Metabolic gene function discovery platform GeneMAP identifies SLC25A48 as necessary for mitochondrial choline import – Nature.com

Posted: July 11, 2024 at 2:43 am

Prosser, G. A., Larrouy-Maumus, G. & de Carvalho, L. P. S. Metabolomic strategies for the identification of new enzyme functions and metabolic pathways. EMBO Rep. 15, 657669 (2014).

Article PubMed PubMed Central Google Scholar

Pizzagalli, M. D., Bensimon, A. & Superti-Furga, G. A guide to plasma membrane solute carrier proteins. FEBS J. 288, 27842835 (2021).

Article PubMed Google Scholar

Wiedmer, T., Ingles-Prieto, A., Goldmann, U., Steppan, C. M. & Superti-Furga, G. Accelerating SLC transporter research: streamlining knowledge and validated tools. Clin. Pharmacol. Ther. 112, 439442 (2022).

Article PubMed PubMed Central Google Scholar

Csar-Razquin, A. et al. A call for systematic research on solute carriers. Cell 162, 478487 (2015).

Article PubMed Google Scholar

Shi, X. et al. Combinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS. Nat. Commun. 13, 2483 (2022).

Article CAS PubMed PubMed Central Google Scholar

Kenny, T. C. et al. Integrative genetic analysis identifies FLVCR1 as a plasma-membrane choline transporter in mammals. Cell Metab. 35, 10571071.e12 (2023).

Article CAS PubMed PubMed Central Google Scholar

Wang, Y. et al. SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells. Nature 599, 136140 (2021).

Article CAS PubMed PubMed Central Google Scholar

Unlu, G. et al. Metabolic-scale gene activation screens identify SLCO2B1 as a heme transporter that enhances cellular iron availability. Mol. Cell 82, 28322843.e7 (2022).

Article CAS PubMed PubMed Central Google Scholar

Dvorak, V. et al. An overview of cell-based assay platforms for the solute carrier family of transporters. Front. Pharmacol. 12, 722889 (2021).

Article CAS PubMed PubMed Central Google Scholar

Barroso, I. & McCarthy, M. I. The genetic basis of metabolic disease. Cell 177, 146161 (2019).

Article PubMed PubMed Central Google Scholar

Rios, S. et al. Plasma metabolite profiles associated with the World Cancer Research Fund/American Institute for Cancer Research lifestyle score and future risk of cardiovascular disease and type 2 diabetes. Cardiovasc. Diabetol. 22, 252 (2023).

Article CAS PubMed PubMed Central Google Scholar

Wang, F. et al. Plasma metabolomic profiles associated with mortality and longevity in a prospective analysis of 13,512 individuals. Nat. Commun. 14, 5744 (2023).

Article CAS PubMed PubMed Central Google Scholar

Schlosser, P. et al. Genetic studies of paired metabolomes reveal enzymatic and transport processes at the interface of plasma and urine. Nat. Genet. 55, 9951008 (2023).

Article CAS PubMed PubMed Central Google Scholar

Yin, X. et al. Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci. Nat. Commun. 13, 1644 (2022).

Article CAS PubMed PubMed Central Google Scholar

Chen, Y. et al. Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases. Nat. Genet. 55, 4453 (2023).

Article PubMed PubMed Central Google Scholar

Surendran, P. et al. Rare and common genetic determinants of metabolic individuality and their effects on human health. Nat. Med. 28, 23212332 (2022).

Article CAS PubMed PubMed Central Google Scholar

Yin, X. et al. Integrating transcriptomics, metabolomics, and GWAS helps reveal molecular mechanisms for metabolite levels and disease risk. Am. J. Hum. Genet. 109, 17271741 (2022).

Lotta, L. A. et al. A cross-platform approach identifies genetic regulators of human metabolism and health. Nat. Genet. 53, 5464 (2021).

Article CAS PubMed PubMed Central Google Scholar

Gamazon, E. R. et al. A gene-based association method for mapping traits using reference transcriptome data. Nat. Genet. 47, 10911098 (2015).

Article PubMed PubMed Central Google Scholar

Gusev, A. et al. Integrative approaches for large-scale transcriptome-wide association studies. Nat. Genet. 48, 245252 (2016).

Article CAS PubMed PubMed Central Google Scholar

Porcu, E. et al. Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits. Nat. Commun. 10, 3300 (2019).

Article PubMed PubMed Central Google Scholar

Barbeira, A. N. et al. Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. Nat. Commun. 9, 1825 (2018).

Article PubMed PubMed Central Google Scholar

Zhou, D. et al. A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis. Nat. Genet. 52, 12391246 (2020).

Article CAS PubMed PubMed Central Google Scholar

Mogil, L. S. et al. Genetic architecture of gene expression traits across diverse populations. PLoS Genet. 14, e1007586 (2018).

Article PubMed PubMed Central Google Scholar

Storey, J. D. & Tibshirani, R. Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA 100, 94409445 (2003).

Article PubMed PubMed Central Google Scholar

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583589 (2021).

Article CAS PubMed PubMed Central Google Scholar

Cheng, J. et al. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science 381, eadg7492 (2023).

