Protein expression profiling of formalin-fixed paraffin-embedded tissue using recombinant antibody microarrays.
Proteomics, the large-scale analysis of proteins, is a rapidly evolving field with an increasing number of key clinical applications, such as diagnosis, prognosis, and classification. In order to generate complete protein expression profiles, or protein atlases, any crude sample format must be addressable in a rapid, multiplex, and sensitive manner. A common and clinically central sample format, formalin-fixed, paraffin-embedded (FFPE) tissue material, holds great potential as a source for disease-associated biomarker signatures. However, despite major efforts, extraction and subsequent profiling of proteins from FFPE tissue has proven to be challenging. In this proof-of-concept study, we have demonstrated for the first time that proteins could be extracted, labeled, and subsequently profiled in a multiplex, sensitive, and reproducible manner using recombinant scFv antibody microarrays. Thus, we have added FFPE samples to the list of sample formats available for high-throughput analysis by affinity proteomics, paving the way for the next generation of biomarker-driven discovery projects.
Department of Immunotechnology, Lund University , Medicon Village, Lund, Sweden.
Frida
F
Pauly
Linda
L
Dexlin-Mellby
Sara
S
Ek
Mats
M
Ohlin
Niclas
N
Olsson
Karin
K
Jirström
Michael
M
Dictor
Saskia
S
Schoenmakers
Carl A K
CA
Borrebaeck
Christer
C
Wingren
D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000276:immunology; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D005260:Female; D005404:Fixatives; D005557:Formaldehyde; D015870:Gene Expression; D020869:Gene Expression Profiling; D006801:Humans; D007135:Immunoglobulin Variable Region / Q000096:biosynthesis / Q000276:immunology; D057230:Limit of Detection; D008224:Lymphoma, Follicular / Q000175:diagnosis / Q000235:genetics* / Q000276:immunology; D020522:Lymphoma, Mantle-Cell / Q000175:diagnosis / Q000235:genetics* / Q000276:immunology; D009363:Neoplasm Proteins / Q000032:analysis* / Q000235:genetics / Q000276:immunology; D016612:Paraffin Embedding; D040081:Protein Array Analysis / Q000295:instrumentation* / Q000379:methods; D011994:Recombinant Proteins / Q000096:biosynthesis / Q000276:immunology; D015203:Reproducibility of Results; D057127:Single-Chain Antibodies / Q000096:biosynthesis / Q000276:immunology; D016707:Tissue Fixation
D005404:Fixatives; D007135:Immunoglobulin Variable Region; D009363:Neoplasm Proteins; D011994:Recombinant Proteins; D057127:Single-Chain Antibodies; D005557:Formaldehyde