Identifying substrates of metabolic gene products is important to understand their function in physiology and disease. We developed GeneMAP, a multiomics platform for predicting metabolic gene functions using models of gene expression. We experimentally validated a top-scoring gene–metabolite association, thereby revealing a role for SLC25A48 in mitochondrial choline import.
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References
César-Razquin, A. et al. A call for systematic research on solute carriers. Cell 162, 478–487 (2015). A perspective article on the need for focused studies on metabolic transporters.
Kenny, T. C. et al. Integrative genetic analysis identifies FLVCR1 as a plasma-membrane choline transporter in mammals. Cell. Metab. 35, 1057–1071.e12 (2023). This paper uses GWAS for gene function discovery.
Gamazon, E. R. et al. A gene-based association method for mapping traits using reference transcriptome data. Nat. Genet. 47, 1091 (2015). This study implements TWAS, the core methodology of GeneMAP, to associate gene variants with traits.
Gusev, A. et al. Integrative approaches for large-scale transcriptome-wide association studies. Nat. Genet. 48, 245–252 (2016). This paper introduced summary-statistics-based TWAS.
Zhou, D. et al. A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis. Nat. Genet. 52, 1239–1246 (2020). This study developed the gene expression models used for GeneMAP.
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This is a summary of: Khan, A. et al. Metabolic gene function discovery platform GeneMAP identifies SLC25A48 as necessary for mitochondrial choline import. Nat. Genet. https://doi.org/10.1038/s41588-024-01827-2 (2024).
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GeneMAP enables discovery of metabolic gene function. Nat Genet 56, 1552–1553 (2024). https://doi.org/10.1038/s41588-024-01828-1
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DOI: https://doi.org/10.1038/s41588-024-01828-1
