Integrative Analysis of Genomics and Proteomics Data on Clinical Breast Cancer Tissue Specimens Extracted with Acid Guanidinium Thiocyanate–Phenol–Chloroform

Acid
guanidinium thiocyanate, phenol, and chloroform extraction
(AGPC) is a commonly used procedure to extract RNA from fresh frozen
tissues and cell lines. In addition, DNA and proteins can be recovered,
which makes AGPC an attractive source for integrative analysis on
tissues of which little material is available, such as clinical specimens.
Despite this potential, AGPC has only scarcely been used for proteomic
analysis, mainly due to difficulties in extracting proteins. We have
used a quantitative mass spectrometry method to show that proteins
can readily be recovered from AGPC extracted tissues with high recovery
and repeatability, which allows this method to be used for global
proteomic profiling. Protein expression data for a selected number
of clinically relevant markers, of which transcript and protein levels
are known to be correlated, were in agreement with genomic and transcriptomic
data obtained from the same AGPC lysate. Furthermore, global proteomic
profiling successfully discriminated breast tumor tissues according
to their clinical subtype. Lastly, a reference gene set of differentially
expressed transcripts was strongly enriched in the differentially
abundant proteins in our cohort. AGPC lysates are therefore well suited
for comparative protein and integrative analyses.