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

De Marchi, Tommaso LU ; Braakman, Rene B H; Stingl, Christoph; van Duijn, Martijn M; Smid, Marcel; Foekens, John A.; Luider, Theo M.; Martens, John W. M. and Umar, Arzu (2016) In Proteomics 16(10). p.85-1474
Abstract

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... (More)

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).

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author
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Contribution to journal
publication status
published
keywords
Biomarkers, Tumor, Breast Neoplasms, Estrogen Receptor alpha, Female, Humans, Laser Capture Microdissection, Proteome, Proteomics, Tandem Mass Spectrometry, Treatment Outcome, Comparative Study, Journal Article, Research Support, Non-U.S. Gov't
in
Proteomics
volume
16
issue
10
pages
85 - 1474
publisher
John Wiley & Sons
external identifiers
  • scopus:84964689645
ISSN
1615-9861
DOI
10.1002/pmic.201600004
language
English
LU publication?
no
id
b418212f-e750-4a65-8d66-671b92bf518e
date added to LUP
2017-06-27 14:33:22
date last changed
2017-10-29 05:03:19
@article{b418212f-e750-4a65-8d66-671b92bf518e,
  abstract     = {<p>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 &lt; 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).</p>},
  author       = {De Marchi, Tommaso and Braakman, Rene B H and Stingl, Christoph and van Duijn, Martijn M and Smid, Marcel and Foekens, John A. and Luider, Theo M. and Martens, John W. M. and Umar, Arzu},
  issn         = {1615-9861},
  keyword      = {Biomarkers, Tumor,Breast Neoplasms,Estrogen Receptor alpha,Female,Humans,Laser Capture Microdissection,Proteome,Proteomics,Tandem Mass Spectrometry,Treatment Outcome,Comparative Study,Journal Article,Research Support, Non-U.S. Gov't},
  language     = {eng},
  number       = {10},
  pages        = {85--1474},
  publisher    = {John Wiley & Sons},
  series       = {Proteomics},
  title        = {The advantage of laser-capture microdissection over whole tissue analysis in proteomic profiling studies},
  url          = {http://dx.doi.org/10.1002/pmic.201600004},
  volume       = {16},
  year         = {2016},
}