖芯片等。这些高通量、高灵敏地检测糖基化的方法为疾病的诊断提供了有效的手段。然而,以凝集素芯片为例,虽然人们做出了很多努力提高它的检测灵敏度、通量以及重现性,但为了满足不断增加的临床应用的需求,我们还需要对其进一步改进,甚至将新涌现的芯片技术用于其中。最后,在糖链结构解析的领域,仍然需要我们在分离方法,质谱串级碎片离子的解析中提供更好的方案以全面地解析糖链结构。
本论文主要是结合生物质谱、分子生物学相关技术,发展新型凝集素芯片技术,致力于揭示具有重要生物学或诊断意义的目标糖蛋白的糖基化特征,对疾病的诊断分子进行糖基化的定性和相对定量研究并且为糖链结构解析提供新的方法。本论文工作的主要贡献是：
(1)首次揭示了人重组膜糖蛋白CD82(KAI1)的N-糖基化特征。通过重组表达以及免疫沉淀,获得了人重组膜蛋白CD82。利用生物质谱和位点突变方法,全面解析了CD82的3个潜在N-糖基化位点。其中一个N-糖基化位点是首次报道。利用液相色质联用技术和凝集素印迹研究了CD82的N-糖链结构。总共获得了27条N-糖链结构信息。同时,还发现一些具有重要功能的糖基化结构,为CD82糖基化功能研究提供了坚实的基础。
(2)首次建立了基于液相悬浮芯片检测系统的新型凝集素液相芯片。将液相悬浮芯片应用于凝集素芯片中,使得凝集素与糖链能够在三维的环境中反应。因而大大地提高了凝集素与糖链的结合亲和力,从而获得了很灵敏的凝集素芯片。通过分析还发现,这一方法具有良好的线性和重现性。这一方法能够反映不同糖蛋白的糖基化特点,体现了该技术的可靠性。将其用于分析正常人和患肝癌人血清免疫球蛋白G(Ig G)的糖基化,发现这一技术能够有效地揭示Ig G的糖基化特征同时能够对正常人和患肝癌人的Ig G糖基化进行相对定量。这一方法为快速、高灵敏、高通量分析临床样品提供了有力的手段。
(3)首次将肽N-糖酰胺酶催化硌O标记N-糖链还原末端与质谱二级碎裂结合,解析N-糖链的碎片离子。在质谱解析糖链时,通常存在碎片较多难以分辨的问题。这些碎片离子可能含有相同的分子量但却由糖链的不同区域碎裂而成。为了避免这个问题,我们将还原末端标记有18O的N-糖链碎裂。碎片离子由于在还原末端含有18O因而可增加2Da,将这一质量增加作为标志,有利于N-糖链结构的解析。这种方法标记容易且非常方便,因而对于辅助碎片解析很有利。其次,我们尝试将HILIC亲水色谱柱与质谱联用分析糖蛋白中的N-糖链。结合正离子和负离子检测模式,我们分析了人血清中Ig G的N-糖链。为以后分离分析N-糖链提供了重要的信息并打下了坚实的基础。
论文一共分为以下四章进行阐述：
第一章绪论：阐述了糖蛋白的重要性,并介绍了目标糖蛋白研究相关领域的发展现状。
蛋白质糖基化是最常见的翻译后修饰之一,目前已知真核蛋白中有超过半数的蛋白存在糖基化修饰。蛋白质的糖基化可以分成N-连接、O-连接、GPI锚定和C-连接四个类型,其中以N-连接、O-连接研究最多。蛋白质的糖基化不仅影响蛋白的可溶性,折叠,定位等性质,而且在分化、发育、肿瘤发生与转移、精卵识别、免疫、传染及再生中发挥重要的作用。一些重要糖蛋白与疾病的发生、发展有很大的相关性。为此,我们有必要研究重要的目标蛋白的糖基化。在这一章中,我们重点介绍了糖蛋白N-糖基化研究的前沿进展,包括了糖蛋白/糖肽的分离与富集、糖基化位点的解析、糖链结构的解析、糖蛋白质组学和糖组学的相对定量技术等。着重在利用质谱以及芯片技术对N-糖基化进行研究。通过揭示N-糖基化研究难点,我们发现不仅要借助质谱技术对N-糖基化的位点和糖链进行研究还需要借助高通量、高灵敏的芯片技术快速检测目标糖蛋白的N-糖基化。而且在利用质谱对N-糖链的结构解析中还存在着很多的困难,比如糖链的碎片离子难以分辨、糖链的分离与检测还需要进一步建立有效的手段等。这些困难都需要我们进一步发展新的方法以及优化现有方法来克服。总地来说,蛋白糖基化修饰的研究还处于发展阶段,充满机遇和挑战。
第二章基于生物质谱的人重组膜蛋白CD82糖基化研究：分为两节：(1)人重组膜蛋白CD82的N-糖基化位点研究；(2)人重组膜蛋白CD82的N-糖链结构解析。
(1)CD82是一个高度糖基化的膜蛋白,其属于跨四膜超家族(tetraspanin)。在多种癌症中,如前列腺,胰腺,肺,胃,肠,肝癌中都发现CD82发挥着肿瘤转移抑制的作用。已有实验证明CD82的N-糖基化在细胞粘附与运动中担任重要的角色。虽然N-糖基化对于CD82发挥其功能至关重要但目前还没有关于其N-糖基化结构解析的报道。我们希望利用生物质谱和分子生物学相关技术全面解析CD82的N-糖基化位点。为了保证CD82有足够的表达量用于后续研究,我们首先建立了膜蛋白CD82的体外表达及免疫沉淀的方法。其次,利用蛋白质组学领域的数据处理软件APEX对免疫沉淀产物进行了相对定量,一方面确定了前期富集CD82方法的有效性,另一方也证明虽然有其他的糖蛋白被鉴定到,但是由于它们量很低而不会干扰后期实验。再次,结合Nano-LC-ESI-MS/MS和位点突变、胶迁移的方法,鉴定到了CD82三个N-糖基化位点。其中Asn157位点是首次报道。而且我们还利用多种Endo糖苷内切酶初步揭示了Asn129和Asn198位点上的特定糖型。
