iTRAQ技术在消化道肿瘤研究中的应用进展

近年来,同位素标记相对和绝对定量(Isobaric tags for relative and absolute quantification,iTRAQ)技术已成为蛋白质组学定量研究中一种强有力的工具,尤其在肿瘤相关领域备受关注,其突出优势为测定蛋白范围广泛、分析结果可靠、精确度高、重复性好等。大量文献也表明,iTRAQ技术在消化道肿瘤,如食管癌、胃癌、肝癌等肿瘤标志物筛查研究、肿瘤发生发展机制研究以及肿瘤治疗预后探索等方面得到广泛应用。在大规模定量生物学时代,iTRAQ技术在分子水平上深入了解消化道肿瘤的相关机制研究中越来越不可或缺。因此本文对iTRAQ技术在消化道肿瘤中的研究进展进行简要综述。     

高通量分析技术在肿瘤MDR中的研究进展

高通量分析技术是近年来肿瘤研究新平台,肿瘤多药耐药(MDR)和耐药逆转药物研究在肿瘤化疗领域亟需解决。现综述基因芯片、蛋白质芯片、组织芯片三大高通量微阵列技术在肿瘤MDR机制、筛选耐药逆转靶点和逆转药物及指导临床个体化治疗等方面的应用。     

DNA芯片技术及其在肿瘤研究中的应用

DNA芯片技术是一项新兴的生物学技术,可在基因组水平上高通量地对基因的表达、突变和多态性进行快速、准确的检测.肿瘤的形成、发展是多步骤、多基因参与的复杂过程,应用DNA芯片技术在基因组水平上对肿瘤进行研究,可以了解肿瘤细胞基因表达谱的改变,解释肿瘤发生、发展的分子机制,为肿瘤的分子病理诊断、临床肿瘤预后判断及治疗方案的选择提供理论指导.本文综述了DNA芯片的技术原理及近年来在肿瘤研究中的应用.     

高通量分析技术在肿瘤MDR中的研究进展

高通量分析技术是近年来肿瘤研究新平台，肿瘤多药耐药（MDR）和耐药逆转药物研究在肿瘤化疗领域亟需解决。现综述基因芯片、蛋白质芯片、组织芯片三大高通量微阵列技术在肿瘤MDR机制、筛选耐药逆转靶点和逆转药物及指导临床个体化治疗等方面的应用。     

单细胞测序技术在乳腺癌研究中的应用进展

乳腺癌是全球女性发病率最高的恶性肿瘤,也是女性癌症相关致死的主要原因之一。乳腺癌是一种高度异质性的疾病,肿瘤间异质性和肿瘤内异质性使得精准分型治疗工作进展缓慢。传统高通量测序技术在乳腺癌研究中的应用已为揭示乳腺癌的发生、发展、驱动基因、精确分型、诊断及治疗方面提供了重要参考,但仍有局限性,无法揭示肿瘤内异质性。近年来兴起的单细胞测序技术在灵敏度、准确度和效率方面都得到了极大的提高,研究人员可以分析复杂混合细胞中的单个细胞的分子生物学信息,该技术在研究肿瘤异质性方面展现出极大的优越性。近年来,单细胞测序技术在乳腺癌研究中的应用已有多项重要研究成果发表,包括从单细胞层面解析乳腺癌转录组图谱、探索乳腺癌微环境异质性、探索乳腺癌耐药发生机制、探索乳腺癌克隆异质性及克隆演化研究,以及综合挖掘单细胞公共数据资源揭示乳腺癌异质性。本文对近年来单细胞测序技术在乳腺癌中的应用相关前沿重要研究进行综述并深入思考,旨在为乳腺癌研究者应用单细胞测序技术提供参考,促进单细胞测序技术在乳腺癌研究中的广泛应用。     

细胞核仁组成区嗜银蛋白在肿瘤病理学上的应用

近年来,国内、外病理学家将细胞核仁组成区嗜银蛋白(AgNOR)技术应用于肿瘤病理学的诊断和研究,发现该技术对区别良、恶性病变以及对肿瘤进行分型和分级等有重要价值。现将该技术在肿瘤病理学上的应用述如下: 一、历史 Henderson等最先应用银染技术报告人类细胞核仁组成区位于近端着丝点染色体(13、14、15、21与22号)短臂的次缢痕区域。过去应用银染来观察核仁功能大多是通过分析核分裂中期染色体上着色的NORs数目等来进行,但此期并无rRNA合成,故有人认为对合成rRNA的分裂间期进行银     

