Combining laser capture microdissection and MALDI mass spectrometry for tissue protein profiling: methodology development and clinical applications

Abstract

The combination of laser capture microdissection (LCM) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) for protein profiling from specific cells of interest within heterogeneous tissue is presented in this thesis. The methodology of direct analysis of laser capture microdissected cells using MALDI MS is described. The sensitivity and reproducibility of this approach were reported. High quality protein expression profiles at the mass range of 2,000 to 50,000 Da are obtained. As the protocols were optimized, three clinical applications were studied: 1) protein biomarkers of normal and neoplastic mouse colon, 2) proteomic patterns of glomerulosclerosis and their use for the prediction of sclerosis progression, and 3) proteomic patterns of human breast tissue aimed at the molecular distinction of breast cancer and normal mammary tissue with classification of in situ tumor and invasive tumor. Statistically significant protein markers were identified for each of the tissue groups by amino acid sequence analysis. Immunostaining studies further confirmed the differential expression of some of these protein markers. In summary, LCM combined with MALDI MS is a sensitive, accurate, fast and reliable method to discover protein biomarkers which can aid in disease diagnosis, discovery of drug targets and advance the understanding of underlying mechanisms of diseases.