(2)由于糖蛋白的糖链具有重要的作用,所以我们希望解析CD82的N-糖链结构。然而,糖链不直接由基因编码,并且含有一些同分异构体和较多的连接位点和分支,造成了糖链结构解析的困难。我们的研究采用凝集素印迹、全甲基化衍生糖链以及反相色谱质谱联用的方法来解析CD82的N-糖链。凝集素印迹能够揭示CD82的N-糖链的结构特征。全甲基化衍生能够增加糖链的离子化效率在串级碎裂中产生更多的碎片并且更加适合于反相色谱分离。我们采用以上方法首次揭示了CD82的N-糖链结构。通过研究,我们发现了CD82总共有27种不同的N-糖链并且可分为三种的不同类型,分别为高甘露糖型,复杂型和杂合型。而其中一些与细胞粘附、癌症转移相关的重要单糖,如唾液酸、核心岩藻糖、平分型N-乙酰葡糖胺的发现为我们后续研究CD82糖基化的重要功能提供了基础。
第三章基于凝集素液相芯片的目标糖蛋白多重检测：分为两节：(1)凝集素液相芯片的建立；(2)凝集素液相芯片的应用。
(1)糖组学(Glycomics)是一门在结构上阐明并描绘自然界中的各种糖结构并且揭示与各项生命过程相关的糖结构时空变换的学科。目前糖组学的发展已进入了第二个黄金期,那就是将临床应用作为糖组学的研究重点。凝集素芯片因其高灵敏、高通量、快速的特性而成为糖组学临床研究的重要手段。许多糖蛋白被认为可以作为疾病相关的生物诊断靶标。为了满足不断增长的临床应用的需要,我们将液相悬浮芯片和凝集素检测相结合,发展了一种新型的液相悬浮凝集素芯片检测系统。我们利用这一方法检测了不同的标准糖蛋白,发现这种方法大大提高了凝集素芯片的灵敏度。同时,这一方法还表现出了良好的重现性和很宽的线性范围。为这一方法应用到临床样品的检测奠定了坚实的基础。
(2)糖基化结构的变化是癌症中一种广泛的标志。一些重要的人血清糖蛋白,如α-甲胎蛋白L3(a-fetoprotein-L3)、α1-酸性糖蛋白(α1-acid glycoprotein)、触珠蛋白(haptoglobin)、免疫球蛋白G (immunoglobulin G)已被广泛用于疾病特异性诊断。特别是免疫球蛋白G(Ig G)在人的免疫系统中扮演重要的角色。同时Ig G上的糖基化也被认为参与调控它的功能。我们从正常人以及患肝癌人血清中获得Ig G,利用我们建立的凝集素液相芯片技术揭示了它的糖基化特点并且比较了正常人及患肝癌人的糖基化差异。我们发现了非常有意义的差异,从而证明了凝集素液相芯片技术的实用性。另外我们还检测了3种糖蛋白,确证了这一方法的可靠性。此外,我们还将多重检测方法应用于凝集素液相芯片中,大大提高了它的检测通量。
第四章基于生物质谱及亲水色谱质谱联用的N-糖链结构解析：分为两节：(1)肽N-糖酰胺酶(PNGase)酶18O标记与串联质谱结合解析N-糖链；(2)采用HILIC色谱柱与质谱联用分析糖蛋白中的N-糖链。
(1)N-糖链结构解析一直是糖基化研究中的一个重要部分。串联质谱解析N-糖链结构是一项有效的手段,目前利用这种方法研究N-糖链结构的实验室也越来越多。然而,糖链碎裂产生的碎片离子有的含有相同的质荷比却是不同的碎片结构。为了帮助分辨碎片离子,我们利用肽N-糖酰胺酶(PNGase)催化的’8O标记N-糖链的还原末端,因此含有还原末端的碎片具有2Da的质量增加。结合串联质谱与这一质量增加标志能够更好地解析N-糖链结构。
(2)N-糖链的分离检测方法是N-糖链结构解析的重要步骤。我们采用HILIC色谱柱与质谱联用分析糖蛋白中的N-糖链。采用HILIC色谱柱可以大大地提高糖链的分离效率,同时结合质谱检测的方法能够高效地对N-糖链结构进行解析。我们分析了标准糖蛋白鸡卵清蛋白以及健康人血清Ig G未衍生糖链的结构。并且通过负离子检测模式发现了Ig G上带唾液酸的糖链。
This thesis presents an interdisciplinary research involved in analytical chemistry, chemical biology and biological chemistry. The application of mass spectrometry (MS), molecular biology technology and the innovation of lectin microarray have been achieved to efficiently reveal the glycosylation of target glycoprotein, including glycosylation sites, glycan structure and the analysis of glycosylation alteration.