基因芯片技术在癌症研究中的应用

新近发展的高通量的基因表达分析平台———基因芯片技术具有多样品并行处理能力、分析速度快、所需样品量少、污染少等优点 ,近年来在临床诊断、药物筛选、寻找新基因等研究领域带来革新性的影响。本文综述用基因芯片技术进行肿瘤研究的新策略和模式。     

液体活检技术应用于肿瘤筛检的研究现状

摘 要：随着社会经济发展、城市化及人口老龄化进程加速、生活方式改变等,恶性肿瘤已成为严重威胁人们健康的重大慢性疾病,而高水准的肿瘤筛检技术可早期发现肿瘤的存在,通过肿瘤早诊早治,改善预后。液体活检技术是新兴的极具潜力的血液检测技术,凭借便捷、无创、经济等特点成为近年来关注的热点,其有望取代传统的肿瘤筛检技术,成为未来主流的筛检方式。全文将液体活检技术在肿瘤筛检中的应用现状进行汇总,并进一步检索在美国临床试验注册平台和中国临床试验注册中心注册的相关研究,深入探讨液体活检技术应用于肿瘤筛检的应用价值、可行性和未来发展方向。     

蛋白质组学及其在恶性肿瘤患者血浆标记物分析中的应用

近年来,蛋白质组学技术已经成为临床肿瘤疾病普查和早期诊断蛋白质标记物的有效工具,同时为研究恶性肿瘤发生和发展机制提供了技术平台。其中双向凝胶电泳一质谱技术具有高敏感性、高准确性、高通量,是研究蛋白组学重要的技术支撑,是筛选血浆肿瘤特异性标记物较为理想的方法。可以通过测定血浆肿瘤标记物来分析病程、监测复发或转移、指导治疗及判断预后。本文就双向凝胶电泳一质谱的蛋白组学技术在筛选血浆肿瘤标记物中的应用及其发展前景做一综述。     

射频消融治疗恶性肿瘤现状

目前,恶性肿瘤的治疗多强调以手术切除为主的多学科综合治疗,而对于一些不能手术切除的肿瘤患者,微创介入疗法是一种较好的肿瘤姑息治疗手段。射频消融(radiofrequency ablation,RFA)是一种针对肿瘤局部的微创介入性疗法,已被证实是一种有效、安全、并发症少、定位准确的治疗恶性实体肿瘤的微创技术。近年来,此项技术已被广泛应用于多种恶性肿瘤,如肝癌、肺癌、乳腺癌等。随着RFA治疗原理研究的不断深入、射频消融技术的不断改进,局部肿瘤治疗的疗效将进一步提高,但仍需要随机化的研究和长期的随访来证实RFA在肿瘤治疗中的重要意义。     

Comparative analysis of the liver and plasma proteomes as a novel and powerful strategy for hepatocellular carcinoma biomarker discovery

The extraordinary developments made in the past decade in proteomic technologies, in particular in mass spectrometry, have enabled investigators to consider designing studies to search for diagnostic and therapeutic biomarkers by scanning complex proteome samples. We developed a method based on extensive fractionation of intact proteins, to comprehensively and quantitatively profile the liver and plasma proteomes in health and disease. We have applied this method to samples collected from patients with early hepatocellular carcinoma (HCC) and from patients with liver cirrhosis as well as to samples collected from three mouse models of HCC. This method allowed for the identification of proteins that differ in expression levels in liver tissue or in plasma with disease progression from liver fibrosis, cirrhosis or steatohepatitis to HCC. The comparative analysis of the liver and plasma proteomes generated from human and mouse specimens, constitutes a novel and powerful strategy for HCC biomarker discovery.     

