A Standardized and Reproducible Workflow for Membrane Glass Slides in Routine Histology and Spatial Proteomics

Defining the molecular phenotype of single cells in situ is key for understanding tissue architecture in health and disease. Advanced imaging platforms have recently been joined by spatial omics technologies, promising unparalleled insights into the molecular landscape of biological samples. Furthermore, high-precision laser microdissection (LMD) of tissue on membrane glass slides is a powerful method for spatial omics technologies and single-cell type spatial proteomics in particular. However, current histology protocols have not been compatible with glass membrane slides and LMD for automated staining platforms and routine histology procedures. This has prevented the combination of advanced staining procedures with LMD. In this study, we describe a novel method for handling glass membrane slides that enables automated eight-color multiplexed immunofluorescence staining and high-quality imaging followed by precise laser-guided extraction of single cells. The key advance is the glycerol-based modification of heat-induced epitope retrieval protocols, termed “G-HIER.” We find that this altered antigen-retrieval solution prevents membrane distortion. Importantly, G-HIER is fully compatible with current antigen retrieval workflows and mass spectrometry–based proteomics and does not affect proteome depth or quality. To demonstrate the versatility of G-HIER for spatial proteomics, we apply the recently introduced deep visual proteomics technology to perform single-cell type analysis of adjacent suprabasal and basal keratinocytes of human skin. G-HIER overcomes previous incompatibility of standard and advanced staining protocols with membrane glass slides and enables robust integration with routine histology procedures, high-throughput multiplexed imaging, and sophisticated downstream spatial omics technologies. [Display omitted] •Glycerol-enhanced antigen retrieval enables membrane slide use in routine histology.•G-HIER is compatible with automated staining platforms and multiplexed imaging.•G-HIER integrates with laser microdissection and spatial omic technologies. Integrating spatial omics with laser microdissection has been challenging due to incompatibility between routine histology and glass membrane slides. We introduce glycerol-modified antigen retrieval. This standardizes membrane slide use in routine histology and aligns with automated staining platforms. Importantly, it enables integration of multiplexed imaging, laser microdissection, and spatial prot