Glycosylation is one of the most important and universal protein post-translational modifications (PTMs) and plays an important role in differentiation, development, the metastasis of tumor, fertilization, immunity, infection and regeneration. The alteration of target glycoproteins provides crucial information for tumor early diagnosis, process monitoring and prognostic evaluation. Therefore, the glycosylation of target protein should be analyzed to reveal its important function. However, studies of the glycosylation of target glycoproteins have often been hampered by low abundance. Several glycoproteins have been expressed with a tag in human cell lines to obtain sufficient abundance for further assay. Several complementary approaches such as mass spectrometry, site-directed mutagenesis, permethylation and lectin blots were used on both glycosylation site and glycan structure analyses to provide a complete understanding of target protein glycosylation. However, it does not supply enough information to focus on the glycan structure. Various kinds of microarray such as antibody microarray, lectin microarray and glycan microarray have been developed for clinical diagnosis of glyco-biomarkers. For example, lectin microarray has been crucial for the disease diagnosis because of its high-throughput and high-sensitivity. However, the sensitivity, reproducibility, and throughput of lectin microarray should still be constantly improved to meet the increasing demand of clinical applications. The application of novel array system is still needed. The last but not the least, the separation, detection and annotation of oligosaccharides should be improved for the comprehensive analysis of glycan structure.
The major contributions of this work are as follows:
(1) The N-glycosylation pattern of recombinant human CD82(KAI1) was revealed for the first time. CD82was expressed in HEK-293T cells with a flag tag to obtain sufficient abundance. CD82was purified from HEK-293T cells. An integrative proteomic and glycomic approach, which combined glycosidase and protease digestions, glycan permethylation, MS analyses, site-directed mutagenesis, and lectin blots, were performed. As a result, we found three N-glycosylation sites and especially Asn157was reported for the first time. Combined lectin blots and LC-MS/MS,27N-glycans structures have been shown for the first time. The presence of some important carbohydrate epitopes provides useful information for understanding and the further investigation of the glycobiological function of CD82.
(2) We applied high-sensitive bead-based suspension array system in lectin microarray for the first time. In this system, lectins were conjugated to different populations of microbeads and incubated with biotin-labeled glycoproteins under a liquid condition. Thus, the lectins bound with the specific glycans of glycoproteins under a three-dimensional condition. Our results showed that the bead-based lectin array had the lowest detection of limit among reported lectin microarrays. Furthermore, it provided good linearity with high reproducibility at two to three orders of magnitude in dynamic range. The specific signal patterns for three biotin-labeled glycoproteins were derived with different immobilized lectins, which proved the reliability. Moreover, the quantitative glycosylation alteration of Ig G enriched from sera of healthy individuals and HCC patients was determined. This study demonstrated that the bead-based lectin array can be carried out in a rapid, sensitive, and high-throughput manner and potentially fulfill qualitative and quantitative analyses of clinical samples.
(3) The combination of PNGase F mediated incorporation of18O into glycans and tandem MS was applied in the N-glycan structure analysis for the first time. The fragments produced by mass spectrometry contain ambiguous information because fragment ions of the same mass and composition can arise from different regions of the molecule. The glycans labeled with18O at the reducing end were collided by tandem MS. The fragment containing the reducing end, which had an increase of2Da, could be distinguished from the other molecular ions. The increase of2Da using as a reliable marker assisted in the analysis of glycan structure. This approach is simple, convenient for the discrimination of the glycan fragments. On the other hand, HILIC-ESI-MS was used to separate and detect the oliogosaccharides of ovalbumin and human serum Ig G. The positive and negative ion mode was operated. This approach supplied the abundant information for the determination of glycan structure.
This thesis consists of four parts which are summarized as follows:
Part1. Introduction:a brief and comprehensive introduction of protein glycosylation and glycoproteomics-related fields.
Glycosylation is a common and highly diverse co-and post-translational protein modification. It has been reported that more than50%of human proteins are likely conjugated with glycans. There are four major types of protein glycosylation; the two mostly studied are N-linked and O-linked glycosylation. The glycosylation of proteins does not only affect the protein solubility, folding and location but also play an important role in differentiation, development, the metastasis of tumor, fertilization, immunity, infection and regeneration. Therefore, the glycosylation of target glycoprotein should be studied. The part one is emphasis on the study of N-glycosylation including the separation and enrichment of glycoproteins and glycopeptides, the analysis of glycosylation sites, the determination of glycan structure and relative quantification of glycoproteomics and glycomics. We found that mass spectrometry and microarray were complementary technologies for the research of N-glycosylation. Antibody, lectin and glycan microarray are high-throughput, sensitive for the detection of glycosylation. Mass spectrometry exhibits difficulty in discriminating structural isomers and annotating data. Thus, we need new technologies to distinguish the fragment and separate isomers. Generally, glycosylation study now is still full of chances and challenges.
Part2. The Study of N-glycosylation Pattern of Recombinant Human CD82(KAI1) by Biological Mass Spectrometry:two sections included (1) determination of CD82N-glycosylation sites;(2) characterization of CD82glycans.
