Residual tissue repositories as a resource for population-based cancer proteomic studies.
Residual tissue repositories as a resource for population-based cancer proteomic studies.
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DOI：
10.1186/s12014-018-9202-4
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发表时间：
2018
影响因子：
3.8
通讯作者：
Rodland KD
中科院分区：
文献类型：
--
作者：
Piehowski PD;Petyuk VA;Sontag RL;Gritsenko MA;Weitz KK;Fillmore TL;Moon J;Makhlouf H;Chuaqui RF;Boja ES;Rodriguez H;Lee JSH;Smith RD;Carrick DM;Liu T;Rodland KD
基于质谱的蛋白质组学已成为从各种生物样本中识别和定量蛋白质的强大工具。迄今为止，大多数利用组织样本的研究都是在前瞻性收集的新鲜冷冻或最佳切割温度 (OCT) 包埋样本上进行的。然而，此类样本通常很难获得，供应有限，而且与银行样本相比，患者的临床信息和结果本质上会延迟。带注释的福尔马林固定石蜡包埋 (FFPE) 肿瘤组织标本可从各种组织库中获取以供研究使用，例如来自监测、流行病学和最终结果 (SEER) 登记处的残留组织存储库。鉴于与此类样本相关的大量结果信息，重复使用存档的 FFPE 块通过质谱技术进行深度蛋白质组表征将为基于人群的癌症研究提供宝贵的资源。此外，由于 FFPE 样本的广泛使用，样本完整性验证为在全球范围内进行数千项研究提供了可能性。为了检查 SEER 存储库组织对蛋白质组和磷酸化蛋白质组分析的适用性，我们分析了 60 个 SEER 患者样本，存储时间从 7 年到 32 年不等；使用同量异位标记，对 60 个表达蛋白质组学样品和 18 个磷酸蛋白质组学样品进行分析。使用线性模型和基因集富集分析来评估收集地点和储存时间的影响。所有样品，无论年龄如何，在提取后都产生了适合表达分析的蛋白质质量，其中 18 个样品产生了足够的质量用于磷酸肽分析。尽管与可比较的 OCT 样本相比，肽、蛋白质和磷酸肽的鉴定结果分别减少了 50%、20% 和 76%，但我们发现与采集地点或样本年龄相关的蛋白质定量没有统计学上的显着差异。 GSEA 对 FFPE 和 OCT 包埋样本之间蛋白质丰度差异的 GO-term 水平测量结果进行分析表明，福尔马林固定过程可能会改变所得数据集中蛋白质类别的表示。这些研究表明，如果与经过严格验证的质谱工作流程配合使用，不同年龄和采集地点的残留 FFPE 组织标本是蛋白质组研究有前途的蛋白质来源。本文的在线版本 (10.1186/s12014-018-9202-4) 包含补充材料，可供授权用户使用。
Mass spectrometry-based proteomics has become a powerful tool for the identification and quantification of proteins from a wide variety of biological specimens. To date, the majority of studies utilizing tissue samples have been carried out on prospectively collected fresh frozen or optimal cutting temperature (OCT) embedded specimens. However, such specimens are often difficult to obtain, in limited in supply, and clinical information and outcomes on patients are inherently delayed as compared to banked samples. Annotated formalin fixed, paraffin embedded (FFPE) tumor tissue specimens are available for research use from a variety of tissue banks, such as from the surveillance, epidemiology and end results (SEER) registries’ residual tissue repositories. Given the wealth of outcomes information associated with such samples, the reuse of archived FFPE blocks for deep proteomic characterization with mass spectrometry technologies would provide a valuable resource for population-based cancer studies. Further, due to the widespread availability of FFPE specimens, validation of specimen integrity opens the possibility for thousands of studies that can be conducted worldwide. To examine the suitability of the SEER repository tissues for proteomic and phosphoproteomic analysis, we analyzed 60 SEER patient samples, with time in storage ranging from 7 to 32 years; 60 samples with expression proteomics and 18 with phosphoproteomics, using isobaric labeling. Linear modeling and gene set enrichment analysis was used to evaluate the impacts of collection site and storage time. All samples, regardless of age, yielded suitable protein mass after extraction for expression analysis and 18 samples yielded sufficient mass for phosphopeptide analysis. Although peptide, protein, and phosphopeptide identifications were reduced by 50, 20 and 76% respectively, from comparable OCT specimens, we found no statistically significant differences in protein quantitation correlating with collection site or specimen age. GSEA analysis of GO-term level measurements of protein abundance differences between FFPE and OCT embedded specimens suggest that the formalin fixation process may alter representation of protein categories in the resulting dataset. These studies demonstrate that residual FFPE tissue specimens, of varying age and collection site, are a promising source of protein for proteomic investigations if paired with rigorously verified mass spectrometry workflows. The online version of this article (10.1186/s12014-018-9202-4) contains supplementary material, which is available to authorized users.
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影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
4.4
作者：
Kennedy, Jacob J.;Whiteaker, Jeffrey R.;Paulovich, Amanda G.
通讯作者：
Paulovich, Amanda G.
DOI：
10.4103/0973-029x.125199
发表时间：
2013-09-01
期刊：
Journal of oral and maxillofacial pathology : JOMFP
影响因子：
--
作者：
Negi, Amita;Puri, Abhiney;Sachdeva, Alisha
通讯作者：
Sachdeva, Alisha
影响因子：
3.7
作者：
Carrick DM;Mehaffey MG;Sachs MC;Altekruse S;Camalier C;Chuaqui R;Cozen W;Das B;Hernandez BY;Lih CJ;Lynch CF;Makhlouf H;McGregor P;McShane LM;Phillips Rohan J;Walsh WD;Williams PM;Gillanders EM;Mechanic LE;Schully SD
通讯作者：
Schully SD
影响因子：
3.8
作者：
Kawashima Y;Kodera Y;Singh A;Matsumoto M;Matsumoto H
通讯作者：
Matsumoto H