Integrating Ambient Ionization Mass Spectrometry Imaging and Spatial Transcriptomics on the Same Cancer Tissues to Identify RNA–Metabolite Correlations

Abstract Innovations in spatial omics technologies applied to human tissues have led to breakthrough discoveries in various diseases, including cancer. Two of these approaches—spatial transcriptomics and spatial metabolomics—have blossomed independently, fueled by technologies such as spatial transcriptomics (ST) and mass spectrometry imaging (MSI). Although powerful, these technologies only offer insights into the spatial distributions of restricted classes of molecules and have not yet been integrated to provide more holistic insights into biological questions. These techniques can be performed on adjacent serial sections from the same sample, but section‐to‐section variability can convolute data integration. We present a novel method combining desorption electrospray ionization mass spectrometry imaging (DESI‐MSI) spatial metabolomics and Visium spatial transcriptomics on the same tissue sections. We show that RNA quality is maintained after performing DESI‐MSI on a tissue under ambient conditions and that ST data is unperturbed following DESI‐MSI. We demonstrate this workflow on human breast and lung cancer tissues and identify novel correlations between metabolites and mRNA transcripts in cancer‐specific tissue regions.