(1) CD82is a highly glycosylated membrane protein belonging to the tetraspanins. It has attracted much attention in various human cancers, such as prostate, pancreatic, lung, gastric, hepatic, and colorectal cancers. Although CD82N-glycosylation profoundly affects cell motility and adhesion, its N-glycosylation pattern has not been described so far. Firstly, CD82was expressed in HEK-293T cells with a flag tag to obtain sufficient and purified using anti-FLAG antibody. Secondly, high-performance MS identification and absolute protein expression measurement were conducted to analyze the immnunoprecipited protein. This result confirms that CD82is obtained with very few glycoprotein impurities and with enough quantity as a glycoprotein for the subsequent assay. Thirdly, the presence of the three N-glycosylation sites at the Asn129, Asn157, and Asn198residues was demonstrated using LC-ESI-MS/MS and site-directed mutagenesis. Furthermore, the site-specific oligosaccharides of the two N-glycosylation sites (Asn129, Asnl98) were shown by the digestion of Endo-β-N-acetylglucosaminidase.
(2) The characterization of CD82glycan was revealed for the first time. Despite the significant role of carbohydrates, studies on glycosylation have been hindered by its structural heterogeneity and diversity caused by its non-template-driven biosynthesis. In our study, a detailed characterization of recombinant human CD82N-linked glycosylation pattern was conducted by employing an integrative approach, including glycan permethylation, MS analyses and lectin-blot. Lectin-blot is a key approach in glycosylation analysis, due to its ability to recognize specific linkages and distinguish isomeric sugars presented in glycans. Permethylation increases ionization efficiency, produces more structural details in tandem MS and are more suitable for the separation of reversed-phase chromatography. Finally, we found27N-glycans structures of recombinant CD82. The discovered N-glycans could be further classified into three types:high-mannose, hybrid and complex-type. The presence of some important carbohydrate epitopes, such as bisecting GlcNAc, NeuAc, and core fucose, were also detected. The interesting epitopes provide useful information for understanding and the further investigation of the glycobiological function of CD82.
Part3. Multiplex Profiling of Glycoproteins Using a Novel Bead-based Lectin Array:two sections included (1) the establishment of bead-based Lectin Array;(2) the application of bead-based Lectin Array.
(1) Glycomics is the study of comprehensive structural elucidation and characterization of all glycoforms found in nature and their dynamic spatiotemporal changes that are associated with biological processes. The development of glycomics has been focused on clinical applications, which are viewed as the second golden age of glycomics. Lectin microarray is an attractive platform for structural profile and screening glycosylation differences on large-scale and high-throughput studies. Some glycoproteins have been widely used as disease-specific biomarkers. We applied high-sensitive bead-based suspension array system in lectin microarray to meet the increasing demand of clinical applications. The analytical performance of this approach was evaluated using model glycoproteins, and the results showed that the sensitivity and throughput were improved significantly. Moreover, a good linear response with high reproducibility was obtained. This approach can be further used in the detection of clinical samples.
(2) The alteration of glycan structures is a universal hallmark of tumors. Some human serum glycoproteins, such as a-fetoprotein-L3, α1-acid glycoprotein, haptoglobin (Hp), and immunoglobulin G (Ig G), have been widely used as disease-specific biomarkers. Ig G plays an important role in the human immune system, and the attached glycans in Ig G have been implicated in modulating its function. The quantitative glycosylation alteration of Ig G enriched from sera of healthy individuals and HCC patients was determined. Three kinds of glycoproteins were selected as representative glycoproteins to test the reliability of bead-based lectin array. The multiplexed assay provided a high-throughput, sample-and reagent-saving method, allowing for simultaneous detection of multiple carbohydrate epitopes in a single reaction vessel.
Part4. The Analysis of N-glycan Chains Using Mass Spectrometry and Hydrophilic Interaction Liquid Chromatography:two sections included (1) the combination of PNGase-mediated incorporation of18O into glycans and tandem MS to analyze the N-glycan structures;(2) the analysis of N-glycan structures using HILIC-ESI-MS.
(1) The analysis of N-glycan structure is an important part of glycosylation research. The fragment collided by mass spectrometry are used to deduce the structure of oligosaccharide. However, the fragments produced by mass spectrometry contain ambiguous information because fragment ions of the same mass and composition can arise from different regions of the molecule. Therefore, we combined PNGase-mediated incorporation of18O into glycans and tandem MS to analyze the N-glycan structures. The glycans labeled with18O at the reducing end were collided by MS2. The increase of2Da using as a reliable marker assisted in the analysis of glycan structure.
(2) The separation and detection of glycan chains is important step for the analysis of glycan structures. We used HILIC-ESI-MS to analyze the N-glycan structures. HILIC improved the separation and the combination of normal-phase chromatography and mass spectrometry enhance the efficiency of the detection. We analyzed the native N-glycan structures of ovalbumin and human sera Ig G. The negative ion mode was operated for the detection of Ig G sialylation.
