PT  - JOURNAL ARTICLE
AU  - Jeremy A. Herrera
AU  - Venkatesh Mallikarjun
AU  - Silvia Rosini
AU  - Maria Angeles Montero
AU  - Stacey Warwood
AU  - Ronan O’Caulian
AU  - David Knight
AU  - Martin A. Schwartz
AU  - Joe Swift
TI  - Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues
AID  - 10.1101/721373
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 721373
4099  - http://biorxiv.org/content/early/2019/08/13/721373.short
4100  - http://biorxiv.org/content/early/2019/08/13/721373.full
AB  - Haematoxylin and eosin (H&E) – which respectively stain nuclei blue and other cellular and stromal material pink – are routinely used for clinical diagnosis based on the identification of morphological features. A richer characterization can be achieved by laser capture microdissection coupled to mass spectrometry (LCM-MS), giving an unbiased assay of the proteins that make up the tissue. However, the process of fixing, and H&E staining of tissues is poorly compatible with standard sample preparation methods for mass spectrometry, resulting in low protein yield. Here we describe a microproteomics technique optimized to analyze H&E-stained, formalin-fixed paraffin-embedded (FFPE) tissues. We advance our methodology by combining 3 techniques shown to individually enhance protein yields (heat extraction, physical disruption, and in column digestion) into one optimized pipeline for the analysis of H&E stained FFPE tissues. Micro-dissected morphologically normal human lung alveoli (0.082 mm3) and human lung blood vessels (0.094 mm3) from FFPE fixed section from Idiopathic Pulmonary Fibrosis (IPF) specimens were then subject to comparative proteomics using this methodology. This approach yielded 1252 differentially expressed proteins including 137 extracellular matrix (ECM) proteins. In addition, we offer proof of principal that MS can identify distinct, characteristic proteomic compositions of anatomical features within complex tissues.