title: Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues.
abstract: Successful treatment of multiple cancer types requires early detection and identification of reliable biomarkers present in specific cancer tissues. To test the feasibility of identifying proteins from archival cancer tissues, we have developed a methodology, termed direct tissue proteomics (DTP), which can be used to identify proteins directly from formalin-fixed paraffin-embedded prostate cancer tissue samples. Using minute prostate biopsy sections, we demonstrate the identification of 428 prostate-expressed proteins using the shotgun method. Because the DTP method is not quantitative, we employed the absolute quantification method and demonstrate picogram level quantification of prostate-specific antigen. In depth bioinformatics analysis of these expressed proteins affords the categorization of metabolic pathways that may be important for distinct stages of prostate carcinogenesis. Furthermore, we validate Wnt-3 as an upregulated protein in cancerous prostate cells by immunohistochemistry. We propose that this general strategy provides a roadmap for successful identification of critical molecular targets of multiple cancer types.
authors.affiliation: Department of Cell Biology, Center for Vascular Biology, University of Connecticut School of Medicine, Farmington, CT 06030, USA.
authors.forename: S-I
authors.initials: SI
authors.lastname: Hwang
authors.forename: J
authors.initials: J
authors.lastname: Thumar
authors.forename: D H
authors.initials: DH
authors.lastname: Lundgren
authors.forename: K
authors.initials: K
authors.lastname: Rezaul
authors.forename: V
authors.initials: V
authors.lastname: Mayya
authors.forename: L
authors.initials: L
authors.lastname: Wu
authors.forename: J
authors.initials: J
authors.lastname: Eng
authors.forename: M E
authors.initials: ME
authors.lastname: Wright
authors.forename: D K
authors.initials: DK
authors.lastname: Han
mesh_terms: D000595:Amino Acid Sequence; D014408:Biomarkers, Tumor / Q000378:metabolism*; D019295:Computational Biology; D005557:Formaldehyde; D006801:Humans; D007150:Immunohistochemistry; D008297:Male; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D009363:Neoplasm Proteins / Q000737:chemistry / Q000378:metabolism*; D016612:Paraffin Embedding; D011471:Prostatic Neoplasms / Q000378:metabolism; D040901:Proteomics
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D005557:Formaldehyde