蛋白质糖基化是最常见的翻译后修饰之一,而糖蛋白则在分化、发育、肿瘤发生与转移、精卵识别、免疫、传染及再生中发挥重要的作用。许多重要的糖蛋白的糖基化变化为肿瘤的早期诊断,进程监测,预后评估提供了重要的信息。因此,我们有必要研究重要目标糖蛋白以揭示其糖基化特征。然而,许多具有重要生理、病理意义的糖蛋白在细胞中的表达量较低,阻碍了糖基化的研究。为了克服这一问题,人们采用重组表达的方式获得足量的糖蛋白。再结合N-糖基化位点突变、凝集素印迹、糖链衍生化等方法,借助生物质谱全面地解析糖蛋白的糖基化位点以及糖链结构。但是仅仅研究目标糖蛋白的糖基化结构对于揭示其如何在疾病中发挥作用是远远不够的。为了研究糖基化的重要生物诊断分子在不同疾病状态下的糖基化变化,人们还发展了一系列芯片技术,如抗体芯片、凝集素芯片以及糖芯片等。这些高通量、高灵敏地检测糖基化的方法为疾病的诊断提供了有效的手段。然而,以凝集素芯片为例,虽然人们做出了很多努力提高它的检测灵敏度、通量以及重现性,但为了满足不断增加的临床应用的需求,我们还需要对其进一步改进,甚至将新涌现的芯片技术用于其中。最后,在糖链结构解析的领域,仍然需要我们在分离方法,质谱串级碎片离子的解析中提供更好的方案以全面地解析糖链结构。
本论文主要是结合生物质谱、分子生物学相关技术,发展新型凝集素芯片技术,致力于揭示具有重要生物学或诊断意义的目标糖蛋白的糖基化特征,对疾病的诊断分子进行糖基化的定性和相对定量研究并且为糖链结构解析提供新的方法。本论文工作的主要贡献是：
(1)首次揭示了人重组膜糖蛋白CD82(KAI1)的N-糖基化特征。通过重组表达以及免疫沉淀,获得了人重组膜蛋白CD82。利用生物质谱和位点突变方法,全面解析了CD82的3个潜在N-糖基化位点。其中一个N-糖基化位点是首次报道。利用液相色质联用技术和凝集素印迹研究了CD82的N-糖链结构。总共获得了27条N-糖链结构信息。同时,还发现一些具有重要功能的糖基化结构,为CD82糖基化功能研究提供了坚实的基础。
(2)首次建立了基于液相悬浮芯片检测系统的新型凝集素液相芯片。将液相悬浮芯片应用于凝集素芯片中,使得凝集素与糖链能够在三维的环境中反应。因而大大地提高了凝集素与糖链的结合亲和力,从而获得了很灵敏的凝集素芯片。通过分析还发现,这一方法具有良好的线性和重现性。这一方法能够反映不同糖蛋白的糖基化特点,体现了该技术的可靠性。将其用于分析正常人和患肝癌人血清免疫球蛋白G(Ig G)的糖基化,发现这一技术能够有效地揭示Ig G的糖基化特征同时能够对正常人和患肝癌人的Ig G糖基化进行相对定量。这一方法为快速、高灵敏、高通量分析临床样品提供了有力的手段。
(3)首次将肽N-糖酰胺酶催化硌O标记N-糖链还原末端与质谱二级碎裂结合,解析N-糖链的碎片离子。在质谱解析糖链时,通常存在碎片较多难以分辨的问题。这些碎片离子可能含有相同的分子量但却由糖链的不同区域碎裂而成。为了避免这个问题,我们将还原末端标记有18O的N-糖链碎裂。碎片离子由于在还原末端含有18O因而可增加2Da,将这一质量增加作为标志,有利于N-糖链结构的解析。这种方法标记容易且非常方便,因而对于辅助碎片解析很有利。其次,我们尝试将HILIC亲水色谱柱与质谱联用分析糖蛋白中的N-糖链。结合正离子和负离子检测模式,我们分析了人血清中Ig G的N-糖链。为以后分离分析N-糖链提供了重要的信息并打下了坚实的基础。
论文一共分为以下四章进行阐述：
第一章绪论：阐述了糖蛋白的重要性,并介绍了目标糖蛋白研究相关领域的发展现状。
蛋白质糖基化是最常见的翻译后修饰之一,目前已知真核蛋白中有超过半数的蛋白存在糖基化修饰。蛋白质的糖基化可以分成N-连接、O-连接、GPI锚定和C-连接四个类型,其中以N-连接、O-连接研究最多。蛋白质的糖基化不仅影响蛋白的可溶性,折叠,定位等性质,而且在分化、发育、肿瘤发生与转移、精卵识别、免疫、传染及再生中发挥重要的作用。一些重要糖蛋白与疾病的发生、发展有很大的相关性。为此,我们有必要研究重要的目标蛋白的糖基化。在这一章中,我们重点介绍了糖蛋白N-糖基化研究的前沿进展,包括了糖蛋白/糖肽的分离与富集、糖基化位点的解析、糖链结构的解析、糖蛋白质组学和糖组学的相对定量技术等。着重在利用质谱以及芯片技术对N-糖基化进行研究。通过揭示N-糖基化研究难点,我们发现不仅要借助质谱技术对N-糖基化的位点和糖链进行研究还需要借助高通量、高灵敏的芯片技术快速检测目标糖蛋白的N-糖基化。而且在利用质谱对N-糖链的结构解析中还存在着很多的困难,比如糖链的碎片离子难以分辨、糖链的分离与检测还需要进一步建立有效的手段等。这些困难都需要我们进一步发展新的方法以及优化现有方法来克服。总地来说,蛋白糖基化修饰的研究还处于发展阶段,充满机遇和挑战。
第二章基于生物质谱的人重组膜蛋白CD82糖基化研究：分为两节：(1)人重组膜蛋白CD82的N-糖基化位点研究；(2)人重组膜蛋白CD82的N-糖链结构解析。