Article CAS PubMed Google Scholar

Rentzsch, P., Schubach, M., Shendure, J. & Kircher, M. CADD-Spliceimproving genome-wide variant effect prediction using deep learning-derived splice scores. Genome Med. 13, 31 (2021).

Article CAS PubMed PubMed Central Google Scholar

Jeong, H., Tombor, B., Albert, R., Oltval, Z. N. & Barabsl, A. L. The large-scale organization of metabolic networks. Nature 407, 651654 (2000).

Article CAS PubMed Google Scholar

Stacey, D. et al. ProGeM: a framework for the prioritization of candidate causal genes at molecular quantitative trait loci. Nucleic Acids Res. 47, e3 (2019).

Article CAS PubMed Google Scholar

Li, F., Chen, Y., Anton, M. & Nielsen, J. GotEnzymes: an extensive database of enzyme parameter predictions. Nucleic Acids Res. 51, D583D586 (2023).

Article CAS PubMed Google Scholar

Aguet, F. et al. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369, 13181330 (2020).

Article CAS Google Scholar

Zeisel, S. H. & Da Costa, K. A. Choline: an essential nutrient for public health. Nutr. Rev. 67, 615623 (2009).

Article PubMed Google Scholar

Combs, G. F. Jr. & McClung, J. P. (eds) in The Vitamins 523589 (Academic Press, 2022).

Kennedy, E. P. & Weiss, S. B. The function of cytidine coenzymes in the biosynthesis of phospholipides. J. Biol. Chem. 222, 193214 (1956).

Article CAS PubMed Google Scholar

Ducker, G. S. & Rabinowitz, J. D. One-carbon metabolism in health and disease. Cell Metab. 25, 2742 (2017).

Article PubMed Google Scholar

Dragolovich, J. Dealing with salt stress in animal cells: the role and regulation of glycine betaine concentrations. J. Exp. Zool. 268, 139144 (1994).

Article CAS Google Scholar

Ueland, P. M. Choline and betaine in health and disease. J. Inherit. Metab. Dis. 34, 315 (2011).

Article CAS PubMed Google Scholar

Chen, W. W., Freinkman, E., Wang, T., Birsoy, K. & Sabatini, D. M. Absolute quantification of matrix metabolites reveals the dynamics of mitochondrial metabolism. Cell 166, 13241337.e11 (2016).

Article CAS PubMed PubMed Central Google Scholar

Palmieri, F. The mitochondrial transporter family SLC25: identification, properties and physiopathology. Mol. Aspects Med. 34, 465484 (2013).

Article CAS PubMed Google Scholar

Chen, S. et al. A genome-wide mutational constraint map quantified from variation in 76,156 human genomes. Preprint at bioRxiv https://doi.org/10.1101/2022.03.20.485034 (2022).

Son, Y., Kenny, T. C., Khan, A., Birsoy, K. & Hite, R. K. Structural basis of lipid head group entry to the Kennedy pathway by FLVCR1. Nature 629, 710716 (2024).

Article CAS PubMed Google Scholar

Ri, K. et al. Molecular mechanism of choline and ethanolamine transport in humans. Nature 630, 501508 (2024).

Verkerke, A. R. P., Shi, X., Abe, I., Gerszten, R. E. & Kajimura, S. Mitochondrial choline import regulates purine nucleotide pools via SLC25A48. Preprint at bioRxiv https://doi.org/10.1101/2023.12.31.573776 (2024).

Patil, S. et al. SLC25A48 is a human mitochondrial choline transporter. Preprint at medRxiv https://doi.org/10.1101/2023.12.04.23299390 (2023).

Ardlie, K. G. et al. The GenotypeTissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348, 648660 (2015).

Article Google Scholar

Giambartolomei, C. et al. Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet. 10, e1004383 (2014).

Article PubMed PubMed Central Google Scholar

Lonsdale, J. et al. The GenotypeTissue Expression (GTEx) project. Nat. Genet. 45, 580585 (2013).

Article CAS Google Scholar

Yavorska, O. O. & Burgess, S. MendelianRandomization: an R package for performing Mendelian randomization analyses using summarized data. Int. J. Epidemiol. 46, 17341739 (2017).

Article PubMed PubMed Central Google Scholar

Burgess, S., Thompson, S. G. & CRP CHD Genetics Collaboration. Avoiding bias from weak instruments in Mendelian randomization studies. Int. J. Epidemiol. 40, 755764 (2011).

Foley, C. N. et al. A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits. Nat. Commun. 12, 764 (2021).

Article CAS PubMed PubMed Central Google Scholar

Wu, P. et al. Mapping ICD-10 and ICD-10-CM codes to phecodes: workflow development and initial evaluation. JMIR Med. Inform. 7, e14325 (2019).

Article PubMed PubMed Central Google Scholar

Wu, M. C. et al. Rare-variant association testing for sequencing data with the sequence kernel association test. Am. J. Hum. Genet. 89, 8293 (2011).

Article PubMed PubMed Central Google Scholar

Choi, S. W. & OReilly, P. F. PRSice-2: polygenic risk score software for biobank-scale data. Gigascience 8, giz082 (2019).

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Metabolic gene function discovery platform GeneMAP identifies SLC25A48 as necessary for mitochondrial choline import - Nature.com

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