人胰腺组织蛋白质组的双向电泳分析

目的利用双向电泳技术建立正常人胰腺组织的蛋白质组表达图谱。方法取正常人胰腺组织3例，经蛋白质的提取、一向、二向电泳、染色、扫描及图像采集分析，对各种条件进行比较优化。结果获得了分辨率及重复性均较好的双向电泳图谱。结论通过对各种条件的优化，初步建立了胰腺的双向电泳技术。     

APC +/- alters colonic fibroblast proteome in FAP

Here we compared the proteomes of primary fibroblast cultures derived from morphologically normal colonic mucosa of familial adenomatous polyposis (FAP) patients with those obtained from unaffected controls. The expression signature of about 19% of total fibroblast proteins separates FAP mutation carriers from unaffected controls (P < 0.01). More than 4,000 protein spots were quantified by 2D PAGE analysis, identifying 368 non-redundant proteins and 400 of their isoforms. Specifically, all three classes of cytoskeletal filaments and their regulatory proteins were altered as were oxidative stress response proteins. Given that FAP fibroblasts showed heightened sensitivity to transformation by KiMSV and SV40 including elevated levels of the p53 protein, events controlled in large measure by the Ras suppressor protein-1 (RSU-1) and oncogenic DJ-1, here we show decreased RSU1 and augmented DJ-1 expression in both fibroblasts and crypt-derived epithelial cells from morphologically normal colonic mucosa of FAP gene-carriers. The results indicate that heterozygosity for a mutant APC tumor suppressor gene alters the proteomes of both colon-derived normal fibroblasts in a gene-specific manner, consistent with a "one-hit" effect.     

Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using <Emphasis Type="Italic">in vitro</Emphasis>cultured epithelial cells derived from the cancer tissues

Background  

Breast carcinomas represent a heterogeneous group of tumors diverse in behavior, outcome, and response to therapy. Identification of proteins resembling the tumor biology can improve the diagnosis, prediction, treatment selection, and targeting of therapy. Since the beginning of the post-genomic era, the focus of molecular biology gradually moved from genomes to proteins and proteomes and to their functionality. Proteomics can potentially capture dynamic changes in protein expression integrating both genetic and epigenetic influences.     

Proteomic analysis of human prostate cancer.

Proteomics is a promising approach in the identification of proteins and biochemical pathways involved in tumorigenesis. In an effort to discover such proteins and pathways that are deregulated in prostate tumorigenesis, cellular proteomes of matched normal prostate epithelial cells and high-grade prostate cancer cells were analyzed by tissue microdissection, two-dimensional electrophoresis, and mass spectrometry. Forty protein alterations were detected in the tumors; however, the majority of these changes were not shared among the 12 neoplasms. In contrast, parallel cDNA microarray analysis identified a number of common gene expression changes. The marked heterogeneity of the observed protein alterations may have significance with regard to tumor biology and research strategies for molecular profiling analyses of human prostate cancer.     

The proteome profile of two cell lines and their xenografts isolated from a patient with clear cell sarcoma (soft tissue melanoma)

We report the establishment of two novel clear cell sarcoma (CCS) cell lines (soft tissue melanoma) from a patient and the production of the corresponding xenografts after xenotransplantation of those cells to NOD/SCID mice. As no comprehensive study on the relevant proteomes of this type of cancer has been reported to date, proteomics technologies were applied in a first attempt to analyze the proteins of the two cell lines and their corresponding primary xenografts. Total protein extracts were separated by two dimensional gel electrophoresis (2-DE) and analysed by MALDI-MS and MALDI-MS-MS following in-gel digestion with trypsin. Protein identification was carried out by peptide mass fingerprint (PMF) and post source decay (PSD), respectively. Comparative analysis revealed that 124 proteins were common between the cell lines and the xenografts; 249 proteins were found to be expressed only in the proteome of the cell lines, while 178 proteins were expressed only in the proteome of xenografts. Our results demonstrated that both cell lines and xenografts were positive for vimentin and S100 reported as markers for CCS. After functional analysis, 27 different protein groups were identified in the analysed proteomes, including apoptosis-related proteins, oncogenes and several proteins closely related to TP-53 and NF-kappa B pathways. Furthermore, the proteins nestin, stem cell growth factor CLC11 and mdr-1, closely related to malignant-melanoma-initiating cells, were found to be expressed in both the cell lines and their corresponding xenografts. Since there are no data concerning protein expression in CCS, this study may contribute to the understanding of the molecular basis of the disease, while the cell lines as well as the developed xenografts may be used as tools for the development of new therapeutic strategies to tackle this rare but fatal malignancy.     