(1)CD82是一个高度糖基化的膜蛋白,其属于跨四膜超家族(tetraspanin)。在多种癌症中,如前列腺,胰腺,肺,胃,肠,肝癌中都发现CD82发挥着肿瘤转移抑制的作用。已有实验证明CD82的N-糖基化在细胞粘附与运动中担任重要的角色。虽然N-糖基化对于CD82发挥其功能至关重要但目前还没有关于其N-糖基化结构解析的报道。我们希望利用生物质谱和分子生物学相关技术全面解析CD82的N-糖基化位点。为了保证CD82有足够的表达量用于后续研究,我们首先建立了膜蛋白CD82的体外表达及免疫沉淀的方法。其次,利用蛋白质组学领域的数据处理软件APEX对免疫沉淀产物进行了相对定量,一方面确定了前期富集CD82方法的有效性,另一方也证明虽然有其他的糖蛋白被鉴定到,但是由于它们量很低而不会干扰后期实验。再次,结合Nano-LC-ESI-MS/MS和位点突变、胶迁移的方法,鉴定到了CD82三个N-糖基化位点。其中Asn157位点是首次报道。而且我们还利用多种Endo糖苷内切酶初步揭示了Asn129和Asn198位点上的特定糖型。
(2)由于糖蛋白的糖链具有重要的作用,所以我们希望解析CD82的N-糖链结构。然而,糖链不直接由基因编码,并且含有一些同分异构体和较多的连接位点和分支,造成了糖链结构解析的困难。我们的研究采用凝集素印迹、全甲基化衍生糖链以及反相色谱质谱联用的方法来解析CD82的N-糖链。凝集素印迹能够揭示CD82的N-糖链的结构特征。全甲基化衍生能够增加糖链的离子化效率在串级碎裂中产生更多的碎片并且更加适合于反相色谱分离。我们采用以上方法首次揭示了CD82的N-糖链结构。通过研究,我们发现了CD82总共有27种不同的N-糖链并且可分为三种的不同类型,分别为高甘露糖型,复杂型和杂合型。而其中一些与细胞粘附、癌症转移相关的重要单糖,如唾液酸、核心岩藻糖、平分型N-乙酰葡糖胺的发现为我们后续研究CD82糖基化的重要功能提供了基础。
第三章基于凝集素液相芯片的目标糖蛋白多重检测：分为两节：(1)凝集素液相芯片的建立；(2)凝集素液相芯片的应用。
(1)糖组学(Glycomics)是一门在结构上阐明并描绘自然界中的各种糖结构并且揭示与各项生命过程相关的糖结构时空变换的学科。目前糖组学的发展已进入了第二个黄金期,那就是将临床应用作为糖组学的研究重点。凝集素芯片因其高灵敏、高通量、快速的特性而成为糖组学临床研究的重要手段。许多糖蛋白被认为可以作为疾病相关的生物诊断靶标。为了满足不断增长的临床应用的需要,我们将液相悬浮芯片和凝集素检测相结合,发展了一种新型的液相悬浮凝集素芯片检测系统。我们利用这一方法检测了不同的标准糖蛋白,发现这种方法大大提高了凝集素芯片的灵敏度。同时,这一方法还表现出了良好的重现性和很宽的线性范围。为这一方法应用到临床样品的检测奠定了坚实的基础。
(2)糖基化结构的变化是癌症中一种广泛的标志。一些重要的人血清糖蛋白,如α-甲胎蛋白L3(a-fetoprotein-L3)、α1-酸性糖蛋白(α1-acid glycoprotein)、触珠蛋白(haptoglobin)、免疫球蛋白G (immunoglobulin G)已被广泛用于疾病特异性诊断。特别是免疫球蛋白G(Ig G)在人的免疫系统中扮演重要的角色。同时Ig G上的糖基化也被认为参与调控它的功能。我们从正常人以及患肝癌人血清中获得Ig G,利用我们建立的凝集素液相芯片技术揭示了它的糖基化特点并且比较了正常人及患肝癌人的糖基化差异。我们发现了非常有意义的差异,从而证明了凝集素液相芯片技术的实用性。另外我们还检测了3种糖蛋白,确证了这一方法的可靠性。此外,我们还将多重检测方法应用于凝集素液相芯片中,大大提高了它的检测通量。
第四章基于生物质谱及亲水色谱质谱联用的N-糖链结构解析：分为两节：(1)肽N-糖酰胺酶(PNGase)酶18O标记与串联质谱结合解析N-糖链；(2)采用HILIC色谱柱与质谱联用分析糖蛋白中的N-糖链。
(1)N-糖链结构解析一直是糖基化研究中的一个重要部分。串联质谱解析N-糖链结构是一项有效的手段,目前利用这种方法研究N-糖链结构的实验室也越来越多。然而,糖链碎裂产生的碎片离子有的含有相同的质荷比却是不同的碎片结构。为了帮助分辨碎片离子,我们利用肽N-糖酰胺酶(PNGase)催化的’8O标记N-糖链的还原末端,因此含有还原末端的碎片具有2Da的质量增加。结合串联质谱与这一质量增加标志能够更好地解析N-糖链结构。
(2)N-糖链的分离检测方法是N-糖链结构解析的重要步骤。我们采用HILIC色谱柱与质谱联用分析糖蛋白中的N-糖链。采用HILIC色谱柱可以大大地提高糖链的分离效率,同时结合质谱检测的方法能够高效地对N-糖链结构进行解析。我们分析了标准糖蛋白鸡卵清蛋白以及健康人血清Ig G未衍生糖链的结构。并且通过负离子检测模式发现了Ig G上带唾液酸的糖链。
This thesis presents an interdisciplinary research involved in analytical chemistry, chemical biology and biological chemistry. The application of mass spectrometry (MS), molecular biology technology and the innovation of lectin microarray have been achieved to efficiently reveal the glycosylation of target glycoprotein, including glycosylation sites, glycan structure and the analysis of glycosylation alteration.
