title: Integrative analysis of genomics and proteomics data on clinical breast cancer tissue specimens extracted with acid guanidinium thiocyanate-phenol-chloroform.
abstract: 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.
authors.affiliation: Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam , Be401, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
authors.forename: René B H
authors.initials: RB
authors.lastname: Braakman
authors.forename: Karel
authors.initials: K
authors.lastname: Bezstarosti
authors.forename: Anieta M
authors.initials: AM
authors.lastname: Sieuwerts
authors.forename: Vanja
authors.initials: V
authors.lastname: de Weerd
authors.forename: Anne M
authors.initials: AM
authors.lastname: van Galen
authors.forename: Christoph
authors.initials: C
authors.lastname: Stingl
authors.forename: Theo M
authors.initials: TM
authors.lastname: Luider
authors.forename: Mieke A M
authors.initials: MA
authors.lastname: Timmermans
authors.forename: Marcel
authors.initials: M
authors.lastname: Smid
authors.forename: John W M
authors.initials: JW
authors.lastname: Martens
authors.forename: John A
authors.initials: JA
authors.lastname: Foekens
authors.forename: Jeroen A A
authors.initials: JA
authors.lastname: Demmers
authors.forename: Arzu
authors.initials: A
authors.lastname: Umar
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D002725:Chloroform / Q000737:chemistry*; D005260:Female; D015894:Genome, Human; D006146:Guanidines / Q000737:chemistry*; D006801:Humans; D019800:Phenol / Q000737:chemistry*; D040901:Proteomics; D013048:Specimen Handling; D013861:Thiocyanates / Q000737:chemistry*
chemical_list: D006146:Guanidines; D013861:Thiocyanates; D019800:Phenol; C054436:guanidine thiocyanate; D002725:Chloroform
keywords: RNA Bee; acid guanidinium phenol-chloroform; breast cancer; genomics; proteomics; sample preparation