Mapping the mammalian dark metabolome by <i>in vivo</i> isotope tracing
isotope tracing to infer the biosynthetic origins of unidentified metabolites. We administered 26 different isotopically labelled nutrients to mice, measured circulating and tissue metabolite labelling by mass spectrometry, and developed a statistical framework to infer the number of carbon atoms incorporated from each of these precursors into more than 4,000 putative metabolites. We show this information can be harnessed for biosynthesis-aware structure elucidation using a multimodal AI model that co-embeds isotopic labelling patterns with chemical structures. This approach revealed several previously unrecognized families of mammalian metabolites, including cysteine-derived alkylthiazolidines, dithioacetal mercapturic acid derivatives, short-chain N-acyltaurines, acylglycyltaurines, and N-oxidized taurines. It further uncovered a family of mevalonate-derived isoprenoid metabolites that includes 2,3-dihydrofarnesoic acid, which is markedly depleted in both mouse and human aging. Age-related depletion of these isoprenoids is driven by impaired coenzyme A synthesis. Our work establishes the biosynthetic precursors for thousands of unidentified metabolites and reveals multiple previously unrecognized branches of mammalian metabolism.
Authors
- Connor S.R. Jankowski (ORCID: https://orcid.org/0000-0003-1247-4548)
- Michael D. Neinast (ORCID: https://orcid.org/0000-0003-4032-8142)
- Christian G. Peace (ORCID: https://orcid.org/0000-0002-5390-6530)
- Jenna E. AbuSalim (ORCID: https://orcid.org/0000-0002-5870-6984)
- Asael Roichman (ORCID: https://orcid.org/0000-0001-9538-0103)
- Michael A. Skinnider (ORCID: https://orcid.org/0000-0002-2168-1621)
- Michael R. MacArthur (ORCID: https://orcid.org/0000-0003-3593-6995)
- Anna M. Oschmann
- Joshua D. Rabinowitz (ORCID: https://orcid.org/0000-0002-1247-4727)
- Justine Raeber (ORCID: https://orcid.org/0000-0003-4732-7484)
- Ricardo A. Cordova (ORCID: https://orcid.org/0000-0003-4959-309X)
- Daniil G. Ivanov (ORCID: https://orcid.org/0000-0003-2987-1048)
- Kellen Olszewski (ORCID: https://orcid.org/0000-0001-9691-0831)
- Laith Z. Samarah (ORCID: https://orcid.org/0000-0003-1358-2727)
- Julien F. Ayroles (ORCID: https://orcid.org/0000-0001-8729-0511)
- Sarah J. Mitchell
- Vanha N. Pham (ORCID: https://orcid.org/0000-0003-2200-9332)
- Hahn Kim (ORCID: https://orcid.org/0000-0003-4180-6038)
- Xi Xing
- Wenyun Lu
- Edmundo Leiva
- Amelia V. Schueppert
- Gianna L. Renzo
- Lucas B. Ayres
- Hantao Qiang
Institutions
- Bar-Ilan University (IL)
- Princeton University (US)
- Ludwig Cancer Research (US)
- University of California, Berkeley (US)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2026-04-02
- DOI
- https://doi.org/10.64898/2026.03.31.713900
- Primary Topic
- Metabolomics and Mass Spectrometry Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00