Coupling metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and human traits.

Pascal Schlosser, Michael Köttgen, Miriam Schmidts, Yannan Xi, Sahar Mozaffari, Casper Wong, Fabian Telkämper, Stefan Haug, Daniel Fässler, Nora Scherer, Yong Li, Kai-Uwe Eckardt, Heike Meiselbach, Anna Köttgen, Anselm Hoppmann, Suraj Patil, Ines Thiele, Johannes Hertel, Matthias Wuttke, Ulla T Schultheiss, Yurong Cheng, Peggy Sekula, Robert Graham, Sarah C Grünert, Felix Knauf, Karol Estrada, Peter J Oefner, Oleg Borisov, Urs Berger

Journal: Nature genetics 2025;57(1):193-205

PMID: 39747595

Abstract

Genetic studies of the metabolome can uncover enzymatic and transport processes shaping human metabolism. Using rare variant aggregation testing based on whole-exome sequencing data to detect genes associated with levels of 1,294 plasma and 1,396 urine metabolites, we discovered 235 gene-metabolite associations, many previously unreported. Complementary approaches (genetic, computational (in silico gene knockouts in whole-body models of human metabolism) and one experimental proof of principle) provided orthogonal evidence that studies of rare, damaging variants in the heterozygous state permit inferences concordant with those from inborn errors of metabolism. Allelic series of functional variants in transporters responsible for transcellular sulfate reabsorption (SLC13A1, SLC26A1) exhibited graded effects on plasma sulfate and human height and pinpointed alleles associated with increased odds of diverse musculoskeletal traits and diseases in the population. This integrative approach can identify new players in incompletely characterized human metabolic reactions and reveal metabolic readouts informative of human traits and diseases.

© 2025. The Author(s).

Address: Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.; Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.; Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany.; Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.; Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.; Centre for Integrative Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.; Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.; Department of Medicine IV, Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.; Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.; Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.; Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.; Department of Medicine IV, Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.; Faculty of Biology, University of Freiburg, Freiburg, Germany.; Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.; Research, Maze Therapeutics, South San Francisco, CA, USA.; Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.; Department of Medicine IV, Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.; SYNLAB MVZ Humangenetik Freiburg, Freiburg, Germany.; Centre for Integrative Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.; Department of General Pediatrics, Adolescent Medicine and Neonatology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.; Centre for Integrative Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.; Department of Medicine IV, Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.; Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.; Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany.; Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.; Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany.; Department of General Pediatrics, Adolescent Medicine and Neonatology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.; School of Medicine, University of Galway, Galway, Ireland.; Ryan Institute, University of Galway, Galway, Ireland.; Division of Microbiology, University of Galway, Galway, Ireland.; APC Microbiome Ireland, Cork, Ireland.; Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany. [email protected].; German Centre for Cardiovascular Research (DZHK), partner site Greifswald, Greifswald, Germany. [email protected].; Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany. [email protected].; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA. [email protected].; Centre for Integrative Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany. [email protected].

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