Spatial Multiomics Lipids and Gene expression using MALDI In Situ Hybridization Mass Spectrometry Imaging

Abstract

Current spatial gene expression methods use DNA microarrays, Next Generation Sequencing (NGS), and fluorescence microscopy to depict the pathological/histological architecture of tissues. While each of these techniques has its own advantages, they are often costly, time intensive, and limit sampling area. A newly developed mass spectrometry-based platform, MADLI ISH MSI, combines in-situ hybridization (ISH) with matrix-assisted laser desorption/ionization (MALDI) to indirectly detect mRNA through an azide-modified photocleavable peptide mass tag using a single RNA targeting probe sequence. To date, 20 photocleavable mRNA probes have been synthesized to provide cellular identity within full sagittal sections of fresh frozen murine brain. This information can then be combined with existing MALDI techniques to overlay metabolomic data, such as lipids, to connect the functional state of a cell with its expressed genes. Future directions include expanding upon the number of genes that can be targeted within a single experiment.