Multiplexed analysis of protein signatures in formalin-fixed breast cancers

Coordinator:		Dr. Peter Porschewski
Institution:		Qiagen GmbH
Homepage:		www1.qiagen.com/

Currently, formalin-fixed and paraffin-embedded (FFPE) tissues from clinical specimens are not routinely used in clinical proteomic workflows, mainly because the macromolecules are crosslinked. These crosslinks render proteins insoluble and therefore make proteins inaccessible for routine biochemical or proteomic analysis. However, this drawback will be circumvented by using protein lysates from FFPE tissues from well-documented breast cancer cohorts prepared with our method. Full-length intact proteins will be resolved in a systematic multiplex approach by 2-D PAGE followed by visualization using different staining methods and fluorescence 2-D difference gel electrophoresis (DIGE). Differentially expressed proteins will be identified by mass spectrometry. Resulting protein signatures will be compared to quantitative data obtained in subproject #2 as well as with retrospective data from patients (e.g. Her2 marker status). Novel identified proteins will be assessed as candidates for new diagnostic markers or drug targets.