Identification of a novel proliferation-related protein, WHSC1 4a, in human gliomas

Dynamic changes in the expression of multiple genes appear to be common features that distinguish transformed cells from their normal counterparts. We compared the proteomic profiles of four glioblastoma multiforme (GBM) tissue samples and four normal brain cortex samples to examine the molecular basis of gliomagenesis. Trypsin-digested protein samples were separated by capillary isoelectric focusing with nano-reversed-phase liquid chromatography and were profiled by mass spectrometric sequencing. Wolf-Hirschhorn syndrome candidate 1 (WHSC1), along with 103 other proteins, was found only in the GBM proteomes. Western blot and immunohistochemistry verified our proteomic findings and demonstrated that 30-kDa WHSC1 expression increases with ascending tumor proliferation activity. RNA interference could suppress glioma cell growth by blocking WHSC1 expression. Our novel findings encourage the application of proteomic techniques in cancer research.     

Clinical proteomics for cancer biomarker discovery and therapeutic targeting

As we emerge into the post-genome era, proteomics finds itself as the driving force field as we translate the nucleic acid information archive into understanding how the cell actually works and how disease processes operate. Even so, the traditionally held view of proteomics as simply cataloging and developing lists of the cellular protein repertoire of a cell are now changing, especially in the sub-discipline of clinical proteomics. The most relevant information archive to clinical applications and drug development involves the elucidation of the information flow of the cell; the "software" of protein pathway networks and circuitry. The deranged circuitry of the cell as the drug target itself as well as the effect of the drug on not just the target, but also the entire network, is what we now are striving towards. Clinical proteomics, as a new and most exciting sub-discipline of proteomics, involves the bench-to-bedside clinical application of proteomic tools. Unlike the genome, there are potentially thousands of proteomes: each cell type has its own unique proteome. Moreover, each cell type can alter its proteome depending on the unique tissue microenvironment in which it resides, giving rise to multiple permutations of a single proteome. Since there is no polymerase chain reaction equivalent to proteomics- identifying and discovering the "wiring diagram" of a human diseased cell in a biopsy specimen remains a daunting challenge. New micro-proteomic technologies are being and still need to be developed to drill down into the proteomes of clinically relevant material. Cancer, as a model disease, provides a fertile environment to study the application of proteomics at the bedside. The promise of clinical proteomics and the new technologies that are developed is that we will detect cancer earlier through discovery of biomarkers, we will discover the next generation of targets and imaging biomarkers, and we can then apply this knowledge to patient-tailored therapy.     

Cancer proteomics and its application to discovery of therapy response markers in human cancer

The administration of chemotherapy either alone or in combination with radiotherapy is an important factor in reducing the mortality and morbidity of cancer patients. Resistance to both chemotherapy and radiotherapy represents a major obstacle to a successful outcome. The identification of novel biomarkers that can be used to predict treatment response would allow therapy to be tailored on an individual patient basis. Although the mechanisms are unclear, it is accepted that development of therapy resistance is a multifactorial phenomenon involving alterations in several cellular pathways. Proteome analysis methods are powerful tools for identifying factors associated with resistance to anticancer therapy because they facilitate the simultaneous analysis of whole proteomes. The current review describes the plethora of existing proteomic approaches and details the studies that have identified biomarkers that may be useful in the prediction of clinical response to anticancer therapy.     

Classical oncogenes and tumor suppressor genes: a comparative genomics perspective

We have curated a reference set of cancer- related genes and reanalyzed their sequences in the light of molecular information and resources that have become available since they were first cloned. Homology studies were carried out for human oncogenes and tumor suppressors, compared with the complete proteome of the nematode, Caenorhabditis elegans, and partial proteomes of mouse and rat and the fruit fly, Drosophila melanogaster. Our results demonstrate that simple, semi-automated bioinformatics approaches to identifying putative functionally equivalent gene products in different organisms may often be misleading. An electronic supplement to this article provides an integrated view of our comparative genomics analysis as well as mapping data, physical cDNA resources and links to published literature and reviews, thus creating a "window" into the genomes of humans and other organisms for cancer biology.