Chromosome-8-Coded Proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with Partial Immunohistochemical Verifications
Chromosome-8-Coded Proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with Partial Immunohistochemical Verifications
复制标题
中国染色体蛋白质组数据集 (CCPD) 2.0 的染色体 8 编码蛋白质组及部分免疫组织化学验证。
DOI：
10.1021/pr400902u
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发表时间：
2014-01-01
影响因子：
4.4
通讯作者：
Zhong, Fan
中科院分区：
文献类型：
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作者：
Liu, Yang;Ying, Wantao;Zhong, Fan
我们使用三种肝细胞癌（HCC）细胞系（即Hep 3B、MHCC 97 H和HCCLM 3）的最新深度分析蛋白质组（CCPD 2013）（ProteomeXchange标识符：PXD 000529、PXD 000533和PXD 000535）将初步CCPD 1.0升级为CCPD 2.0。CCPD 2.0共覆盖了63.6%（438/689）的8号染色体编码蛋白和62.6%（439/701）的8号染色体编码蛋白编码基因。有趣的是，我们发现缺失的蛋白质表现出在染色体中形成簇区域的趋势，例如第8染色体中的两个β-防御素簇，这可能是由它们的炎症相关特征引起的。对41个以前鉴定较弱或几乎不鉴定的Chr.8编码蛋白，我们在30对癌/癌旁HCC和20例非癌肝组织中进行了免疫组化（IHC）验证，证实了它们在组织样本中的表达证据和出现比例。我们还使用IHC验证了CCPD 1.0中报告的13个8号染色体编码的HCC肿瘤发生相关的耗竭或缺陷蛋白，并从CCPD 2013的大规模无标记蛋白质组定量数据中筛选了16个阳性和24个阴性HCC转移潜力相关蛋白。我们的研究结果表明，选择合适的样品和方法来寻找目标缺失的蛋白质，应仔细考虑在进一步验证剩余的Chr.8编码的蛋白质。
We upgraded the preliminary CCPD 1.0 to CCPD 2.0 using the latest deep-profiling proteome (CCPD 2013) of three hepatocellular carcinoma (HCC) cell lines, namely, Hep3B, MHCC97H, and HCCLM3 (ProteomeXchange identifiers: PXD000529, PXD000533, and PXD000535). CCPD 2.0 totally covered 63.6% (438/689) of Chr. 8-coded proteins and 62.6% (439/701) of Chr. 8-coded protein-coding genes. Interestingly, we found that the missing proteins exhibited a tendency to form a cluster region in chromosomes, such as two β-defensins clusters in Chr. 8, caused perhaps by their inflammation-related features. For the 41 Chr. 8-coded proteins being weakly or barely identified previously, we have performed an immunohistochemical (IHC) verification in 30 pairs of carcinoma/para-carcinoma HCC and 20 noncancerous liver tissues and confirmed their expressional evidence and occurrence proportions in tissue samples. We also verified 13 Chr. 8-coded HCC tumorigenesis-associated depleting or deficient proteins reported in CCPD 1.0 using IHC and screened 16 positive and 24 negative HCC metastatic potential-correlated proteins from large-scale label-free proteome quantitation data of CCPD 2013. Our results suggest that the selection of proper samples and the methodology to look for targeted missing proteins should be carefully considered in further verifications for the remaining Chr. 8-coded proteins.