The advantage of laser-capture microdissection over whole tissue analysis in proteomic profiling studies

被引:30
作者
De Marchi, Tommaso [1 ]
Braakman, Rene B. H. [1 ,4 ]
Stingl, Christoph [2 ]
van Duijn, Martijn M. [2 ]
Smid, Marcel [1 ]
Foekens, John A. [1 ]
Luider, Theo M. [2 ]
Martens, John W. M. [1 ,3 ]
Umar, Arzu [1 ]
机构
[1] Erasmus Univ, Med Ctr, Erasmus MC Canc Inst, Dept Med Oncol, Wytemaweg 80, NL-3015 CN Rotterdam, Netherlands
[2] Erasmus Univ, Med Ctr Rotterdam, Dept Neurol, Rotterdam, Netherlands
[3] Canc Genom Netherlands, Utrecht, Netherlands
[4] TNO Rijswijk, CBRN Protect, Rijswijk, Netherlands
关键词
Bioinformatics; Biomarker; Label-free quantification; Laser-capture microdissection; Orbitrap mass spectrometry; Tissue heterogeneity; HUMAN PLASMA PROTEOME; CANCER TISSUES; DRAFT; COLON;
D O I
10.1002/pmic.201600004
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Laser-capture microdissection (LCM) offers a reliable cell population enrichment tool and has been successfully coupled to MS analysis. Despite this, most proteomic studies employ whole tissue lysate (WTL) analysis in the discovery of disease biomarkers and in profiling analyses. Furthermore, the influence of tissue heterogeneity in WTL analysis, nor its impact in biomarker discovery studies have been completely elucidated. In order to address this, we compared previously obtained high resolution MS data from a cohort of 38 breast cancer tissues, of which both LCM enriched tumor epithelial cells and WTL samples were analyzed. Label-free quantification (LFQ) analysis through MaxQuant software showed a significantly higher number of identified and quantified proteins in LCM enriched samples (3404) compared to WTLs (2837). Furthermore, WTL samples displayed a higher amount of missing data compared to LCM both at peptide and protein levels (p-value<0.001). 2D analysis on co-expressed proteins revealed discrepant expression of immune system and lipid metabolisms related proteins between LCM and WTL samples. We hereby show that LCM better dissected the biology of breast tumor epithelial cells, possibly due to lower interference from surrounding tissues and highly abundant proteins. All data have been deposited in the ProteomeXchange with the dataset identifier PXD002381 (http://proteomecentral.proteomexchange.org/dataset/PXD002381).
引用
收藏
页码:1474 / 1485
页数:12
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