Genome-scale identification of membrane-associated human mRNAs.
Genome-scale identification of membrane-associated human mRNAs.
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DOI：
10.1371/journal.pgen.0020011
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发表时间：
2006-01
期刊：
影响因子：
4.5
通讯作者：
Brown PO
中科院分区：
文献类型：
--
作者：
Diehn M;Bhattacharya R;Botstein D;Brown PO
蛋白质的亚细胞定位对其生物学作用至关重要。此外，蛋白质是膜结合的、分泌的还是细胞内的影响了使用蛋白质作为诊断标志物或治疗靶标的有用性和策略。我们采用了一种快速有效的实验方法，将数千种人类基因产物分为"膜相关/分泌"（MS）或"细胞溶质/核"（CN）。使用亚细胞分级分离方法，我们将与膜相关的mRNA与可溶性胞质组分相关的mRNA分离，并通过与DNA微阵列的比较杂交来分析这两个池。对代表淋巴、骨髓、乳腺、卵巢、肝脏、结肠和前列腺组织的11种不同人类细胞系的分析，以高置信水平鉴定了5，000多个先前未表征的MS和6，400多个推定的CN基因。实验确定的定位与信号肽和跨膜结构域的计算机预测相关，但也显着增加了可被归类为编码MS或CN蛋白的人类基因的数量。使用来自各种原发性人类恶性肿瘤和正常组织的基因表达数据，我们合理地鉴定了数百种MS基因产物，与正常组织相比，这些基因产物在肿瘤中显著过表达，因此代表了血清诊断测试或基于单克隆抗体的治疗的候选者。最后，我们使用CN基因产物的目录来产生器官特异性组织损伤的候选标记物的集合。大规模注释的亚细胞定位报告将作为一个参考数据库，并将有助于合理设计的诊断测试和分子治疗的各种疾病。当前生物学研究的一个重要目标是用相关描述符和属性注释人类基因。生物学家和医学研究人员感兴趣的一个关键特性是基因产物的亚细胞定位，因为这影响蛋白质的生物学作用和我们将其用作治疗靶点的能力。这项研究使用了一种基于微阵列的功能基因组学方法，可以快速，大规模地识别亚细胞定位，使作者能够注释数千种以前未表征的人类基因产物的定位。然后，作者提供了一个例子，说明如何将这些数据应用于寻找肿瘤特异性标志物。利用来自肿瘤和正常组织中数百个全球基因表达模式的DNA微阵列谱的数据，他们确定了编码在肿瘤中高度过表达的膜相关和分泌蛋白的候选基因，因此可能是诊断测试或分子治疗的特别好的靶点。基于这些标志物的诊断测试可能使癌症能够比目前更早地被检测到，并且针对这些基因产物的分子疗法可能对相应的癌症具有高度特异性。
The subcellular localization of proteins is critical to their biological roles. Moreover, whether a protein is membrane-bound, secreted, or intracellular affects the usefulness of, and the strategies for, using a protein as a diagnostic marker or a target for therapy. We employed a rapid and efficient experimental approach to classify thousands of human gene products as either “membrane-associated/secreted” (MS) or “cytosolic/nuclear” (CN). Using subcellular fractionation methods, we separated mRNAs associated with membranes from those associated with the soluble cytosolic fraction and analyzed these two pools by comparative hybridization to DNA microarrays. Analysis of 11 different human cell lines, representing lymphoid, myeloid, breast, ovarian, hepatic, colon, and prostate tissues, identified more than 5,000 previously uncharacterized MS and more than 6,400 putative CN genes at high confidence levels. The experimentally determined localizations correlated well with in silico predictions of signal peptides and transmembrane domains, but also significantly increased the number of human genes that could be cataloged as encoding either MS or CN proteins. Using gene expression data from a variety of primary human malignancies and normal tissues, we rationally identified hundreds of MS gene products that are significantly overexpressed in tumors compared to normal tissues and thus represent candidates for serum diagnostic tests or monoclonal antibody-based therapies. Finally, we used the catalog of CN gene products to generate sets of candidate markers of organ-specific tissue injury. The large-scale annotation of subcellular localization reported here will serve as a reference database and will aid in the rational design of diagnostic tests and molecular therapies for diverse diseases. An important goal of current biological research is annotation of human genes with relevant descriptors and properties. One critical property of interest to biologists and medical researchers is the subcellular localization of gene products, as this affects a protein's biological role and our ability to use it as a therapeutic target. This study used a microarray-based functional genomic method that allows rapid, large-scale identification of subcellular localization, enabling the authors to annotate the localization of thousands of previously uncharacterized human gene products. The authors then provide an example of how these data can be used by applying them to the search for tumor-specific markers. Using data from hundreds of DNA microarray profiles of global gene expression patterns in tumors and normal tissues, they identify candidate genes encoding membrane-associated and secreted proteins that are highly overexpressed in tumors and that might therefore be particularly good targets for diagnostic tests or molecular therapies. Diagnostic tests based on these markers could potentially enable cancers to be detected earlier than is currently possible, and molecular therapies targeting the products of these genes could have high specificity for the corresponding cancers.
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DOI：
10.1073/pnas.0437875100
发表时间：
2003-02-18
影响因子：
11.1
作者：
Bohen, SP;Troyanskaya, OG;Levy, R
通讯作者：
Levy, R
影响因子：
30.8
作者：
Hieronymus, H;Silver, PA
通讯作者：
Silver, PA
影响因子：
14.9
作者：
Gollub, J;Ball, CA;Sherlock, G
通讯作者：
Sherlock, G
影响因子：
7.5
作者：
Friedrichs, N;Jäger, R;Buettner, R
通讯作者：
Buettner, R
DOI：
10.1073/pnas.241500798
发表时间：
2001-11-20
影响因子：
11.1
作者：
Garber, ME;Troyanskaya, OG;Petersen, I
通讯作者：
Petersen, I