Glycosylation is one of the most important and universal protein post-translational modifications (PTMs) and plays an important role in differentiation, development, the metastasis of tumor, fertilization, immunity, infection and regeneration. The alteration of target glycoproteins provides crucial information for tumor early diagnosis, process monitoring and prognostic evaluation. Therefore, the glycosylation of target protein should be analyzed to reveal its important function. However, studies of the glycosylation of target glycoproteins have often been hampered by low abundance. Several glycoproteins have been expressed with a tag in human cell lines to obtain sufficient abundance for further assay. Several complementary approaches such as mass spectrometry, site-directed mutagenesis, permethylation and lectin blots were used on both glycosylation site and glycan structure analyses to provide a complete understanding of target protein glycosylation. However, it does not supply enough information to focus on the glycan structure. Various kinds of microarray such as antibody microarray, lectin microarray and glycan microarray have been developed for clinical diagnosis of glyco-biomarkers. For example, lectin microarray has been crucial for the disease diagnosis because of its high-throughput and high-sensitivity. However, the sensitivity, reproducibility, and throughput of lectin microarray should still be constantly improved to meet the increasing demand of clinical applications. The application of novel array system is still needed. The last but not the least, the separation, detection and annotation of oligosaccharides should be improved for the comprehensive analysis of glycan structure.
The major contributions of this work are as follows:
(1) The N-glycosylation pattern of recombinant human CD82(KAI1) was revealed for the first time. CD82was expressed in HEK-293T cells with a flag tag to obtain sufficient abundance. CD82was purified from HEK-293T cells. An integrative proteomic and glycomic approach, which combined glycosidase and protease digestions, glycan permethylation, MS analyses, site-directed mutagenesis, and lectin blots, were performed. As a result, we found three N-glycosylation sites and especially Asn157was reported for the first time. Combined lectin blots and LC-MS/MS,27N-glycans structures have been shown for the first time. The presence of some important carbohydrate epitopes provides useful information for understanding and the further investigation of the glycobiological function of CD82.
(2) We applied high-sensitive bead-based suspension array system in lectin microarray for the first time. In this system, lectins were conjugated to different populations of microbeads and incubated with biotin-labeled glycoproteins under a liquid condition. Thus, the lectins bound with the specific glycans of glycoproteins under a three-dimensional condition. Our results showed that the bead-based lectin array had the lowest detection of limit among reported lectin microarrays. Furthermore, it provided good linearity with high reproducibility at two to three orders of magnitude in dynamic range. The specific signal patterns for three biotin-labeled glycoproteins were derived with different immobilized lectins, which proved the reliability. Moreover, the quantitative glycosylation alteration of Ig G enriched from sera of healthy individuals and HCC patients was determined. This study demonstrated that the bead-based lectin array can be carried out in a rapid, sensitive, and high-throughput manner and potentially fulfill qualitative and quantitative analyses of clinical samples.
(3) The combination of PNGase F mediated incorporation of18O into glycans and tandem MS was applied in the N-glycan structure analysis for the first time. The fragments produced by mass spectrometry contain ambiguous information because fragment ions of the same mass and composition can arise from different regions of the molecule. The glycans labeled with18O at the reducing end were collided by tandem MS. The fragment containing the reducing end, which had an increase of2Da, could be distinguished from the other molecular ions. The increase of2Da using as a reliable marker assisted in the analysis of glycan structure. This approach is simple, convenient for the discrimination of the glycan fragments. On the other hand, HILIC-ESI-MS was used to separate and detect the oliogosaccharides of ovalbumin and human serum Ig G. The positive and negative ion mode was operated. This approach supplied the abundant information for the determination of glycan structure.
This thesis consists of four parts which are summarized as follows:
Part1. Introduction:a brief and comprehensive introduction of protein glycosylation and glycoproteomics-related fields.
Glycosylation is a common and highly diverse co-and post-translational protein modification. It has been reported that more than50%of human proteins are likely conjugated with glycans. There are four major types of protein glycosylation; the two mostly studied are N-linked and O-linked glycosylation. The glycosylation of proteins does not only affect the protein solubility, folding and location but also play an important role in differentiation, development, the metastasis of tumor, fertilization, immunity, infection and regeneration. Therefore, the glycosylation of target glycoprotein should be studied. The part one is emphasis on the study of N-glycosylation including the separation and enrichment of glycoproteins and glycopeptides, the analysis of glycosylation sites, the determination of glycan structure and relative quantification of glycoproteomics and glycomics. We found that mass spectrometry and microarray were complementary technologies for the research of N-glycosylation. Antibody, lectin and glycan microarray are high-throughput, sensitive for the detection of glycosylation. Mass spectrometry exhibits difficulty in discriminating structural isomers and annotating data. Thus, we need new technologies to distinguish the fragment and separate isomers. Generally, glycosylation study now is still full of chances and challenges.
