Integrating Ambient Ionization Mass Spectrometry Imaging and Spatial Transcriptomics on the Same Cancer Tissues to Identify RNA–Metabolite Correlations
This study presents a novel workflow for mapping the location and abundance of mRNA and metabolites from the same tissue section, allowing identification of thousands of spatially correlating genes and metabolites.
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While recent innovations in spatial omics technologies have led to breakthrough discoveries in various human diseases, different spatial technologies have largely been developed and applied separately, such spatial transcriptomics, derived from mini-bulk NGS or in-situ hybridization, and spatial metabolomics, from mass spectrometry imaging (MSI). Combining spatial metabolomics and spatial transcriptomics can reveal powerful connections between gene expression and metabolism in heterogeneous tissues, however most studies to date have been performed on adjacent serial sections which can convolute data integration.
This study presents a novel approach, whereby Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI) spatial metabolomics and Visium Spatial Transcriptomics (VST) are sequentially performed on the same tissue section. RNA quality is maintained after performing DESI-MSI on a tissue under ambient conditions, as demonstrated on human breast and lung cancer tissues. Aspect Analytics conducted the data integration and downstream data analysis of the spatial transcriptomics, spatial metabolomics and histology datasets, allowing the detection of thousands of spatially correlating metabolite-mRNA pairs in cancer-specific tissue regions.
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Publication Details: Trevor M. Godfrey1, Yasmin Shanneik1, Wanqiu Zhang2, Thao Tran2, Nico Verbeeck2, Nathan H. Patterson2, Faith E. Jackobs1, Chandandeep Nagi3, Maheshwari Ramineni3, Livia S. Eberlin1, Integrating Ambient Ionization Mass Spectrometry Imaging and Spatial Transcriptomics on the Same Cancer Tissues to Identify RNA–Metabolite Correlations. Angew Chem Int Ed Engl. 2025 Apr 11;e202502028. doi: 10.1002/anie.202502028.
AFFILIATIONS
1. Department of Surgery, Baylor College of Medicine, Houston, TX, 77030, USA.
2. Aspect Analytics NV, Genk 3600, Belgium.
3. Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA.