Subnuclear Proteomics in Colorectal Cancer IDENTIFICATION OF PROTEINS ENRICHED IN THE NUCLEAR MATRIX FRACTION AND REGULATION IN ADENOMA TO CARCINOMA PROGRESSION
Subnuclear Proteomics in Colorectal Cancer IDENTIFICATION OF PROTEINS ENRICHED IN THE NUCLEAR MATRIX FRACTION AND REGULATION IN ADENOMA TO CARCINOMA PROGRESSION
复制标题
DOI：
10.1074/mcp.m900546-mcp200
复制
发表时间：
2010-05-01
影响因子：
7
通讯作者：
Jimenez, Connie R.
中科院分区：
文献类型：
--
作者：
Albrethsen, Jakob;Knol, Jaco C.;Jimenez, Connie R.
核表型和染色体结构异常是癌细胞的关键特征。研究癌症细胞核亚组分的蛋白质决定簇可以从分子水平上了解异常染色体功能和染色质组织，此外还可以产生早期癌症检测的生物标志物。在这里，我们评估蛋白质组学的工作流程分析蛋白质成分在亚核结构域的结直肠癌组织和应用此工作流程的比较分析结直肠腺瘤和癌组织样本的核基质分数。首先，我们建立了整个工作流程的可重复性。在从相同结肠肿瘤匀浆中独立分离的三种核基质组分的再现性分析中，1，047种蛋白质中的889种（85%）在高置信度下可再现地鉴定（在蛋白质水平上，每种蛋白质至少两种肽，置信区间为99%），每种蛋白质标准化光谱计数数的平均方差系数为30%。这表明从生物化学分离到nano-LC-MS/MS分析的整个工作流程具有良好的重现性。第二，使用光谱计数结合统计，我们确定了显着富集在核基质组分相对于两个早期的馏分（染色质结合和中间丝馏分）从六个结直肠组织样本分离的蛋白质。总数据集包含2，059个非冗余蛋白质。对核基质富集蛋白的基因本体挖掘和蛋白质网络分析表明，核基质富集了参与“RNA加工”和“mRNA代谢"过程的蛋白质。最后，对结直肠腺瘤和癌组织中的核基质蛋白质组进行了探索性比较，发现了许多以前与肿瘤发生有关的蛋白质以及新的候选蛋白质。这些差异表达的蛋白质的子集也表现出相应的变化在mRNA水平。总之，这些结果表明，肿瘤组织的亚核蛋白质组学是可行的，是探索肿瘤发生的一条有前途的途径。Molecular & Cellular Proteomics 9：988-1005，2010.
Abnormalities in nuclear phenotype and chromosome structure are key features of cancer cells. Investigation of the protein determinants of nuclear subfractions in cancer may yield molecular insights into aberrant chromosome function and chromatin organization and in addition may yield biomarkers for early cancer detection. Here we evaluate a proteomics work flow for profiling protein constituents in subnuclear domains in colorectal cancer tissues and apply this work flow to a comparative analysis of the nuclear matrix fraction in colorectal adenoma and carcinoma tissue samples. First, we established the reproducibility of the entire work flow. In a reproducibility analysis of three nuclear matrix fractions independently isolated from the same colon tumor homogenate, 889 of 1,047 proteins (85%) were reproducibly identified at high confidence (minimally two peptides per protein at 99% confidence interval at the protein level) with an average coefficient of variance for the number of normalized spectral counts per protein of 30%. This indicates a good reproducibility of the entire work flow from biochemical isolation to nano-LC-MS/MS analysis. Second, using spectral counting combined with statistics, we identified proteins that are significantly enriched in the nuclear matrix fraction relative to two earlier fractions (the chromatin-binding and intermediate filament fractions) isolated from six colorectal tissue samples. The total data set contained 2,059 non-redundant proteins. Gene ontology mining and protein network analysis of nuclear matrix-enriched proteins revealed enrichment for proteins implicated in "RNA processing" and "mRNA metabolic process." Finally, an explorative comparison of the nuclear matrix proteome in colorectal adenoma and carcinoma tissues revealed many proteins previously implicated in oncogenesis as well as new candidates. A subset of these differentially expressed proteins also exhibited a corresponding change at the mRNA level. Together, the results show that subnuclear proteomics of tumor tissue is feasible and a promising avenue for exploring oncogenesis. Molecular & Cellular Proteomics 9:988-1005, 2010.