Micro-structure Proteins Characterization in Tissue Sections and Clinical Biopsy Samples by a Novel Spatial Proteomic Method Named AutoSTOMP

Abstract

Abstract We aim at structure determining immunological machinery using a novel spatial selective proteomic tool, autoSTOMP, developed in Ewald lab. AutoSTOMP comprises of UV initiated biotin tagging by confocal microscopy, affinity isolation, and peptide identification by the mass spectrometer, rendering a precise characterization of micro-structures of interest (mSOIs) at intracellular organelle scale excluding surrounding area with the decent signal-to-noise ratio. Previously, autoSTOMP was employed to investigate the parasitophorous vacuole membrane, a unique intracellular membrane structure in apicomplexan infected cells. We broaden the application of autoSTOMP to respond to the calls from the research or clinical laboratory for a reliable, repeatable, and re-constructible protocol to explore the mSOIs of an animal specimen or a patient biopsy. We demonstrated, in the cardiac infarcted tissue in ischemic injured rat, the mSOIs stained against the macrophage/monocyte marker, CD68, are enriched in lysosomal proteins, and characteristic proteins involved in the Fcγ receptor-activated macrophage deformation, migration, and phagocytosis. Furthermore, in eosinophilic esophagitis (EoE) biopsy, we identify the lgG4+ cell-cluster structures are enriched in eosinophil-derived granule proteins and lgE receptor FcɛRI signaling associated proteins as well as food allergens to build up the correlation between patient’s diet with EoE progression.