Part2. The Study of N-glycosylation Pattern of Recombinant Human CD82(KAI1) by Biological Mass Spectrometry:two sections included (1) determination of CD82N-glycosylation sites;(2) characterization of CD82glycans.
(1) CD82is a highly glycosylated membrane protein belonging to the tetraspanins. It has attracted much attention in various human cancers, such as prostate, pancreatic, lung, gastric, hepatic, and colorectal cancers. Although CD82N-glycosylation profoundly affects cell motility and adhesion, its N-glycosylation pattern has not been described so far. Firstly, CD82was expressed in HEK-293T cells with a flag tag to obtain sufficient and purified using anti-FLAG antibody. Secondly, high-performance MS identification and absolute protein expression measurement were conducted to analyze the immnunoprecipited protein. This result confirms that CD82is obtained with very few glycoprotein impurities and with enough quantity as a glycoprotein for the subsequent assay. Thirdly, the presence of the three N-glycosylation sites at the Asn129, Asn157, and Asn198residues was demonstrated using LC-ESI-MS/MS and site-directed mutagenesis. Furthermore, the site-specific oligosaccharides of the two N-glycosylation sites (Asn129, Asnl98) were shown by the digestion of Endo-β-N-acetylglucosaminidase.
(2) The characterization of CD82glycan was revealed for the first time. Despite the significant role of carbohydrates, studies on glycosylation have been hindered by its structural heterogeneity and diversity caused by its non-template-driven biosynthesis. In our study, a detailed characterization of recombinant human CD82N-linked glycosylation pattern was conducted by employing an integrative approach, including glycan permethylation, MS analyses and lectin-blot. Lectin-blot is a key approach in glycosylation analysis, due to its ability to recognize specific linkages and distinguish isomeric sugars presented in glycans. Permethylation increases ionization efficiency, produces more structural details in tandem MS and are more suitable for the separation of reversed-phase chromatography. Finally, we found27N-glycans structures of recombinant CD82. The discovered N-glycans could be further classified into three types:high-mannose, hybrid and complex-type. The presence of some important carbohydrate epitopes, such as bisecting GlcNAc, NeuAc, and core fucose, were also detected. The interesting epitopes provide useful information for understanding and the further investigation of the glycobiological function of CD82.
Part3. Multiplex Profiling of Glycoproteins Using a Novel Bead-based Lectin Array:two sections included (1) the establishment of bead-based Lectin Array;(2) the application of bead-based Lectin Array.
(1) Glycomics is the study of comprehensive structural elucidation and characterization of all glycoforms found in nature and their dynamic spatiotemporal changes that are associated with biological processes. The development of glycomics has been focused on clinical applications, which are viewed as the second golden age of glycomics. Lectin microarray is an attractive platform for structural profile and screening glycosylation differences on large-scale and high-throughput studies. Some glycoproteins have been widely used as disease-specific biomarkers. We applied high-sensitive bead-based suspension array system in lectin microarray to meet the increasing demand of clinical applications. The analytical performance of this approach was evaluated using model glycoproteins, and the results showed that the sensitivity and throughput were improved significantly. Moreover, a good linear response with high reproducibility was obtained. This approach can be further used in the detection of clinical samples.
(2) The alteration of glycan structures is a universal hallmark of tumors. Some human serum glycoproteins, such as a-fetoprotein-L3, α1-acid glycoprotein, haptoglobin (Hp), and immunoglobulin G (Ig G), have been widely used as disease-specific biomarkers. Ig G plays an important role in the human immune system, and the attached glycans in Ig G have been implicated in modulating its function. The quantitative glycosylation alteration of Ig G enriched from sera of healthy individuals and HCC patients was determined. Three kinds of glycoproteins were selected as representative glycoproteins to test the reliability of bead-based lectin array. The multiplexed assay provided a high-throughput, sample-and reagent-saving method, allowing for simultaneous detection of multiple carbohydrate epitopes in a single reaction vessel.
Part4. The Analysis of N-glycan Chains Using Mass Spectrometry and Hydrophilic Interaction Liquid Chromatography:two sections included (1) the combination of PNGase-mediated incorporation of18O into glycans and tandem MS to analyze the N-glycan structures;(2) the analysis of N-glycan structures using HILIC-ESI-MS.
(1) The analysis of N-glycan structure is an important part of glycosylation research. The fragment collided by mass spectrometry are used to deduce the structure of oligosaccharide. However, the fragments produced by mass spectrometry contain ambiguous information because fragment ions of the same mass and composition can arise from different regions of the molecule. Therefore, we combined PNGase-mediated incorporation of18O into glycans and tandem MS to analyze the N-glycan structures. The glycans labeled with18O at the reducing end were collided by MS2. The increase of2Da using as a reliable marker assisted in the analysis of glycan structure.
(2) The separation and detection of glycan chains is important step for the analysis of glycan structures. We used HILIC-ESI-MS to analyze the N-glycan structures. HILIC improved the separation and the combination of normal-phase chromatography and mass spectrometry enhance the efficiency of the detection. We analyzed the native N-glycan structures of ovalbumin and human sera Ig G. The negative ion mode was operated for the detection of Ig G sialylation.
引文
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